Abstract
BackgroundSince outbreak in December 2019, the highly infectious and pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused over a million deaths globally. With increasing burden, the novel coronavirus has posed a dire threat to public health, social interaction, and global economy. Mutations in the SARS-CoV-2 genome are moderately evolving which might have contributed to its genome variability, transmission, replication efficiency, and virulence in different regions of the world.ResultsThe present study elucidated the mutational landscape in the SARS-CoV-2 genome among the African populace, which may have contributed to the virulence, spread, and pathogenicity observed in the region. A total of 3045 SARS-CoV-2 complete protein sequences with the reference viral sequence (EPI_ISL_402124) were mined and analyzed. SARS-CoV-2 ORF1ab, spike, ORF3, ORF8, and nucleocapsid proteins were observed as mutational hotspots in the African population and may be of keen interest in understanding the viral host relationship, while there is conservation in the ORF6, ORF7a, ORF7b, ORF10, envelope, and membrane proteins.ConclusionsThe accumulation of moderate mutations (though slowly), in the SARS-CoV-2 genome as seen in this present study, could be a promising strategy to develop antiviral drugs or vaccines. These antiviral interventions should target viral conserved domains and host cellular proteins and/or receptors involved in viral invasion and replication to avoid a new viral wave due to drug resistance and vaccine evasion.
Highlights
Since outbreak in December 2019, the highly infectious and pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused over a million deaths globally
COVID-19 burden differs across regions and countries [3]; primarily due to incidence of index cases, countries’ demographic structure, life expectancy, level of adherence to public health guidelines, and the measures put in place to curtail sporadic community transmission [4, 5]
African countries studied highlights high rate recurrent mutations observed at the following genomic sites in the SARS-CoV-2 ORF1ab polyprotein site: nsp2 region; T265I (197 viral sequences), 3 chymotrypsin-like proteinase region (3CLpro); G3278S (191 viral sequences), nsp6; L3606F (152 viral sequences), and RNA dependent
Summary
Since outbreak in December 2019, the highly infectious and pathogenic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused over a million deaths globally. The viral infection caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2) was initially referred to as the Wuhan seafood market pneumonia virus before it was officially named by World Health Organization (WHO) on February. COVID-19 burden differs across regions and countries [3]; primarily due to incidence of index cases, countries’ demographic structure, life expectancy, level of adherence to public health guidelines, and the measures put in place to curtail sporadic community transmission [4, 5]. Coronaviruses have the largest genome (about 26 to kb) among all RNA viruses. It encodes ORF1ab, ORF3a, ORF6, ORF7a/b, ORF8, spike (S), envelope (E), membrane (M), and nucleocapsid (N) gene (Fig. 1) [6, 7]
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