44 2033180199

The popular 3675SGF deletion in nsp6 domain of ORF1ab polyprotein of SARS-CoV-2 was spread into Alpha, Beta, Gamma, Iota and Omicron variants except highly infectious and death promoting Delta variant

Asit Kumar Chakraborty

The SARS-CoV-2 was appeared in mid-2020 but the first RNA sequence was available since December, 2020. The higher transmission and disease severity were seen since acquisition of D614G dominant point mutation in spike protein as well as P4715L point mutation in the RNA-dependent RNA polymerase (RdRp). The next event occurred in B.1.1.7 Alpha variant was acquisition of N501Y point mutation and 69HV two AAs deletion in the spike protein. Interestingly, 3675SGF three AAs deletions were also occurred in ORF1ab polyprotein in B.1.1.7 variants. The appearance of notorious Delta variant in Mid-2021 was shocking as too many deaths happened worldwide. The Delta variants (B.1.617.2 and AY.X) acquired 157FR two AAs deletion instead 69HV in B.1.1.7 variant. Here, we showed that Delta variant was spread worldwide but has no 3675SGF deletion. Moreover, 3675SGF deletion was found in all Omicron variants which were appeared in December, 2021 and its subvariants BA.2.75, BA. (BF.7), BQ.1, BQ.1.1 and XBB.1.5 which were spreading now worldwide with mild infections. Thus, Delta variant has very complete ORF1ab protein (9096 AAs) to attend high titre and to infect more human lung cells. Further, 119DF deletion in ORF8 activator protein and 157FR deletion in spike might be contributed to higher pathogenicity in Delta including P2046L and P2287S mutations in nsp3 main protease, P4715L and G5063S mutations in RdRp and P6128S and A6319V mutations in nsp14 Ribonuclease. Further, complete attenuation of Delta corona virus spread recently likely due to herd immunity and wide spread inoculation with COVID-19 vaccine.

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