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FTR #1121 More than One “Flu” Over the Cuckoo’s Nest, Part 2

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FTR #1121 This pro­gram was record­ed in one, 60-minute seg­ment

Intro­duc­tion: Oya­Gen, Inc. has used a drug devel­oped, test­ed and FDA-approved that suc­cess­ful­ly treats and–apparently–cures Covid-19. Inter­est­ing­ly and, per­haps, sig­nif­i­cant­ly, the tri­als were con­duct­ed at Fort Det­rick. As seen in FTR #‘s 1119 and 1120, the mil­i­tary has been heav­i­ly involved in research­ing virus­es of this type.

There con­tin­ues to be enor­mous empha­sis on Gilead Sci­ences by hedge funds includ­ing Renais­sance Tech­nolo­gies. Robert Mer­cer stepped down as CEO of the firm at the end of 2017, as pub­lic­i­ty around Cam­bridge Ana­lyt­i­ca and the fall­out from the Char­lottesville march made him some­thing of a PR lia­bil­i­ty. Usu­al­ly in such sit­u­a­tions, peo­ple like Mer­cer remain as key investors.

In FTR #1118, we not­ed that the Board of Direc­tors of the firm is “inter­est­ing.” The “dis­ap­point­ing” per­for­mance of Gilead Sci­ences changed dra­mat­i­cal­ly with the Covid-19 out­break. ” . . . . Until Mon­day, when it fell in a bru­tal mar­ket rout, Gilead’s stock price had defied the over­all mar­ket decline of recent weeks, ris­ing almost 20 per­cent from Feb. 21 to March 6, on hopes that the drug could pro­vide the first treat­ment for covid-19. The lack of treat­ment helps explain why. The stock price increased 5 per­cent on Feb. 24 alone when a top offi­cial of the World Health Orga­ni­za­tion pinned much of the world’s hopes for a treat­ment on the drug. . . .”

Again, in FTR #‘s 1119 and 1120 we looked at the pro­found involve­ment of the Pen­ta­gon in research­ing coro­n­avirus­es like Covid-19, as well as DARPA’s deep involve­ment with com­pa­nies approved to begin work­ing on vac­cines. Now, Med­ica­go, anoth­er DARPA-fund­ed com­pa­ny, claims to have a vac­cine ready for tri­al. . . . . Using plants and genet­i­cal­ly engi­neered agrobac­te­ria works faster than eggs also makes the vac­cine much eas­i­er to pro­duce at scale, which, in part, is why the U.S. mil­i­tary has invest­ed in the com­pa­ny. In 2010, the Defense Advanced Research Projects Agency, or DARPA, put togeth­er a $100 mil­lion pro­gram dubbed Blue Angel to look into new forms of vac­cine dis­cov­ery and pro­duc­tion. A big chunk of that mon­ey went to Med­ica­go to build a facil­i­ty in North Car­oli­na, where they showed that they could find a vac­cine in just 20 days, then rapid­ly scale up pro­duc­tion. . . .”

Next, we turn to an arti­cle not­ing that the char­ac­ter­is­tics of the COVID-19 dis­ease has remark­able over­lap with a hypo­thet­i­cal dis­ease, dubbed “Dis­ease X.” In 2018, the World Health Orga­ni­za­tion empha­sized an alarm­ing char­ac­ter­is­tic of “hypo­thet­i­cal” “Dis­ease X” that appears to be shared with SARS-CoV­‑2: the abil­i­ty to rapid­ly morph from a mild to dead­ly dis­ease. The sud­den turn towards a dead­ly dis­ease appears to be due, in part, to an over­ly aggres­sive immune response that ends up rav­aging the lungs. As one expert points out, this is the same pat­tern seen in the 1918 “Span­ish flu” pan­dem­ic.

In FTR #1117, we reviewed the fact that mil­i­tary researchers had suc­cess­ful­ly recov­ered DNA from that infa­mous 1918 flu virus. as will be seen below, that virus was re-cre­at­ed in a lab­o­ra­to­ry in 2005.

So the WHO warned a cou­ple years ago about a hypo­thet­i­cal “Dis­ease X” dis­ease that was high­ly con­ta­gious with the abil­i­ty to spread with asymp­to­mati­cal­ly, is mild in most cas­es but with the abil­i­ty to sud­den­ly turn dead­ly. And here we are two years lat­er with a dis­ease that fits that pro­file. It was a pret­ty pre­scient pre­dic­tion.

Note, also, that Mar­i­on Koopmans–head of viro­science at Eras­mus Med­ical Cen­ter in Rot­ter­dam and one of the WHO per­son­nel who opined that Covid-19 was “Dis­ease X” worked at the same insti­tu­tion as the researchers who per­formed gain-of-func­tion exper­i­ments on the HN51 Avian Bird Flu virus, adapt­ing to fer­rets and mak­ing it com­mu­ni­ca­ble through casu­al res­pi­ra­to­ry activ­i­ty. Those GOF experiements were also dis­cussed in FTR #1117.

” . . . . From recent reports about the stealthy ways the so-called Covid-19 virus spreads and maims, a pic­ture is emerg­ing of an enig­mat­ic pathogen whose effects are main­ly mild, but which occa­sion­al­ly — and unpre­dictably — turns dead­ly in the sec­ond week. . . . The doc­tor [Li Wen­liang], who was in good health pri­or to his infec­tion, appeared to have a rel­a­tive­ly mild case until his lungs became inflamed, lead­ing to the man’s death two days lat­er, said Lin­fa Wang, who heads the emerg­ing infec­tious dis­ease pro­gram at Duke-Nation­al Uni­ver­si­ty of Sin­ga­pore Med­ical School. A sim­i­lar pat­tern of inflam­ma­tion not­ed among Covid-19 patients was observed in those who suc­cumbed to the 1918 ‘Span­ish flu’ pan­dem­ic . . .”

We won­der if vari­ants of the Covid-19 may have been mod­i­fied to infect the upper res­pi­ra­to­ry tract and/or mod­i­fied with DNA from the res­ur­rect­ed 1918 “Span­ish Flu”?

Peter Daszak of the WHO once again, voiced the (self-ful­fill­ing?) opinion/prophecy that Covid-19 is indeed “Dis­ease X.”

A key fac­tor spurring our sus­pi­cion con­cern­ing genet­ic-engi­neer­ing of one or more vari­ant of the Covid-19 virus con­cerns a 2015 Gain-of-Func­tion exper­i­ment: “Ralph Bar­ic, an infec­tious-dis­ease researcher at the Uni­ver­si­ty of North Car­oli­na at Chapel Hill, last week (Novem­ber 9) pub­lished a study on his team’s efforts to engi­neer a virus with the sur­face pro­tein of the SHC014 coro­n­avirus, found in horse­shoe bats in Chi­na, and the back­bone of one that caus­es human-like severe acute res­pi­ra­to­ry syn­drome (SARS) in mice. The hybrid virus could infect human air­way cells and caused dis­ease in mice. . . . The results demon­strate the abil­i­ty of the SHC014 sur­face pro­tein to bind and infect human cells, val­i­dat­ing con­cerns that this virus—or oth­er coro­n­avirus­es found in bat species—may be capa­ble of mak­ing the leap to peo­ple with­out first evolv­ing in an inter­me­di­ate host, Nature report­ed. They also reignite a debate about whether that infor­ma­tion jus­ti­fies the risk of such work, known as gain-of-func­tion research. ‘If the [new] virus escaped, nobody could pre­dict the tra­jec­to­ry,’ Simon Wain-Hob­son, a virol­o­gist at the Pas­teur Insti­tute in Paris, told Nature. . . .”

The above-men­tioned Ralph Bar­ic–who did the gain-of-func­tion mod­i­fi­ca­tion on the Horse­shoe Bat coro­n­avirus, has been select­ed to engi­neer the Covid-19.

Note what might be termed a “viro­log­ic Juras­sic Park” man­i­fes­ta­tion: ” . . . . . . . . The tech­nol­o­gy imme­di­ate­ly cre­at­ed bio-weapon wor­ries. . . . Researchers at the US Cen­ters for Dis­ease Con­trol and Pre­ven­tion (CDC) drove that point home in 2005 when they res­ur­rect­ed the influen­za virus that killed tens of mil­lions in 1918–1919. . . .

1a. Oya­Gen, Inc. has used a drug devel­oped, test­ed and FDA-approved that suc­cess­ful­ly treats and–apparently–cures Covid-19. Inter­est­ing­ly and, per­haps, sig­nif­i­cant­ly, the tri­als were con­duct­ed at Fort Det­rick. As seen in FTR #‘s 1119 and 1120, the mil­i­tary has been heav­i­ly involved in research­ing virus­es of this type.

“ROC biotech com­pa­ny says lab tests of for­mer can­cer drug con­firm it stops COVID-19” by Jane Flasch; 13WHAM News; 03/11/2020

A vac­cine for COVID-19 is like­ly years away. Yet a drug test­ed in a lab three weeks ago has been found to stop the virus from spread­ing from cell to cell.

The stun­ning announce­ment comes from a Rochester biotech com­pa­ny called Oya­Gen, Inc. The com­pa­ny is seek­ing to fast-track the for­mu­la to treat peo­ple who become infect­ed.

“A treat­ment right now is the pri­or­i­ty,” said Dr. Harold Smith of Oya­Gen. He added the drug already has FDA approval for anoth­er use.

The tests were con­duct­ed at the fed­er­al government’s inte­grat­ed research facil­i­ty in Fort Det­rick, Md. A drug called Oya 1 had already been proven in lab tests there to be effec­tive against Ebo­la.

“If it worked for Ebo­la, is it absolute­ly unique to Ebo­la, or would it work on oth­er virus­es?” asked Dr. Smith – though he said an actu­al drug for human con­sump­tion was nev­er pur­sued.

The coro­n­avirus was still new and con­tained to Wuhan, Chi­na when a sam­ple of the live virus was shipped to the gov­ern­ment lab for test­ing with Oya 1. Test sam­ples viewed under a micro­scope show a clear “before” and “after” that indi­cates prop­er­ties that allowed the virus to grow and spread were neu­tral­ized.

“The drug was so effec­tive that, even though we got through our dose-test­ing, we had lit­er­al­ly ster­il­ized the cul­ture of the virus, so we knew this was a pow­er­ful thing,” said Dr. Smith.

Under a dif­fer­ent name, Oya‑1 was first devel­oped in the 1960s as a treat­ment for can­cer. It was lat­er shelved as inef­fec­tive, but not before it received approval from the Food and Drug Admin­is­tra­tion. Safe dosage lev­els were deter­mined for men, women and chil­dren.

“Clin­i­cal tri­als have already been done on this com­pound and, if safe­ty is a main issue, we feel safe­ty has been addressed years ago,” said Dr. Smith.

He said pre­lim­i­nary research indi­cates a sin­gle dose of the med­i­cine stops the pro­gres­sion of COVID-19 for eight days and con­tin­ues to work at half-strength for anoth­er four days.

The ques­tion is whether the drug will react to the virus the same way in the body as it has in the lab. When an approved drug is pro­posed for a new use, the FDA usu­al­ly requires new clin­i­cal tri­als.

Oya­Gen says the live virus tests were con­duct­ed and val­i­dat­ed by a third par­ty – the U‑S gov­ern­ment, and argue that is also a rea­son the drug should be fast-tracked.

“You’ve got this com­pound that’s absolute­ly lethal to the virus, and we know it has a mar­gin of safe­ty in peo­ple,” said Dr. Smith. “What are we wait­ing for?”

1b. There con­tin­ues to be enor­mous empha­sis on Gilead Sci­ences by hedge funds includ­ing Renais­sance Tech­nolo­gies. Robert Mer­cer stepped down as CEO of the firm at the end of 2017, as pub­lic­i­ty around Cam­bridge Ana­lyt­i­ca and the fall­out from the Char­lottesville march made him some­thing of a PR lia­bil­i­ty. Usu­al­ly in such sit­u­a­tions, peo­ple like Mer­cer remain as key investors.

In FTR #1118, we not­ed that the Board of Direc­tors of the firm is “inter­est­ing.”

“2019 Review: Most Favored Hedge Fund Stocks vs. Gilead Sci­ences, Inc. (GILD)” by Asma UL Hus­na in Hedge Funds; Insid­er Mon­key; 12/29/2019

It has been a fan­tas­tic year for equi­ty investors as Don­ald Trump pres­sured Fed­er­al Reserve to reduce inter­est rates and final­ized the first leg of a trade deal with Chi­na. If you were a pas­sive index fund investor, you had seen gains of 31% in your equi­ty port­fo­lio in 2019. How­ev­er, if you were an active investor putting your mon­ey into hedge funds’ favorite stocks, you had seen gains of more than 41%. In this arti­cle we are going to take a look at how hedge funds feel about a stock like Gilead Sci­ences, Inc. (NASDAQ:GILD) and com­pare its per­for­mance against hedge funds’ favorite stocks.

Gilead Sci­ences, Inc. (NASDAQ:GILD) was in 58 hedge funds’ port­fo­lios at the end of the third quar­ter of 2019. GILD has seen an increase in hedge fund inter­est recent­ly. . . .

. . . . The largest stake in Gilead Sci­ences, Inc. (NASDAQ:GILD) was held by Renais­sance Tech­nolo­gies, which report­ed hold­ing $933.9 mil­lion worth of stock at the end of Sep­tem­ber. It was fol­lowed by D E Shaw with a $349.9 mil­lion posi­tion. . . . Oth­er investors bull­ish on the com­pa­ny includ­ed Two Sig­ma Advi­sors, AQR Cap­i­tal Man­age­ment, and GLG Part­ners. In terms of the port­fo­lio weights assigned to each posi­tion Coper­ni­cus Cap­i­tal Man­age­ment allo­cat­ed the biggest weight to Gilead Sci­ences, Inc. (NASDAQ:GILD), around 11.67% of its 13F port­fo­lio. Health­care Val­ue Cap­i­tal is also rel­a­tive­ly very bull­ish on the stock, ear­mark­ing 8.01 per­cent of its 13F equi­ty port­fo­lio to GILD.

. . . . Our cal­cu­la­tions showed that top 20 most pop­u­lar stocks among hedge funds returned 41.1% in 2019 through Decem­ber 23rd and out­per­formed the S&P 500 ETF (SPY) by 10.1 per­cent­age points. Unfor­tu­nate­ly GILD wasn’t near­ly as pop­u­lar as these 20 stocks and hedge funds that were bet­ting on GILD were dis­ap­point­ed as the stock returned 10.8% so far in 2019 (through 12/23) and trailed the mar­ket. . . . .

1c. The “dis­ap­point­ing” per­for­mance of Gilead Sci­ences changed dra­mat­i­cal­ly with the Covid-19 out­break. ” . . . . Until Mon­day, when it fell in a bru­tal mar­ket rout, Gilead’s stock price had defied the over­all mar­ket decline of recent weeks, ris­ing almost 20 per­cent from Feb. 21 to March 6, on hopes that the drug could pro­vide the first treat­ment for covid-19. The lack of treat­ment helps explain why. The stock price increased 5 per­cent on Feb. 24 alone when a top offi­cial of the World Health Orga­ni­za­tion pinned much of the world’s hopes for a treat­ment on the drug. . . .”

“The best hope for coro­n­avirus treat­ment is an exper­i­men­tal drug that fiz­zled against Ebo­la” by Christo­pher Row­land; The Wash­ing­ton Post; 03/11/2020

. . . . Now the drug, [remde­sivir] cre­at­ed by phar­ma­ceu­ti­cal giant Gilead Sci­ences, is being test­ed in new clin­i­cal tri­alsand glob­al health author­i­ties deem it the most promis­ing of pos­si­ble treat­ments for peo­ple who are severe­ly ill with the nov­el coro­n­avirus, which caus­es the covid-19 dis­ease. Because it is a “broad spec­trum’’ drug that has been effec­tive against mul­ti­ple viral tar­gets in the lab and in ani­mals, the strat­e­gy could work, experts said. . . .

