Origin of SARS-CoV-2, the virus behind COVID-19 or coronavirus pandemic: facts, assumptions and myths

Updated: 3.6.2020

How did the novel coronavirus, SARS-CoV-2, originate at all? Where? How? When? From which source?

These are some questions about which media and social media have been carrying numerous posts, with versions ranging from a fluke transfer from wild animals in a local Chinese market to a stupid reaction by local police, an embarrassing mistake, an experiment gone haywire and creation of a biological war agent. Some government agencies and world leaders have also expressed their opinions in a way that adds muck to an already murky narrative. Domestic politics also decides what view leaders and people of a particular political party (also media and people on the social media,  with political leanings) take on a sensitive subject. So, what is floating around us is a big heap of fiction, with some shards of truth scattered here and there. This article is an attempt to separate truth from outright fiction, also to highlight things about which we do not know yet.

Before doing the sifting, let me draw you attention to the fact that Chinese authorities have not been forthright about various facts and figures. That is one reason for so much confusion. Though Chinese government agencies/ spokesmen/ representatives have tried to clarify their position, they went further and joined a vehement war of words with others. If you believe the Chinese version, they themselves are a big victim; but not being transparent from the beginning has generated many conspiracy theories against them. A sort of ban on reporting on the epidemic within China and disappearance of a couple of reporters also increased suspicion that everything was not that clean about the virus, and China could be hiding much more than just an embarrassingly big number of deaths.

Let us now look at the facts, myths and unproven hypotheses circulating on the origin of coronavirus. For clarity, I have made the proven facts green, highly plausible hypotheses blue, postulates that need much corroboration orange and very unlikely assumptions as red. These are based purely on my understanding of the subject.
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At the outset, let me explain some terms so that things do not get mixed up:

  • Coronavirus is a family of many viruses. These are grouped into many sub-families and genera. The most common virus of this family is the one causing common cold.
  • COVID-19 is the disease caused by coronavirus, which originated in Wuhan in 2019 and has spread across the globe. 
  • SARS-CoV-2 is the universally accepted name of the virus that causes COVID-19. Its initial name was 2019-n-CoV. Initially, it was also called as novel coronavirus.
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There is no doubt that SARS-CoV-2, the virus responsible for COVID-19, is a coronavirus (CoV), i.e. one of those with protein spikes on its body and responsible for various types of flu. Genetic sequencing has determined that SARS-CoV-2 belongs to a group of genetically related viruses that includes the SARS virus, SARS-CoV.

When did the first infection happen to a human being? The spillover from an animal source i.e. bat to humans seems to have happened during the last quarter of 2019. There are reports that suggest that it might have happened as early as September, 2019. Another set of reports indicate that a person was identified as early as November 17 in Hubei province where Wuhan is located. From that date onward, one to five new cases were reported each day. Chinese authorities say, in late December 2019, the Wuhan Center for Disease Control and Prevention (CDC) in central China's Hubei Province detected cases of pneumonia of unknown cause - that's what came to be known later as COVID-19.

The first patient (=patient zero) or the place of first infection by SARS-CoV-2 may never be found out precisely, partly because the first patient(s) might have developed no/minor symptoms and might not have been admitted to a hospital with typical symptoms.

The most popular theory is that COVID-19 spread from the local Huanan Wholesale Seafood Market that sold a variety of animals and animal products including wild animals. Out of the first 41 cases reported officially, while 27 had a relationship with this market, 14 had no direct contact with that market. It is logical that once someone was infected in this market (from an internal or external source), the crowding might have led to its fast spread among shopkeepers as well as buyers.

It is highly likely that novel coronavirus or COVID-19 originated in Wuhan, China. There are a number of hypotheses including one that it was transported to Wuhan during research or as part of a deliberate act to infect the population. I will come to such assumptions later and presently go with the likely hypothesis that it originated within Wuhan.

