The extent of molecular variation in novel SARS-CoV-2 after the six-month global spread

Haplotype distribution of SARS-CoV-2 variants in low and high vaccination rate countries during ongoing global COVID-19 pandemic in early 2021

“…2 , Table 1 ). The haplotype and sub-haplotype distribution of the variants from global areas post 1-year spread from January 2021 to March 2021 was an observable change compared to the previous data post-6-month spread from December 2019 to June 2020 ( Bui et al, 2021 ). Haplotype 1 with the mutation at ORF8 L84S was prevalent post-6-month spread (25.34%) but rarely identified post-1-year pandemic (1.19%).…”

“…3 , Table 1 , Table 2 ). For instance, the haplotype 2A variants defined post-6-month outbreak in our prior report ( Bui et al, 2021 ) progressed into three sub-haplotypes, in which sub-haplotype 2A_1 (B.1.1.7, Alpha) variants emerged in January 2021 had 17 new mutations, became highly prevalent in the high partly vaccinated rate countries (US, Canada, and Germany) in May 2021 ( Table 2 ). Especially, sub-haplotype 2C_3 (B.1.617.2, Delta) variants with 22 to 24 amino acid changes unexpectedly became the mainly circulating variant in the low vaccination-rate group (particularly in India) in May 2021 ( Fig.…”

“…Since the 100 replicates of phylogenetic tree analysis produced stable bootstrap values ( Pattengale et al, 2010 ), the bootstrap consensus tree of 100 replicates was inferred using the NJ for analyzing 117 and 420 complete proteomes of variants that emerged in 2020 and 2021, respectively. Finally, the phylogenetic tree was validated by comparing with our prior report in that the bootstrap consensus tree of 1000 replicates of NJ and MCL method for analyzing the variants collected post-six-month spread ( Bui et al, 2021 ). The Poisson correction method was computed to see the evolutionary distance.…”

Relation between ORF8a and the mitochondrial protein TOM70 in SARS‐CoV‐2 infection

“…The SARS‐CoV‐2 contains a single ORF8 protein which is various from SARS‐CoV which has two ORF8s (ORF8a and ORF8b). 5 ORF8 is considered as one of the most relevant genes that have previously reported as genetic change during human‐to‐human transmission of the SARS‐CoV epidemic. 6 No motif such as VLVVL (75‐79aa) or known functional domain has been observed in the ORF8 of SARS‐CoV‐2 that activates the nucleotide‐binding domain and leucine‐rich repeat‐containing protein 3 (NLRP3) inflammasomes or bind to the interferon regulatory factor (IRF) domain (IAD) region of IRF3 then inactivates interferon signalling.…”

“… 6 No motif such as VLVVL (75‐79aa) or known functional domain has been observed in the ORF8 of SARS‐CoV‐2 that activates the nucleotide‐binding domain and leucine‐rich repeat‐containing protein 3 (NLRP3) inflammasomes or bind to the interferon regulatory factor (IRF) domain (IAD) region of IRF3 then inactivates interferon signalling. 5 …”