U.S. funded discovery of close COVID-19 relative at the center of origins controversy

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Updated: 3:23 p.m.

By Karolina Corin and Emily Kopp

American ties to coronavirus research at the pandemic’s epicenter in Wuhan are closer than previously understood.

The U.S. government underwrote the discovery of the closest relative of SARS-CoV-2 known before the pandemic’s start.

The Wuhan Institute of Virology’s U.S. partners claimed the discovery of the close cousin virus in a letter to a member of Congress about U.S. Agency for International Development achievements, and listed a research paper detailing its discovery in grant progress reports to the National Institutes of Health.

The cousin virus is 96 percent similar to SARS-CoV-2, the virus that causes COVID-19, and has been at the center of speculation about the pandemic’s origin.

The close relative — RaTG13 — was found in a mineshaft where six miners became sick with severe pneumonia. Three of the six miners died. Yet this extraordinary finding was not widely shared with the scientific community. It was uncovered after the emergence of COVID-19 by the independent research group DRASTIC.

Experts agree that RaTG13 could not have been the direct progenitor of COVID-19. The differences between the two viruses are spread across the genome, and evolution from one to the other could require decades. Other viruses circulating in Southeast Asia have since been shown to have slightly more similar genomes, though phylogenetic analyses still place RaTG13 as the closest relative. However, its existence has fueled speculation about whether a closer relative could be among the unpublished viruses under study at the WIV.

Recent reporting citing anonymous sources alleges that researchers at the Wuhan Institute of Virology working with RaTG13 and a related clade of viruses may have been among the first infected with COVID-19. Their research papers and grant proposals show that they were interested in bat coronaviruses with features shared by SARS-CoV-2, like a furin cleavage site and the ability to infect human cells through a receptor called ACE2.

EcoHealth Alliance was the U.S. conduit between both funders and the Wuhan lab. EcoHealth Alliance, its president Peter Daszak, and NIAID have not responded to requests for comment. USAID did not respond to questions about RaTG13 but did provide a statement.

“The work through the PREDICT project ended in 2020,” a spokesperson said. “USAID is committed to keeping Americans and the world safe and secure from health outbreaks and pandemic threats by working with countries around the world to strengthen global health security, prioritize critical gaps, and build and measure strengthened capacities to identify and contain.”

NIH concern

Within weeks of the pandemic’s outbreak, Wuhan Institute of Virology Senior Scientist Shi Zhengli published a preprint about RaTG13 and submitted its sequence to a public database.

Its resemblance to the novel coronavirus gripping the globe set off sirens among top virologists and NIH leaders Francis Collins and Anthony Fauci, their emails show.

“In case you haven’t seen this preprint from one week ago,” Collins said in a February 1, 2020, email to Fauci obtained by U.S. Right to Know.

“No evidence this work was supported by NIH,” he said.

The NIH leaders joined a teleconference hours later with top virologists concerned about signs SARS-CoV-2 was engineered, which included discussion of similarities between the emerging novel virus and RaTG13.

Neither the Wuhan Institute of Virology’s preprint nor the final version published in February 2020 acknowledged any U.S. funding.

However, an addendum published nine months later revealed that the WIV partially sequenced RaTG13 in a 2016 study under its original name, RaBtCoV/4991.

This 2016 study did acknowledge funding from an NIH grant to EcoHealth Alliance, a longtime partner of the WIV lab.

U.S. ties to COVID cousin

Documents obtained and analyzed by U.S. Right to Know confirm that the U.S. government helped fund the discovery of RaTG13.

Progress reports for the NIH grant awarded to EcoHealth Alliance confirm that the 2016 study was “published from work funded by this NIAID R01 [grant].”

A University of California Davis letter to Sen. Dianne Feinstein, D-Calif., goes further, suggesting that USAID may have been involved with its discovery.

“In China alone, we sampled >10,000 bats and ~2,000 other mammals, using PREDICT protocols to discover 52 novel SARS related-CoV’s [coronaviruses], including the closest relative of the Wuhan nCoV [SARS-CoV-2],” reads the letter.

The letter also reports “supplemental funding from NIH” to Shi Zhengli.

PREDICT was USAID’s $200 million, 10 year virus-hunting program, which had the aim of predicting zoonotic diseases and also coincided with a boom in U.S. biodefense efforts after 9/11.

While the letter to Feinstein suggests that PREDICT helped find or sequence RaTG13, the program’s role in RaTG13’s discovery is not certain.

Only NIH funding is mentioned in grants and publications connected to RaTG13, but EcoHealth often used funds from both NIH and USAID to search for new SARS-like coronaviruses.

RaTG13 was also sampled and partially sequenced while the PREDICT project was active, but, according to their naming scheme, no novel SARS-like coronaviruses in China appear to be mentioned in PREDICT’s final reports or datasets.

However, peer-reviewed papers show that numerous novel SARS-like coronaviruses were found in China with PREDICT funding before the pandemic began.

The 52 novel SARS-like coronaviruses mentioned in the letter also appear to result from Daszak’s 2014 grant.

“Since then, under an R01 [NIH grant] awarded in 2014, we have discovered >50 bat SARSr-CoVs in southern China,” claims the proposal to renew the grant.

Conflicting statements on RaTG13’s discovery

EcoHealth Alliance President Peter Daszak — who has been at the center of the lab leak controversy — has made conflicting statements about whether or not his research group aided in the virus’ discovery.

The same day the letter to Senator Feinstein is dated, Science published an article that repeated PREDICT’s claims and specifically named RaTG13 as one of the viruses found by Daskak and Shi.

“Daszak and Shi’s group … have found some 500 novel coronaviruses, about 50 of which fall relatively close to the SARS virus on the family tree, including RaTG13,” reads the story.

In interviews through April 2020 to other media outlets, Daszak continued to claim credit for the discovery of RaTG13.

Yet in August 2020, after the NIH suspended EcoHealth’s grant and reinstatement appeared tenuous, Daszak denied involvement in the 2016 study, pointing out that the sample containing RaBtCoV/4991 was collected before the grant started.

“We were not part of this work,” Daszak tweeted in August 2020. “Samples [were] collected prior to our grant so clearly outside NIH’s remit.”

Though the NIH grant in question began in 2014, EcoHealth started receiving funds in 2009 from USAID’s PREDICT program to sample coronaviruses in partnership with the WIV. A previous NIH grant from 2008 to 2013 was also used to finance the discovery of novel SARS-like coronaviruses.

Daszak did state that NIH grant money was used to pay staff salaries while the 2016 paper was being written, but remained adamant that EcoHealth did not collect the sample and had no authority over it.

“RaTG13 was not from a sample collected under the NIH grant. So we didn’t have any oversight on that or any knowledge of it,” he repeated in a 2022 interview with The Intercept.

Some documents used in this report were obtained by U.S. Right to Know through a California Public Records Act request to UC Davis.

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