Where did COVID come from? Are infected animals or a lab leak to blame for the pandemic?
Preliminary re-analysis of genomic data collected at the Wuhan market suggests that the initial transmission of the SARS-CoV-2 virus from an infected animal to a human, which started the COVID-19 pandemic, occurred right there. On the other hand, a recent thorough analysis of bat coronavirus genomes studied at the Wuhan Institute of Virology did not confirm that the strains under investigation belonged to the closest ancestors of SARS-CoV-2. Is it finally clear how the pandemic originated?
Coronavirus and animals at the market
At the beginning of December, a conference titled "Preparing for the next pandemic: Evolution, pathogenesis, and virology of coronaviruses" was held in Awaji, Japan.
An international team of virologists presented preliminary results of sample analysis collected at the Huanan wholesale seafood market. This market was associated with the first cases of COVID-19 at the start of the pandemic. Although many studies have confirmed the presence of both the SARS-CoV-2 virus and animals susceptible to infection at the market, it has not yet been confirmed that the animals were indeed infected with the virus.
Important Samples
Shortly after the closure of the Huanan market in early January 2020, a group of scientists from the Chinese Center for Disease Control and Prevention took swabs from the surfaces of stalls, walls, trash bins, sewage pits, and animal products stored in freezers. They sequenced the DNA and RNA present in the samples, and the sequencing results were made available to scientists in a genomic database.
Virologist Angela Rasmussen from the University of Saskatchewan decided to study this database in detail to find a potential animal transmitter. She focused on animals susceptible to SARS-CoV-2 infection: minks, stoats, masked palm civets, raccoon dogs, foxes, and badgers. She found the same RNA expression pattern characteristic of infection by SARS-CoV-2 or its close relatives in samples from market visitors and raccoon dogs and white-throated badgers.
These results confirmed that the immune system of some animals was activated, suggesting that they were indeed infected with the coronavirus. However, the presence of SARS-CoV-2 infection in these animals has still not been directly confirmed.
Data from the Wuhan Institute of Virology
Most researchers agree that SARS-CoV-2 originates from animals. However, since no direct ancestor of the virus has been found in any analyzed animal, some still believe that the virus could have escaped—either accidentally or deliberately—from the Wuhan Institute of Virology.
At the conference in Awaji, a contribution from Professor Zhengli Shi, who specializes in bat coronaviruses, was also discussed. It was speculated that SARS-CoV-2 might have escaped from her high-biosafety-level laboratory at the Wuhan Institute of Virology. Although Professor Shi has consistently reiterated that she never studied this virus in her lab, some scientists still wonder whether any of the bat strains she studied are closely related to the causative agent of COVID-19.
Thousands of Studied Bats
The virologist sequenced the entire genome of 56 new betacoronaviruses that her lab collected between 2004 and 2021. She found no new sequences that were more closely related to the viruses SARS-CoV-1 or 2. The closest relatives of the SARS-CoV-2 virus were found in bats in the southern Chinese provinces of Laos and Yunnan, but years, if not decades, have passed since they shared a common ancestor with the causative agent of COVID-19.
Over the years, Professor Shi's team collected more than 15,000 bat swabs. They tested them for the presence of coronaviruses and performed genomic sequencing on positive samples. The database of these samples has expanded our knowledge of coronavirus diversity. Based on a broader analysis of 233 sequences, some of which have already been published, the team was able to identify 7 virus lineages.
The analysis also provided new evidence of ongoing extensive recombination, that is, the exchange of RNA segments among these viruses. The yet unpublished analysis also assesses the risks of these viruses transmitting to humans and identifies potential therapeutic targets.
Editorial Team, Medscope.pro
Sources:
- Mallapaty S. Sick animals suggest COVID pandemic started in Wuhan market. Nature 2024 Dec; 636 (8042): 284–285, doi: 10.1038/d41586-024-03968-0.
- Mallapaty S. Wuhan lab samples hold no close relatives to virus behind COVID. Nature 2024 Dec; 636 (8043): 531–532, doi: 10.1038/d41586-024-03982-2.)
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