A question that currently remains unanswered is the origin of SARS CoV-2, the causative agent of the COVID-19 disease. Despite the virus governing every aspect of our lives, we are yet to discover the factors that allowed it to successfully infect a human host. As the virus spread all over the globe, so have a myriad of theories pertaining to its origin. In addition to battling a pandemic, fact-checkers work to curb the rampant “infodemic” that arises due to the influx of various conspiracy theories about the origin of the coronavirus. As of the date of publication of the article, these are the theories that have been debunked, and origin-hypotheses that still stand.

Who is Patient 0 (zero)?

The term Patient 0 is given to the first person to be afflicted by a disease. Tracking the first patient provides clues to the potential origin of the virus and offers evidence on the mutation pathway of the virus as it made its way to infect more than 7 million across the globe.

In this situation, what makes tracking Patient 0 particularly difficult is that the SARS CoV-2 has only been recently classified as a the 7th member of the family of coronaviruses. When the virus broke out in the Hubei province in China, the gaps in the knowledge of the virus meant that individuals who showed symptoms were deemed as being afflicted with a “mysterious pneumonia-like phenomenon”, allowing for undetected spread. Scientists cannot be certain as to when exactly the first patient was afflicted.

Despite the virus governing every aspect of our lives, we are yet to discover the factors that allowed it to successfully infect a human host.

Two candidates for Patient 0 arise. A study in Lancet medical journal by Chinese scientists, claims that the first person diagnosed with COVID-19 was identified on December 1, as an old man who had no ties to the Huanan Seafood Wholesale wet market in Wuhan. The second candidate for Patient 0, as reported by the Wall Street Journal, deemed a 57-year-old female shrimp seller at the Huanan wet market, named Wei Guixian, who developed what she thought to be a cold, on December 10.

 The Wet Market

A wet market refers to a space comprising of open-air stalls that sell fresh meat products and other perishable goods. Some markets may house live animals for on-site slaughter. The close proximity of the live animals and humans provides ample conditions for genetic mechanisms such as mutations, recombination and re-assortment to take effect and allow the successful transmissions of viral pathogens to a human host.

Chinese wet markets have been implicated in previous outbreaks such as the Severe Acute Respiratory Syndrome (SARS) in 2002, and the avian influenza H5N1 outbreak in 2008. According to a report published on 24 January in Lancet by Chinese scientists from Wuhan, of the first 41 patients to be identified as of January 2, 27 out of the 41 patients had been exposed to the seafood market (65.85%). In response to an epidemiological alert issued on 31 December 2019, the Huanan seafood market was shut down on 1 January 2020. Shortly after, samples were collected from the market and a deep cleaning procedure was performed.

A study in Lancet medical journal by Chinese scientists, claims that the first person diagnosed with COVID-19 was identified on December 1

Upon testing the samples of various livestock and wildlife sold at the market, results have come back negative for the presence of the coronavirus, according to the Chinese Centre for Disease Control (CDC). The director of the Chinese CDC, Gao Fu, ascertained that “It now turns out that the market is one of the victims.” Scientists from the Wuhan Institute of Virology (WIV) have asserted that to prove a virus’ jump from an animal to a human, it needs to be present in an intermediate animal host. The samples collected from the Huanan seafood market, comprised of samples from various animals housed in the vicinity as well swabs from the market’s surfaces, were all tested negative for the coronavirus. This allowed the Chinese CDC to declare that the coronavirus did not originate in the Huanan seafood market.

Finding a guilty bat

Studies undertaken in response to the Severe Acute Respiratory Syndrome (SARS) outbreak of 2002 that arose in Southeast Asia cited that bats (the natural reservoirs of these viruses) possess a large number of different coronaviruses. Furthermore, the studies highlighted the potential of these viruses to spread to humans, via an intermediate host.

A study published by Chinese scientists in the Nature journal on 3 February cited evidence that SARS CoV-2 samples taken from five patients at the early stage of the outbreak showed 96% similarity to a coronavirus called RATG13 isolated from a bat species called Rhinolophus affinis from Yunnan province (1887.2 km from Wuhan city).