Gilead, the Nation­al Insti­tutes of Health and Chi­nese health author­i­ties are rac­ing to test it on hun­dreds of peo­ple in con­trolled clin­i­cal tri­als, includ­ing a patient who was quar­an­tined in Nebras­ka after being removed from the Dia­mond Princess cruise ship. Axios report­ed this month that Gilead act­ed so quick­ly that it did not even wait for required approval by the Food and Drug Admin­is­tra­tion before it shipped dos­es to Chi­na. Asked to respond, Gilead said it thinks its “lim­it­ed ship­ments’’ were made in com­pli­ance with U.S. law.

. . . . Until Mon­day, when it fell in a bru­tal mar­ket rout, Gilead’s stock price had defied the over­all mar­ket decline of recent weeks, ris­ing almost 20 per­cent from Feb. 21 to March 6, on hopes that the drug could pro­vide the first treat­ment for covid-19.

The lack of treat­ment helps explain why. The stock price increased 5 per­cent on Feb. 24 alone when a top offi­cial of the World Health Orga­ni­za­tion pinned much of the world’s hopes for a treat­ment on the drug.

“There is only one drug right now that we think may have real effi­ca­cy, and that’s remde­sivir,” said Bruce Ayl­ward, WHO’s assis­tant direc­tor gen­er­al. Ten days lat­er, RBC Cap­i­tal Mar­kets gave it only a 50 per­cent chance of suc­ceed­ing as a treat­ment.

The mixed sig­nals have done lit­tle to damp­en inter­est. There have been des­per­ate pleas for sup­plies to treat patients on a ‘com­pas­sion­ate use’ basis.

. . . . But drug com­pa­nies also have been accused of not pur­su­ing vac­cines and antivi­ral treat­ments aggres­sive­ly because the com­mer­cial mar­kets for such drugs are weak. . . .

. . . . Giv­en the large degree of pub­lic finan­cial sup­port, debates are already flar­ing about how much Gilead should charge for its treat­ment if it ever makes it to mar­ket.

Con­gress and Pres­i­dent Trump autho­rized up to $3 bil­lion last week for efforts by aca­d­e­m­ic researchers and drug com­pa­nies to devel­op vac­cines and treat­ments for coro­n­avirus, part of an $8.3 bil­lion emer­gency spend­ing bill. The indus­try suc­cess­ful­ly opposed efforts by some House Democ­rats to attach guar­an­tees for afford­able prices for vac­cines or treat­ments that result. . . .”

1d. Again, in FTR #‘s 1119 and 1120 we looked at the pro­found involve­ment of the Pen­ta­gon in research­ing coro­n­avirus­es like Covid-19, as well as DARPA’s deep involve­ment with com­pa­nies approved to begin work­ing on vac­cines. Now, Med­ica­go, anoth­er DARPA-fund­ed com­pa­ny, claims to have a vac­cine ready for tri­al. . . . . Using plants and genet­i­cal­ly engi­neered agrobac­te­ria works faster than eggs also makes the vac­cine much eas­i­er to pro­duce at scale, which, in part, is why the U.S. mil­i­tary has invest­ed in the com­pa­ny. In 2010, the Defense Advanced Research Projects Agency, or DARPA, put togeth­er a $100 mil­lion pro­gram dubbed Blue Angel to look into new forms of vac­cine dis­cov­ery and pro­duc­tion. A big chunk of that mon­ey went to Med­ica­go to build a facil­i­ty in North Car­oli­na, where they showed that they could find a vac­cine in just 20 days, then rapid­ly scale up pro­duc­tion. . . .”

“We’ve Got the Vac­cine, Says Pen­ta­gon-Fund­ed Com­pa­ny” by Patrick Tuck­er; Defense One; 3/12/2020.

A Cana­di­an com­pa­ny says that it haspro­duced a COVID-19 vac­cine just 20 days after receiv­ing the coronavirus’s genet­ic sequence, using a unique tech­nol­o­gy that they soon hope to sub­mit for FDA approval.

Med­ica­go CEO Bruce Clark said his com­pa­ny could pro­duce as many as 10 mil­lion dos­es a month. If reg­u­la­to­ry hur­dles can be cleared, he said in a Thurs­day inter­view, the vac­cine could start to become avail­able in Novem­ber 2021. . . .

. . . . Using plants and genet­i­cal­ly engi­neered agrobac­te­ria works faster than eggs also makes the vac­cine much eas­i­er to pro­duce at scale, which, in part, is why the U.S. mil­i­tary has invest­ed in the com­pa­ny. 

In 2010, the Defense Advanced Research Projects Agency, or DARPA, put togeth­er a $100 mil­lion pro­gram dubbed Blue Angel to look into new forms of vac­cine dis­cov­ery and pro­duc­tion. A big chunk of that mon­ey went to Med­ica­go to build a facil­i­ty in North Car­oli­na, where they showed that they could find a vac­cine in just 20 days, then rapid­ly scale up pro­duc­tion. . . .

1d. Next, we turn to an arti­cle not­ing that the char­ac­ter­is­tics of the COVID-19 dis­ease has remark­able over­lap with a hypo­thet­i­cal dis­ease, dubbed “Dis­ease X.” In 2018, the World Health Orga­ni­za­tion empha­sized an alarm­ing char­ac­ter­is­tic of “hypo­thet­i­cal” “Dis­ease X” that appears to be shared with SARS-CoV­‑2: the abil­i­ty to rapid­ly morph from a mild to dead­ly dis­ease. The sud­den turn towards a dead­ly dis­ease appears to be due, in part, to an over­ly aggres­sive immune response that ends up rav­aging the lungs. As one expert points out, this is the same pat­tern seen in the 1918 “Span­ish flu” pan­dem­ic.

In FTR #1117, we reviewed the fact that mil­i­tary researchers had suc­cess­ful­ly recov­ered DNA from that infa­mous 1918 flu virus. as will be seen below, that virus was re-cre­at­ed in a lab­o­ra­to­ry in 2005.

So the WHO warned a cou­ple years ago about a hypo­thet­i­cal “Dis­ease X” dis­ease that was high­ly con­ta­gious with the abil­i­ty to spread with asymp­to­mati­cal­ly, is mild in most cas­es but with the abil­i­ty to sud­den­ly turn dead­ly. And here we are two years lat­er with a dis­ease that fits that pro­file. It was a pret­ty pre­scient pre­dic­tion.

Note, also, that Mar­i­on Koopmans–head of viro­science at Eras­mus Med­ical Cen­ter in Rot­ter­dam and one of the WHO per­son­nel who opined that Covid-19 was “Dis­ease X” worked at the same insti­tu­tion as the researchers who per­formed gain-of-func­tion exper­i­ments on the HN51 Avian Bird Flu virus, adapt­ing to fer­rets and mak­ing it com­mu­ni­ca­ble through casu­al res­pi­ra­to­ry activ­i­ty. Those GOF experiements were also dis­cussed in FTR #1117.

” . . . . From recent reports about the stealthy ways the so-called Covid-19 virus spreads and maims, a pic­ture is emerg­ing of an enig­mat­ic pathogen whose effects are main­ly mild, but which occa­sion­al­ly — and unpre­dictably — turns dead­ly in the sec­ond week. . . . The doc­tor [Li Wen­liang], who was in good health pri­or to his infec­tion, appeared to have a rel­a­tive­ly mild case until his lungs became inflamed, lead­ing to the man’s death two days lat­er, said Lin­fa Wang, who heads the emerg­ing infec­tious dis­ease pro­gram at Duke-Nation­al Uni­ver­si­ty of Sin­ga­pore Med­ical School. A sim­i­lar pat­tern of inflam­ma­tion not­ed among Covid-19 patients was observed in those who suc­cumbed to the 1918 ‘Span­ish flu’ pan­dem­ic . . .”

We won­der if vari­ants of the Covid-19 may have been mod­i­fied to infect the upper res­pi­ra­to­ry tract and/or mod­i­fied with DNA from the res­ur­rect­ed 1918 “Span­ish Flu”?

“Coro­n­avirus May Be ‘Dis­ease X’ Health Experts Warned About” By Jason Gale; Bloomberg; 02/22/2020

* Pic­ture is emerg­ing of an unpre­dictable, enig­mat­ic pathogen
* SARS-like lung inflam­ma­tion seen in severe Covid-19 cas­es

The World Health Orga­ni­za­tion cau­tioned years ago that a mys­te­ri­ous “dis­ease X” could spark an inter­na­tion­al con­ta­gion. The new coro­n­avirus ill­ness, with its abil­i­ty to quick­ly morph from mild to dead­ly, is emerg­ing as a con­tender.

From recent reports about the stealthy ways the so-called Covid-19 virus spreads and maims, a pic­ture is emerg­ing of an enig­mat­ic pathogen whose effects are main­ly mild, but which occa­sion­al­ly — and unpre­dictably — turns dead­ly in the sec­ond week. In less than three months, it’s infect­ed almost 78,000 peo­ple, most­ly in Chi­na, and killed more than 2,300. Emerg­ing hot spots in South Korea, Iran and Italy have stoked fur­ther alarm.

“Whether it will be con­tained or not, this out­break is rapid­ly becom­ing the first true pan­dem­ic chal­lenge that fits the dis­ease X cat­e­go­ry,” Mar­i­on Koop­mans, head of viro­science at Eras­mus Uni­ver­si­ty Med­ical Cen­ter in Rot­ter­dam, and a mem­ber of the WHO’s emer­gency com­mit­tee, wrote Wednes­day in the jour­nal Cell.

The dis­ease has now spread to more than two dozen coun­tries and ter­ri­to­ries. Some of those infect­ed caught the virus in their local com­mu­ni­ty and have no known link to Chi­na, the U.S. Cen­ters for Dis­ease Con­trol and Pre­ven­tion said.

“We are not see­ing com­mu­ni­ty spread here in the Unit­ed States yet, but it’s very pos­si­ble — even like­ly — that it may even­tu­al­ly hap­pen,” Nan­cy Mes­son­nier, direc­tor of the CDC’s Nation­al Cen­ter for Immu­niza­tion and Res­pi­ra­to­ry Dis­eases, told reporters Fri­day.

Unlike SARS, its viral cousin, the Covid-19 virus repli­cates at high con­cen­tra­tions in the nose and throat akin to the com­mon cold, and appears capa­ble of spread­ing from those who show no, or mild, symp­toms. That makes it impos­si­ble to con­trol using the fever-check­ing mea­sures that helped stop SARS 17 years ago.

Spread­ing Sur­rep­ti­tious­ly

A clus­ter of cas­es with­in a fam­i­ly liv­ing in the Chi­nese city of Anyang is pre­sumed to have begun when a 20-year-old woman car­ried the virus from Wuhan, the outbreak’s epi­cen­ter, on Jan. 10 and spread it while expe­ri­enc­ing no ill­ness, researchers said Fri­day in the Jour­nal of the Amer­i­can Med­ical Asso­ci­a­tion.

Five rel­a­tives sub­se­quent­ly devel­oped fever and res­pi­ra­to­ry symp­toms. Covid-19 is less dead­ly than SARS, which had a case fatal­i­ty rate of 9.5%, but appears more con­ta­gious. Both virus­es attack the res­pi­ra­to­ry and gas­troin­testi­nal tracts, via which they can poten­tial­ly spread.

While more than 80% of patients are report­ed to have a mild ver­sion of the dis­ease and will recov­er, about one in sev­en devel­ops pneu­mo­nia, dif­fi­cul­ty breath­ing and oth­er severe symp­toms. About 5% of patients have crit­i­cal ill­ness, includ­ing res­pi­ra­to­ry fail­ure, sep­tic shock and mul­ti-organ fail­ure.

“Unlike SARS, Covid-19 infec­tion has a broad­er spec­trum of sever­i­ty rang­ing from asymp­to­matic to mild­ly symp­to­matic to severe ill­ness that requires mechan­i­cal ven­ti­la­tion,” doc­tors in Sin­ga­pore said in a paper in the same med­ical jour­nal Thurs­day. “Clin­i­cal pro­gres­sion of the ill­ness appears sim­i­lar to SARS: patients devel­oped pneu­mo­nia around the end of the first week to the begin­ning of the sec­ond week of ill­ness.”

Unpre­dictable Ill­ness

Old­er adults, espe­cial­ly those with chron­ic con­di­tions, such as hyper­ten­sion and dia­betes, have been found to have a high­er risk of severe ill­ness. Still, “the expe­ri­ence to date in Sin­ga­pore is that patients with­out sig­nif­i­cant co-mor­bid con­di­tions can also devel­op severe ill­ness,” they said.

Li Wen­liang, the 34-year-old oph­thal­mol­o­gist who was one of the first to warn about the coro­n­avirus in Wuhan, died ear­li­er this month after receiv­ing anti­bod­ies, antivi­rals, antibi­otics, oxy­gen and hav­ing his blood pumped through an arti­fi­cial lung.

Update: Li Wen­liang is cur­rent­ly in crit­i­cal con­di­tion. His heart report­ed­ly stopped beat­ing at around 21:30. He was then giv­en treat­ment with ECMO(extra-corporeal mem­brane oxy­gena­tion). https://t.co/ljhMSwHBXB
— Glob­al Times (@globaltimesnews) Feb­ru­ary 6, 2020

The doc­tor, who was in good health pri­or to his infec­tion, appeared to have a rel­a­tive­ly mild case until his lungs became inflamed, lead­ing to the man’s death two days lat­er, said Lin­fa Wang, who heads the emerg­ing infec­tious dis­ease pro­gram at Duke-Nation­al Uni­ver­si­ty of Sin­ga­pore Med­ical School.

A sim­i­lar pat­tern of inflam­ma­tion not­ed among Covid-19 patients was observed in those who suc­cumbed to the 1918 “Span­ish flu” pan­dem­ic, said Gre­go­ry A. Poland, the Mary Low­ell Leary emer­i­tus pro­fes­sor of med­i­cine, infec­tious dis­eases, and mol­e­c­u­lar phar­ma­col­o­gy and exper­i­men­tal ther­a­peu­tics at the Mayo Clin­ic in Rochester, Min­neso­ta.

“When­ev­er, you have an infec­tion, you have a bat­tle going on,” Poland said in a phone inter­view Thurs­day. “And that bat­tle is a bat­tle between the dam­age that the virus is doing, and the dam­age the body can do when it tries to fight it off.” . . . .

2. Peter Daszak of the WHO once again, voiced the (self-ful­fill­ing?) opinion/prophecy that Covid-19 is indeed “Dis­ease X.”

“We Knew Dis­ease X Was Com­ing. It’s Here Now.” by Peter Daszak; The New York Times; 02/27/2020

In ear­ly 2018, dur­ing a meet­ing at the World Health Orga­ni­za­tion in Gene­va, a group of experts I belong to (the R&D Blue­print) coined the term “Dis­ease X”: We were refer­ring to the next pan­dem­ic, which would be caused by an unknown, nov­el pathogen that hadn’t yet entered the human pop­u­la­tion. As the world stands today on the edge of the pan­dem­ic precipice, it’s worth tak­ing a moment to con­sid­er whether Covid-19 is the dis­ease our group was warn­ing about.

