The origin of the SARS-CoV-2 virus is still not determined

None of these scenarios have been ruled out:

  1. The virus is of completely natural origin, most likely originating in a bat population, possibly crossing over another species and finally to humans.
    The original virus or bat population has yet to be found.
  2. The virus is a result of random gain-of-function processes in a laboratory, in an attempt to see what evolutionary possibilities a common coronavirus found in bats.
    Despite a USA-China collaboration of this process was done in Wuhan, no-one has admitted to or found the virus in its pre-release state.
  3. The virus is a result of deliberate gene-engineering in an attempt to create a new coronavirus, based on a common coronavirus found in bats.
    There is currently no evidence of this.

Either way, the origin is important and Jesse D. Bloom has published a new paper where he discusses his find of gene-sequences originally shared from China but later deleted. He was able to find those gene-sequences and compare them to the public gene-sequences, which might enable us to trace the virus back to an origin.

For those os us not well-versed in gene-sequences, he summarised his findings on Twitter:

Now I need to give background to explain a confusing scientific mystery about other early #SARSCoV2 sequences. Although events that led to emergence of #SARSCoV2 in Wuhan are unclear (zoonosis vs lab accident), everyone agrees deep ancestors are coronaviruses from bats.

Therefore, we’d expect the first #SARSCoV2 sequences would be more similar to bat coronaviruses, and as #SARSCoV2 continued to evolve it would become more divergent from these ancestors. But that is *not* the case!

Instead, early Huanan Seafood Market #SARSCoV2 viruses are more different from bat coronaviruses than #SARSCoV2 viruses collected later in China and even other countries. @lpipes @ras_nielsen give nice technical analysis at academic.oup.com/mbe/article/38…

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