Origin of SARS-CoV-2 Coronavirus—Part 2: Interpret New Findings

Authored by Venkat Rao

Part 1 of my report on the origin of SARS-CoV-2 coronavirus examined that question in light of a new study recently published in Science citing a previously undisclosed 2020 study conducted by Chinese investigators during the early stages of the COVID-19 pandemic on genetic data from the Huanan Seafood Wholesale Market, in Wuhan, China.

To recap from Part 1, the 2020 study by Chinese investigators on the source and origin of SARS-CoV-2 virus collected and analyzed 1,380 samples from the wildlife food and general environment in the Huanan Seafood Wholesale Market, in Wuhan, China, and found that the none of the wildlife food samples tested positive for the virus. In contrast, 73 of the 1,380 samples collected from the general environment at the seafood food market tested positive for SARS-CoV-2 and three live viruses were successfully isolated with a genetic makeup showing a 99.99% match with the virus isolated from COVID-19 human patient samples. No virus was detected in the wild food samples collected in the course of this study. For clarification, Huanan Seafood Wholesale Market in Wuhan sells both seafood and mammalian wildlife meat for human and animal consumption.

These results present a complicated interpretation of the key finding on the presence of SARS-CoV-2 virus at the Huanan Seafood Market. Chinese CDC interpretation that illegal wildlife meat dealing may be linked to the presence of virus and subsequent action by shutting down the market in March 2020 without additional information leaves the key findings unanswered: If illegal animal dealing was the source then why none of the 1,380 wildlife food samples tested positive but 73 samples from the general environment detected SARS-CoV-2 with the exact genetic composition of the virus collected from COVID-19 patients?

Environmental scientists will attest to the fact that contaminants, be it a hazardous chemical or a biological pathogen such as SARS-CoV-2 virus when detected in the general environmental samples such as air, water, hard surfaces, etc. would have to be generated or released from a source. Food items, be it poultry, meat, or vegetables contaminated with virus or bacteria would not serve as source for the release of the pathogens into the general ambient (air) environment, unless the contaminated food source was chopped and processed at the market at the point of sale creating an aerosol carrying live virus at the vicinity, in which case at least some food samples would have tested positive as well as the environmental samples for the presence of the virus. That was not the case, as reported in the 2020 study.

The “origin” and “source” are two interrelated issues, but not the same. As to the origin of the SARS-CoV-2 virus we do not yet know conclusively where the virus originated. The scientific evidence obtained thus far seem to indicate that the virus may have originated from an animal source. But origin is only a partial answer to the more crucial next question: What was the source of SARS-CoV-2 virus in the Huanan Seafood Wholesale Market, in Wuhan, China, that is accepted as the epicenter for the first cluster of COVID-19 infection leading to a global pandemic?

As a toxicologist, having performed numerous biosafety and biological risk assessments on biological pathogens such as viruses and bacteria, bring a unique perspective to interpret the seemingly contradictory reports on the source of SARS-CoV-2 virus at the seafood market, setting aside the question on the origin of the virus.

The biological risk assessments I refer to are conducted as part of biotechnology facility regulatory compliance requirements with biosafety guidelines and environmental regulations.

The biological risk assessment would involve worst-case scenarios, usually referred to as Maximum Credible Event, created by a laboratory accident such as an improperly balanced centrifuge breaking up and releasing the biological material into the laboratory environment, or a failure in the Heating, Ventilation, and Air Conditioning (HVAC) system in the high-containment facility resulting in a catastrophic release of dangerous pathogens inside the facility and spilling into the general environment outside. Another common scenario considered involve failure by laboratory workers to strictly adhere to the biosafety procedures resulting in general contamination and workers unintentionally walking out of the high-containment laboratory areas to other places within the facility carrying the pathogens on their clothes and personal belonging contaminating others and the general environment. These are the sorts of likely worst-case scenarios invoked as part of biological risk assessment to evaluate the adequacy of biosafety mitigating capabilities at the facility in terms of engineering infrastructure, strict adherence to biosafety procedures, employee training and awareness of management to the crucial need for strict biosafety and biosecurity at biological laboratories handling, manipulating, and storing dangerous pathogens.

The focus of biological risk assessment at laboratory facilities is to ensure strict compliance with existing biosafety guidelines for biological laboratories and to comply with local environmental regulations. Note that most of these theoretical scenarios involving release of biological pathogens resulted in contaminated ambient (air) general environment within the laboratory, or contaminated clothing and personal possession of staff members that gets carried outside the lab and into the general environment. If the worst-case analysis scenario involves a highly dangerous pathogen, or large volumes released during a manufacturing operation, the resulting accident and spillover is postulated as “likely” to enter outside general environment.

In the following section, I will describe one such real accident that occurred at a biowarfare laboratory.

Sverdlovsk, now known as Yekaterinburg is a city of 2.2 million in Russia. As the third largest city ranked by its economy, Russians refer to Sverdlovsk (Yekaterinburg) as the “Third capital of Russia.” Nevertheless, this city has the dubious distinction of facing the deadliest anthrax epidemic, in 1979, which was linked to a former Soviet biological weapons research facility, leading to an officially declared death of 68 people, although real numbers are likely to be even higher.

