Last time, we talked about the vindication of the lab leak theory, as a growing number of investigative articles have pointed to a lab accident as the cause of the COVID-19 pandemic. Now,we turn to the role risky gain-of-function research may have played in the affair.

To understand why some in the U.S. government and the NIH want to downplay funding of gain-of-function research, we need to understand what exactly it is.

All viruses mutate, some faster than others. Influenza is one of the fastest mutating viruses, followed by HIV. SARS-CoV-2 mutates slower than both viruses, which is why many scientists believe vaccine booster shots will likely be every few years, rather than annually, like the flu.

Scientists need to understand how viruses mutate because mutations produce variants of the virus. When it comes to producing a flu vaccine, researchers look at which variant is likely to be the dominant variant in a flu season. In the case of SARS-CoV-2, most of the variants are inconsequential. However, some variants, like the UK variant (also known as the alpha variant or B.1.1.7) have one or more mutations in the region coding for the spike protein that cause the virus to be more transmissible. Other variants, such as the India variant (also known as delta variant or B.1.617.2), are potentially more resistant to antibody treatment or vaccines and have been found to be more transmissible.

Studying mutations and predicting variants is not particularly controversial. But scientists don’t just want to predict known viruses for vaccines and therapeutics. They also want to predict new viruses, especially those that may cause a pandemic. Past pandemics have happened when a virus jumps from animal to human. The Ebola outbreak in West Africa several years ago was traced to a boy who was bit by a fruit bat. New influenza viruses can come from birds (avian flu) or pigs (swine flu), so this is a legitimate concern. SARS-CoV (2002) originated in bats, then jumped to civet cats, and then humans. MERS-CoV (2012) spread to humans from camels. Scientists were concerned that a pandemic may be caused by another coronavirus like MERS or SARS.

Gain-of-function studies take known viruses and investigate which mutations cause them to become transmissible to humans. This is done either by transmitting the virus from one cell to another and across different species, as what happened in the wild with the original SARS-CoV virus, or by making genetic changes to a virus genome and then exposing it to either a human cell or “humanized mice” (i.e., mice with the ACE2 gene) to see if it enters human cells. These genetic changes to a virus either combine the genes of one known virus with another through recombinant methods, or the genetic change is inserted directly into the genome of a virus using gene editing tools like CRISPR. 

So, what kinds of changes would someone want to make? Consider MERS-CoV. It has something called a “polybasic furin cleavage site” in the portion of its genome that codes for the spike protein—that would be the spike protein that gives coronaviruses their namesake. The furin cleavage site has been shown to make coronaviruses more transmissible to human cells, especially human lung cells. MERS-CoV naturally developed this type of furin cleavage site. What gain-of-function studies can do is use one of the methods above to cause a different coronavirus to gain something like the type of furin cleavage site found in MERS-CoV. This would theoretically make the modified coronavirus more susceptible to infecting human lung cells.

Here’s what Peter Daszak had to say in a 2019 interview about these studies. This was prior to the pandemic:

Spike protein drives a lot of what happen with coronavirus, in zoonotic risk. So you can get the sequence, you can build the protein, and we work a lot with Ralph Baric at UNC to do this. Insert into the backbone of another virus and do some work in the lab. So you can get more predictive when you find a sequence. You’ve got this diversity. Now the logical progression for vaccine is, if you are going to develop a vaccine for SARS, people are going to use pandemic SARS, but let’s insert some of these other things and get a better vaccine.

quoted in “The origin of COVID: Did people or nature open Pandora’s box at Wuhan?” by Nicholas Wade, Bulletin of the Atomic Scientists

Some scientists, including those quoted in Nicholas Wade’s article, think SARS-CoV-2 could be a result of gain-of-function studies rather than naturally occurring because SARS-CoV-2 has a furin cleavage site, one of the “things” Peter Daszak was talking about:

“When I first saw the furin cleavage site in the viral sequence, with its arginine codons, I said to my wife it was the smoking gun for the origin of viruses,” said David Baltimore, an eminent virologist and former president of CalTech. “These features make a powerful challenge to the idea of a natural origin for SARS2,” he said.

“The origin of COIVD: Did people or nature open Pandora’s box at Wuhan?” by Nicholas Wade, Bulletin of the Atomic Scientists

Here’s where it gets tricky and why different people will draw different conclusions: The furin cleavage site is found in other naturally occurring coronaviruses, like MERS-CoV (and two viruses labeled HCoV-OC43 and MHV-A59; see here and here), but the furin cleavage site with its specific arginine codons has not been found in SARS-like coronaviruses that come from bats. Furthermore, the specific codons for arginine are not typically found in bat coronaviruses, although that codon (CGG) has been found in bat coronaviruses before. Some people see this as evidence that SARS-CoV-2 was the result of a gain-of-function study; others say because it can be found in other coronaviruses, it could have occurred naturally.

To make things more confusing, another possibility is SARS-CoV-2 may have been a naturally occurring virus, but one that was accidentally released from the Wuhan Institute of Virology. Shi Zheng-Li’s group had collected hundreds of bat samples from the Yunnan mine, which included a virus that has over 96% genetic similarity to SARS-CoV-2. They identified several new coronaviruses from the bat samples, but the online records of those viruses were taken down in September 2019. Shi’s group could have been studying a novel virus that they found in the Yunnan mine, and sloppy lab techniques, which the lab has been dinged for in the past, led to infection and eventual spread. (See here for a 2018 paper providing technical details about the relationship between MERS and bat coronaviruses found by Shi’s group).

Others have said that unlike SARS-CoV, SARS-CoV-2 was too well-adapted for human transmission from the beginning of the pandemic to have been a naturally occurring virus that first came from an animal. Wade makes a compelling case for why it is highly unlikely that a furin cleavage site naturally evolved from a bat coronavirus.

Whether a lab-made virus from gain-of-function studies or a newly discovered virus, neither case absolves the Wuhan Institute of Virology if the pandemic started from a lab accident. It also puts the NIH in a tough spot for funding such research.

Next: The U.S. ponders what to do about gain-of-function research.

You may also wish to read the first article in this three-part series:

Lab Leak Theory Vindicated: What That Means for Fighting COVID-19. Vanity Fair adds to the growing number of investigative articles pointing to a lab accident as the cause of the COVID-19 pandemic. This article looks at the U.S. government’s role in downplaying that lab leak theory. (Heather Zeiger)