Dis­ease X, we said back then, would like­ly result from a virus orig­i­nat­ing in ani­mals and would emerge some­where on the plan­et where eco­nom­ic devel­op­ment dri­ves peo­ple and wildlife togeth­er. Dis­ease X would prob­a­bly be con­fused with oth­er dis­eases ear­ly in the out­break and would spread quick­ly and silent­ly; exploit­ing net­works of human trav­el and trade, it would reach mul­ti­ple coun­tries and thwart con­tain­ment. Dis­ease X would have a mor­tal­i­ty rate high­er than a sea­son­al flu but would spread as eas­i­ly as the flu. It would shake finan­cial mar­kets even before it achieved pan­dem­ic sta­tus.

In a nut­shell, Covid-19 is Dis­ease X. . . .

3. A key fac­tor spurring our sus­pi­cion con­cern­ing genet­ic-engi­neer­ing of one or more vari­ant of the Covid-19 virus con­cerns a 2015 Gain-of-Func­tion exper­i­ment: “Ralph Bar­ic, an infec­tious-dis­ease researcher at the Uni­ver­si­ty of North Car­oli­na at Chapel Hill, last week (Novem­ber 9) pub­lished a study on his team’s efforts to engi­neer a virus with the sur­face pro­tein of the SHC014 coro­n­avirus, found in horse­shoe bats in Chi­na, and the back­bone of one that caus­es human-like severe acute res­pi­ra­to­ry syn­drome (SARS) in mice. The hybrid virus could infect human air­way cells and caused dis­ease in mice. . . . The results demon­strate the abil­i­ty of the SHC014 sur­face pro­tein to bind and infect human cells, val­i­dat­ing con­cerns that this virus—or oth­er coro­n­avirus­es found in bat species—may be capa­ble of mak­ing the leap to peo­ple with­out first evolv­ing in an inter­me­di­ate host, Nature report­ed. They also reignite a debate about whether that infor­ma­tion jus­ti­fies the risk of such work, known as gain-of-func­tion research. ‘If the [new] virus escaped, nobody could pre­dict the tra­jec­to­ry,’ Simon Wain-Hob­son, a virol­o­gist at the Pas­teur Insti­tute in Paris, told Nature. . . .”

“Lab-Made Coro­n­avirus Trig­gers Debate” by Jef Akst; The Sci­en­tist; 11/16/2015

Ralph Bar­ic, an infec­tious-dis­ease researcher at the Uni­ver­si­ty of North Car­oli­na at Chapel Hill, last week (Novem­ber 9) pub­lished a study on his team’s efforts to engi­neer a virus with the sur­face pro­tein of the SHC014 coro­n­avirus, found in horse­shoe bats in Chi­na, and the back­bone of one that caus­es human-like severe acute res­pi­ra­to­ry syn­drome (SARS) in mice. The hybrid virus could infect human air­way cells and caused dis­ease in mice, accord­ing to the team’s results, which were pub­lished in Nature Med­i­cine.

The results demon­strate the abil­i­ty of the SHC014 sur­face pro­tein to bind and infect human cells, val­i­dat­ing con­cerns that this virus—or oth­er coro­n­avirus­es found in bat species—may be capa­ble of mak­ing the leap to peo­ple with­out first evolv­ing in an inter­me­di­ate host, Nature report­ed. They also reignite a debate about whether that infor­ma­tion jus­ti­fies the risk of such work, known as gain-of-func­tion research. “If the [new] virus escaped, nobody could pre­dict the tra­jec­to­ry,” Simon Wain-Hob­son, a virol­o­gist at the Pas­teur Insti­tute in Paris, told Nature.

In Octo­ber 2013, the US gov­ern­ment put a stop to all fed­er­al fund­ing for gain-of-func­tion stud­ies, with par­tic­u­lar con­cern ris­ing about influen­za, SARS, and Mid­dle East res­pi­ra­to­ry syn­drome (MERS). “NIH [Nation­al Insti­tutes of Health] has fund­ed such stud­ies because they help define the fun­da­men­tal nature of human-pathogen inter­ac­tions, enable the assess­ment of the pan­dem­ic poten­tial of emerg­ing infec­tious agents, and inform pub­lic health and pre­pared­ness efforts,” NIH Direc­tor Fran­cis Collins said in a state­ment at the time. “These stud­ies, how­ev­er, also entail biosafe­ty and biose­cu­ri­ty risks, which need to be under­stood bet­ter.”

Baric’s study on the SHC014-chimeric coro­n­avirus began before the mora­to­ri­um was announced, and the NIH allowed it to pro­ceed dur­ing a review process, which even­tu­al­ly led to the con­clu­sion that the work did not fall under the new restric­tions, Bar­ic told Nature. But some researchers, like Wain-Hob­son, dis­agree with that deci­sion.

The debate comes down to how infor­ma­tive the results are. “The only impact of this work is the cre­ation, in a lab, of a new, non-nat­ur­al risk,” Richard Ebright, a mol­e­c­u­lar biol­o­gist and biode­fence expert at Rut­gers Uni­ver­si­ty, told Nature.

But Bar­ic and oth­ers argued the study’s impor­tance. “[The results] move this virus from a can­di­date emerg­ing pathogen to a clear and present dan­ger,” Peter Daszak, pres­i­dent of the Eco­Health Alliance, which sam­ples virus­es from ani­mals and peo­ple in emerg­ing-dis­eases hotspots across the globe, told Nature.

4. The above-men­tioned Ralph Baric–who did the gain-of-func­tion mod­i­fi­ca­tion on the Horse­shoe Bat coro­n­avirus, has been select­ed to engi­neer the Covid-19.

Note what might be termed a “viro­log­ic Juras­sic Park” man­i­fes­ta­tion: ” . . . . . . . . The tech­nol­o­gy imme­di­ate­ly cre­at­ed bio-weapon wor­ries. . . . Researchers at the US Cen­ters for Dis­ease Con­trol and Pre­ven­tion (CDC) drove that point home in 2005 when they res­ur­rect­ed the influen­za virus that killed tens of mil­lions in 1918–1919. . . .

“Biol­o­gists rush to re-cre­ate the Chi­na coro­n­avirus from its DNA code” by Anto­nio Regal­a­do; MIT Tech­nol­o­gy Review; 02/15/2020

The world is watch­ing with alarm as Chi­na strug­gles to con­tain a dan­ger­ous new virus, now being called SARS-CoV­‑2. It has quar­an­tined entire cities, and the US has put a blan­ket ban on trav­ellers who’ve been there. Health offi­cials are scram­bling to under­stand how the virus is trans­mit­ted and how to treat patients.

But in one Uni­ver­si­ty of North Car­oli­na lab, there’s a dif­fer­ent race. Researchers are try­ing to cre­ate a copy of the virus. From scratch.

Led by Ralph Bar­ic, an expert in coronaviruses—which get their name from the crown-shaped spike they use to enter human cells—the North Car­oli­na team expects to recre­ate the virus start­ing only from com­put­er read­outs of its genet­ic sequence post­ed online by Chi­nese labs last month.

The remark­able abil­i­ty to “boot up” virus­es from genet­ic instruc­tions is made pos­si­ble by com­pa­nies that man­u­fac­ture cus­tom DNA mol­e­cules, such as Inte­grat­ed DNA Tech­nol­o­gy, Twist Bio­science, and Atum. By order­ing the right genes, which cost a few thou­sand dol­lars, and then stitch­ing them togeth­er to cre­ate a copy of the coro­n­avirus genome, it’s pos­si­ble to inject the genet­ic mate­r­i­al into cells and jump-start the virus to life.

The abil­i­ty to make a lethal virus from mail-order DNA was first demon­strat­ed 20 years ago. It’s enough of a bioter­ror­ism con­cern that com­pa­nies care­ful­ly mon­i­tor who is order­ing which genes. But it’s also an impor­tant way to respond to a sud­den out­break, since syn­thet­ic virus recipes give researchers pow­er­ful ways to study treat­ments, vac­cines, and how muta­tions could make it more dan­ger­ous.

When a syn­thet­ic virus is bet­ter than the real thing

Baric’s North Car­oli­na lab, which spe­cial­izes in engi­neer­ing virus­es, has pre­vi­ous­ly butted heads with Wash­ing­ton agen­cies over the work, which has includ­ed syn­the­siz­ing new, nev­er before seen coro­n­avirus­es that can infect mice. In 2014, the Nation­al Insti­tutes of Health froze fund­ing to sev­er­al labs, includ­ing Baric’s, over con­cerns that such research was too risky. The fund­ing was lat­er rein­stat­ed.

For the Chi­na virus, Bar­ic said in a tele­phone inter­view, his team placed an order for match­ing DNA from a man­u­fac­tur­er last month. Their first step was to go online and look at genet­ic sequences of the virus. They then com­pared sev­er­al avail­able sequences, which dif­fer slight­ly, and picked a “con­sen­sus” ver­sion to have man­u­fac­tured. . . .

. . . . The tech­nol­o­gy imme­di­ate­ly cre­at­ed bio-weapon wor­ries. What if ter­ror­ists used the tech­nique to res­ur­rect small­pox? That hasn’t hap­pened, but it does mean that scourges like polio, smallpox—and now the Chi­nese coronavirus—cannot now ever be tru­ly wiped out. Researchers at the US Cen­ters for Dis­ease Con­trol and Pre­ven­tion (CDC) drove that point home in 2005 when they res­ur­rect­ed the influen­za virus that killed tens of mil­lions in 1918–1919. . . .

To keep the tech­nol­o­gy out of the hands of evil-doers, com­pa­nies that man­u­fac­ture DNA band­ed togeth­er a few years ago to lim­it access to dan­ger­ous genes. The big US play­ers have all agreed to com­pare incom­ing DNA orders to a data­base of about 60 lethal germs and tox­ins called “select agents” so that only autho­rized labs can ever obtain the DNA need­ed to res­ur­rect them. . . .

 

Discussion

5 comments for “FTR #1121 More than One “Flu” Over the Cuckoo’s Nest, Part 2”

  1. Well, looks like ol’ Dov “Project For A New Amer­i­can Cen­tu­ry” Zakheim is advis­ing Herr Trump on invok­ing the Cold-War mon­stros­i­ty that is the “Defense Pro­duc­tion Act” on order to “aug­ment” civil­ian hos­pi­tal’s abil­i­ty to cope with the com­ing pan­dem­ic:

    https://news.yahoo.com/pressure-grows-on-trump-to-invoke-defense-production-act-for-coronavirus-response-004710535.html

    Posted by Booji Boy | March 18, 2020, 1:42 am
  2. Here’s an inter­est­ing piece in the Atlantic describ­ing some of what’s been learned about what makes the SARS-CoV­‑2 virus that caus­es COVID-19 dif­fer­ent from oth­er coro­n­avirus­es known to infect humans. The arti­cle men­tions some of what we’ve already heard, like how this virus unusu­al­ly infects both the upper and low­er res­pi­ra­to­ry tracts and describes the biol­o­gy of why that hap­pens. It turns out the ‘spike’ part of the SARS-CoV­‑2 virus is unusu­al­ly good at latch­ing into a pro­tein called ACE2 which is found on the exte­ri­or of the cells in human air­ways. This abil­i­ty to latch onto ACE2 is like­ly a big fac­tor in what has allowed the virus to infect upper air­ways. It’s thought that the virus like­ly infects the upper air­ways first and then, as cells in the air­way die and are sloughed off, the virus makes its way down to the low­er res­pi­ra­to­ry tract and lungs where the dead­ly infec­tions might occur. It’s this pat­tern of first infect­ing the upper res­pi­ra­to­ry tract before mak­ing its way down to the lungs that has giv­en the virus the abil­i­ty to silent­ly spread while it’s in a rel­a­tive­ly asymp­to­matic ini­tial phase before it sud­den­ly turns much more vicious and dead­ly.

    But that abil­i­ty to latch strong­ly on the ACE2 pro­tein in human air­ways is just one of the muta­tions that has made this virus excep­tion­al at spread­ing among humans. Anoth­er key fea­ture has to do with a pro­tein bridge that con­nects two halves of the virus’s spike. When the spike gets acti­vate the virus injects its pay­load into the cell. Acti­vat­ing the spike requires the cleav­age of a pro­tein bridge con­nect­ing the two halves of the spike and it turns out this pro­tein bridge is cleav­able by the enzyme furin which is ubiq­ui­tous in human cells. This was­n’t the case for SARS, which had a pro­tein bridge that was less like­ly to be cleaved. So SARS-CoV­‑2 can first latch onto to human upper air­way cells more effec­tive­ly than SARS and once there is read­i­ly acti­vat­ed much more eas­i­ly than SARS.

    But here is per­haps the most notable obser­va­tion made about this virus thus far: it does­n’t appear to be muta­tion in any mean­ing­ful ways. Out of the 100-plus muta­tions that have been observed in wild so far, none of those viral strains has emerged as a dom­i­nant strain. That’s unusu­al­ly for a virus that appar­ent­ly only recent­ly jumped to humans and has been spread­ing at a wild rate. It’s as if the virus is already evo­lu­tion­ar­i­ly opti­mized for spread­ing among humans and there are no ‘gain-of-fuc­tion’ muta­tions left for it acquire. As Lisa Gralin­s­ki, a coro­n­avirus expert at the Uni­ver­si­ty of North Car­oli­na Chapel Hill, described it, “The virus has been remark­ably sta­ble giv­en how much trans­mis­sion we’ve seen...That makes sense, because there’s no evo­lu­tion­ary pres­sure on the virus to trans­mit bet­ter. It’s doing a great job of spread­ing around the world right now.” Note that Gralin­sky works close­ly with Ralph Bar­ic’s lab. Recall that Bar­ic is the researcher who con­struct­ed a chimeric virus out of a SARS virus and horse­shoe bat coro­n­avirus in 2015, so Bar­ic and Gralin­s­ki are going to be world lead­ing experts on coro­n­avirus­es. They lit­er­al­ly build news ones. So when some­one like Gralin­s­ki observes that the it makes sense that the virus would­n’t feel any evo­lu­tion­ary pres­sure to spread more read­i­ly because it’s already doing such a good job that’s quite a state­ment. Evo­lu­tion does­n’t stop just because it’s already doing a real­ly good job. If there was a muta­tion that would allow the virus to spread even more read­i­ly that would hap­pen. And nor­mal­ly does hap­pen. But it has­n’t hap­pened so for SARS-CoV­‑2 because it’s appar­ent­ly already at some sort of coro­n­avirus evo­lu­tion­ary peak:

    The Atlantic

    Why the Coro­n­avirus Has Been So Suc­cess­ful

    We’ve known about SARS-CoV­‑2 for only three months, but sci­en­tists can make some edu­cat­ed guess­es about where it came from and why it’s behav­ing in such an extreme way.

    Ed Yong
    March 20, 2020

    One of the few mer­cies dur­ing this cri­sis is that, by their nature, indi­vid­ual coro­n­avirus­es are eas­i­ly destroyed. Each virus par­ti­cle con­sists of a small set of genes, enclosed by a sphere of fat­ty lipid mol­e­cules, and because lipid shells are eas­i­ly torn apart by soap, 20 sec­onds of thor­ough hand-wash­ing can take one down. Lipid shells are also vul­ner­a­ble to the ele­ments; a recent study shows that the new coro­n­avirus, SARS-CoV­‑2, sur­vives for no more than a day on card­board, and about two to three days on steel and plas­tic. These virus­es don’t endure in the world. They need bod­ies.

    But much about coro­n­avirus­es is still unclear. Susan Weiss, of the Uni­ver­si­ty of Penn­syl­va­nia, has been study­ing them for about 40 years. She says that in the ear­ly days, only a few dozen sci­en­tists shared her interest—and those num­bers swelled only slight­ly after the SARS epi­dem­ic of 2002. “Until then peo­ple looked at us as a back­ward field with not a lot of impor­tance to human health,” she says. But with the emer­gence of SARS-CoV‑2—the cause of the COVID-19 disease—no one is like­ly to repeat that mis­take again.

