Emergence in late 2020 of multiple lineages of SARS-CoV-2 Spike protein variants affecting amino acid position 677.

Autor:	Hodcroft EB; Institute of Social and Preventive Medicine, University of Bern, Switzerland., Domman DB; University of New Mexico Health Sciences Center, Albuquerque, NM, USA., Snyder DJ; Microbial Genome Sequencing Center, LLC, Pittsburgh, PA, USA., Oguntuyo KY; Icahn Mt Sinai School of Medicine, New York, New York. USA., Van Diest M; Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA., Densmore KH; Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA., Schwalm KC; University of New Mexico Health Sciences Center, Albuquerque, NM, USA., Femling J; University of New Mexico Health Sciences Center, Albuquerque, NM, USA., Carroll JL; Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA., Scott RS; Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA., Whyte MM; Louisiana Department of Health. Minden, LA, USA., Edwards MW; New Mexico Department of Health, Albuquerque, NM, USA., Hull NC; Wyoming Public Health Laboratory, Cheyenne, WY, USA., Kevil CG; Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA., Vanchiere JA; Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA., Lee B; Microbial Genome Sequencing Center, LLC, Pittsburgh, PA, USA., Dinwiddie DL; University of New Mexico Health Sciences Center, Albuquerque, NM, USA., Cooper VS; University of Pittsburgh, School of Medicine, Pittsburgh, PA, USA., Kamil JP; Louisiana State University Health Sciences Center, Shreveport, Shreveport, LA, USA.
Jazyk:	angličtina
Zdroj:	MedRxiv : the preprint server for health sciences [medRxiv] 2021 Feb 21. Date of Electronic Publication: 2021 Feb 21.
DOI:	10.1101/2021.02.12.21251658
Abstrakt:	The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) spike protein (S) plays critical roles in host cell entry. Non-synonymous substitutions affecting S are not uncommon and have become fixed in a number of SARS-CoV-2 lineages. A subset of such mutations enable escape from neutralizing antibodies or are thought to enhance transmission through mechanisms such as increased affinity for the cell entry receptor, angiotensin-converting enzyme 2 (ACE2). Independent genomic surveillance programs based in New Mexico and Louisiana contemporaneously detected the rapid rise of numerous clade 20G (lineage B.1.2) infections carrying a Q677P substitution in S. The variant was first detected in the US on October 23, yet between 01 Dec 2020 and 19 Jan 2021 it rose to represent 27.8% and 11.3% of all SARS-CoV-2 genomes sequenced from Louisiana and New Mexico, respectively. Q677P cases have been detected predominantly in the south central and southwest United States; as of 03 Feb 2021, GISAID data show 499 viral sequences of this variant from the USA. Phylogenetic analyses revealed the independent evolution and spread of at least six distinct Q677H sub-lineages, with first collection dates ranging from mid-August to late November 2020. Four 677H clades from clade 20G (B.1.2), 20A (B.1.234), and 20B (B.1.1.220, and B.1.1.222) each contain roughly 100 or fewer sequenced cases, while a distinct pair of clade 20G clusters are represented by 754 and 298 cases, respectively. Although sampling bias and founder effects may have contributed to the rise of S:677 polymorphic variants, the proximity of this position to the polybasic cleavage site at the S1/S2 boundary are consistent with its potential functional relevance during cell entry, suggesting parallel evolution of a trait that may confer an advantage in spread or transmission. Taken together, our findings demonstrate simultaneous convergent evolution, thus providing an impetus to further evaluate S:677 polymorphisms for effects on proteolytic processing, cell tropism, and transmissibility. Competing Interests: Conflicts of Interest. V.S.C. and D.J.S. are co-founders of Microbial Genome Sequencing Center, LLC. All other authors declare no conflicts of interest.
Databáze:	MEDLINE
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