Upon testing the samples of various livestock and wildlife sold at the market, results have come back negative for the presence of the coronavirus…

It is important to note that although the virus originated in bats, it still needs an intermediate host to inhabit before successfully passing to a human host. The intermediate host will house an identical strain of the virus as seen in humans. The causative agent of the SARS outbreak of 2002, SARS CoV-1, originated in a horseshoe bat genus, Rhinolophus but it was only through civets cats (an intermediate host), that it was able to spread to humans. A study undertaken at the time confirmed that the SARS virus in civet cats and humans showed a 99.8% similarity in their genomic sequences. Similarly, camels acted as the intermediate hosts in the Middle East respiratory syndrome (MERS) outbreak in Saudi Arabia in 2014.

The 96% similarity between the virus isolated in Rhinolophus affinis and the causative agent of COVID-19 prove that the virus originated in bats but it does not reveal how the virus acquired mutations to successfully spread to humans. Evidence that implicates pangolins as a potential intermediate host has been polarising as no clear path has been established as to how the virus made its way from bats to pangolins to humans.

Implicating a pangolin

Initially, at a press briefing conducted by the South China Agricultural University in Guangzhou on 7 February, scientists mistakenly declared that the coronavirus isolated from pangolins showed a 99% similarity to the SARS CoV-2 virus circulating in humans. However, the scientists behind the study later clarified that the similarity was centred on the receptor-binding domain (RBD) of the viruses as opposed to the entire genomic sequence. The RBD is the location of the characteristic spike seen on the surface of the coronavirus, however, the scientists argue that the same viral machinery does not provide sufficient evidence to justify genomic similarity. A full genome analysis in the study showed that there was only a 90.3% similarity between coronaviruses in pangolins and humans. Two other studies conducted this year on coronaviruses isolated from pangolins also showed 90.23-91.02% similarity. In order to be considered as the intermediate host, the similarity would have to surpass 96% (as found in bats).

It is important to note that although the virus originated in bats, it still needs an intermediate host to inhabit before successfully passing to a human host.

The pangolin has been prized for its meat, and scales for use in Chinese medicine. The Municipality government in Wuhan adopted a law that came into effect from 13 May that banned the sale, consumption, promotion and rearing of wild animals on land as well as endangered and protected wild aquatic species. Researchers who intend on using wild-life species for research are required to obtain special licenses to carry out the research.

The Wuhan Lab next to the market

Shi Zhengli, a Wuhan-based virologist who directs the Centre for Emerging Infectious Diseases at the Wuhan Institute of Virology (WIV), was responsible for submitting the first genome sequence of the novel coronavirus when the outbreak first started in Wuhan. Dr Zhengli is renowned for her extensive research on the presence of coronaviruses in bats for 16 years, to the point of being nicknamed as “bat woman”, by the scientific sphere. Dr Zhengli was also responsible for discovering the origin of SARS CoV-1 (causative agent of SARS outbreak in 2004) in one of the bat expeditions she conducted. In an interview conducted in February with Jane Qiu, a writer for Scientific American Magazine, Dr Zhengli recalls that when she was first notified of the outbreak, she questioned as to whether it could have come from her lab. Many allegations were thrown at the WIV for either accidentally or purposely releasing a viral sample in a bid to unleash a bio war.

Shi Zhengli, a Wuhan-based virologist who directs the Centre for Emerging Infectious Diseases at the Wuhan Institute of Virology (WIV), was responsible for submitting the first genome sequence of the novel coronavirus when the outbreak first started in Wuhan.

During the initial onset of the outbreak, Dr Zhengli asserted that she went through all lab records to identify any potential malpractices and mishandling of experimental samples. Furthermore, Dr Zhengli confirmed that the sample of SARS CoV-2, did not match any samples contained in the lab.

Dr Zhengli also expressed surprise in discovering the spread in Wuhan citing that subtropical Chinese provinces such as Guangdong and Yunnan (where the horseshoe bat species resided), would have had a higher potential for the outbreak of SARS related outbreaks as opposed to the Hubei province (situated 1887.2km away), that did not house any bat species that were reservoirs of coronaviruses.

An origin outside of Wuhan or China

Scientists have weighed in on the possibility that the Huanan wet market merely provided a place for a super spreader event that could have created a cluster of cases that arose over a short span of time, effectively framing the seafood market as the origin.