    To be clear, SARS-CoV­‑2 is not the flu. It caus­es a dis­ease with dif­fer­ent symp­toms, spreads and kills more read­i­ly, and belongs to a com­plete­ly dif­fer­ent fam­i­ly of virus­es. This fam­i­ly, the coro­n­avirus­es, includes just six oth­er mem­bers that infect humans. Four of them—OC43, HKU1, NL63, and 229E—have been gen­tly annoy­ing humans for more than a cen­tu­ry, caus­ing a third of com­mon colds. The oth­er two—MERS and SARS (or “SARS-clas­sic,” as some virol­o­gists have start­ed call­ing it)—both cause far more severe dis­ease. Why was this sev­enth coro­n­avirus the one to go pan­dem­ic? Sud­den­ly, what we do know about coro­n­avirus­es becomes a mat­ter of inter­na­tion­al con­cern.

    The struc­ture of the virus pro­vides some clues about its suc­cess. In shape, it’s essen­tial­ly a spiky ball. Those spikes rec­og­nize and stick to a pro­tein called ACE2, which is found on the sur­face of our cells: This is the first step to an infec­tion. The exact con­tours of SARS-CoV‑2’s spikes allow it to stick far more strong­ly to ACE2 than SARS-clas­sic did, and “it’s like­ly that this is real­ly cru­cial for per­son-to-per­son trans­mis­sion,” says Angela Ras­mussen of Colum­bia Uni­ver­si­ty. In gen­er­al terms, the tighter the bond, the less virus required to start an infec­tion.

    There’s anoth­er impor­tant fea­ture. Coro­n­avirus spikes con­sist of two con­nect­ed halves, and the spike acti­vates when those halves are sep­a­rat­ed; only then can the virus enter a host cell. In SARS-clas­sic, this sep­a­ra­tion hap­pens with some dif­fi­cul­ty. But in SARS-CoV­‑2, the bridge that con­nects the two halves can be eas­i­ly cut by an enzyme called furin, which is made by human cells and—crucially—is found across many tis­sues. “This is prob­a­bly impor­tant for some of the real­ly unusu­al things we see in this virus,” says Kris­t­ian Ander­sen of Scripps Research Trans­la­tion­al Insti­tute.

    For exam­ple, most res­pi­ra­to­ry virus­es tend to infect either the upper or low­er air­ways. In gen­er­al, an upper-res­pi­ra­to­ry infec­tion spreads more eas­i­ly, but tends to be milder, while a low­er-res­pi­ra­to­ry infec­tion is hard­er to trans­mit, but is more severe. SARS-CoV­‑2 seems to infect both upper and low­er air­ways, per­haps because it can exploit the ubiq­ui­tous furin. This dou­ble wham­my could also con­ceiv­ably explain why the virus can spread between peo­ple before symp­toms show up—a trait that has made it so dif­fi­cult to con­trol. Per­haps it trans­mits while still con­fined to the upper air­ways, before mak­ing its way deep­er and caus­ing severe symp­toms. All of this is plau­si­ble but total­ly hypo­thet­i­cal; the virus was only dis­cov­ered in Jan­u­ary, and most of its biol­o­gy is still a mys­tery.

    The new virus cer­tain­ly seems to be effec­tive at infect­ing humans, despite its ani­mal ori­gins. The clos­est wild rel­a­tive of SARS-CoV­‑2 is found in bats, which sug­gests it orig­i­nat­ed in a bat, then jumped to humans either direct­ly or through anoth­er species. (Anoth­er coro­n­avirus found in wild pan­golins also resem­bles SARS-CoV­‑2, but only in the small part of the spike that rec­og­nizes ACE2; the two virus­es are oth­er­wise dis­sim­i­lar, and pan­golins are unlike­ly to be the orig­i­nal reser­voir of the new virus.) When SARS-clas­sic first made this leap, a brief peri­od of muta­tion was nec­es­sary for it to rec­og­nize ACE2 well. But SARS-CoV­‑2 could do that from day one. “It had already found its best way of being a [human] virus,” says Matthew Frie­man of the Uni­ver­si­ty of Mary­land School of Med­i­cine.

    This uncan­ny fit will doubtless­ly encour­age con­spir­a­cy the­o­rists: What are the odds that a ran­dom bat virus had exact­ly the right com­bi­na­tion of traits to effec­tive­ly infect human cells from the get-go, and then jump into an unsus­pect­ing per­son? “Very low,” Ander­sen says, “but there are mil­lions or bil­lions of these virus­es out there. These virus­es are so preva­lent that things that are real­ly unlike­ly to hap­pen some­times do.”

    Since the start of the pan­dem­ic, the virus hasn’t changed in any obvi­ous­ly impor­tant ways. It’s mutat­ing in the way that all virus­es do. But of the 100-plus muta­tions that have been doc­u­ment­ed, none has risen to dom­i­nance, which sug­gests that none is espe­cial­ly impor­tant. “The virus has been remark­ably sta­ble giv­en how much trans­mis­sion we’ve seen,” says Lisa Gralin­s­ki of the Uni­ver­si­ty of North Car­oli­na. “That makes sense, because there’s no evo­lu­tion­ary pres­sure on the virus to trans­mit bet­ter. It’s doing a great job of spread­ing around the world right now.”

    There’s one pos­si­ble excep­tion. A few SARS-CoV­‑2 virus­es that were iso­lat­ed from Sin­ga­pore­an COVID-19 patients are miss­ing a stretch of genes that also dis­ap­peared from SARS-clas­sic dur­ing the late stages of its epi­dem­ic. This change was thought to make the orig­i­nal virus less vir­u­lent, but it’s far too ear­ly to know whether the same applies to the new one. Indeed, why some coro­n­avirus­es are dead­ly and some are not is unclear. “There’s real­ly no under­stand­ing at all of why SARS or SARS-CoV­‑2 are so bad but OC43 just gives you a run­ny nose,” Frie­man says.

    Researchers can, how­ev­er, offer a pre­lim­i­nary account of what the new coro­n­avirus does to the peo­ple it infects. Once in the body, it like­ly attacks the ACE2-bear­ing cells that line our air­ways. Dying cells slough away, fill­ing the air­ways with junk and car­ry­ing the virus deep­er into the body, down toward the lungs. As the infec­tion pro­gress­es, the lungs clog with dead cells and flu­id, mak­ing breath­ing more dif­fi­cult. (The virus might also be able to infect ACE2-bear­ing cells in oth­er organs, includ­ing the gut and blood ves­sels.)

    The immune sys­tem fights back and attacks the virus; this is what caus­es inflam­ma­tion and fever. But in extreme cas­es, the immune sys­tem goes berserk, caus­ing more dam­age than the actu­al virus. For exam­ple, blood ves­sels might open up to allow defen­sive cells to reach the site of an infec­tion; that’s great, but if the ves­sels become too leaky, the lungs fill even more with flu­id. These dam­ag­ing over­re­ac­tions are called cytokine storms. They were his­tor­i­cal­ly respon­si­ble for many deaths dur­ing the 1918 flu pan­dem­ic, H5N1 bird flu out­breaks, and the 2003 SARS out­break. And they’re prob­a­bly behind the most severe cas­es of COVID-19. “These virus­es need time to adapt to a human host,” says Akiko Iwasa­ki of the Yale School of Med­i­cine. “When they’re first try­ing us out, they don’t know what they’re doing, and they tend to elic­it these respons­es.”

    Dur­ing a cytokine storm, the immune sys­tem isn’t just going berserk but is also gen­er­al­ly off its game, attack­ing at will with­out hit­ting the right tar­gets. When this hap­pens, peo­ple become more sus­cep­ti­ble to infec­tious bac­te­ria. The storms can also affect oth­er organs besides the lungs, espe­cial­ly if peo­ple already have chron­ic dis­eases. This might explain why some COVID-19 patients end up with com­pli­ca­tions such as heart prob­lems and sec­ondary infec­tions.

    But why do some peo­ple with COVID-19 get incred­i­bly sick, while oth­ers escape with mild or nonex­is­tent symp­toms? Age is a fac­tor. Elder­ly peo­ple are at risk of more severe infec­tions pos­si­bly because their immune sys­tem can’t mount an effec­tive ini­tial defense, while chil­dren are less affect­ed because their immune sys­tem is less like­ly to progress to a cytokine storm. But oth­er factors—a person’s genes, the vagaries of their immune sys­tem, the amount of virus they’re exposed to, the oth­er microbes in their bodies—might play a role too. In gen­er­al, “it’s a mys­tery why some peo­ple have mild dis­ease, even with­in the same age group,” Iwasa­ki says.

    Coro­n­avirus­es, much like influen­za, tend to be win­ter virus­es. In cold and dry air, the thin lay­ers of liq­uid that coat our lungs and air­ways become even thin­ner, and the beat­ing hairs that rest in those lay­ers strug­gle to evict virus­es and oth­er for­eign par­ti­cles. Dry air also seems to damp­en some aspects of the immune response to those trapped virus­es. In the heat and humid­i­ty of sum­mer, both trends reverse, and res­pi­ra­to­ry virus­es strug­gle to get a foothold.

    Unfor­tu­nate­ly, that might not mat­ter for the COVID-19 pan­dem­ic. At the moment, the virus is tear­ing through a world of immuno­log­i­cal­ly naive peo­ple, and that vul­ner­a­bil­i­ty is like­ly to swamp any sea­son­al vari­a­tions. After all, the new virus is trans­mit­ting read­i­ly in coun­tries like Sin­ga­pore (which is in the trop­ics) and Aus­tralia (which is still in sum­mer). And one recent mod­el­ing study con­clud­ed that “SARS-CoV­‑2 can pro­lif­er­ate at any time of year.” “I don’t have an immense amount of con­fi­dence that the weath­er is going to have the effect that peo­ple hope it will,” Gralin­s­ki says. “It may knock things down a lit­tle, but there’s so much per­son-to-per­son trans­mis­sion going on that it may take more than that.” Unless peo­ple can slow the spread of the virus by stick­ing to phys­i­cal-dis­tanc­ing rec­om­men­da­tions, the sum­mer alone won’t save us.

    ...

    ———–

    “Why the Coro­n­avirus Has Been So Suc­cess­ful” Ed Yong; The Atlantic; 03/20/2020

    “Since the start of the pan­dem­ic, the virus hasn’t changed in any obvi­ous­ly impor­tant ways. It’s mutat­ing in the way that all virus­es do. But of the 100-plus muta­tions that have been doc­u­ment­ed, none has risen to dom­i­nance, which sug­gests that none is espe­cial­ly impor­tant. “The virus has been remark­ably sta­ble giv­en how much trans­mis­sion we’ve seen,” says Lisa Gralin­s­ki of the Uni­ver­si­ty of North Car­oli­na. “That makes sense, because there’s no evo­lu­tion­ary pres­sure on the virus to trans­mit bet­ter. It’s doing a great job of spread­ing around the world right now.”

    No evo­lu­tion­ary pres­sure to trans­mit bet­ter. It’s already evolved the abil­i­ty to latch onto ACE2 far more strong­ly than SARS. And once it latch­es onto those ACE2 pro­teins in the upper res­pi­ra­to­ry tract, the virus is able to acti­vate itself more eas­i­ly than SARS with the help of a ubiq­ui­tous human pro­tein furin that will come along and cleave the spike pro­tein bridge required to acti­vate the virus. Those two evo­lu­tion­ary fea­tures appear to be crit­i­cal for giv­ing this virus its remark­ably high lev­els of infec­tious­ness.

    ...
    The struc­ture of the virus pro­vides some clues about its suc­cess. In shape, it’s essen­tial­ly a spiky ball. Those spikes rec­og­nize and stick to a pro­tein called ACE2, which is found on the sur­face of our cells: This is the first step to an infec­tion. The exact con­tours of SARS-CoV‑2’s spikes allow it to stick far more strong­ly to ACE2 than SARS-clas­sic did, and “it’s like­ly that this is real­ly cru­cial for per­son-to-per­son trans­mis­sion,” says Angela Ras­mussen of Colum­bia Uni­ver­si­ty. In gen­er­al terms, the tighter the bond, the less virus required to start an infec­tion.

    There’s anoth­er impor­tant fea­ture. Coro­n­avirus spikes con­sist of two con­nect­ed halves, and the spike acti­vates when those halves are sep­a­rat­ed; only then can the virus enter a host cell. In SARS-clas­sic, this sep­a­ra­tion hap­pens with some dif­fi­cul­ty. But in SARS-CoV­‑2, the bridge that con­nects the two halves can be eas­i­ly cut by an enzyme called furin, which is made by human cells and—crucially—is found across many tis­sues. “This is prob­a­bly impor­tant for some of the real­ly unusu­al things we see in this virus,” says Kris­t­ian Ander­sen of Scripps Research Trans­la­tion­al Insti­tute.

    For exam­ple, most res­pi­ra­to­ry virus­es tend to infect either the upper or low­er air­ways. In gen­er­al, an upper-res­pi­ra­to­ry infec­tion spreads more eas­i­ly, but tends to be milder, while a low­er-res­pi­ra­to­ry infec­tion is hard­er to trans­mit, but is more severe. SARS-CoV­‑2 seems to infect both upper and low­er air­ways, per­haps because it can exploit the ubiq­ui­tous furin. This dou­ble wham­my could also con­ceiv­ably explain why the virus can spread between peo­ple before symp­toms show up—a trait that has made it so dif­fi­cult to con­trol. Per­haps it trans­mits while still con­fined to the upper air­ways, before mak­ing its way deep­er and caus­ing severe symp­toms. All of this is plau­si­ble but total­ly hypo­thet­i­cal; the virus was only dis­cov­ered in Jan­u­ary, and most of its biol­o­gy is still a mys­tery.
    ...

    And then we have the oblig­a­tory assur­ances that, despite the seem­ing improb­a­bil­i­ty of a virus jump­ing from ani­mals to humans already hav­ing the key fea­tures that make it seem­ing­ly opti­mized for spread­ing between peo­ple, we should­n’t jump to con­clu­sions like the obvi­ous pos­si­bil­i­ty that the virus was man-made. Instead, we’re remind­ed that while the odds of an indi­vid­ual virus acquir­ing these muta­tions and then jump­ing to humans is “very low”, ran­dom low prob­a­bil­i­ty events do hap­pen. That’s the assur­ance. A reminder that even the improb­a­ble is pos­si­ble:

    ...
    The new virus cer­tain­ly seems to be effec­tive at infect­ing humans, despite its ani­mal ori­gins. The clos­est wild rel­a­tive of SARS-CoV­‑2 is found in bats, which sug­gests it orig­i­nat­ed in a bat, then jumped to humans either direct­ly or through anoth­er species. (Anoth­er coro­n­avirus found in wild pan­golins also resem­bles SARS-CoV­‑2, but only in the small part of the spike that rec­og­nizes ACE2; the two virus­es are oth­er­wise dis­sim­i­lar, and pan­golins are unlike­ly to be the orig­i­nal reser­voir of the new virus.) When SARS-clas­sic first made this leap, a brief peri­od of muta­tion was nec­es­sary for it to rec­og­nize ACE2 well. But SARS-CoV­‑2 could do that from day one. “It had already found its best way of being a [human] virus,” says Matthew Frie­man of the Uni­ver­si­ty of Mary­land School of Med­i­cine.

