Extensive genetic diversity with novel mutations in spike glycoprotein of SARS-CoV-2, Bangladesh in late 2020

Afrin, Sultana Zahura; Paul, Shyamal Kumar; Begum, Jahan Ara; Nasreen, Syeda Anjuman; Ahmed, Salma; Ahmad, Fahim Uddin; Aziz, Md. Abdul; Parvin, Rokshana; Aung, Meiji Soe; Kobayashi, Nobumichi

In Bangladesh, COVID-19 has been highly prevalent during late 2020, causing nearly 500,000 confirmed cases. In the present study, spike (S) protein of severe acute respiratory coronavirus 2 (SARS-CoV-2) circulating in Bangladesh was genetically investigated to elucidate diversity of mutations and their prevalence. Nucleotide sequence of S protein gene was determined for 15 SARS-CoV-2 samples collected from 8 divisions in Bangladesh, and analyzed for mutations comparing with that of reference strain (hCoV-19/Wuhan/WIV04/2019). All the SARS-CoV-2 S genes were assigned to B.1 lineage in G clade, and individual S proteins had 1-25 mutations causing amino acid substitution/deletion. Total 133 mutations were detected in 15 samples, with G614D being present in all the samples, while 53 novel mutations as of Jan. 2021 were detected. On receptor-binding domain, 21 substitutions including ten novel mutations were identified. Other novel mutations were located on N-terminal domain (S1 subunit) and dispersed sites in S2 subunit, including two substitutions that remove potential N-glycosylation sites. P681R substitution adjacent to furin cleavage site was detected in one sample. All the mutations detected were located on positions that are functionally linked to host transition, antigenic drift, host surface receptor binding or antibody recognition sites, and viral oligomerization interfaces, which presumably related to viral transmission and pathogenic capacity.