The genome of SARS-CoV-2 closely resembles that of the coronaviruses isolated from bat populations. In a prominently quoted study, the genome sequence of SARS-CoV-2 was found to be 96.2% identical to a bat CoV, RaTG13. Scientists have concluded that bat is almost certainly the primary ecological source or reservoir for this virus. If bat is considered the most likely  primary source, the virus jumped to humans either directly or through an intermediary animal. 

A good deal of research shows that perhaps an intermediary animal that consumes bats was responsible for its transmission to humans. The closely related SARS virus is also known to have come to humans from bats through an intermediary, civet cat. Pangolin, a scaly ant-eater that looks like a big lizard, is supposed to be the intermediary, because coronaviruses found in pangolin too are quite similar to SARS-CoV-2. The fact that possible intermediaries such as turtles, pangolin and snakes were traded in the market, not bats, were sold in the Huanan Wholesale Seafood Market in Wuhan also leads towards this probability. It has also been stated, based on genetic studies, that pangolin may indeed be the reservoir rather than an intermediary

One scientific assumption is that because the virus is closely related to those found in pangolins and also in bats, it could have originated by recombination between the two types of viruses in an animal that was infected by both strains simultaneously

Eating habits of the Chinese have come in focus. They are known to consume a variety of animals, even wild animals, sometimes even without proper cooking. However, whether the infection occurred due to eating of wild animals is not clear; it could be physical contact with live or dead animals. There also is this hypothesis, which you cannot brush aside just like that: The infection occurred from the droppings of bats instead of through eating bats or coming in contact with their meat/ dead bodies. It is reported that bat droppings are collected by a large number of farmers in that part of the globe for use as manure. Scientists from the Wuhan lab (sell below) have also been collecting samples of bats from different parts of China, and it is reported that they sometimes did not follow enough safety measures.

Now comes the big question: Whether the virus, SARS-CoV-2, jumped to humans naturally from an animal or it happened due to some human actions - deliberate or otherwise?

A number of scientists from different countries have come on record saying that based on the structure of backbone derived from the viral genome and the way the viral spikes attack human respiratory tract cells, there is firm evidence that the virus originated from a natural source and an evolutionary mutation in its parent has created this virus. They claim to have minutely studied the genetic data shared by the Chinese researchers and come to this conclusion. They have also said that a genetically engineered virus would not have the characteristics that SARS-CoV-2 exhibits.

A scientist has said, there is no system in existence that would cause the changes that are seen on this virus as compared to those found naturally in bats. It is also said that if humans were to clone a virus, they would not take the route that would result in a virus like SARS-CoV-2. Scientists have also said that the sample of bat virus RaTG13 kept in the P4 lab of Wuhan Institute of Virology, which is suspect in the eyes of those saying it is human created, cannot result in SARS-CoV-2 through plausible genetic engineering.

Based on detailed study of the property of SARS-CoV-2 to bind with human receptors, it has been postulated that the source coronavirus gained the ability to infect humans through the genetic process of recombination with Pangolin virus followed by natural selection.

A group of 27 scientists from around the world have gone to the extent of making a joint statement stating that they "overwhelmingly conclude" that the virus originated in wildlife and that "...Conspiracy theories do nothing but create fear, rumours and prejudice that jeopardise our global collaboration in the fight against this virus..."

In fact, scientists have gone on to say that the only thing to be examined is whether the mutation that makes the virus so highly pathogenic occurred after it migrated from bats to the intermediary, inside the intermediary or after it entered the first human. According to this version, if the virus mutated before entering humans, there would be possibility of another outbreak because it would be spreading widely in the wild animal population and would jump to humans at the next opportunity.

The World Health Organization (WHO) has also stated that all available evidence indicates that SARS-CoV-2 originated in the wild and not in a lab.


Let us examine the stories floating on web media and television about human involvement in the origin of this virus. The culprit here is mostly a Chinese lab, also the US army. I will finish the latter first because it is less prominent and so can be dealt with quickly.

One report circulating on social media is that the US army was behind the introduction of virus in China. This was suggested by a Chinese official, saying that the virus had appeared in the US before it was observed in Wuhan. Authorised Chinese officials did not refute it; instead they evaded a comment and insisted that the truth about the origin of virus could come out only through scientific investigation.