    This uncan­ny fit will doubtless­ly encour­age con­spir­a­cy the­o­rists: What are the odds that a ran­dom bat virus had exact­ly the right com­bi­na­tion of traits to effec­tive­ly infect human cells from the get-go, and then jump into an unsus­pect­ing per­son? “Very low,” Ander­sen says, “but there are mil­lions or bil­lions of these virus­es out there. These virus­es are so preva­lent that things that are real­ly unlike­ly to hap­pen some­times do.”
    ...

    And while that’s cer­tain­ly true that low prob­a­bil­i­ty events can indeed hap­pen, that’s not exact­ly a com­pelling counter argu­ment to sus­pi­cious that the virus was man-made. After all, what’s more improb­a­ble: that an incred­i­bly low-prob­a­bly event hap­pened where this virus just hap­pened to have all of these opti­mized fea­tures for humans when it jumped from anoth­er ani­mal vs the prob­a­bly that it was made in a lab. Which sce­nario is less like­ly?

    Also keep in mind that, while the large num­ber of virus­es that get pro­duced means high­ly improb­a­bly events can real­is­ti­cal­ly hap­pen, let’s not for­get that the same prin­ci­ple should apply when it comes to new vari­ants of the virus emerg­ing with new func­tion­al muta­tions. Like a new dom­i­nant strain with a muta­tion that allows it to spread more quick­ly and become a dom­i­nant strain. That’s not hap­pen­ing. Why aren’t those low prob­a­bly events dri­ving the evo­lu­tion of this virus? Might the virus already have had its evo­lu­tion sped up? Don’t for­get that the noto­ri­ous “gain-of-func­tion” exper­i­ments involv­ing H5N1 were exper­i­ments that sped up the evo­lu­tion of the virus. That’s how the gain of func­tion was hap­pen­ing. Sped up evo­lu­tion exper­i­ments. So if you just sped a virus’s evo­lu­tion up long enough with these kinds of exper­i­ments would you hit a point where the virus does­n’t evolve any­more and is basi­cal­ly already opti­mized? Might a lack of viral evo­lu­tion be an indi­rect sign that it’s already man-made? Who knows, but it’s worth not­ing the one sil­ver lin­ing in all this: at least it does­n’t sound like the virus itself will get much worse. Because it can’t get any bet­ter.

    Posted by Pterrafractyl | March 23, 2020, 2:12 pm
  3. Here’s a pair of research pub­li­ca­tions that are just get­ting released that expand on the obser­va­tion that SARS-CoV­‑2 virus has two key fea­tures that caus­es COVID-19 to be much more infec­tious in humans than the SARS-CoV virus that cause the SARS out­break in 2003:

    First, recall how SARS-CoV­‑2 appears to stick to the ACE2 recep­tors on the cell walls of human air­ways much more effec­tive­ly than SARS-CoV. This helps the virus infect the upper res­pi­ra­to­ry tract unlike SARS. Also recall how SARS-CoV­‑2 has a cleav­age site on its spike pro­tein that can be cleaved by the human pro­tein furin. This is seen as cru­cial for its infec­tious­ness because cleav­age of the spike pro­tein is required for the virus to inject its pay­load into the cell and furin is ubiq­ui­tous on the sur­face of human air­way cells. The orig­i­nal SARS-CoV virus from 2003 does­n’t have that furin cleav­age site. These are two key fea­tures that have made COVID-19 much more infec­tious than SARS.

    So the first pub­li­ca­tion below expands on how anom­alous it is for the SARS-CoV­‑2 to pos­sess that furin cleav­age site on the spike pro­tein when you look at the entire fam­i­ly of known coro­n­avirus­es and the sub­group that SARS-CoV­‑2 falls into. The paper uses the label 2019-nCoV for the SARS-CoV­‑2 virus (which is the more wide­ly used label), so the nam­ing can get a lit­tle con­fus­ing.

    There are dif­fer­ent gen­eras (fam­i­lies) of coro­n­avirus­es. SARS-CoV­‑2 (2019-nCoV) belongs to the Beta­coro­n­avirus fam­i­ly which has dif­fer­ent lin­eages. Click here to see a visu­al­iza­tion from the paper of the phy­lo­ge­net­ic coro­n­avirus fam­i­ly tree for dif­fer­ent coro­n­avirus­es in the Alpha­coro­n­avirus and Beta­coro­n­avirus fam­i­lies. You can see that the Beta­coro­n­avirus fam­i­ly has four dif­fer­ence lin­eages (a, b, c, d). SARS-CoV­‑2 belongs to the b lin­eage, which includes the SARS-CoV virus from 2003. The b lin­eage also includes the CoV ZXC21 bat virus, which is one of the virus­es most close­ly relat­ed to SARS-CoV­‑2 which is the major rea­son for the ini­tial sus­pi­cions that the virus jumped from bats to humans.

    Now, one would expect SARS-CoV­‑2 to be more sim­i­lar to oth­er virus­es in that same lin­eage than it is to the virus­es in oth­er lin­eages or gen­eras since it’s assumed they emerged from a com­mon ances­tor. And for the most part that’s true, with the major excep­tion of that cleav­age site on SARS-CoV­‑2. It turns out that no oth­er known virus­es in that b lin­eage of Beta­coro­n­avirus­es pos­sess the furin cleav­age site. There are Beta­coro­n­avirus­es in dif­fer­ent lin­eages that do poss­es the furin cleav­age site, but none in the b lin­eage. It’s pret­ty odd.

    The authors in the paper spec­u­late that this addi­tion of the furin cleav­age site in SARS-CoV­‑2 rep­re­sents a gain-of-func­tion muta­tion for the virus that allows it to infect humans more effi­cient­ly. So why is it that no oth­er coro­n­avirus­es in the b lin­eage of Beta­coro­n­avirus­es have the furin cleav­age site? Well, the authors spec­u­late that this might be an exam­ple of con­ver­gent evo­lu­tion tak­ing place between SARS-CoV­‑2 and oth­er coro­n­avirus­es out­side of the b lin­eage that also pos­sess the furin cleav­age sites. Con­ver­gent evo­lu­tion is a well known phe­nom­e­na in nature where dif­fer­ent organ­isms inde­pen­dent­ly evolve to pos­sess sim­i­lar fea­tures. And if we assume that SARS-CoV­‑2 isn’t a man-made virus then con­ver­gent evo­lu­tion is a rea­son­able sus­pi­cion. Of course, in the era of syn­thet­ic biol­o­gy and ‘gain-of-func­tion’ tech­niques in the lab, that assump­tion that this isn’t man-made is becom­ing an increas­ing­ly ten­u­ous assump­tion. More gen­er­al­ly, when we have to fall back on assump­tions of con­ver­gent evo­lu­tion to explain an appar­ent gain-of-func­tion adap­ta­tion it high­lights how unusu­al SARS-CoV­‑2 is com­pared to its clos­est viral cousins.

    Now, in the sec­ond pub­li­ca­tion below, the authors sug­gest a dif­fer­ent nat­ur­al mech­a­nism that could have result­ed in the evo­lu­tion­ar­i­ly unusu­al SARS-CoV­‑2 virus: recom­bi­na­tion. That’s a process that can hap­pen in the same ani­mal gets infect­ed by two RNA dif­fer­ent virus­es at the same time, result­ing a new chimeri­ca virus that a com­bi­na­tion of the two viral genomes. The authors observe that the genet­ic sequence of the Pan­golin-CoV virus — the coro­n­avirus that infects Pan­golins — is the sec­ond most sim­i­lar so SARS-CoV­‑2 after the horse­shoe bat ver­sion. But one part of the the S‑protein (the pro­tein with the furin cleav­age site) in SARS-CoV­‑2 is actu­al­ly much more close­ly relat­ed to the S‑protein in Pan­golin-CoV than to the horse­shoe bat ver­sion of the virus. The S‑protein con­sists of two sub­units (S1 and S2) that are gen­er­at­ed when the pro­tein is cleaved. The S1 sub­unit con­tains the part of the pro­tein that rec­og­nizes the ACE2 recep­tor on mam­malian cells. The S1 sub­unit also con­tains the furin cleav­age site in SARS-CoV­‑2, but not Pan­golin-CoV. Recall how Pan­golins have been sus­pect­ed to be an inter­me­di­ate host between bats and humans if we assume this real­ly did jump to humans from the wild. And yet even Pan­golin-CoV virus’s S‑protein does­n’t have the furin cleav­age site.

    The authors try to explain the sud­den emer­gence of the furin cleav­age site by sug­gest­ing that anoth­er coro­n­avirus with a furin cleav­age site infect­ed an ani­mal (a Pan­golin or bat) at the same time it was infect­ed with the Pan­golin or bat coro­n­avirus and that result­ed in a recom­bi­na­tion even and the inser­tion of that cleav­age site in Pan­golin-CoV, result­ing in SARS-CoV­‑2 (or an inter­me­di­ate) emerg­ing. And while it’s pos­si­ble recom­bi­na­tion was what led to the sud­den addi­tion of pre­cise­ly the adap­ta­tion that allows the virus to infect humans high­ly effi­cient­ly, it’s still a low prob­a­bil­i­ty event that we’re talk­ing about. After all, that furin cleav­age site is in an S‑protein that’s almost iden­ti­cal between SARS-CoV­‑2 and Pan­golin-CoV, imply­ing that if a recom­bi­na­tion event took place it did­n’t change the Pan­golin-CoV S‑protein very much. So what are the odds that the change just hap­pened to include this cru­cial furin cleav­age site? That seems like awful luck. Now, if we lat­er dis­cov­er a coro­n­avirus that has an S‑protein genet­ic sequence that’s an even clos­er match to the SARS-CoV­‑2 S‑protein sequence and con­tains that furin cleav­age site, well that would make a recom­bi­na­tion event sce­nario more plau­si­ble. But unless we find an exam­ple of an exist­ing virus with a close S‑protein match it seems like just hor­ri­ble luck that the furin cleav­age site just hap­pened to be part of the mys­tery coro­n­avirus that got recom­bined into the bat or Pan­golin ver­sions.

    Also note that falling back on the recom­bi­na­tion expla­na­tion is part­ly appeal­ing in this case between that furin cleav­age site is can­non­i­cal accord­ing to the first arti­cle below. It’s like exact­ly what you would need for furin to latch onto the spike pro­tein and not a less potent vari­ant. We would expect a can­non­i­cal cleav­age site in a virus that’s had a long time to evolve with­in a human host. That’s just evo­lu­tion in action. But in this case it’s like the virus had that evo­lu­tion­ar­i­ly opti­mized site right away, which is why it’s tempt­ing to assume it acquired it from a dif­fer­ent virus that already had an evo­lu­tion­ar­i­ly opti­mized site. It’s pos­si­ble, but real­ly bad luck.

    And that appears to be the gen­er­al theme for explain­ing the unex­pect­ed genet­ic char­ac­ter­is­tics of the SARS-CoV­‑2 virus caus­ing the COVID-19 pan­dem­ic: if this hap­pened nat­u­ral­ly, it was a very unlucky turn of events both because of the extreme neg­a­tive con­se­quences and because of how improb­a­ble it was to hap­pen in the first place. That’s not to say that viral pan­demics of this nature were improb­a­ble. On the con­trary, future pan­demics are a cer­tain­ty. It was just a mat­ter of when and how. But hav­ing this virus emerge with seem­ing­ly opti­mized genet­ics for infect­ing humans with­out first going through an ear­li­er, less infec­tious strain, is just hor­ri­ble luck if that’s what hap­pened.

    Now, it’s also pos­si­ble there was an evo­lu­tion­ary inter­me­di­ary we just haven’t found yet. For exam­ple, let’s say SARS-CoV­‑2 real­ly did emerge from Pan­golin-CoV. There could have been an ear­li­er ver­sion we nev­er detect­ed that had non-can­non­i­cal furin cleav­age sites that furin could only weak­ly act upon. Per­haps this hypo­thet­i­cal ear­li­er ver­sion of the virus has been infect­ing peo­ple for a while with­out caus­ing sig­nif­i­cant symp­toms and allow­ing evo­lu­tion to play out in the human host. This would be the con­ver­gent evo­lu­tion sce­nario involv­ing an unknown inter­me­di­ary. It’s a pos­si­ble sce­nario, espe­cial­ly if the weak­er ver­sion of the virus did­n’t real­ly cause sig­nif­i­cant dis­ease. In that case there would­n’t have been any rea­son for doc­tors to zero in on it and sequence its genome. But so far we have no evi­dence of that ear­li­er ver­sion of this virus float­ing around. It’s still just a hypo­thet­i­cal.

    So when it comes to the ques­tion of whether or not this is a man-made virus, we appear to be a sit­u­a­tion where we’re forced to gues­ti­mate the rel­a­tive like­li­hood that this virus could have emerged nat­u­ral­ly vs being made in a lab. We know it could emerge nat­u­ral­ly. There are known mech­a­nisms for doing that. We also know it could obvi­ous­ly have been built in a lab, which would cer­tain­ly explain the unex­pect­ed char­ac­ter­is­tics of this virus. Which of those sce­nar­ios is most like­ly?

    Ok, here’s the first arti­cle in Antivi­ral Research that describes how the SARS-CoV­‑2 virus (2019-nCov) is the only virus in the b lin­eage of the Beta­coro­n­avirus gen­era with that furin cleav­age site. A furin cleav­age site that hap­pens to be a can­non­i­cal site which means its basi­cal­ly evo­lu­tion­ar­i­ly opti­mized for furin to latch onto. As the authors put it, this rep­re­sents a gain-of-func­tion for SARS-CoV­‑2 (2019-nCov) and since sim­i­lar furin cleav­age sites have been observed in dif­fer­ent lin­eages of Beta­coro­n­avirus this may be an exam­ple of con­ver­gent evo­lu­tion in action:

    Antivi­ral Research

    The spike gly­co­pro­tein of the new coro­n­avirus 2019-nCoV con­tains a furin-like cleav­age site absent in CoV of the same clade

    B.Coutard, C.Valle, X.de Lam­bal­lerie, B.Canard, N.G.Seidah, E.Decroly
    Vol­ume 176, April 2020

    High­lights

    • The genom­ic sequence of 2019-nCoV indi­cates that the virus clus­ters with beta­coro­n­avirus­es of lin­eage b.
    • 2019-nCoV S‑protein sequence has a spe­cif­ic furin-like cleav­age site absent in lin­eage b CoV includ­ing SARS-CoV sequences.
    • The furin-like cleav­age site in the S‑protein of 2019-nCoV may have impli­ca­tions for the viral life cycle and path­o­genic­i­ty.
    • Cam­paigns to devel­op anti-2019-nCoV ther­a­peu­tics should include the eval­u­a­tion of furin inhibitors.

    Abstract

    In 2019, a new coro­n­avirus (2019-nCoV) infect­ing Humans has emerged in Wuhan, Chi­na. Its genome has been sequenced and the genom­ic infor­ma­tion prompt­ly released. Despite a high sim­i­lar­i­ty with the genome sequence of SARS-CoV and SARS-like CoVs, we iden­ti­fied a pecu­liar furin-like cleav­age site in the Spike pro­tein of the 2019-nCoV, lack­ing in the oth­er SARS-like CoVs. In this arti­cle, we dis­cuss the pos­si­ble func­tion­al con­se­quences of this cleav­age site in the viral cycle, path­o­genic­i­ty and its poten­tial impli­ca­tion in the devel­op­ment of antivi­rals.