A paper published in the journal Proceedings of the National Academy of Sciences by geneticist, Peter Forster, at the University of Cambridge, argues of a possibility that the virus might not have originated in Wuhan. Using 44 genome samples of the coronavirus obtained from early cases in China, coupled with samples from other cases, worldwide, Forster was able to find three varying strands (A, B and C). He affirmed that strain A was the most similar to the RATG13 strand isolated in the Rhinolophus affinis bat species, meaning that strand A was the founding strand (first strand to emerge in humans). The paper stated that of the 23 samples collected from Wuhan, only 3 showed to be strain A, while other parts of China such as Guangdong province, saw a larger number of strain A samples. The notion that strain A was circulating in other parts of China with higher frequency unearths a possibility that Wuhan may not have been where the virus originated.

Amidst the growing tensions between USA and China, Chinese propaganda has alleged that the virus did not originate in their country, during the crossfire of blame for the origin of the coronavirus. Zhao Lijian, a Chinese foreign ministry spokesman, has fanned the flames of conspiracies by alleging that the US army brought the virus into Wuhan upon one of their visits last year.

An aura of disinformation

A Harvard Medical School cites the influx of vehicles in car parks of 6 speciality hospitals (determined via satellite imagery), as an impetus for a rise in hospital visits and an influx of patients from August to December. Furthermore, upon analysing search queries on the Chinese search engine, Baidu, it was found that searches for “diarrhoea” and “cough”, were prominent. Using these pieces of evidence, the study alleges that the virus was circulating in China long-before the official date released by the Chinese CDC, effectively painting China in a light of disinformation.

Scientists have weighed in on the possibility that the Huanan wet market merely provided a place for a super spreader event…

Furthermore, another study highlights discrepancies between China’s release of COVID-19 figures and estimated COVID-19 figures based on social movements and Chinese buying patterns. As per Chinese tradition, funerals take place in the mornings as the norm, hence crematoriums operate only 4 hours in the morning. Figures from 8 of the major crematoriums in Wuhan show that the crematoriums were operating on a 24-hour basis, due to high demand. Additionally, data was obtained to show mass orders for urns. Based on this data, scientists conclude that China has drastically downplayed the toll of COVID-19 on its people. By painting China in a light of disinformation, it sets the stage for whether or not China has been honest with its divulging of information and conduction of studies on the origin of the coronavirus.

In both instances, Chinese doctors and scientist have rebuked the studies and alleged that they “attempt to throw mud at China’s hard-won battle against COVID-19”. Scientists argue that the satellite pictures used for the study have been purposefully taken at obscure angles to induce the image of a full parking lot. Furthermore, the figures obtained from crematoriums are cited as falsified by Chinese scientists.

Furthermore, another study highlights discrepancies between China’s release of COVID-19 figures and estimated COVID-19 figures based on social movements and Chinese buying patterns.

A conflagration of conspiracies

Bill Gates’ TED talk in 2015 on pandemic preparedness, hinted that the world would suffer pandemic that they were ill-equipped to handle. This situation has effectively set the stage for conspiracy theorists to speculate that Gates knew or had some involvement in lab-engineering the virus.

During a question and answer session in the ’r/AskMeAnything’ forum on Reddit, Bill Gates had revealed that a potential initiative to create digital certificates to keep track of those who have been vaccinated against the coronavirus. Conspiracy theorists like Fox News host, Laura Ingraham, argue that a hypothetical mass vaccination campaign that this could create sets the stage for global digital surveillance that could store huge volumes of information about an individual that could be used against them. Theorists claim that advance of such a system, in conjunction with the belt of powerful businessmen who would oversee it, could be used to enforce a class system based on a digital ID. Bill Gates’ consistent silence on the claims has been used against him to fan the flames of conspiracy theories. On 3 June, in an interview with Business Insider, Gates refuted the conspiracy theories and responded by asserting that “It’s almost hard to deny this stuff because it’s so stupid or strange.”

The Wuhan Institute of Virology (WIV) has also been a centre of conspiracies after the director, Shi Zhengli, confirmed that the lab engaged in vigorous studies pertaining to coronaviruses in bats. Amidst the tensions between the USA and China, many global superpowers have accused China of engineering or purposefully releasing the virus as a mechanism of bio-warfare. Scientists have debunked this rhetoric by asserting that the mechanism to synthetically induce pathogenicity is still unavailable at the present time.

Bill Gates’ TED talk in 2015 on pandemic preparedness, hinted that the world would suffer pandemic that they were ill-equipped to handle.

