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How the SARS-CoV-2 virus arose

The SARS-CoV-2 virus has managed to change the world. It is hard to believe that a nucleotide sequence was able to do so. It has caused a global pandemic that as of today, September 5, 2021 has a total of  221 million  confirmed cases and  4.5 million  deaths.

This article will comment on the latest findings on the origin of the pandemic caused by the SARS-CoV-2 virus have recently been published in scientific journals. Being such a complex disease and with hundreds of scientific articles that come out every day to the media is an explanation today, but it does not mean that tomorrow something new will be discovered that changes the version of this article.

This article published in the journal Biorxiv.org -> https://www.biorxiv.org/content/10.1101/2021.06.18.449051v2 with doi: https://doi.org/10.1101/2021.06.18.449051, written by  Jesse D. Bloom of the Fred Hutchinson Cancer Research Center in Seattle, United States, is taken as a starting point.

A Wuhan market

It all started in a Market in Wuhan. Or at least that’s what we’ve been told many times. For example, wikipedia collects that it was ground zero for the spread of the virus.  

Knowing the origin of the spread of the virus is crucial to discover traceability and get to know who was the patient zero that caused the entire pandemic. And above all, what was the vector, the intermediary animal, that transferred the virus to humans. The first reports in late 2019 emphasized the role of a Huanan fish market  in wuhan city,  whichwas credited with the onset of this zoonosis (animal disease that is transmitted to man).

However, this theory of the origin of the virus is increasingly losing strength and it is believed that rather the market was a victim, but not the origin of the pandemic. The virus already existed before its appearance in that fish market.

Before the market

An article in the journal Lancet  described a confirmed case with no association with the market whose symptoms began on December 1(Huang et al. 2020). Hong Kong’s  South China Morning Post  described nine cases from November 2019, including details about the patient’s age and sex, noting that none were confirmed as “patient zero.”

Several Chinese professors indicated details of possible patients in mid-November and a suspected case from September 29, 2020. However, no cases have been confirmed, and China’s CDC  ordered not to share this type of information without approval by this body.

In 2021, a WHO-China report ruled out all cases reported before December 8 as non-COVID-19 and revived the theory that the virus could have originated in the Huanan seafood market(WHO 2021).

Study of the epidemiology of the virus

In other outbreaks where direct identification of early cases has been complicated, it is increasingly possible to use genomic epidemiology to infer the timing and dynamics of spread from viral sequence analysis. For example, analysis of SARS-CoV-2 sequences has allowed the reconstruction of the initial spread of SARS-CoV-2 in North America  and  Europe (Bedford  et al.   2020;  Worobey  et al. 2020;  Deng  et al. 2020;  Fauver  et al. 2020).

But in the case of Wuhan, genomic epidemiology has proven frustratingly inconclusive. Some of the problems are simply limited data: even though Wuhan has advanced virology laboratories, there are only irregular samples of SARS-CoV-2 sequences from the first months of the city’s explosive outburst. Another than a set of multiple sequence samples collected in late December 2019 from a dozen patients connected to Huanan Seafood Market (OMS 2021), only a handful of Wuhan sequences are available from before the end of January 2020.

This shortage of sequences could be due in part to an order that unauthorized Chinese laboratories destroyed all coronavirus samples from the early stages of the outbreak, supposedly reasons of “laboratory biological safety.”

Discovering the lost sequences of SARS-CoV-2 virus

However, the Wuhan sequences that are available also confusing phylogenetic analyses designed to infer the “progenitor” of SARS-CoV-2, which is the sequence from which all other currently known sequences descend(Kumar et al.2021). Although there is debate about exactly how SARS-CoV-2 entered the human population, it is universally accepted that the ancestors of the virus are bat coronaviruses (Lytras  et al. 2021). But the earliest known sequences of SARS-CoV-2, which come mainly from the Huanan seafood market, are noticeably more different from these bat coronaviruses than other sequences collected at later dates outside Wuhan.

Summary

The origin and early spread of SARS-CoV-2 remains a mystery. In the work presented in this article, a dataset containing SARS-CoV-2 sequences from the early Wuhan epidemic that had been removed from the NIHSequence Reading Archive wereidentified.

Deleted files were recovered from Google Cloud and partial sequences of 13 early epidemic viruses were reconstructed. Phylogenetic analysis of these sequences suggests that the Huanan seafood market sequences that are the focus of the joint WHO-China report are not fully representative of the viruses in Wuhan at the beginning of the epidemic. In contrast, the progenitor of known sequences of the SARS-CoV-2 virus probably contained three mutations relative to the viruses on the market that made it more similar to the bat coronavirus relatives of SARS-CoV-2.

Therefore, we are still far from knowing exactly what was the origin of the pandemic that has caused COVID-19. However, each new article brings us closer to knowing where and when it emerged.

References

  1. https://en.wikipedia.org/wiki/Huanan_Seafood_Wholesale_Market
  2. https://pubmed.ncbi.nlm.nih.gov/32015508/
  3. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7094943/pdf/41586_2020_Article_2008.pdf
  4. https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30183-5/fulltext
  5. https://www.who.int/medicines/publications/druginformation/issues/WHO_DI_34-3_PL124-SpecialEdition.pdf
  6. https://montoliu.naukas.com/2020/12/27/la-ciencia-que-hay-detras-de-la-primera-vacuna-contra-la-covid-19/
  7. https://www.biorxiv.org/content/10.1101/2021.06.18.449051v1?fbclid=IwAR0CgoclCVNsnPQybYUcWYH1MpVclGilauPHUOEVy3X9khAIRVZJyzeX25s
  8. https://www.who.int/publications/i/item/who-convened-global-study-of-origins-of-sars-cov-2-china-part

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