    Human coro­n­avirus­es (CoV) are enveloped pos­i­tive-strand­ed RNA virus­es belong­ing to the order Nidovi­rales, and are most­ly respon­si­ble for upper res­pi­ra­to­ry and diges­tive tract infec­tions. Among them SARS-CoV and MERS-CoV that spread in 2002 and 2013 respec­tive­ly, have been asso­ci­at­ed with severe human ill­ness­es, such as severe pneu­mo­nia and bron­chi­oli­tis, and even menin­gi­tis in more vul­ner­a­ble pop­u­la­tions (de Wit et al., 2016). In Decem­ber 2019, a new CoV (2019-nCoV) has been detect­ed in the city of Wuhan, and this emerg­ing viral infec­tion was asso­ci­at­ed with severe human res­pi­ra­to­ry dis­ease with a ~2–3% fatal­i­ty rate (Li et al., 2020). The virus that was pre­sumed to have ini­tial­ly been trans­mit­ted from an ani­mal reser­voir to humans pos­si­bly via an ampli­fy­ing host. How­ev­er human-to-human trans­mis­sion has been report­ed, lead­ing to a sus­tained epi­dem­ic spread with >31,000 con­firmed human infec­tions, includ­ing >640 deaths, report­ed by the WHO in ear­ly Feb­ru­ary 2020. The esti­mat­ed effec­tive repro­duc­tive num­ber ® val­ue of ~2.90 (95%: 2.32–3.63) at the begin­ning of the out­break rais­es the pos­si­bil­i­ty of a pan­demics (Zhao et al., 2020). This prompt­ed WHO to declare it as a Pub­lic Health Emer­gency of Inter­na­tion­al Con­cern. This is espe­cial­ly rel­e­vant because so far there are no spe­cif­ic antivi­ral treat­ments avail­able or vac­cine. Based on its genome sequence, 2019-nCoV belongs to lin­eage b of Beta­coro­n­avirus (Fig. 1A), which also includes the SARS-CoV and bat CoV ZXC21, the lat­ter and CoV ZC45 being the clos­est to 2019-nCoV. 2019-nCoV shares ~76% amino acid sequence iden­ti­ty in the Spike (S)-protein sequence with SARS-CoV and 80% with CoV ZXC21 (Chan et al., 2020). In this arti­cle, we focus on a spe­cif­ic furin-like pro­tease recog­ni­tion pat­tern present in the vicin­i­ty of one of the mat­u­ra­tion sites of the S pro­tein (Fig. 1B) that may have sig­nif­i­cant func­tion­al impli­ca­tions for virus entry.

    The pro­pro­tein con­ver­tases (PCs; genes PCSKs) con­sti­tute a fam­i­ly of nine ser­ine secre­to­ry pro­teas­es that reg­u­late var­i­ous bio­log­i­cal process­es in both healthy and dis­ease states (Sei­dah and Prat, 2012). By pro­te­ol­y­sis, PCs are respon­si­ble for the acti­va­tion of a wide vari­ety of pre­cur­sor pro­teins, such as growth fac­tors, hor­mones, recep­tors and adhe­sion mol­e­cules, as well as cell sur­face gly­co­pro­teins of infec­tious virus­es (Sei­dah and Chre­tien, 1999) (Table 1). Sev­en PCs cleave pre­cur­sor pro­teins at spe­cif­ic sin­gle or paired basic amino acids (aa) with­in the motif (R/K)-(2X)n-(R/K)↓, where n = 0, 1, 2, or 3 spac­er aa (Sei­dah and Chre­tien, 1999). Because of their role in the pro­cess­ing of many crit­i­cal cell sur­face pro­teins PCs, espe­cial­ly furin, have been impli­cat­ed in viral infec­tions. They have the poten­tial to cleave specif­i­cal­ly viral enve­lope gly­co­pro­teins, there­by enhanc­ing viral fusion with host cell mem­branes (Iza­guirre, 2019; Moulard and Decroly, 2000). In the case of human-infect­ing coro­n­avirus­es such as HCoV-OC43 (Le Coupanec et al., 2015), MERS-CoV (Mil­let and Whit­tak­er, 2014), and HKU1 (Chan et al., 2008) the spike pro­tein has been demon­strat­ed to be cleaved at an S1/S2 cleav­age site (Fig. 2) gen­er­at­ing the S1 and S2 sub­units. The above three virus­es dis­play the canon­i­cal (R/K)-(2X)n-(R/K)↓ motif (Table 1). Addi­tion­al­ly, it has been demon­strat­ed that vari­a­tion around the viral enve­lope gly­co­pro­tein cleav­age site plays a role in cel­lu­lar tro­pism and patho­gen­e­sis. For instance, the patho­gen­e­sis of some CoV has been pre­vi­ous­ly relat­ed to the pres­ence of a furin-like cleav­age site in the S‑protein sequence. For exam­ple, the inser­tion of a sim­i­lar cleav­age site in the infec­tious bron­chi­tis virus (IBV) S‑protein results in high­er path­o­genic­i­ty, pro­nounced neur­al symp­toms and neu­rotro­pism in infect­ed chick­ens (Cheng et al., 2019).

    Sim­i­lar­ly, in the case of influen­za virus, low-path­o­genic­i­ty forms of influen­za virus con­tain a sin­gle basic residue at the cleav­age site, which is cleaved by trypsin-like pro­teas­es and the tis­sue dis­tri­b­u­tion of the acti­vat­ing protease(s) typ­i­cal­ly restricts infec­tions to the res­pi­ra­to­ry and/or intesti­nal organs (Sun et al., 2010). Con­verse­ly, the high­ly path­o­gen­ic forms of influen­za have a furin-like cleav­age site cleaved by dif­fer­ent cel­lu­lar pro­teas­es, includ­ing furin, which are expressed in a wide vari­ety of cell types allow­ing a widen­ing of the cell tro­pism of the virus (Kido et al., 2012). Fur­ther­more the inser­tion of a multi­ba­sic motif RERRRKKR↓GL at the H5N1 hemag­glu­tinin HA cleav­age site was like­ly asso­ci­at­ed with the hyper-vir­u­lence of the virus dur­ing the Hong Kong 1997 out­break Claas et al., 1998). This motif exhibits the crit­i­cal Arg at P1 and basic residues at P2 and P4, as well as P6 and P8 and an aliphat­ic Leu at P2’ posi­tions (Table 1) (Schechter and Berg­er nomen­cla­ture (Schechter and Berg­er, 1968)), typ­i­cal of a furin-like cleav­age speci­fici­ty (Braun and Sauter, 2019; Iza­guirre, 2019; Sei­dah and Prat, 2012).

    The coro­n­avirus S‑protein is the struc­tur­al pro­tein respon­si­ble for the crown-like shape of the CoV viral par­ti­cles, from which the orig­i­nal name “coro­n­avirus” was coined. The ~1200 aa long S‑protein belongs to class‑I viral fusion pro­teins and con­tributes to the cell recep­tor bind­ing, tis­sue tro­pism and patho­gen­e­sis (Lu et al., 2015; Mil­let and Whit­tak­er, 2014). It con­tains sev­er­al con­served domains and motifs (Fig. 2). The tri­met­ric S‑protein is processed at the S1/S2 cleav­age site by host cell pro­teas­es, dur­ing infec­tion. Fol­low­ing cleav­age, also known as prim­ing, the pro­tein is divid­ed into an N‑terminal S1-ectodomain that recog­nis­es a cog­nate cell sur­face recep­tor and a C‑terminal S2-mem­brane-anchored pro­tein involved in viral entry. The SARS-CoV S1-pro­tein con­tains a con­served Recep­tor Bind­ing Domain (RBD), which recog­nis­es the angiotensin-con­vert­ing enzyme 2 (ACE2) (Li et al., 2003). The SARS-CoV binds to both bat and human cells, and the virus can infect both organ­isms (Ge et al., 2013; Kuhn et al., 2004). The RBD sur­face of S1/ACE2 impli­cates 14 aa in the S1 of SARS-CoV (Li et al., 2005). Among them, 8 residues are strict­ly con­served in 2019-nCoV, sup­port­ing the hypoth­e­sis that ACE2 is also the recep­tor of the new­ly emerged nCoV (Wan et al., 2020). The S2-pro­tein con­tains the fusion pep­tide (FP), a sec­ond pro­te­olyt­ic site (S2’), fol­lowed by an inter­nal fusion pep­tide (IFP) and two hep­tad-repeat domains pre­ced­ing the trans­mem­brane domain ™ (Fig. 2). Notably, the IFPs of the 2019-nCoV and SARS-CoV are iden­ti­cal, dis­play­ing char­ac­ter­is­tics of viral fusion pep­tides (Fig. 2). While the mol­e­c­u­lar mech­a­nism involved in cell entry is not yet ful­ly under­stood, it is like­ly that both FP and IFP par­tic­i­pate in the viral entry process (Lu et al., 2015) and thus the S‑protein must like­ly be cleaved at both S1/S2 and S2’ cleav­age sites for virus entry. The furin-like S2’ cleav­age site at KR↓SF with P1 and P2 basic residues and a P2’ hydropho­bic Phe (Sei­dah and Prat, 2012), down­stream of the IFP is iden­ti­cal between the 2019-nCoV and SARS-CoV (Fig. 2). In the MERS-CoV and HCoV-OC43 the S1/S2 site is replaced by RXXR↓SA, with P1 and P4 basic residues, and an Ala (not aliphat­ic) at P2’, sug­gest­ing a some­what less favourable cleav­age by furin. How­ev­er, in the oth­er less path­o­gen­ic cir­cu­lat­ing human CoV, the S2’ cleav­age site only exhibits a monoba­sic R↓S sequence (Fig. 2) with no basic residues at either P2 and/or P4 need­ed to allow furin cleav­age, sug­gest­ing a less effi­cient cleav­age or high­er restric­tion at the entry step depend­ing on the cog­nate pro­teas­es expressed by tar­get cells. Even though pro­cess­ing at S2’ in 2019-nCoV is expect­ed to be a key event for the final acti­va­tion of the S‑protein, the protease(s) involved in this process have not yet been con­clu­sive­ly iden­ti­fied. Based on the 2019-nCoV S2’ sequence and the above argu­ments, we pro­pose that one or more furin-like enzymes would cleave the S2’ site at KR↓SF. In con­trast to the S2’, the first cleav­age between the RBD and the FP (S1/S2 cleav­age site, Fig. 2) has been exten­sive­ly stud­ied for many CoVs (Lu et al., 2015). Inter­est­ing­ly the S1/S2 pro­cess­ing site exhibits dif­fer­ent motifs among coro­n­avirus­es (Fig. 2, site 1 & site 2), with many of them dis­play­ing cleav­age after a basic residue. It is thus like­ly that the prim­ing process is ensured by dif­fer­ent host cell pro­teas­es depend­ing on the sequence of the S1/S2 cleav­age site. Accord­ing­ly the MERS-CoV S‑protein, which con­tains a RSVR↓SV motif is cleaved dur­ing virus egress, prob­a­bly by furin (Mille and Whit­tak­er, 2014). Con­verse­ly the S‑protein of SARS-CoV remains large­ly uncleaved after biosyn­the­sis, pos­si­bly due to the lack of a favourable furin-like cleav­age site (SLLR-ST). In this case, it was report­ed that fol­low­ing recep­tor bind­ing the S‑protein is cleaved at a con­served sequence AYT↓M (locat­ed 10 aa down­stream of SLLR-ST) by tar­get cells’ pro­teas­es such as elas­tase, cathep­sin L or TMPRSS2 (Bosch et al., 2008; Mat­suya­ma et al., 2010, 2005; Mil­let and Whit­tak­er, 2015). As the prim­ing event is essen­tial for virus entry, the effi­ca­cy and extent of this acti­va­tion step by the pro­teas­es of the tar­get cells should reg­u­late cel­lu­lar tro­pism and viral patho­gen­e­sis. In the case of the 2019-nCoV S‑protein, the con­served site 2 sequence AYT↓M may still be cleaved, pos­si­bly after the pre­ferred furin-cleav­age at the site 1 (Fig. 2).

    Since furin is high­ly expressed in lungs, an enveloped virus that infects the res­pi­ra­to­ry tract may suc­cess­ful­ly exploit this con­ver­tase to acti­vate its sur­face gly­co­pro­tein (Bassi et al., 2017; Mbikay et al., 1997). Before the emer­gence of the 2019-nCoV, this impor­tant fea­ture was not observed in the lin­eage b of beta­coro­n­avirus­es. How­ev­er, it is shared by oth­er CoV (HCoV-OC43, MERS-CoV, MHV-A59) har­bour­ing furin-like cleav­age sites in their S‑protein (Fig. 2; Table 1), which were shown to be processed by furin exper­i­men­tal­ly (Le Coupanec et al., 2015; Mille and Whit­tak­er, 2014). Strik­ing­ly, the 2019-nCoV S‑protein sequence con­tains 12 addi­tion­al nucleotides upstream of the sin­gle Arg↓ cleav­age site 1 (Fig. 1, Fig. 2) lead­ing to a pre­dic­tive­ly sol­vent-exposed PRRAR↓SV sequence, which cor­re­sponds to a canon­i­cal furin-like cleav­age site (Braun and Sauter, 2019; Iza­guirre, 2019; Sei­dah and Prat, 2012). This furin-like cleav­age site, is sup­posed to be cleaved dur­ing virus egress (Mille and Whit­tak­er, 2014) for S‑protein “prim­ing” and may pro­vide a gain-of-func­tion to the 2019-nCoV for effi­cient spread­ing in the human pop­u­la­tion com­pared to oth­er lin­eage b beta­coro­n­avirus­es. This pos­si­bly illus­trates a con­ver­gent evo­lu­tion path­way between unre­lat­ed CoVs. Inter­est­ing­ly, if this site is not processed, the S‑protein is expect­ed to be cleaved at site 2 dur­ing virus endo­cy­to­sis, as observed for the SARS-CoV.

    Obvi­ous­ly much more work is need­ed to demon­strate exper­i­men­tal­ly our asser­tion, but the inhi­bi­tion of such pro­cess­ing enzyme(s) may rep­re­sent a poten­tial antivi­ral strat­e­gy. Indeed, it was recent­ly shown that in an effort to lim­it viral infec­tions, host cells that are infect­ed by a num­ber of virus­es pro­voke an inter­fer­on response to inhib­it the enzy­mat­ic activ­i­ty of furin-like enzymes. It was also demon­strat­ed that HIV infec­tion induces the expres­sion of either the pro­tease acti­vat­ed recep­tor 1 (PAR1) (Kim et al., 2015) or guany­late bind­ing pro­teins 2 and 5 (GBP2,5) (Braun and Sauter, 2019) that restrict the traf­fick­ing of furin to the trans Gol­gi net­work (PAR1) or to ear­ly Gol­gi com­part­ments (GBP2,5) where the pro­pro­tein con­ver­tase remains inac­tive. Alto­geth­er, these obser­va­tions sug­gest that inhibitors of furin-like enzymes may con­tribute to inhibit­ing virus prop­a­ga­tion.

    ...

