Genetic Diversity of SARS-CoV-2 over a One-Year Period of the COVID-19 Pandemic: A Global Perspective

Abstract

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused a global pandemic of coronavirus disease in 2019 (COVID-19). Genome surveillance is a key method to track the spread of SARS-CoV-2 variants. Genetic diversity and evolution of SARS-CoV-2 were analyzed based on 260,673 whole-genome sequences, which were sampled from 62 countries between 24 December 2019 and 12 January 2021. We found that amino acid (AA) substitutions were observed in all SARS-CoV-2 proteins, and the top six proteins with the highest substitution rates were ORF10, nucleocapsid, ORF3a, spike glycoprotein, RNA-dependent RNA polymerase, and ORF8. Among 25,629 amino acid substitutions at 8484 polymorphic sites across the coding region of the SARS-CoV-2 genome, the D614G (93.88%) variant in spike and the P323L (93.74%) variant in RNA-dependent RNA polymerase were the dominant variants on six continents. As of January 2021, the genomic sequences of SARS-CoV-2 could be divided into at least 12 different clades. Distributions of SARS-CoV-2 clades were featured with temporal and geographical dynamics on six continents. Overall, this large-scale analysis provides a detailed mapping of SARS-CoV-2 variants in different geographic areas at different time points, highlighting the importance of evaluating highly prevalent variants in the development of SARS-CoV-2 antiviral drugs and vaccines.

Disease waves of SARS-CoV-2 in Iran closely mirror global pandemic trends

“…The 19B clade did not rise in Iran, while in February 2021 resurgence of this clade was reported in some countries (dominated by A.23.1, A.27 and, A.2.5 lineages) (Murall et al 2021). From mid-September 2020 onward, the pandemic was dominated by 20E clade, while we detected 20B dominancy, which is more similar to the pandemic in Asia, in which 20B was the leading clade in January (Miao et al 2021).…”

“…The observed difference is largely caused by the different time intervals of the two cohorts rather than the distinct genetic diversity of SARS-CoV-2 in Iran compared to the world. Miao et al investigated 260,673 sequences between December 2019-12 January 2021, before the dominancy of B.1.1.7 lineage in the world (Miao et al 2021).…”

“…Today; over one year after the declaration of the COVID-19 pandemic by WHO, genome surveillance projects are frequently performed in all countries with the intention of tracking the spread of SARS-CoV-2 variants (Miao et al 2021). The current study is the report of complete genome sequencing of 369 SARS-CoV-2 viral isolates of the Iranian outbreak from March 2020 till the end of May 2021.…”

The Algerian Chapter of SARS-CoV-2 Pandemic: An Evolutionary, Genetic, and Epidemiological Prospect

“…The same results were observed in a similar study on SARS-CoV-2 in a Canadian population conducted by Zhang et al [ 47 ]. In addition, a recent analysis performed on 260,673 whole-genome sequences to study the selection pressure among the coding genes highlighted the rarity of positive selection in SARS-CoV-2 protein-coding genes [ 48 ].…”

Whole-Genome Sequences of SARS-CoV-2 Isolates from Ethiopian Patients

“…The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) that emerged in Wuhan, China, is an RNA virus that belongs to the genus Betacoronavirus , in the family Coronaviridae ( 1 ). Like most RNA viruses, SARS-CoV-2 is expected to display a relatively high rate of genetic mutations, which may influence viral transmission and pathogenesis, enable escape from host defenses, and negatively affect the efficacy of vaccines and molecular diagnostic tools ( 2 ). Thus, enhancing genomic capacity is important to investigate the transmission and to monitor the evolution and mutational patterns of SARS-CoV-2 in this country.…”