It was also said that only because the epidemic was reported first in China does not mean it originated in China. This has also been supported by a researcher drawing inference after examination of different variants of SARS-CoV-2 that the variant that infected Wuhan was not the original one. This has even been linked to the participation by the US army in the Military World Games held in Wuhan in October 2019.

To say that the US army created the virus and introduced it in Wuhan looks too far fetched, like saying that the Chinese army did so (discussed later).

Now let's look at the leads/ inferences put forth by those claiming that the virus started its journey from a Chinese lab. If you take this hypothesis to be valid, there emerge a number of scenarios:
  • The virus was being created as a biological weapon by manipulating its genome.
  • It came out of the lab by mistake (by contaminating things that came out of the lab).
  • It was purposely spread by a rogue researcher.
  • It infected a researcher and spread from him.
  • It was purposely spread out for testing but went out of control.
  • It spread from bats disposed of within the lab but not properly.
  • It spread from bats that, after experiments, were sold/ distributed in the Seafood Market or elsewhere.
So, there are two sets of postulates: 1, that it was a deliberate act on the part of Chinese authorities, and 2, that it was an accident.

Was it a deliberate act? There are suggestions to this, as I will place below. However, even the US intelligence experts have generally not found favour with this line. They have rather said, they cannot rule out anything as of now.

Many experts dismiss the hypothesis of China deliberately introducing the virus into humans saying that if they wanted it, they would not have spread it among their own people - an act that does not help authorities in any way.

But that does not discount the hypothesis that it might have leaked from the lab due to insufficient precautions or serious indiscretion.

One big reason for suspicion of human involvement in origin of SARS-CoV-2 is the effort on the part of Chinese health authorities to veer public attention towards the Huanan Seafood Market as the ground zero.

The local health authorities and later higher authorities kept on harping that the Seafood Market is the likely place of origin of COVID-19. Observers find it intriguing that in the middle of January the Chinese national health authorities issued diagnostic criteria that mandated only such cases to be reported in which the patients had a history of contact with the market (in addition to fever and whole genome sequencing), even though by that time it was crystal clear that a third of cases were not related to the market. It might have been done to cover up the actual source, and if so, there must be a reason behind that, skeptics say.

For discounting the Seafood Market as the primary and only source of infection, it is also pointed out that the market did not trade in bats or pangolins - the most probable sources of the virus. Those knowing about the working of the market, however, say a huge variety of live and dead animals were routinely sold for which there was no permission, and bats (or any intermediary animal for SARS-CoV-2) were no exception.

The majority of observers are almost sure that having a source different from the Seafood Market does not mean the second source was the lab. They also say that there was strong logic behind thinking that the Seafood Market was the source because the most number of cases were reported from the market and it sold all types of animals. In hindsight, that seems to be a hasty conclusion, even if not intentional.

The second is the presence of a highly sophisticated lab in Wuhan in which a lot of research was actually being carried out in viruses very similar to SARS-CoV-2.

This is a fact that an institute, Wuhan Institute of Virology (WIV) , operates in Wuhan and it has a lab - National Biosafety Laboratory or P4 - which is equipped to handle viruses. This research facility was created with US and French collaboration. US has been funding research in the institute even now.

It is also true that a large number of research papers on coronaviruses have been published by scientists of this institute, in internationally reputed journals. The Institute uses this fact to claim that it has been transparent about its research and has been sharing data and research with others. It says, it follows strict regulations and code of conduct.

On the type of research being conducted at WIV, the arguments against the institute go like this:

Scientists working in WIV seem to know too much about coronaviruses. They have been successful in re-engineering virus genomes. Some such experiments had, in the past, generated concern about emergence of a new type of powerful virus. A number of research papers came out in years and months preceding February 2020, on genome sequencing and other research on coronaviruses. One of the scientists working in WIV had been publishing a large number of research papers on SARS, starting 2010.

