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How common is for SARS coronaviruses to share the same envelope proteins? I downloaded 200 CoV envelope proteins from NCBI, and I couldn't find any pair of iden

How common is for SARS coronaviruses to share the same envelope proteins? I downloaded 200 CoV envelope proteins from NCBI, and I couldn't find any pair of identical proteins. As someone unfamiliar with virology, I'm curious if there are any explanations for how come the protein envelope of 2019-nCoV[1] is the same as the protein envelope described by the Institute of Military Medicine Nanjing Command 2 years ago in the unpublished paper "Genomic characterization and infectivity of a novel SARS-like coronavirus in Chinese bats"[3]? Is it just a coincidence? The bats used in the paper were from Zhejiang not Hubei. [1] https://www.ncbi.nlm.nih.gov/protein/YP_009724392.1 https://www.ncbi.nlm.nih.gov/protein/YP_009724392.1 [2] https://www.ncbi.nlm.nih.gov/protein/AVP78033.1 https://www.ncbi.nlm.nih.gov/protein/AVP78033.1 [3] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6135831/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6135831/

lol768 7y ago
Some additional information: this paper cites the unpublished paper you mention ("Genomic characterization and infectivity of a novel SARS-like coronavirus in Chinese bats"): https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30154-9/fulltext https://www.thelancet.com/journals/lancet/article/PIIS0140-6... With regard to ZC45, which your paper discusses, it states: > The genome of our virus strains are phylogenetically closest to the bat SARS-related coronaviruses first found in the Chinese horseshoe bats, Rhinolophus sinicus, captured in Zhoushan, Zhejiang province, China, between 2015 and 2017. The full virus genome had about an 89% nucleotide identity with bat-SL-CoVZC45, which makes it a new species. Moreover, the Spike protein of our virus has an 84% nucleotide identity with the bat-SL-CoVZC45 coronavirus and an 78% nucleotide identity with the human SARS coronavirus. Doesn't answer your question as to how common this is, but provides some additional context on the extent of similarities.
throwawaylolx 7y ago
Quick update: after analyzing about 3,500 strains of coronaviruses, I found several that shared the same envelope proteins despite being different strains e.g. https://www.ncbi.nlm.nih.gov/ipg/?term=ABP38309.1 https://www.ncbi.nlm.nih.gov/ipg/?term=ABP38309.1 My quick-and-dirty estimate from my data is that about 0.1% share the same envelope protein with other viruses, but this was just rushed amateur work, so don't take the number too seriously.
busymom0 7y ago
Comparison between "Bat SARS-like coronavirus" and the "Wuhan seafood market pneumonia virus" seems to show a 100% match: https://blast.ncbi.nlm.nih.gov/Blast.cgi?RID=2PUA1EJK114&CMD=Get https://blast.ncbi.nlm.nih.gov/Blast.cgi?RID=2PUA1EJK114&CMD... Bat SARS-like coronavirus WIV1 has been known since at least 2013. https://en.wikipedia.org/wiki/Bat_SARS-like_coronavirus_WIV1 https://en.wikipedia.org/wiki/Bat_SARS-like_coronavirus_WIV1
- throwawaylolx 7y ago
  Yes, these are the two strains I was referring to in my original post. They share the same sequence of 75 aminoacids for their envelope proteins despite differing slightly in the nucleotide sequences.
akiselev 7y ago
It's almost certainly a coincidence. Bats don't have an inflammatory response to viral infections like other mammals [1] so viruses are basically harmless to them and they are perfect carriers, with many species having life expectancies reaching 2-3 decades. Studies of regional populations of bats have found that if a virus makes it into a bat population, it will usually spread to 50-90% of the total population (where virus = rabies and region = Western Europe) [2]. This Wuhan virus evolving from another SARS-like virus while maintaining surface markers is squarely in the realm of possibility. [1] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6410205/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6410205/ [2] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1539106/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1539106/
- deleted 7y ago
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lol768 7y ago

Some additional information: this paper cites the unpublished paper you mention ("Genomic characterization and infectivity of a novel SARS-like coronavirus in Chinese bats"): https://www.thelancet.com/journals/lancet/article/PIIS0140-6736(20)30154-9/fulltext https://www.thelancet.com/journals/lancet/article/PIIS0140-6... With regard to ZC45, which your paper discusses, it states: > The genome of our virus strains are phylogenetically closest to the bat SARS-related coronaviruses first found in the Chinese horseshoe bats, Rhinolophus sinicus, captured in Zhoushan, Zhejiang province, China, between 2015 and 2017. The full virus genome had about an 89% nucleotide identity with bat-SL-CoVZC45, which makes it a new species. Moreover, the Spike protein of our virus has an 84% nucleotide identity with the bat-SL-CoVZC45 coronavirus and an 78% nucleotide identity with the human SARS coronavirus. Doesn't answer your question as to how common this is, but provides some additional context on the extent of similarities.

throwawaylolx 7y ago

Quick update: after analyzing about 3,500 strains of coronaviruses, I found several that shared the same envelope proteins despite being different strains e.g. https://www.ncbi.nlm.nih.gov/ipg/?term=ABP38309.1 https://www.ncbi.nlm.nih.gov/ipg/?term=ABP38309.1 My quick-and-dirty estimate from my data is that about 0.1% share the same envelope protein with other viruses, but this was just rushed amateur work, so don't take the number too seriously.

busymom0 7y ago

Comparison between "Bat SARS-like coronavirus" and the "Wuhan seafood market pneumonia virus" seems to show a 100% match: https://blast.ncbi.nlm.nih.gov/Blast.cgi?RID=2PUA1EJK114&CMD=Get https://blast.ncbi.nlm.nih.gov/Blast.cgi?RID=2PUA1EJK114&CMD... Bat SARS-like coronavirus WIV1 has been known since at least 2013. https://en.wikipedia.org/wiki/Bat_SARS-like_coronavirus_WIV1 https://en.wikipedia.org/wiki/Bat_SARS-like_coronavirus_WIV1

throwawaylolx 7y ago
Yes, these are the two strains I was referring to in my original post. They share the same sequence of 75 aminoacids for their envelope proteins despite differing slightly in the nucleotide sequences.

akiselev 7y ago

It's almost certainly a coincidence. Bats don't have an inflammatory response to viral infections like other mammals [1] so viruses are basically harmless to them and they are perfect carriers, with many species having life expectancies reaching 2-3 decades. Studies of regional populations of bats have found that if a virus makes it into a bat population, it will usually spread to 50-90% of the total population (where virus = rabies and region = Western Europe) [2]. This Wuhan virus evolving from another SARS-like virus while maintaining surface markers is squarely in the realm of possibility. [1] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6410205/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6410205/ [2] https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1539106/ https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1539106/

deleted 7y ago
[deleted]