Raccoon canines didn’t begin COVID-19, new research says

The raccoon canine did it: That was the explosive takeaway of a genomic evaluation performed in March by a trio of scientists who had scrutinized information from a market in Wuhan, China, the place the pandemic was thought to have begun.

Till then, proof for that conviction had been scant.

“This can be a actually sturdy indication that animals on the market have been contaminated,” virologist Angela Rasmussen informed the Atlantic, which was first to report on the raccoon dog study. “There’s actually no different rationalization that makes any sense.”

Others equally felt it was a landmark second. For months, momentum had been behind a countervailing speculation {that a} laboratory accident, not an animal, had prompted the pandemic. The brand new raccoon canine evaluation appeared to rule out that chance.

“The COVID lab leak idea is useless,” declared Edward Holmes, one of many researchers concerned within the raccoon canine research.

Solely his evaluation gave the impression to be untimely.

New proof for market origin

In January, a trove of knowledge from the Huanan Seafood Wholesale Market in Wuhan appeared on the worldwide database GISAID, seemingly by chance. On this batch have been genetic samples from swabs taken in market stalls in early January 2020, earlier than many of the world had even heard of the coronavirus.

An evolutionary biologist in France named Florence Débarre noticed the brand new information and, in response to the Atlantic, notified colleagues all over the world. With their monumental assortment of genetic materials from totally different species, the GISAID samples have been a chronicle of the Huanan market within the earliest days of the pandemic. Right here, probably, within the limitless string of genetic sequences, lay hidden the origin story of SARS-CoV-2.

Chinese language scientists had already analyzed all of the Huanan swabs, surmising that “the market might [have] acted as an amplifier of transmission as a result of excessive variety of guests day-after-day.” Their research explicitly discounted the chance that the virus had jumped from an animal to people.

Now, working with the uncooked information, Kristian Andersen, Michael Worobey and Holmes got here to a completely totally different conclusion. They believed that the pandemic had begun in stall 29, on the southwestern edge of the market.

In that stall sat caged raccoon canines.

“The Strongest Proof But That an Animal Began the Pandemic,” mentioned the headline of the Atlantic article that broke the information.

A 3-year debate seemingly settled

From the beginning, the controversy about how the pandemic started was as ferocious because it was inconclusive.

At first, pangolins bought on the Huanan market have been thought to have been the intermediate species. Bats, that are inclined to coronaviruses, have been one other apparent suspect.

Andersen, Worobey and Holmes have been a part of a gaggle that had maintained from virtually the beginning of the pandemic that solely a market origin made sense, a conviction that detractors thought had an oddly dogmatic high quality. And for all their confidence, the proponents of a market origin lacked the one factor that might persuade skeptics: proof.

One other group of virologists maintained {that a} extra seemingly candidate was the close by Wuhan Institute of Virology, which was well-known to conduct analysis on bat coronaviruses — and the place, in November 2019, three researchers had come down with a mysterious illness.

Biosecurity on the Wuhan institute was reportedly lax (a standard downside in Western laboratories as well), making an accident all too believable.

To the proponents of this lab leak speculation, trying to find an intermediate species was futile at finest, misdirection at worst. Making their case was tough, nonetheless, with then-President Trump commonly launching vituperative assaults on China, baselessly suggesting that the virus was deliberately created as a bioweapon. Few scientists sought affiliation, nonetheless oblique, with the likes of Alex Jones and different figures on the conspiratorial fringe.

Nonetheless, proponents of a market origin failed to provide any convincing clues, resembling a reservoir of animals within the wild contaminated with the unique, “wild sort” SARS-CoV-2 pressure. It appeared lower than believable that solely a single animal had been contaminated with a virus as extremely transmissible as SARS-CoV-2.

The raccoon canine research was, because the Atlantic identified, probably the most persuasive argument in favor of a market origin.

That’s, if its conclusions held.

A single molecule amongst thousands and thousands

In 2021, computational virologist Jesse Bloom of the Fred Hutchinson Most cancers Heart gained acclaim (and notoriety) by discovering that coronavirus genetic sequences from the early days of the pandemic had been deleted from a Nationwide Institutes of Well being archive — on the request of Chinese language scientists, it will prove. These sequences, Bloom noted in a paper, bore uncommon similarity to bat coronaviruses.