WIV has been conducting experiments on samples collected from bats in 28 Chinese provinces, even from caves as far as Yunnan in China for many years. Chinese scientists are also supposed to have access to virus samples available in the US. It is being suggested that mix-and-match experiments with different viruses is very much possible in WIV.

Those believing in the lab-to-human hypothesis also refer to a 2015 case of the US. The University of North Carolina was then working on the spike protein of SARS and the virus modified by the team during experiments was pathogenic to humans. Scientists from WIV were part of the research, and virus from Chinese bats was used. Following serious concerns about the research, it was finally abandoned.

These observers also say, WIV is not a mere academic institute. Though it collaborated with France and gets funds from the US, these are treated as outsiders while military experts are routinely roped in, in virus research.

So, research and experimentation on SARS viruses was indeed being carried out in WIV very aggressively. The inference here is, even if there was no warfare or other sinister angle to it, this over-zealousness might have been to prove their supremacy in research into coronaviruses at molecular/ genetic level.

Now come to the safety levels maintained in WIV labs. There are independent reports suggesting that the safety levels in Chinese labs dealing with such deadly viruses are not up to the level, and there have been instances of careless collection of bat samples, and bio-safety of level 2 (BSL 2) being followed by these labs instead of BSL 4. It is also being pointed out that there have been at least two earlier incidences of SARS virus escaping from a Beijing lab. The potential harm was quickly contained, though.

China issued belated instructions on strengthening bio-security management in microbiology labs that handle advanced viruses like the novel coronavirus. It is pointed out that there was no need for such instructions if there was no breach in the past. Also, that these instructions are focused on WIV because only that facility has been dealing with coronavirus; making it applicable to 'labs' in general is for avoiding a direct reference to WIV.

A prominent news website has brought to attention that in 2018, the US embassy in China had  sent a message to US authorities pointing towards poor safety procedures being maintained at the Wuhan lab.

Let's come to indiscretion on the part of researchers or other staff in the institute. It is reported that some Chinese researchers have been selling laboratory animals to street vendors after finishing their  experiments. The incentive could be financial and not a motive to spread an infection. But if that happened in the present case, that could explain why the virus spread in areas near the institute.

It is also reported that a Beijing researcher made a million dollars selling monkeys and rats in a live animal market before he was caught.

The recent posting of a top military officer, who is a virologist, to head WIV is seen by some as a proof that something serious has happened in the lab and the officer has been posted there for damage control.

The Institute has repeatedly and categorically said that the virus has not spread from the lab either by mistake, misadventure or authorised action.

The US Director of National Intelligence issued a statement on May 1, 2020 saying that "COVD-19 virus originated in China", "The Intelligence Community concurs with the wide scientific consensus that the COVID-19 virus was not manmade or genetically modified" and “The IC will continue to rigorously examine emerging information and intelligence to determine whether the outbreak began through contact with infected animals or if it was the result of an accident at a laboratory in Wuhan.”

The third 'proof' given for the virus having arisen through a human act is the unusual genome sequence of SARS-CoV-2 as compared to other coronaviruses.

A research paper published sometime back said, SARS-CoV-2 genome has inserts from HIV, which is an evidence that tinkering with the natural viral genome has been done. The paper was retracted later. Yet, some kept insisting that the unusually fast spread of the virus, its extra-ordinary capacity to attach to human cells and its attack on the human immune system (as in the case of HIV) could not have been without some sort of tinkering in the lab. They also say that experiments with SARS virus including genetic recombination were not unusual in WIT. 

One report says, the high degree of closeness between genome sequence of SARS-CoV-2 and that of Yunnan bats (not the bats found in Wuhan, but the ones brought to WIV by researchers from Yunnan) may not be a mere natural occurrence.

But, as I have already said above, these theories have been debunked by not only Chinese researchers but also a large number of scientists and the WHO. As regards 'inserts' noticed in SARS-CoV-2, these are said to be seen in other bat viruses, some bacteria and even shark.

It is also reported that when, on knowing about a new pneumonia virus spreading in Wuhan, the US wanted China to share the samples of initial infection so that it worked on finding cures, it did not get the samples. China has not only denied that but insisted that it has been sharing samples and data with US researchers, as early as it could, in a transparent manner.

