Origin of SARS-CoV-2 Coronavirus—Part 1:New Developments

Authored by: Venkat Rao

There are new developments on the origin of SARS-CoV-2, the coronavirus responsible for the COVID-19 global pandemic. Origin of SARS-CoV-2 remains unsettled as a highly controversial topic across the geopolitical and scientific community. According to a recent report in Science magazine, a French scientist has accidentally identified previously undisclosed genetic data from the Huanan Seafood Market in Wuhan, China. Early reports on COVID-19 outbreak in December 2019 were linked to a contact history leading up to the Huanan market. According to this report, investigators, in early 2020, had collected as many as 1380 samples from wildlife and the general environment within the market for genetic analysis and found 73 samples tested positive for SARS-CoV-2. The viruses detected in the environmental samples were a 99.99% match with the virus isolated from COVID-19 human patient samples. Surprisingly, no SARS-CoV-2 virus was detected in the 18 species of animals sampled during this investigation. Note for the moment that only environmental samples tested positive for the SARS-CoV-2 virus.

Since the food samples from the market tested negative, while general environmental samples tested positive for the virus, the 2020 January study conclusion by the Chinese investigators was that humans brought the virus to the market and that the marketplace was not the origin of the pandemic. The 2020 January study makes a key observation that the virus could have come from human sources to the market and not from the animal food sources sold in the market. The seafood market may have amplified the scale of human infections but was not the source is how they concluded three years ago, although the supportive data to this very important conclusion was not made public.

The study, although not yet published, indicated that SARS-CoV-2 virus was in circulation in the Huanan Seafood Market during the early 2020 phase of the COVID-19 outbreak. The study conclusion is ambivalent as to whether COVID-19 virus was in circulation in the general environment outside of the seafood market, or was introduced into the general environment from human sources, or possibly from an accidental release from a nearby laboratory facility remains open for debate. A key observation from the 2020 unpublished study is that the animal meat samples tested were negative, but environmental samples were positive for the SARS-CoV-2 virus. What could have been the source for SARS-CoV-2 virus in the general environment at the seafood market?

Compare this finding with an earlier report published in the same Science Magazine last year that concluded the origin of COVID-19 pandemic may have been initiated at the Huanan Seafood Market resulting in two cases of the virus jumping from live animal hosts to humans working or shopping at the market. This observation contradicts the just released report that the virus was not detected in the animal meat sources, but was present in the general environmental samples. Absence of viruses in the food samples and presence in the general environment brings up unsettling questions on the source and origin of the virus.

Several researchers presented these findings past fortnight to the World Health Organization’s Scientific Advisory Group for the Origin of Novel Pathogens (SAGO). Soon after the past fortnight briefing by the French team, the WHO has requested the Chinese Center for Disease Control to share genomic data with the WHO and the international community. WHO clarified in the public statement that “these data do not provide a definitive answer to the question of where the pandemic began, but every piece of data is important in moving us closer to that answer”. In the March 17th remarks, WHO stated that China could have and should have shared this data three years ago.

Given the unsolved mystery of SARS-CoV-2 origin, it is unclear why the Chinese Center for Disease Control did not make the sequences public earlier absolving China from international criticism of laboratory leak and negligence as the origin of global COVID-19 pandemic. It is unclear why the Chinese CDC claimed illegal animal dealing was the reason why the market was shut down on 2 March 2020, without providing additional information on the Huanan Seafood Market investigations.

Before we get too far to conclude whether the natural food sources at the Wuhan seafood market was the source and origin of COVID-19 virus, or a different source of release introduced the virus into the general environment of the market as detected from the recent French study, let us review the background and other contradictory data.

Ever since, December 31, 2019, the first outbreak of a respiratory illness later determined to be caused by a novel coronavirus, first reported in Wuhan, a city of Hubei province in China, the source and origin of the virus has remained a frontline topic with no clear and conclusive evidence on whether the virus was of natural origin, or, as reported in the recent US Department of Energy report, due to a lab leak.at the Wuhan Institute of Virology, in China.

According to the unclassified summary of a US Director of National Intelligence report, SARS-CoV-2 virus probably emerged from the Wuhan lab causing a minor infection episode in November 2019, when the first cluster of the disease outbreak was reported in Wuhan on December 19, 2019. However, the IC report did not conclusively state that the virus was part of a biological weapons research at the Wuhan lab, although the veracity of available data was weak to make a conclusive determination either way. The IC report did not arrive at a conclusive determination on two lines of argument: origin from a natural source involving contact with an infected animal or a laboratory-associated incident resulting in the release of a lab constructed virus into the nearby wildlife meat market.

Analysis by the US Intel community was based on the weight-of-evidence from various published scientific sources, intelligence reporting and scientific gaps interpreted by subject matter experts.

The level of confidence used by analysts simply denotes the strength and veracity of the data they were able to obtain and use in these analyses to arrive at conclusions. Nevertheless, due to lack of data, these analyses resulted in divergent conclusions with one intelligence entity concluding at a moderate-level of confidence that the SARS-CoV-2 virus originated from a laboratory associated incident, probably involving experimentation, animal handling or sampling from various natural sources for research at the highest biological containment research laboratory in Wuhan.

Contrast this to another set of analysis by four different intelligence community entities that concluded at a low- to moderate-level of confidence that the initial SARS-CoV-2 infection occurred through natural exposure to an infected animal, perhaps to a viral variant very close to the human virus that causes COVID-19.This line of analysis accepts to a considerable level the official Chinese explanation that they were unaware of the numerous natural sources of the virus circulating in the wildlife meat market at the vicinity of the Wuhan Institute of Virology, from where the initial contact with infected wildlife meat source may have happened with unsuspecting shoppers leading to the initial outbreak of COVID-19 disease cluster in Wuhan around December of 2019.

Lack of transparency on the part of the Chinese public health authorities greatly contributed to the raging controversy on the source and origin of SARS-CoV-2 virus with no clear, conclusive evidence either way.

The source of COVID-19 pandemic is a pertinent question as the global damage caused is immense. As of today, over 684 million cases of confirmed COVID-19 are reported from across the globe and over 6.8 million deaths and associated global economic damage estimated at $16 trillion and counting. COVID-19 is considered the greatest threat to prosperity and wellbeing of the United States since the Great Depression.

When Charles Darwin published his groundbreaking book, “Origin of Species” in 1859, he provided a detailed outline for evolutionary biology. His research provided the fundamental theoretical framework for “evolution” of life, and not “origin” of life. The difference between biological evolution, be it a virus or a monkey, is not the same as its “origin”.

In Part 2, I will provide a more detailed delineation of these aspects with SARS-CoV-2, to better understand what we know about its origin and rapid transformation to genomic variants responsible for the global pandemic.