Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India

Genes

Saurabh Saigal¹  Debasis Biswas²  Shashwati Nema²  Prem Shankar²  Ashvini Kumar Yadav²  Arun Raghuvanshi²  Sarman Singh²  Anvita Gupta Malhotra²  Dipesh Kale²  Leena Lokhande²  Jitendra Singh³ 

[1] Department of Anesthesia and Critical Care, All India Institute of Medical Sciences, Bhopal 462020, India;Department of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, India;Translational Medicine Centre, All India Institute of Medical Sciences, Bhopal 462020, India;

关键词: COVID-19;    SARS-CoV-2 genome;    next generation sequencing;    ion torrent;    alpha variant;    kappa variant and delta variant;   

DOI  :  10.3390/genes12111803

来源: DOAJ

【 摘 要 】

India experienced a tragic second wave after the end of March 2021, which was far more massive than the first wave and was driven by the emergence of the novel delta variant (B.1.617.2) of the SARS-CoV-2 virus. In this study, we explored the local and national landscape of the viral variants in the period immediately preceding the second wave to gain insight into the mechanism of emergence of the delta variant and thus improve our understanding of the causation of the second wave. We randomly selected 20 SARS-CoV-2 positive samples diagnosed in our lab between 3 February and 8 March 2021 and subjected them to whole genome sequencing. Nine of the 20 sequenced genomes were classified as kappa variant (B.1.617.1). The phylogenetic analysis of pan-India SARS-CoV-2 genome sequences also suggested the gradual replacement of the α variant with the kappa variant during this period. This relative consolidation of the kappa variant was significant, since it shared 3 of the 4 signature mutations (L452R, E484Q and P681R) observed in the spike protein of delta variant and thus was likely to be the precursor in its evolution. This study demonstrates the predominance of the kappa variant in the period immediately prior to the second wave and underscores its role as the “bridging variant” between the α and delta variants that drove the first and second waves of COVID-19 in India, respectively.

【 授权许可】

Unknown