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According to the below paper, the coronavirus spike protein sequence was available to scientists by end of february 2020 - the begin of march 2020 timeline. I had this question that why does sequencing of a virus protein take so much time (I am a software engineer, currently studying molecular biology to better understand the pandemic, hence I am seriously unaware!) ? The reason of asking is because, in case of another epidemic, we might need to spend again a lot of time to sequence the protein. This might be a real concern!

https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7151553/#:~:text=At%20the%20time%20of%20the,remain%20identical%20or%20almost%20so.

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  • $\begingroup$ Note that the protein sequence is inferred from a DNA sequencing experiment, not sequenced separately. $\endgroup$ – Maximilian Press Nov 21 at 22:53
  • $\begingroup$ @MaximilianPress Yes, that is an important point, and one that I neglected to state explicitly in my answer. Thank you for clarifying in yours -- Protein sequences are inferred from the DNA sequence using gene/ORF calling software. $\endgroup$ – acvill Nov 21 at 23:50
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    $\begingroup$ You really can’t expect us to read through this paper to discover what exactly is the time period between what events you feel is “so much time”. Sequencing the genome of a virus in itself can be done very quickly. I suspect that you may be confusing stalking the deer with cooking the venison. If you don’t know where the meat got to before it got to the supermarket, perhaps you need to do some reading. Biology perhaps? $\endgroup$ – David Nov 22 at 9:37
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Sequencing a viral genome requires isolation of the virus, propagation in cell culture, extraction of nucleic acids, and preparation of a sequencing library. Once sequences are obtained, a genome can be assembled de novo using (untargeted) shotgun reads, and gaps in the genome can be spanned with (targeted) Sanger sequencing. This process can take weeks to months depending on the availability of resources and the growth characteristics of the virus.

For details on how the 2019-nCoV genome was sequenced, see Zhu et al., published January 2020:

A Novel Coronavirus from Patients with Pneumonia in China, 2019

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  • $\begingroup$ Thanks @acvill, that answers my question. So, "the availability of resources and the growth characteristics of the virus" are the reasons. Thanks again!!! $\endgroup$ – harry potter Nov 23 at 4:51
  • $\begingroup$ Note that mine is a very general answer and is indeed pessimistic about processing times. Your question would be much improved if you walked us through your logic in deducing what you describe as "so much time", per David's comment. $\endgroup$ – acvill Nov 23 at 14:46
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Sequencing DNA (which is what was done for the COVID virus, post reverse transcription as it is an RNA virus) does not take very long. A NextSeq instrument can provide results in <24 hours. Protein sequences are inferred from the DNA sequence using gene/ORF calling software.

SOme of this is suggested by @acvill, though I think that they are pessimistic about time estimates. Viral genomes are pretty easy to assemble (matter of hours). In principle you can dispense with the isolation step too, though that makes the analysis more complex.

It is all the medical and bioinformatic stuff around the sequencing, e.g. isolation and analysis and ethical paperwork (necessary!), which takes time.

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  • $\begingroup$ Thanks @Maximilian Press, that was very informative! "A NextSeq instrument can provide results in <24 hours" was useful information to know. Thanks again!!! $\endgroup$ – harry potter Nov 23 at 4:53

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