    ————

    “The spike gly­co­pro­tein of the new coro­n­avirus 2019-nCoV con­tains a furin-like cleav­age site absent in CoV of the same clade” by B.Coutard, C.Valle, X.de Lam­bal­lerie, B.Canard, N.G.Seidah, E.Decroly; Antivi­ral Research; April 2020

    “Since furin is high­ly expressed in lungs, an enveloped virus that infects the res­pi­ra­to­ry tract may suc­cess­ful­ly exploit this con­ver­tase to acti­vate its sur­face gly­co­pro­tein (Bassi et al., 2017; Mbikay et al., 1997). Before the emer­gence of the 2019-nCoV, this impor­tant fea­ture was not observed in the lin­eage b of beta­coro­n­avirus­es. How­ev­er, it is shared by oth­er CoV (HCoV-OC43, MERS-CoV, MHV-A59) har­bour­ing furin-like cleav­age sites in their S‑protein (Fig. 2; Table 1), which were shown to be processed by furin exper­i­men­tal­ly (Le Coupanec et al., 2015; Mille and Whit­tak­er, 2014). Strik­ing­ly, the 2019-nCoV S‑protein sequence con­tains 12 addi­tion­al nucleotides upstream of the sin­gle Arg↓ cleav­age site 1 (Fig. 1, Fig. 2) lead­ing to a pre­dic­tive­ly sol­vent-exposed PRRAR↓SV sequence, which cor­re­sponds to a canon­i­cal furin-like cleav­age site (Braun and Sauter, 2019; Iza­guirre, 2019; Sei­dah and Prat, 2012). This furin-like cleav­age site, is sup­posed to be cleaved dur­ing virus egress (Mille and Whit­tak­er, 2014) for S‑protein “prim­ing” and may pro­vide a gain-of-func­tion to the 2019-nCoV for effi­cient spread­ing in the human pop­u­la­tion com­pared to oth­er lin­eage b beta­coro­n­avirus­es. This pos­si­bly illus­trates a con­ver­gent evo­lu­tion path­way between unre­lat­ed CoVs. Inter­est­ing­ly, if this site is not processed, the S‑protein is expect­ed to be cleaved at site 2 dur­ing virus endo­cy­to­sis, as observed for the SARS-CoV.”

    As the authors put it, the obser­va­tion of the of an addi­tion­al 12 nucleotides (encod­ing for four addi­tion­al amino acids) that hap­pens to encode for a furin cleav­age site right in the S‑protein (the pro­tein that needs to be cleaved for the virus to inject its pay­load) is strik­ing. It’s strik­ing, in part because it’s not found in the close­ly relat­ed bat coro­n­avirus or any oth­er virus­es in the b lin­eage of Beta­coro­n­avirus­es. And strik­ing because the furin cleav­age site encod­ed by these 12 nucleotides is the can­non­i­cal site. That’s why con­ver­gent evo­lu­tion is pro­posed as an expla­na­tion: it’s one of the nat­ur­al process­es that could explain this strik­ing obser­va­tion that SARS-CoV­‑2 some­how acquired a can­non­i­cal furin cleav­age site despite the sites’s absence in all of the virus­es in the b lin­eage that the virus is assumed to have evolved from.

    But as the sec­ond paper below indi­cates, coevo­lu­tion isn’t the only pos­si­ble nat­ur­al expla­na­tion for this strik­ing obser­va­tion. It’s pos­si­ble there was a recom­bi­na­tion event. That’s what they spec­u­lat­ed when observ­ing that the S‑protein of SARS-CoV­‑2 — the pro­tein that con­tains this furin cleav­age site — is even more close­ly relat­ed to the S‑protein found in the Pan­golin-CoV than the bat ver­sion. The Recep­tor Bind­ing Domain (RBD) of SARS-CoV­‑2 and Pan­golin-CoV — the parts of the virus that rec­og­nize and stick to the ACE2 recep­tor on human cells — are almost iden­ti­cal. All indi­ca­tion from the genet­ics make Pan­golin-CoV the like­li­est known pre­cur­sor to SARS-CoV­‑2. But even with Pan­golin-CoV the S‑protein does­n’t have that furin cleav­age site. But instead of sug­gest­ing the seem­ing­ly sud­den addi­tion to the furin cleav­age site may have arisen through evo­lu­tion (con­ver­gent evo­lu­tion in this case), the authors spec­u­late that per­haps a recom­bi­na­tion even took place where a Pan­golin, or some oth­er inter­me­di­ate host, got infect­ed with both Pan­golin-CoV and a dif­fer­ent virus with does have the furin cleav­age site and SARS-CoV­‑2 emerged:

    Cur­rent Biol­o­gy
    Issue 30, pages 1–6

    Prob­a­ble Pan­golin Ori­gin of SARS-CoV­‑2 Asso­ci­at­ed with the COVID-19 Out­break

    Tao Zhang, Qun­fu Wu, Zhi­gang Zhang
    April 6, 2020

    High­lights

    • Pan­golin-CoV is 91.02% iden­ti­cal to SARS-CoV­‑2 at the whole-genome lev­el
    • Pan­golin-CoV is the sec­ond clos­est rel­a­tive of SARS-CoV­‑2 behind RaTG13
    • Five key amino acids in the RBD are con­sis­tent between Pan­golin-CoV and SARS-CoV­‑2
    • Only SARS-CoV­‑2 con­tains a poten­tial cleav­age site for furin pro­teas­es

    Sum­ma­ry

    An out­break of coro­n­avirus dis­ease 2019 (COVID-19) caused by the 2019 nov­el coro­n­avirus (SARS-CoV­‑2) began in the city of Wuhan in Chi­na and has wide­ly spread world­wide. Cur­rent­ly, it is vital to explore poten­tial inter­me­di­ate hosts of SARS-CoV­‑2 to con­trol COVID-19 spread. There­fore, we rein­ves­ti­gat­ed pub­lished data from pan­golin lung sam­ples from which SARS-CoV-like CoVs were detect­ed by Liu et al. [1]. We found genom­ic and evo­lu­tion­ary evi­dence of the occur­rence of a SARS-CoV-2-like CoV (named Pan­golin-CoV) in dead Malayan pan­golins. Pan­golin-CoV is 91.02% and 90.55% iden­ti­cal to SARS-CoV­‑2 and Bat­CoV RaTG13, respec­tive­ly, at the whole-genome lev­el. Aside from RaTG13, Pan­golin-CoV is the most close­ly relat­ed CoV to SARS-CoV­‑2. The S1 pro­tein of Pan­golin-CoV is much more close­ly relat­ed to SARS-CoV­‑2 than to RaTG13. Five key amino acid residues involved in the inter­ac­tion with human ACE2 are com­plete­ly con­sis­tent between Pan­golin-CoV and SARS-CoV­‑2, but four amino acid muta­tions are present in RaTG13. Both Pan­golin-CoV and RaTG13 lost the puta­tive furin recog­ni­tion sequence motif at S1/S2 cleav­age site that can be observed in the SARS-CoV­‑2. Con­clu­sive­ly, this study sug­gests that pan­golin species are a nat­ur­al reser­voir of SARS-CoV-2-like CoVs.

    Results and Dis­cus­sion

    Sim­i­lar to the case for SARS-CoV and MERS-CoV [2], the bat is still a prob­a­ble species of ori­gin for 2019 nov­el coro­n­avirus (SARS-CoV­‑2) because SARS-CoV­‑2 shares 96% whole-genome iden­ti­ty with a bat CoV, Bat­CoV RaTG13, from Rhi­nolo­phus affi­nis from Yun­nan Province [3]. How­ev­er, SARS-CoV and MERS-CoV usu­al­ly pass into inter­me­di­ate hosts, such as civets or camels, before leap­ing to humans [4]. This fact indi­cates that SARS-CoV­‑2 was prob­a­bly trans­mit­ted to humans by oth­er ani­mals. Con­sid­er­ing that the ear­li­est coro­n­avirus dis­ease 2019 (COVID-19) patient report­ed no expo­sure at the seafood mar­ket [5], it is vital to find the inter­me­di­ate SARS-CoV­‑2 host to block inter­species trans­mis­sion. On 24 Octo­ber 2019, Liu and his col­leagues from the Guang­dong Wildlife Res­cue Cen­ter of Chi­na [1] first detect­ed the exis­tence of a SARS-CoV-like CoV from lung sam­ples of two dead Malayan pan­golins with a frothy liq­uid in their lungs and pul­monary fibro­sis, and this fact was dis­cov­ered close to when the COVID-19 out­break occurred. Using their pub­lished results, we showed that all virus con­tigs assem­bled from two lung sam­ples (lung07 and lung08) exhib­it­ed low iden­ti­ties, rang­ing from 80.24% to 88.93%, with known SARSr-CoVs. Hence, we con­jec­tured that the dead Malayan pan­golins may car­ry a new CoV close­ly relat­ed to SARS-CoV­‑2.

    Assess­ing the Prob­a­bil­i­ty of SARS-CoV-2-like CoV Pres­ence in Pan­golin Species

    To con­firm our assump­tion, we down­loaded raw RNA sequenc­ing (RNA-seq) data (SRA: PRJNA573298) for those two lung sam­ples from the SRA and con­duct­ed con­sis­tent qual­i­ty con­trol and con­t­a­m­i­nant removal, as described by Liu’s study [1]. We found 1,882 clean reads from the lung08 sam­ple that mapped to the SARS-CoV­‑2 ref­er­ence genome (Gen­Bank: MN908947) [6] and cov­ered 76.02% of the SARS-CoV­‑2 genome. We per­formed de novo assem­bly of those reads and obtained 36 con­tigs with lengths rang­ing from 287 bp to 2,187 bp, with a mean length of 700 bp. Via Blast analy­sis against pro­teins from 2,845 CoV ref­er­ence genomes, includ­ing RaTG13, SARS-CoV-2s, and oth­er known CoVs, we found that 22 con­tigs were best matched to SARS-CoV-2s (70.6%–100% amino acid iden­ti­ty; aver­age: 95.41%) and that 12 con­tigs matched to bat SARS-CoV-like CoV (92.7%–100% amino acid iden­ti­ty; aver­age: 97.48%) (Table S1). These results indi­cate that the Malayan pan­golin might car­ry a nov­el CoV (here named Pan­golin-CoV) that is sim­i­lar to SARS-CoV­‑2.

    Draft Genome of Pan­golin-CoV and Its Genom­ic Char­ac­ter­is­tics

    Using a ref­er­ence-guid­ed scaf­fold­ing approach, we cre­at­ed a Pan­golin-CoV draft genome (19,587 bp) based on the above 34 con­tigs. To reduce the effect of raw read errors on scaf­fold­ing qual­i­ty, small frag­ments that aligned against the ref­er­ence genome with a length less than 25 bp were man­u­al­ly dis­card­ed if they were unable to be cov­ered by any large frag­ments or ref­er­ence genome. Remap­ping 1,882 reads against the draft genome result­ed in 99.99% genome cov­er­age (cov­er­age depth range: 1X–47X) (Fig­ure 1A). The mean cov­er­age depth was 7.71X across the whole genome, which was two times high­er than the low­est com­mon 3X read cov­er­age depth for SNP call­ing based on low-cov­er­age sequenc­ing in the 1000 Genomes Project pilot phase [7]. Sim­i­lar cov­er­age lev­els are also suf­fi­cient to detect rare or low-abun­dance micro­bial species from metage­nom­ic datasets [8], indi­cat­ing that our assem­bled Pan­golin-CoV draft genome is reli­able for fur­ther analy­ses. Based on Sim­plot analy­sis [9], Pan­golin-CoV showed high over­all genome sequence iden­ti­ty to RaTG13 (90.55%) and SARS-CoV­‑2 (91.02%) through­out the genome (Fig­ure 1B), although there was a high­er iden­ti­ty (96.2%) between SARS-CoV­‑2 and RaTG13 [3]. Oth­er SARS-CoV-like CoVs sim­i­lar to Pan­golin-CoV were bat SARSr-CoV ZXC21 (85.65%) and bat SARSr-CoV ZC45 (85.01%). While this man­u­script was under review, two sim­i­lar preprint stud­ies found that CoVs in pan­golins shared 90.3% [10] and 92.4% [11] DNA iden­ti­ty with SARS-CoV­‑2, approx­i­mat­ing the 91.02% iden­ti­ty to SARS-CoV­‑2 observed here and sup­port­ing our find­ings. Tak­en togeth­er, these results indi­cate that Pan­golin-CoV might be the com­mon ori­gin of SARS-CoV­‑2 and RaTG13.

    The Pan­golin-CoV genome orga­ni­za­tion was char­ac­ter­ized by sequence align­ment against SARS-CoV­‑2 (Gen­Bank: MN908947) and RaTG13. The Pan­golin-CoV genome con­sists of six major open read­ing frames (ORFs) com­mon to CoVs and four oth­er acces­so­ry genes (Fig­ure 1C; Table S2). Fur­ther analy­sis indi­cat­ed that Pan­golin-CoV genes aligned to SARS-CoV­‑2 genes with cov­er­age rang­ing from 45.8% to 100% (aver­age cov­er­age 76.9%). Pan­golin-CoV genes shared high aver­age nucleotide and amino acid iden­ti­ty with both SARS-CoV­‑2 (Gen­Bank: MN908947) (93.2% nucleotide/94.1% amino acid iden­ti­ty) and RaTG13 (92.8% nucleotide/93.5% amino acid iden­ti­ty) genes (Fig­ure 1C; Table S2). Sur­pris­ing­ly, some Pan­golin-CoV genes showed high­er amino acid sequence iden­ti­ty to SARS-CoV­‑2 genes than to RaTG13 genes, includ­ing orf1b (73.4%/72.8%), the spike (S) pro­tein (97.5%/95.4%), orf7a (96.9%/93.6%), and orf10 (97.3%/94.6%). The high S pro­tein amino acid iden­ti­ty implies func­tion­al sim­i­lar­i­ty between Pan­golin-CoV and SARS-CoV­‑2.

    Phy­lo­ge­net­ic Rela­tion­ships among Pan­golin-CoV, RaTG13, and SARS-CoV­‑2

    To deter­mine the evo­lu­tion­ary rela­tion­ships among Pan­golin-CoV, SARS-CoV­‑2, and pre­vi­ous­ly iden­ti­fied CoVs, we esti­mat­ed phy­lo­ge­net­ic trees based on the nucleotide sequences of the whole-genome sequence, RNA-depen­dent RNA poly­merase gene (RdRp), non-struc­tur­al pro­tein genes ORF1a and ORF1b, and main struc­tur­al pro­teins encod­ed by the S and M genes. In all phy­lo­ge­nies, Pan­golin-CoV, RaTG13, and SARS-CoV­‑2 were clus­tered into a well-sup­port­ed group, here named the “SARS-CoV­‑2 group” (Fig­ures 2, S1, and S2). This group rep­re­sents a nov­el Beta­coro­n­avirus group. With­in this group, RaTG13 and SARS-CoV­‑2 were grouped togeth­er, and Pan­golin-CoV was their clos­est com­mon ances­tor. How­ev­er, whether the basal posi­tion of the SARS-CoV­‑2 group is SARSr-CoV ZXC21 and/or SARSr-CoV ZC45 is still under debate. Such debate also occurred in both the Wu et al. [6] and Zhou et al. [3] stud­ies. A pos­si­ble expla­na­tion is a past his­to­ry of recom­bi­na­tion in the Beta­coro­n­avirus group [6]. It is note­wor­thy that the dis­cov­ered evo­lu­tion­ary rela­tion­ships of CoVs shown by the whole genome, RdRp gene, and S gene were high­ly con­sis­tent with those exhib­it­ed by com­plete genome infor­ma­tion in the Zhou et al. study [3]. This cor­re­spon­dence indi­cates that our Pan­golin-CoV draft genome has enough genom­ic infor­ma­tion to trace the true evo­lu­tion­ary posi­tion of Pan­golin-CoV in CoVs.