Ken Alibek, formerly the deputy director of Biopreparat, the former Soviet agency that oversaw the largest and most sophisticated offensive biological warfare program the world has ever seen, describes in chilling detail in the book, Biohazard, he wrote and published in 1999 about the 1979 laboratory incident at the Soviet Biowarfare Laboratory in Sverdlovsk.

The book is aptly titled, “Biohazard: The Chilling True Story of the Largest Covert Biological Weapons Program in the World—Told from the Inside By the Man Who Ran It.” In this book the author describes the accident that took place in 1979 at this covert biological weapons research facility leading to the release of Anthrax spores into city of Sverdlovsk (Yekaterinburg). The incident was the focus of major controversy during the 1980s between Washington and Moscow.

The supportive documents unearthed during years-long investigation in the 1980s provided highly valuable information on the Sverdlovsk anthrax accident as it opened up serious conversation that remains relevant even to this day.

What do we know about this incident, and why I am bringing it up here?

Without going in to great details on the background and related data, which are available for curious readers, here, here and here.

According to these published reports, this is what happened on April 2, 1979: Anthrax spores of Bacillus anthracis (the bacterial pathogen linked to anthrax) were accidentally released from the military research facility of the former Soviet Union into the city of Sverdlovsk. At first, Soviet authorities refused to acknowledge the laboratory origin of a spate of anthrax cases in the city but instead falsely placed the blame on consumption of tainted meat and exposure due to butchers handling the tainted meat. The real situation was entirely different. The anthrax outbreak in the city was unusual, in that, the type of anthrax reported was inhalational anthrax, which one does not contract by consuming contaminated meat products. Inhalational anthrax must involve breathing air contaminated with anthrax spores. Anthrax most often present in contaminated meat and poultry foods remain in the vegetative form of the bacterium and not as spores, meaning exposure to contaminated meat cannot cause inhalational anthrax as falsely alleged by the Soviet authorities.

When anthrax outbreak cases were mapped together with the weather and wind map on April 2, 1979, the trajectory of the anthrax plume appeared as a narrow zone originating from the laboratory and northerly wind during the accident period carried the spores in the north and northwestern direction from the research laboratory and towards the southern city limit (graphic from Science, 1994).

Most of the Anthrax victims were laboratory workers, or residents in the narrow zone extending into the southern city limit that also included death of livestock in the plume zone. Based on these reports and analysis by the US agencies and others, it was concluded that an aerosol of anthrax spores released from the military research facility caused the 1979 Sverdlovsk outbreak. Note that Anthrax spores are not replicative and the disease is not contagious. Only those who inhaled Anthrax spore-contaminated air in the plume zone contracted the disease, but it did not spread beyond the plume zone. For theoretical comparison, a plume containing highly contagious virus such as SARS-CoV-2 presents the risk of infection not only for those in the plume zone, but to others from those infected first and carrying the replicative virus into the general population.

As Ken Alibek writes in his book, Biohazard, a reliably conclusive determination was made possible on the Sverdlovsk anthrax incident since after the fall of the Soviet Union more details on the biowarfare laboratory began to emerge in the 1990s and improved information sharing by the Russian authorities as part of a goodwill measure to broaden cooperation with the West. In comparison, the current situation regarding transparency and data sharing by the Chinese authorities remains poor, without which our current understanding on the source and origin remains largely speculative. On top of it, most research publications focus on genetics and evolutionary biology based on a combination of big data analysis and modeling techniques. As mentioned upfront, these studies focus on the question of biological origin using genomic and evolutionary biology techniques concluding that the virus may have originated from a natural source, This is only a partial answer to the problem. I have not seen a serious research publication from the Environmental Sciences perspective on how the Huanan Seafood Wholesale Market became the focal point for origin of the pandemic.

Notably, the unpublished version of the 2020 Chinese study concludes in verbatim as follows, “In summary, this study provided convincing evidence of the prevalence of SARS-CoV-2 in the Huanan Seafood Market during the early stage of COVID-19 outbreak” without making any conclusion that animal meat sold at the market was the source of the pandemic. However, the paper published in Science states upfront in the title, Unearthed genetic sequences from China market may point to animal origin of COVID-19”. The key paper by the Chinese investigators in 2020 does not make such a conclusion, as I have quoted directly from the paper. If only environmental samples tested positive for the virus, and not wildlife animal meat sold in the market (in early 2020), then how could a conclusion be made that the virus is of animal origin actually explains its presence in the market triggering the pandemic? Animal origin, or not, is only a secondary question in this case.

It is possible the virus originated from a natural source, but the 2020 Chinese study addresses a different angle of the problem. Direct sampling and analysis of the general environment and mammalian meat sold at the seafood market presents a strong case for a thorough environmental sciences study of the problem to answer the most important question facing the scientific community and global health agencies: What is the source of SARS-CoV-2 at the Huanan Seafood Market?

Investigating biological origin of SARS-CoV-2 is an important endeavor, but continued effort to study the source at the epicenter of the pandemic is equally important to get a full picture of the problem.

As pointed out in Part 1 of this article, evolutionary “origin” of a species is different from its “arrival” in an ecosystem. Even if it is conclusively proven that the SARS-CoV-2 virus originated in an animal species, it does not explain how the virus entered the environment of a seafood market causing first-line infection triggering the COVID-19 global pandemic. These are two different, but interrelated questions to address. We need additional environmental data to better understand how the virus entered the seafood market environment. This missing piece of information may help get a closure this painful chapter in global health history