The suppression of information, including research and public information, is being used for inferring that there is something fishy about coronavirus research and the origin of the virus. Even high-pitch political calls are being made, asking China to come clean.

The local health authorities tried every means to cover up the spread of disease even after it had become a sort of endemic. What puts the veracity of Chinese assertions in serious doubt is that China has revised its mortality figures by as much as 50%, after 3 months. Officials say, the revision had to be done because of incorrect or delayed reporting and not because information was suppressed.

A doctor on December 30 discussed on a chat group about a possible outbreak of an illness that resembled SARS. The way he was treated by Wuhan authorities (warned, made to sign statement) and his subsequent death due to COVID-19 also raise questions. Around that time, the authorities also banned testing of samples of the mysterious disease.

After WIV labs started publishing research on, and genome sequence of, SARS-CoV-2, an official directive was issued in January 2020 asking that existing virus samples must be destroyed. Information about the samples, related papers and data were prohibited from release even to Chinese health system. In April, publication of research on coronaviruses was banned without approval of national authorities.

On Chinese social media, it circulated for some time that a female graduate was patient zero as she got infected in a lab in WIV. Her details were removed from official website of the institute, and the institute refuted these 'rumours'.

On the web, you can find reports that some researchers had blown the whistle about the virus having leaked from P4 lab, even naming the person responsible for the leak. These have not been substantiated.

The questions being asked are like this: Where was the need to clamp down on information if the infection in Wuhan was a natural occurrence? Was it to confuse or mis-direct the world community and scientists? Were the data and samples wiped, and research censored, to hide something that would incriminate or at least embarrass Chinese authorities?

One argument given in defence of the Chinese authorities is that censoring of research articles could be in response to wide-spread mis-representation of data by those wanting to prove the Chinese guilty for something they did not do. If there was aggressive exhibition of research by some scientists and they were getting papers published without due caution, that also needed to be curbed.

A large number of observers do not think that there is a link between the suppression of information and  the origin of SARS-CoV-2. They point to the way the Chinese system works, and it worked the same way here too, by first under-stating the damage, then trying to control the issue by themselves before raising alarm. Moreover, the infection started in Wuhan when the Chinese Spring Festival was on and Christmas and New Year were in the offing; a heightened alarm could have caused chaos all around.

Whether it was done for suppressing any vital facts or due to pocedural/ bureaucratic factors, it is very clear that China did not share all facts relating to genome and early spread proactively with the World Health Organization. A detailed report by the Associalted Press states that China did not share the genome of SARS-CoV-2 with the world for many weeks.

Finally, one important link the 'conspiracy theory' believers would not like you to overlook: the military link with virus research in WIV.

It is reported that military wing dealing with virus-related research had been working closely with WIV. The posting of a serving military general, who is also a virologist and has worked on Ebola and anthrax, as head of the Institute in February 2020 supports the hypothesis that military has a strong interest in the research being conducted at WIV.

It is also said that biological warfare has been high on the agenda of the Chinese military and is being actively pursued in a number of labs. There is much more written on Chinese activities on chemical and biological warfare. These mostly go into geopolitics and strategy - areas beyond the present discussion.

I have not seen response of the Chinese side on the reports of linkage between military and the origin of SARS-CoV-2. Those who see the link between military and WIV not too unusual say, in most countries, military and civilian research bodies collaborate on dual-use (in areas that have military as well as civilian use, e.g. atomic research, space research, metallurgy) technologies.

As mentioned above, the reaction to 'conspiracy theories' has been strong from Chinese officials and a group of scientists. It is also reported that a video issued by a US newspaper, trying to prove that a human action was responsible for origin of the virus was being shared on Facebook, and that Facebook has marked it fake and removed all references to it from its platform.

