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Review
. 2021 Jan 1;17(1):97-106.
doi: 10.7150/ijbs.47827. eCollection 2021.

SARS-CoV-2 variants evolved during the early stage of the pandemic and effects of mutations on adaptation in Wuhan populations

Annoor Awadasseid  1   2 , Yanling Wu  3 , Yoshimasa Tanaka  4 , Wen Zhang  1
Affiliations
Review

SARS-CoV-2 variants evolved during the early stage of the pandemic and effects of mutations on adaptation in Wuhan populations

Annoor Awadasseid et al. Int J Biol Sci. .

Abstract

The outbreak of the coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The pandemic apparently started in December 2019 in Wuhan, China, and has since affected many countries worldwide, turning into a major global threat. Chinese researchers reported that SARS-CoV-2 could be classified into two major variants. They suggest that investigating the variations and characteristics of these variants might help assess risks and develop better treatment and prevention strategies. The two variants were named L-type and S-type, in which L-type was prevailed in an initial outbreak in Wuhan, Central China's Hubei Province, and S-type was phylogenetically older than L-type and less prevalent at an early stage, but with a later increase in frequency in Wuhan. There were 149 mutations in 103 sequenced SARS-CoV-2 genomes, 83 of which were nonsynonymous, leading to alteration in the amino acid sequence of proteins. Much effort is currently being devoted to elucidate whether or not these mutations affect viral transmissibility and virulence. In this review, we summarize the mutations in SARS-CoV-2 during the early phase of virus evolution and discuss the significance of the gene alterations in infections.

Keywords: COVID-19; SARS-CoV-2; bioinformatics; genomes; mutations.

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Conflict of interest statement

Competing Interests: The authors have declared that no competing interest exists.

Figures

Figure 1
Figure 1
Three-dimensional conformation shifts of the spike protein of the SARS-CoV-2 virus as it binds to the human ACE2 receptor.
Figure 2
Figure 2
Phylogenetic relationship of SARS-CoV-2-L-type. The SARS-CoV-2-L-type full genome sequences were collected from the National Center for Biotechnology Information search engine (http:/www.ncbi.nim.nih.gov/). The phylogenetic tree was built with 1000 bootstrapped value help and a Poisson correction utilizing the MEGA 5.0 software package and neighbor-joining program (http:/www.megasoftware.net). The bootstrap values are provided at nodes higher than 50%. The scale bar displays the range of phylogenetic variations calculated from the number of changes. The genome sequence accession numbers at NCBI GenBank are MT027062 (2019-nCoV/USA-CA3/2020), MT027063 (2019-nCoV/USA-CA4/2020), LR757996 (BetaCoV/Wuhan/WH-03/2019), LC521925 (BetaCoV/Japan/AI/I-004/2020), MT027064 (2019-nCoV/USA-CA5/2020), MT019532 (BetaCoV/Wuhan/IPBCAMS-WH-04/2019), MN996529 (WIV05), MT019531 (BetaCoV/Wuhan/IPBCAMS-WH-03/2019), MT066176 (BetaCov/Taiwan/NTU02/2020), MN996527 (WIV02), MT039887 (2019-nCoV/USA-WI1/2020), MT019529 (BetaCoV/Wuhan/IPBCAMS-WH-01/2019), MN988669 (2019-nCoV_WHU02), MN996530 (WIV06), LC522972 (2019-nCoV/Japan/KY/V-029/2020), MT044258 (SARS-CoV-2/CA6/human/2020/USA), LR757998 (BetaCoV/Wuhan/WH-01/2019), MN988668 (2019-nCoV_WHU01), MT019533 (BetaCoV/Wuhan/IPBCAMS-WH-05/2020), MT039873 (20cov-1L), MT039888 (2019-nCoV/USA-MA1/2020), MN996528 (WIV04), MN996531 (WIV07), MN988713 (2019-nCoV/USA-IL1/2020), MT019530 (BetaCoV/Wuhan/ IPBCAMS-WH-02/2019), NC_045512 (Severe_acute_respiratory_syndrome_ coronavirus_2_ isolate_Wuhan-Hu-1_complete_genome), MN908947 (Wuhan-Hu-1), MT072688 (SARS0CoV-2/61-TW/human/2020/_NPL), MT007544 (BetaCoV/Australia/VIC01/2020), MN994468 (2019-nCoV/USA-CA2/2020), and MT039890 (SNU01).
Figure 3
Figure 3
Phylogenetic relationship among SARS-CoV-2-S-type genomes. The SARS-CoV-2-S-type full genome sequences were collected from the National Center for Biotechnology Information search engine (http:/www.ncbi.nim.nih.gov/). The phylogenetic tree was built with 1000 bootstrapped value help and a Poisson correction utilizing the MEGA 5.0 software package and neighbor-joining program (http:/www.megasoftware.net). The bootstrap values are provided at nodes higher than 50%. The scale bar displays the range of phylogenetic variations calculated from the number of changes. The genome sequence accession numbers at NCBI GenBank are LC522973 (2019-nCoV/Japan/TY/WK-012/2020), LC522975 (2019-nCoV/Japan/TY/WK-521/2020), LC522974 (2019-nCoV/Japan/TY/WK-501/2020), MN975262 (2019-nCoV_HKU-SZ-005b_2020), MN938384 (2019-nCoV_HKU-SZ-002a_2020), MN997409 (2019-nCoV/USA-AZ1/2020), MT049951 (SARS-CoV-2/human/CHN/Yunnan-01/2020), LR757995 (BetaCoV/Wuhan/WH-04/2019), MN985325 (2019-nCoV/USA-WA1/2020), MT020880 (BetaCoV/USA/WA1-A12/2020), MT020881 (BetaCoV/USA/WA1-F6/2020), MT066175 (Taiwan/NTU01/2020), MN994467 (2019-nCoV/USA-CA1/2020), and MT044257 (SARS-CoV-2/IL2/human/2020/USA).
Figure 4
Figure 4
An overview of therapeutic strategies to treat SARS-CoV-2 infection based on virus-cell interaction. Host-targeted strategies include RBD mimetics and antibody fragments, such as scFv. Virally-targeted strategies include antibodies or antibody fragments, such as Fc. In both cases, the ACE2-RBD interaction is inhibited, preventing infection.
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References

    1. Tang X, Wu C, Li X, Song Y, Yao X, Wu X, On the origin and continuing evolution of SARS-CoV-2. National Science Review. 2020. https://doi.org/10.1093/nsr/nwaa036. - PMC - PubMed
    1. Control ECfDPa. European Centre for Disease Prevention and Control. 2020. https://www.ecdc.europa.eu/en/geographical-distribution-2019-ncov-cases.
    1. Li Q, Guan X, Wu P, Wang X, Zhou L, Tong Y. et al. Early transmission dynamics in Wuhan, China, of novel coronavirus-infected pneumonia. New England Journal of Medicine. 2020 DOI: 10.1056/NEJMoa2001316. - PMC - PubMed
    1. Zhou P, Yang X-L, Wang X-G, Hu B, Zhang L, Zhang W, A pneumonia outbreak associated with a new coronavirus of probable bat origin. Nature. 2020. p:1-4. https://doi.org/10.1038/s41586-020-2012-7. - PMC - PubMed
    1. Xiao K, Zhai J, Feng Y, Zhou N, Zhang X, Zou J-J, Isolation and characterization of 2019-nCoV-like coronavirus from Malayan pangolins. bioRxiv. 2020. https://doi.org/10.1101/2020.02.17.951335.

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