Substantiation of its natural origin

Most scientists in the virology sphere cite a natural origin for the virus and rebuke theories of a lab-engineered virus. Professor Wanda Markotter, the Director of the University of Pretoria’s Centre for Viral Zoonoses asserts that “If someone wanted to make a virus through a genetic reverse system, an available betacoronavirus backbone would have been the obvious choice,” which she mentions is unlikely as the scientific community was not aware of SARS CoV-2 before this outbreak, with the bat and pangolin viruses that have been reported recently as related, were only published after the outbreak.

Furthermore, Prof Markotter explains that “The closest other coronavirus to SARS CoV-2 that was known before the COVID19 outbreak , is SARS CoV -1 that caused the previous outbreak more than a decade ago.” She mentions that the amino acid sequence in the receptor domain of both these viruses, is different, citing that this is the domain that recognises the ACE2 receptor on human cells allowing it to infect humans.

Furthermore, Prof Markotter said that “Biochemical and structural studies suggest that SARS CoV 2 binds with high affinity but computational analyses predict it is not ideal compared to SARS CoV-1. Why would someone engineer a virus if analyses show it may be less optimal for human infection than SARS that caused an outbreak previously? If you want to do this in a lab, you will make the best virus possible with the information available. This is strong evidence that SARS CoV-2 adapted through natural selection to infect human cells optimally.”

Most scientists in the virology sphere cite a natural origin for the virus and rebuke theories of a lab-engineered virus.

Research at UP

 Professor Markotter is currently undertaking research related to the presence of different types of zoonotic viruses (with the coronavirus being one of them) present in bats and other terrestrial mammals in Africa. Using this information, the study aims to analyse the potential sources of transmission to other animals which will allow scientists to garner an understanding of how Severe Acute Respiratory Syndrome (SARS) related viruses afflict humans. The outcomes of research initiatives like these will enable scientific communities to contain potential emergences of other pandemics in future.

PDBY posed several questions to Prof Markotter concerning the zoonotic studies currently being undertaken at UP.  Prof Markotter’s research venture seeks to look at the presence of coronaviruses in animal species that have been previously implicated in zoonotic events in the world or species that have been known to possess zoonotic pathogens. Prof Markotter confirmed that some of the animal species that have been studied in the venture include “the Egyptian fruit bat that has been linked to Marburg outbreaks, Rhinolophus (Horseshoe bats) genus (linked to coronavirus spillovers) and long-fingered bats implicated as a potential host of Ebola.” All of which are widespread in the African region including South Africa.

A few bio-surveillance studies have confirmed that a particular genus of horseshoe bats, known as Rhinolophus, possess the closest related SARS CoV-2 virus strand to humans. Prof Markotter stated that the biosurveillance study being undertaken at UP also looks at horseshoe bats to detect the presence of coronaviruses but asserted that the study is yet to find SARS related coronavirus in bats in Southern Africa. Furthermore, Prof Markotter confirmed that the biosurveillance is currently being expanded on.

The outcomes of research initiatives like these will enable scientific communities to contain potential emergences of other pandemics in future.

UN probe/ investigation

A draft resolution that has been backed by 110 countries, has called for an independent probe into the global response to the pandemic. The draft resolution was presented at the World Health Assembly (the governing body of the World Health Organization) on 18 May and has been adopted by the World Health Organization (WHO). As of date of publication of this article, a date had not been announced for the commencement of the probe nor has the mode of operation of the independent investigation been announced. However, it was agreed upon that this would take priority once an end was in sight for the current pandemic.

Although the final resolution does not explicitly mention an independent investigation into the origin of the coronavirus, it is speculated that this may be one of the investigation divisions in an effort to conduct “a stepwise process of impartial, independent and comprehensive evaluation”, as stipulated in the 9(10) of the final resolution.

A draft resolution that has been backed by 110 countries, has called for an independent probe into the global response to the pandemic.

Although we have a myriad of theories on the origin of the virus, how exactly this spillover to a human host occurred is still unknown. The gaps in our knowledge have provided the impetus for conspiracy theories to play on the human psyche and encourage a sentiment of Sinophobia in the face of the pandemic. In the midst of combating the pandemic, conducting research on possible vaccines has been prioritised over research into its potential origin. An independent probe into the global response to the pandemic may provide clarity to the origin of the virus.

Visual: Kayla Thomas

SUSANNA ANBU

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