In contrast to another researchers in search of the pandemic’s origins, Bloom was not a self-promoter. He didn’t assault critics on Twitter or make wild, unsupportable claims. “He’s probably the most moral scientist I do know. He desires to dig deep and uncover the reality,” a fellow scientist told Vanity Fair.

The raccoon canine revelation gave Bloom a brand new mission. The info utilized by the Worobey group had been faraway from GISAID, solely to materialize there once more in additional fulsome kind in late March. Whereas the raccoon canine group had labored with 227 FASTQ information — the format used to retailer lengthy strings of genetic code — there have been 696 FASTQ information within the Huanan sequences that reappeared on GISAID a number of weeks later.

Working with the larger database, Bloom processed an astonishing three terabytes of knowledge from the Huanan Market — genetic sequences from the identical swabs taken in early 2020 that Worobey and his collaborators thought pointed to raccoon canines.

Bloom’s evaluation didn’t merely have a look at the place coronavirus and animal genetic materials commingled but in addition at how thorough that commingling had been. And whereas the Worobey group had solely examined mammalian DNA, Bloom sifted via each strand of genetic materials, no matter whether or not it got here from a hen, a human or a lower of beef.

In a paper published in late April, Bloom wrote that “the samples that comprise plentiful materials from raccoon canines and different non-human inclined species usually comprise little or no SARS-CoV-2 reads.”

Bloom paid explicit consideration to pattern Q61, which had been collected on Jan. 12, 2020. That day, Chinese language investigators had taken 70 samples from the western fringe of the market, a sizzling spot of viral exercise, together with from the infamous 29th stall that housed raccoon dogs.

Six of these samples had examined constructive for SARS-CoV-2. And of the six, a single one — Q61 — additionally contained the DNA of raccoon canines, in addition to geese.

It appeared that the raccoon canine declare originated from Q61. However in his personal sequencing, Bloom discovered that out of 200 million “reads,” or discrete viral samples, on the swab, solely a single one was constructive for the coronavirus. On condition that the coronavirus was already spreading all through Wuhan for a number of months by then, that particle was way more seemingly deposited by an unsuspecting human than by a sick animal.

In different phrases, the Chinese language researchers who had been the primary to check the swabs, and had concluded that people carried the virus to the market, appeared to have been appropriate all alongside.

As for the raccoon canine, it was unquestionably harmless. “There’s a damaging correlation between the abundance of SARS-CoV-2 and mitochondrial materials from raccoon canines,” Bloom wrote.

Essentially the most viral materials got here from swabs with DNA from stalls the place seafood resembling catfish and largemouth bass have been bought.

“Clearly largemouth bass didn’t begin the pandemic,” Bloom informed Yahoo Information. “What these findings recommend is solely that by the point the Huanan market environmental samples have been collected, the virus had been unfold broadly throughout the market by people, so colocalization of viral and animal genetic materials in samples can’t point out whether or not or not any animal was contaminated.”

Worobey, Andersen and Holmes didn’t reply to a request for remark. Nor did a number of different researchers listed as co-authors on the raccoon canine paper. Alexander Crits-Christoph of Johns Hopkins was the only respondent. He despatched Yahoo Information an insulting electronic mail in response to questions raised by the brand new research.

So what concerning the raccoon canine?

From the beginning, skeptics maintained that there have been scant grounds for the assertion that raccoon canines have been the pandemic’s intermediate species, if the one proof for that declare was the presence of viral and animal DNA in the identical market stall.

In a crowded market, there have been myriad methods for the DNA of various species to finish up in the identical place, combined in with genetic traces of the coronavirus.

“The raccoon canine staff made an enormous fuss out of what’s almost definitely a contaminated pattern,” molecular biologist Alina Chan of the Broad Institute of MIT and Harvard informed Yahoo Information.

“Not solely is there no correlation between raccoon canine and virus genetic materials, however even the one pattern with each raccoon canine and virus was seemingly cross-contaminated throughout the pattern processing,” she mentioned.

In his paper, Bloom argues that his research doesn’t contradict the raccoon canine speculation however, somewhat, merely factors out the close to impossibility of utilizing the market swabs to succeed in any significant conclusion about viral origins.

“A cautious evaluation of those samples doesn’t show or disprove any explicit situation for a way the virus entered the market,” Bloom informed Yahoo Information, “however does recommend that genetic evaluation of the samples will not be immediately informative for answering that query.”

