Emergence of a novel SARS-CoV-2 Pango lineage B.1.1.526 in West Bengal, India

Abstract

Background Since its inception in late 2019, SARS-CoV-2 has been evolving continuously by procuring mutations, leading to emergence of numerous variants, causing second wave of pandemic in many countries including India in 2021. To control this pandemic continuous mutational surveillance and genomic epidemiology of circulating strains is very important to unveil the emergence of the novel variant and also monitor the evolution of existing variants. Methods SARS-CoV-2 sequences were retrieved from GISAID database. Sequence alignment was performed with MAFT version 7. Phylogenetic tree was constructed by MEGA version 7 and UShER. Results In this study, we reported the emergence of a novel variant of SARS-CoV-2 named B.1.1.526 in India. This novel variant encompasses 129 SARS-CoV-2 strains which are characterized by the presence of 11 coexisting mutations including D614G, P681H and V1230L in S-glycoprotein. Out of these 129 sequences, 27 sequences also harbored E484K mutation in the S glycoprotein. Phylogenetic analysis revealed strains of this novel variant emerged from GR clade and formed a new cluster. Geographical distribution showed, out of 129 sequences, 126 were found in seven different states of India. Rest 3 sequences were observed in USA. Temporal analysis revealed this novel variant was first collected from Kolkata district of West Bengal, India. Conclusions The D614G, P618H and E484K mutations have previously reported to favor increased transmissibility, enhanced infectivity and immune invasion, respectively. The transmembrane domain (TM) of S2 subunit anchors S glycoprotein to the virus envelope. The V1230L mutation present within the TM domain of S glycoprotein might strengthen the interaction of S protein with the viral envelope and increase S protein deposition to the virion, resulting in more infectious virion. Therefore, the new variant having D614 G, P618H, V1230L and E484K may have higher infectivity, transmissibility and immune invasion characteristics and thus need to be monitored closely.

Mutational and phylogenetic analyses of the two lineages of the Omicron variant

“…Therefore, in the present study, we have performed the whole‐genome mutational mapping and phylogenetic analysis of BA.1 and BA.2 lineages. We have downloaded 6 genome sequences each of BA.1 and BA.2, and also the genome sequence of the prototype strain (hCoV‐19/Wuhan/WIV04/2019) from the Global Initiative on Sharing All Influenza Data (GISAID) and performed whole‐genome mutational analysis according to the protocol described in Sarkar et al 5 , 6 Each of the six genomes of both BA.1 and BA.2 lineages was found to have 51 mutations dispersed throughout the genome, 32 of which are common to both lineages, whereas each lineage has 19 signature mutations. Among 32 common mutations, 21 are present in the S glycoprotein and the rest 11 are present in the other four coding regions (ORF1ab, E, M, and N).…”

“…Nineteen unique mutations of BA.1 include 13 in the S glycoprotein and that of BA.2 includes 7 in the S glycoprotein (Table 1 ). Phylogenetic analysis of 12 genome sequences of Omicron variant, encompassing 6 genomes each of BA.1 and BA.2, along with the 2000 genomes of 25 different clades by Ultrafast Sample placement of Existing tRees, 6 , 7 revealed that genomes of Omicron variant formed a new cluster that emerged from the 20B clade (also known as GR) and also subdivided into two different subclusters (BA.1 and BA.2) based on the unique mutations (Figure 1 ).…”

Omicron BA.2 lineage predominance in severe acute respiratory syndrome coronavirus 2 positive cases during the third wave in North India

“…Delta variant (B.1.617) was responsible for this deadly second wave of COVID-19 and was associated with breakthrough infections in the country ( 8 ). Previous studies have reported various circulating double-mutant (B.1.617) and triple-mutant strains (B.1.618) of SARS-CoV-2 across different regions of India, which are more pathogenic than the initial strains such as B.1.1.7 (Alpha), B.1.351 (Beta), and P.1 (Gamma) ( 9 ). After surviving the first and second waves of the SARS-CoV-2 virus, India was hit by a vicious third wave in January 2022.…”