Geographical distribution of SARS-CoV-2 amino acids mutations and the concomitant evolution of seven distinct clades in non-human hosts.
Zoonoses Public Health
; 69(7): 816-825, 2022 11.
Article
in English
| MEDLINE | ID: covidwho-1864196
ABSTRACT
Since its first emergence in December 2019, the world has witnessed the eruption of mutations in the SARS-CoV-2 genome that have led to increased viral transmissibility and pathogenicity due to sustained local viral transmission. Zooanthroponotic and zoonotic transmissions have further raised concerns as they could result in the emergence of viral variants with a novel antigenicity and transmissibility that could jeopardize the vaccine efficacy. To understand the viral evolution during such transmissions, 1016 whole-genome sequences (deposited in GISAID as of March 7, 2022) (from 18 countries) corresponding to mink, cat, deer, dog, hyena, tiger, lion, gorilla, Syrian hamster, leopard cat, fishing cat, bear cat, coati, ferret, snow leopard and green monkey have been analysed here. Intriguingly, phyloproteome analysis indicate that Nsp2R218C, Nsp2D268-(deletion), SpikeD614G, Nsp12P323L, Nsp2A192V, ORF3a proteinQ57H, N proteinR203K and N proteinG204R/L, SpikeA222V, ORF10 proteinV30L and N proteinA220V are moderate or high recurring and clade decisive mutations, leading to 6 primary clades during the early stage of pandemic. Most interestingly, the human evolved delta variant having a combination of 26 (clade decisive) mutations defines the seventh clade and transmits to non-human hosts across the globe without exhibiting any country-specific mutation(s). Nonetheless, SpikeD614G and Nsp12P323L together with (i)N proteinR203K,N proteinG204R/L,SpikeV70-, SpikeH69-, Nsp12T739I, and Nsp1M85-, (ii)Nsp2A192V, Nsp3D178Y, (iii)Nsp2T85I, N proteinP67S and ORF3a proteinQ57H and (iv)SpikeA222V, ORF10 proteinV30L, N proteinA220V and SpikeF486I are specific to Denmark, Netherlands, USA and Latvia respectively and, (v)Nsp2D268- and Nsp13R292C that are devoid of SpikeD614G and Nsp12P323L is specific to Netherlands. SARS-CoV-2 variants consisting of these mutations are also seen in the human SARS-CoV-2 sequences from the same country. Independent country-specific SARS-CoV-2 variant evolution further indicates distinct epidemiological dynamics during zooanthroponotic and zoonotic transmissions. Thus, the results presented here indicate the need for the surveillance of viral evolution in non-human hosts also during the future pandemic.
Keywords
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Deer
/
Dog Diseases
/
COVID-19
Topics:
Vaccines
/
Variants
Limits:
Animals
/
Humans
Language:
English
Journal:
Zoonoses Public Health
Journal subject:
Veterinary Medicine
/
Public Health
Year:
2022
Document Type:
Article
Affiliation country:
Zph.12971
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