So, the view that SARS-CoV-2 arose due to genetic modification of one or more existing viruses, done to create a biological warfare agent seems pure speculation. The other possibility - that it was created deliberately towards controlling research in this highly sophisticated area - even if with the good intention of producing cure against virus diseases - looks highly specious. What perhaps needs further scrutiny is whether it was created/ spread accidentally or due to indiscretion on the part of some rogue scientist.

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"It is improbable that SARS-CoV-2 emerged through laboratory manipulation of a related SARS-CoV-like coronavirus...The RBD of SARS-CoV-2 is optimized for binding to human ACE2 with an efficient solution different from those previously predicted7. Furthermore, if genetic manipulation had been performed, one of the several reverse-genetic systems available for betacoronaviruses would probably have been used. However, the genetic data irrefutably show that SARS-CoV-2 is not derived from any previously used virus backbone. Instead, we propose two scenarios that can plausibly explain the origin of SARS-CoV-2: (i) natural selection in an animal host before zoonotic transfer; and (ii) natural selection in humans following zoonotic transfer.": paper in Nature, published on 17.3.2020
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SOURCES, REFERENCES

On web media, opinions have been expressed by virologists, infectious disease specialists, epidemiologists, genetic engineers, other researchers, biological warfare analysts, also economic and political analysts, politicians, journalists of all kinds and self-styled experts. These opinions have been commented upon and shared all over social media.

The following are the prominent web resources I have used here:

As U.S. investigates Wuhan lab leak theory, senior china researcher says allegations are 'malicious, impossible' [newsweek.com]
China clamps curbs on publication of research papers on coronavirus origin: Report [deccanherald.com]
China delayed releasing coronavirus info, frustrating WHO [apnews.com]
China publishes timeline on COVID-19 information sharing, int'l cooperation [xinhuanet.com]
Chinese diplomat promotes conspiracy theory that US military brought coronavirus to Wuhan [edition.cnn.com]
Coronavirus origins: genome analysis suggests two viruses may have combined [weforum.org]
Coronavirus: China’s first confirmed Covid-19 case traced back to November 17 [scmp.com]
COVID-19 coronavirus epidemic has a natural origin [sciencedaily.com]
Don’t buy China’s story: The coronavirus may have leaked from a lab [nypost.com]
Emergence of SARS-CoV-2 through recombination and strong purifying selection [sciencemag.org]
How did coronavirus break out? Theories abound as researchers race to solve genetic detective story [edition.cnn.com]
How did covid-19 begin? Its initial origin story is shaky. [washingtonpost.com]
Intelligence Community Statement on Origins of COVID-19 [odni.gov]
No proof that COVID-19 originated in Wuhan: Peter Forster (video) [youtube.com]
Origin of SARS-CoV-2 (26 March 2020) [who.int]
Rare footage shows scientists working at controversial Wuhan virus lab as the head of the institute says 'there's no way' coronavirus originated there [dailymail.co.uk]
Scientists ‘strongly condemn’ rumors and conspiracy theories about origin of coronavirus outbreak [sciencemag.org]
Scientists Are Tired of Explaining Why The COVID-19 Virus Was Not Made in a Lab [sciencealert.com]
Sources believe coronavirus originated in Wuhan lab as part of China's efforts to compete with US [foxla.com]
Sources believe coronavirus outbreak originated in Wuhan lab as part of China's efforts to compete with US [foxnews.com]
The coronavirus was not engineered in a lab. Here's how we know. [livescience.com]
The proximal origin of SARS-CoV-2  [nature.com]
Tracking Down the Origin of Wuhan Coronavirus (video) [theepochtimes.com]
WHO Timeline - COVID-19 [who.int]
Wuhan lab was performing coronavirus experiments on bats from the caves where the disease is believed to have originated - with a £3m grant from the US [dailymail.co.uk]

DISCLAIMER

This article is meant purely to bring forth the facts and hypotheses connected with the origin of the virus that has caused COVID-19. The information shared here is in the nature of web-research. I have tried to avoid politics or geo-politics out of the discussion. I have made some inferences based on material in hand and my understanding of the subject and these do not represent views of organization(s) I may be associated with in my professional/ official capacity.

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