    Dual­ism of the S Pro­tein of Pan­golin-CoV

    The CoV S pro­tein con­sists of two sub­units (S1 and S2), medi­ates infec­tion of recep­tor-express­ing host cells, and is a crit­i­cal tar­get for antivi­ral neu­tral­iz­ing anti­bod­ies [12]. S1 con­tains a recep­tor-bind­ing domain (RBD) that con­sists of an approx­i­mate­ly 193 amino acid frag­ment, which is respon­si­ble for rec­og­niz­ing and bind­ing the cell sur­face recep­tor [13, 14]. Zhou et al. exper­i­men­tal­ly con­firmed that SARS-CoV­‑2 is able to use human, Chi­nese horse­shoe bat, civet, and pig ACE2 pro­teins as an entry recep­tor in ACE2-express­ing cells [3], sug­gest­ing that the RBD of SARS-CoV­‑2 medi­ates infec­tion in humans and oth­er ani­mals. To gain sequence-lev­el insight into the path­o­gen­ic poten­tial of Pan­golin-CoV, we first inves­ti­gat­ed the amino acid vari­a­tion pat­tern of the S1 pro­teins from Pan­golin-CoV, SARS-CoV­‑2, RaTG13, and oth­er rep­re­sen­ta­tive SARS/SARSr-CoVs. The amino acid phy­lo­ge­net­ic tree showed that the S1 pro­tein of Pan­golin-CoV is more close­ly relat­ed to that of 2019-CoV than to that of RaTG13. With­in the RBD, we fur­ther found that Pan­golin-CoV and SARS-CoV­‑2 were high­ly con­served, with only one amino acid change (500H/500Q) (Fig­ure 3), which is not one of the five key residues involved in the inter­ac­tion with human ACE2 [3, 14]. These results indi­cate that Pan­golin-CoV could have path­o­gen­ic poten­tial sim­i­lar to that of SARS-CoV­‑2. In con­trast, RaTG13 has changes in 17 amino acid residues, 4 of which are among the key amino acid residues (Fig­ure 3). There are evi­dences sug­gest­ing that the change of 472L (SARS-CoV) to 486F (SARS-CoV­‑2) (cor­re­spond­ing to the sec­ond key amino acid residue change in Fig­ure 3) may make stronger van der Waals con­tact with M82 (ACE2) [15]. Besides, the major sub­sti­tu­tion of 404V in the SARS-CoV-RBD with 417K in the SARS-CoV-2-RBD (see 420 align­ment posi­tion in Fig­ure 3 and with­out amino acid change between the SARS-CoV­‑2 and RaTG13) may result in tighter asso­ci­a­tion because of the salt bridge for­ma­tion between 417K and 30D of ACE2 [15]. Nev­er­the­less, fur­ther inves­ti­ga­tion is still need­ed about whether those muta­tions affect the affin­i­ty for ACE2. Whether the Pan­golin-CoV or RaTG13 are poten­tial infec­tious agents to humans remains to be deter­mined.

    The S1/S2 cleav­age site in the S pro­tein is also an impor­tant deter­mi­nant of the trans­mis­si­bil­i­ty and path­o­genic­i­ty of SARS-CoV­/SARS-CoVr virus­es [16]. The tri­met­ric S pro­tein is processed at the S1/S2 cleav­age site by host cell pro­teas­es dur­ing infec­tion. Fol­low­ing cleav­age, also known as prim­ing, the pro­tein is divid­ed into an N‑terminal S1-ectodomain that rec­og­nizes a cog­nate cell sur­face recep­tor and a C‑terminal S2-mem­brane anchored pro­tein that dri­ves fusion of the viral enve­lope with a cel­lu­lar mem­brane. We found that the SARS-CoV­‑2 S pro­tein con­tains a puta­tive furin recog­ni­tion motif (PRRARSV) (Fig­ure 4) sim­i­lar to that of MERS-CoV, which has a PRSVRSV motif that is like­ly cleaved by furin [16, 17] dur­ing virus egress. Con­verse­ly, the furin sequence motif at the S1/S2 site is miss­ing in the S pro­tein of Pan­golin-CoV and all oth­er SARS/SARSr-CoVs. This dif­fer­ence indi­cates the SARS-CoV­‑2 might gain a dis­tinct mech­a­nism to pro­mote its entry into host cells [18]. Inter­est­ing­ly, aside from MERS-CoV, sim­i­lar sequence pat­terns to the SARS-CoV­‑2 were also pre­sent­ed in some mem­bers of Alpha­coro­n­avirus, Beta­coro­n­avirus, and Gamm­coro­n­avirus [19], rais­ing an inter­est­ing ques­tion regard­ing whether this furin sequence motif in SARS-CoV­‑2 might be derived from those exist­ing S pro­teins of oth­er coro­n­avirus­es or alter­na­tive­ly if the SARS-CoV­‑2 might be the recom­bi­nant of Pan­golin-CoV or RaTG13 and oth­er coro­n­avirus­es with a sim­i­lar furin recog­ni­tion motif in the unknown inter­me­di­ate host.

    ...

    Con­clu­sion

    Based on pub­lished metage­nom­ic data, this study pro­vides the first report on a poten­tial close­ly relat­ed kin (Pan­golin-CoV) of SARS-CoV­‑2, which was dis­cov­ered from dead Malayan pan­golins after exten­sive res­cue efforts. Aside from RaTG13, the Pan­golin-CoV is the CoV most close­ly relat­ed to SARS-CoV­‑2. Due to unavail­abil­i­ty of the orig­i­nal sam­ple, we did not per­form fur­ther exper­i­ments to con­firm our find­ings, includ­ing PCR val­i­da­tion, sero­log­i­cal detec­tion, or even iso­la­tion of the virus par­ti­cles. Our dis­cov­ered Pan­golin-CoV genome showed 91.02% nucleotide iden­ti­ty with the SARS-CoV­‑2 genome. How­ev­er, whether pan­golin species are good can­di­dates for SARS-CoV­‑2 ori­gin is still under debate. Con­sid­er­ing the wide spread of SARSr-CoVs in nat­ur­al reser­voirs, such as bats, camels, and pan­golins, our find­ings would be mean­ing­ful for find­ing nov­el inter­me­di­ate SARS-CoV­‑2 hosts to block inter­species trans­mis­sion.

    ————

    “Prob­a­ble Pan­golin Ori­gin of SARS-CoV­‑2 Asso­ci­at­ed with the COVID-19 Out­break” by Tao Zhang, Qun­fu Wu, Zhi­gang Zhang; Cur­rent Biol­o­gy issue 30, pages 1–6; 04/06/2020

    “The CoV S pro­tein con­sists of two sub­units (S1 and S2), medi­ates infec­tion of recep­tor-express­ing host cells, and is a crit­i­cal tar­get for antivi­ral neu­tral­iz­ing anti­bod­ies [12]. S1 con­tains a recep­tor-bind­ing domain (RBD) that con­sists of an approx­i­mate­ly 193 amino acid frag­ment, which is respon­si­ble for rec­og­niz­ing and bind­ing the cell sur­face recep­tor [13, 14]. Zhou et al. exper­i­men­tal­ly con­firmed that SARS-CoV­‑2 is able to use human, Chi­nese horse­shoe bat, civet, and pig ACE2 pro­teins as an entry recep­tor in ACE2-express­ing cells [3], sug­gest­ing that the RBD of SARS-CoV­‑2 medi­ates infec­tion in humans and oth­er ani­mals. To gain sequence-lev­el insight into the path­o­gen­ic poten­tial of Pan­golin-CoV, we first inves­ti­gat­ed the amino acid vari­a­tion pat­tern of the S1 pro­teins from Pan­golin-CoV, SARS-CoV­‑2, RaTG13, and oth­er rep­re­sen­ta­tive SARS/SARSr-CoVs. The amino acid phy­lo­ge­net­ic tree showed that the S1 pro­tein of Pan­golin-CoV is more close­ly relat­ed to that of 2019-CoV than to that of RaTG13. With­in the RBD, we fur­ther found that Pan­golin-CoV and SARS-CoV­‑2 were high­ly con­served, with only one amino acid change (500H/500Q) (Fig­ure 3), which is not one of the five key residues involved in the inter­ac­tion with human ACE2 [3, 14]. These results indi­cate that Pan­golin-CoV could have path­o­gen­ic poten­tial sim­i­lar to that of SARS-CoV­‑2. In con­trast, RaTG13 has changes in 17 amino acid residues, 4 of which are among the key amino acid residues (Fig­ure 3). There are evi­dences sug­gest­ing that the change of 472L (SARS-CoV) to 486F (SARS-CoV­‑2) (cor­re­spond­ing to the sec­ond key amino acid residue change in Fig­ure 3) may make stronger van der Waals con­tact with M82 (ACE2) [15]. Besides, the major sub­sti­tu­tion of 404V in the SARS-CoV-RBD with 417K in the SARS-CoV-2-RBD (see 420 align­ment posi­tion in Fig­ure 3 and with­out amino acid change between the SARS-CoV­‑2 and RaTG13) may result in tighter asso­ci­a­tion because of the salt bridge for­ma­tion between 417K and 30D of ACE2 [15]. Nev­er­the­less, fur­ther inves­ti­ga­tion is still need­ed about whether those muta­tions affect the affin­i­ty for ACE2. Whether the Pan­golin-CoV or RaTG13 are poten­tial infec­tious agents to humans remains to be deter­mined.”

    So Pan­golin-CoV­’s S1 sub­unit is the most close­ly relat­ed to SARS-CoV-2’s S1 sub­unit. And that’s the part of the S‑protein that con­tains the furin cleav­age site in SARS-CoV­‑2 but not in any oth­er b lin­eage Beta­coro­n­avirus­es. But the furin cleav­age site is found in more dis­tant­ly relat­ed coro­n­avirus­es. That’s why the authors sug­gest SARS-CoV­‑2 may have arisen from a recom­bi­na­tion event:

    ...
    The S1/S2 cleav­age site in the S pro­tein is also an impor­tant deter­mi­nant of the trans­mis­si­bil­i­ty and path­o­genic­i­ty of SARS-CoV­/SARS-CoVr virus­es [16]. The tri­met­ric S pro­tein is processed at the S1/S2 cleav­age site by host cell pro­teas­es dur­ing infec­tion. Fol­low­ing cleav­age, also known as prim­ing, the pro­tein is divid­ed into an N‑terminal S1-ectodomain that rec­og­nizes a cog­nate cell sur­face recep­tor and a C‑terminal S2-mem­brane anchored pro­tein that dri­ves fusion of the viral enve­lope with a cel­lu­lar mem­brane. We found that the SARS-CoV­‑2 S pro­tein con­tains a puta­tive furin recog­ni­tion motif (PRRARSV) (Fig­ure 4) sim­i­lar to that of MERS-CoV, which has a PRSVRSV motif that is like­ly cleaved by furin [16, 17] dur­ing virus egress. Con­verse­ly, the furin sequence motif at the S1/S2 site is miss­ing in the S pro­tein of Pan­golin-CoV and all oth­er SARS/SARSr-CoVs. This dif­fer­ence indi­cates the SARS-CoV­‑2 might gain a dis­tinct mech­a­nism to pro­mote its entry into host cells [18]. Inter­est­ing­ly, aside from MERS-CoV, sim­i­lar sequence pat­terns to the SARS-CoV­‑2 were also pre­sent­ed in some mem­bers of Alpha­coro­n­avirus, Beta­coro­n­avirus, and Gamm­coro­n­avirus [19], rais­ing an inter­est­ing ques­tion regard­ing whether this furin sequence motif in SARS-CoV­‑2 might be derived from those exist­ing S pro­teins of oth­er coro­n­avirus­es or alter­na­tive­ly if the SARS-CoV­‑2 might be the recom­bi­nant of Pan­golin-CoV or RaTG13 and oth­er coro­n­avirus­es with a sim­i­lar furin recog­ni­tion motif in the unknown inter­me­di­ate host.
    ...

    Might we be deal­ing with a virus that’s a con­se­quence of real­ly bad evo­lu­tion­ary luck? If we assume this virus arose nat­u­ral­ly then those are the kinds of sce­nar­ios we need to assumed hap­pened. Real­ly bad luck sce­nar­ios.

    A man-made virus could also be seen as a dif­fer­nt kind of real­ly bad luck sce­nario although that’s not real­ly luck. It’s just real­ly bad. Luck does­n’t have that much to do with it. So what’s more like­ly: a real­ly bad luck nat­ur­al sce­nario or a real­ly bad no-luck-involved man-made sce­nario? That’s kind of the meta ques­tion involved year. Grant, if this is a man-made sce­nario we have got­ten very lucky so far in that that virus has­n’t mutat­ed into some­thing worse as it blows up and spreads across the globe. Although that lack of observed evo­lu­tion appears to have more to do with the virus already being opti­mized for spread­ing among humans, which is pret­ty bad as far good luck goes.

    Posted by Pterrafractyl | March 26, 2020, 2:49 pm
  4. @Pterrafractyl–

    It is impor­tant to remem­ber that this did NOT occur in a vac­u­um, but in the con­text of a full-court press desta­bi­liza­tion effort against Chi­na, head­ed by white nation­al­ist Steve Ban­non, whose pri­ma­ry political/philosophical ref­er­ence is Julius Evola. Evola orig­i­nal­ly like Mus­soli­ni, but thought he was too soft and grav­i­tat­ed to the Nazi SS, who financed his work by the end of the war. https://spitfirelist.com/for-the-record/ftr-947-evola-on-our-minds/

    In July of last year, Ban­non said ” . . . . ‘These are two sys­tems that are incom­pat­i­ble,’ Mr. Ban­non said of the Unit­ed States and Chi­na. ‘One side is going to win, and one side is going to lose.’ . . . .”

    https://www.nytimes.com/2019/07/20/us/politics/china-red-scare-washington.html

    That is a dec­la­ra­tion of totaler krieg–total war!

    The “bad luck” hypoth­e­sis reminds me of “The New York Times’s” reac­tion to the Dal­las Police Depart­ment dictabelt record­ing that indi­cat­ed at least four shots fired in Dealy Plaza on 11/22/1963, there­by dis­prov­ing the War­ren Com­mis­sion’s hypoth­e­sis.

    They opined that this sim­ply meant that there were two, appar­ent­ly uncon­nect­ed “lone nuts” at work in Dal­las on that day.

    Now that is REALLY bad luck, indeed!

    In the age of gene edit­ing, “bad luck” does­n’t cut it.

    Using recom­bi­nant DNA in an inter­me­di­ate host could very eas­i­ly be engi­neered as well.

    More on that in a minute.

    Best,

    Dave

    Posted by Dave Emory | March 27, 2020, 5:02 pm
  5. @Pterrafractyl–

    Note that the “pan­golin-host research” falls in line with some of the DARPA-fund­ed research Whit­ney Webb dis­cuss­es:

    https://spitfirelist.com/news/disturbing-article-about-darpa-and-bat-borne-coronaviruses/

    ” . . . . .For instance, DARPA spent $10 mil­lion on one project in 2018 ‘to unrav­el the com­plex caus­es of bat-borne virus­es that have recent­ly made the jump to humans, caus­ing con­cern among glob­al health offi­cials.” Anoth­er research project backed by both DARPA and NIH saw researchers at Col­orado State Uni­ver­si­ty exam­ine the coro­n­avirus that caus­es Mid­dle East Res­pi­ra­to­ry Syn­drome (MERS) in bats and camels ‘to under­stand the role of these hosts in trans­mit­ting dis­ease to humans.’  . . . For instance, one study con­duct­ed in South­ern Chi­na in 2018 result­ed in the dis­cov­ery of 89 new “nov­el bat coro­n­avirus” strains that use the same recep­tor as the coro­n­avirus known as Mid­dle East Res­pi­ra­to­ry Syn­drome (MERS). That study was joint­ly fund­ed by the Chi­nese government’s Min­istry of Sci­ence and Tech­nol­o­gy, USAID — an orga­ni­za­tion long alleged to be a front for U.S. intel­li­gence, and the U.S. Nation­al Insti­tute of Health — which has col­lab­o­rat­ed with both the CIA and the Pen­ta­gon on infec­tious dis­ease and bioweapons research.. . . .”

    Damn, what bad luck!

    Posted by Dave Emory | March 27, 2020, 5:31 pm

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