The media’s function

From the beginning, the narrative of how the coronavirus originated was a media story, one formed largely by attitudes about Trump. The heated and at instances ugly rhetoric he deployed at the beginning of the pandemic — the brand new virus was a “kung flu,” he was fond of claiming within the pandemic’s early days — made it tough to scrutinize China with out fueling what was then a rising tide of animosity towards Asian Individuals.

FactCheck.org labeled the notion that the coronavirus originated in a laboratory a “baseless conspiracy theory,” placing credible questions on a lab leak into the identical class as clearly unfaithful claims that the SARS-CoV-2 virus contained strains of HIV.

However then President Biden took workplace, promising to extra completely and systematically tackle the pandemic — together with the query of the way it started. Two months into his presidency, he ordered the intelligence neighborhood to look at whether or not the coronavirus could have emerged from a laboratory experiment gone horribly awry.

A number of months later, comic Jon Stewart appeared on Stephen Colbert’s late night time discuss present. Because the dialog turned to the pandemic, Stewart joked about how implausible it was that the virus had originated from animals: “Possibly a bat flew into the cloaca of a turkey after which it sneezed into my chili and now all of us have coronavirus?”

Colbert appeared uneasy however Stewart persevered, declaring {that a} coronavirus outbreak originating just some miles away from a laboratory investigating coronaviruses appeared an odd coincidence, no less than to him.

“There’s been an outbreak of chocolatey goodness close to Hershey, Pennsylvania, what do you assume occurred? I don’t know, possibly a steam shovel mated with a cocoa bean,” Stewart mentioned together with his signature outrage. “Or it’s the f***ing chocolate manufacturing unit!”

Republicans’ takeover of the Home of Representatives the next 12 months all however assured that, even because the pandemic grew to become a background concern for a lot of Individuals, its supply would stay a subject of intense competition on Capitol Hill — and within the information media.

Chan of the Broad Institute, one of the earliest and most outspoken proponents of a lab leak, informed Yahoo Information that the raccoon canine controversy was proof of how badly an authoritative investigation was wanted.

“The origin of COVID-19 debate has gotten so fierce that there are stable scientists on each side who will take any probability to say there’s new proof bolstering their most well-liked speculation,” she mentioned. “A proper fee must be established to carry scientists from each side to place out a joint evaluation of the out there proof. This could assist the general public to see what the details are, free from extrapolation and exaggeration.”

She and others faulted the media for persevering with to favor the market origin — and for not making use of adequate scrutiny to the raccoon canine declare.

Dissenting opinion

In his paper, Bloom makes no conclusions about how the pandemic started. If something, he cautions towards doing so. “We’re unlikely to get conclusive solutions about origin of an outbreak that began in Nov 2019 (or earlier) by taking a look at samples collected in Jan 2020,” he wrote on Twitter.

Nonetheless, some scientists have challenged his conclusions.

Frederic Bushman, a College of Pennsylvania microbiologist, told the New York Times that Bloom had set overly “aggressive” thresholds for deeming a pattern virus-positive. “I don’t assume the Bloom paper modifications my considering that a lot,” he informed the Occasions.

Christopher Mason, a geneticist at Weill Cornell Drugs, informed the Occasions that Bloom’s evaluation might not have absolutely accounted for the rapidity with which coronavirus RNA might have degraded within the days and even weeks earlier than researchers got here to the Huanan market to swab for samples.

These criticisms underscore how tough it’s to re-create the trail SARS-CoV-2 took from a market stall, or a laboratory cubicle, into the human inhabitants.

What’s subsequent?

Home Republicans are persevering with to analyze the origins of the pandemic, although their hearings have to date yielded little new perception.

In the meantime, a brand new report from the COVID Disaster Group (an unbiased consortium of 34 consultants), “Classes From the COVID Conflict,” argues that “each theories stay believable” and supply “pressing insights for motion.”

Common laboratory security pointers are badly wanted, particularly with regards to the riskiest sort of viral analysis. On the identical time, the interactions of animals and people additionally deserve larger scrutiny. And when an outbreak does happen, open and sincere communication is a should.

In impact, each fashions of how the coronavirus unfold must be handled as believable, as a result of each situations will virtually actually materialize throughout a future outbreak.