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

Jitendra Singh,Dipesh Kale,Arun Raghuvanshi,Anvita Gupta Malhotra,Sarman Singh,Saurabh Saigal,Debasis Biswas,Prem Shankar,Shashwati Nema,Leena Lokhande,Ashvini Kumar Yadav

doi:10.3390/genes12111803

Abstract

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.

Highlights

As of 1 August 2021, the ongoing COVID-19 pandemic had infected more than 200 million individuals and resulted in more than 4 million deaths globally
To map the variant distribution at the national level during the same time span, we analyzed all SARS-CoV-2 whole genome sequences submitted to the GISAID. Comparing this profile of variants, with the same encountered after the first wave and that observed during the second wave, we report here that the massive second wave in India was pre-dated by a relative consolidation of the kappa variant which overhauled the erstwhile α variant and acted as a harbinger of the delta variant; and the delta variant subsequently drove the second wave and swiftly progressed to become the dominant variant of the pandemic
The overall distribution of the different variants across India during these periods revealed that the B.1.1.7 (α) variant was predominant during the first wave, while the second wave was characterized by an overwhelming excess of B.1.617.2 variant and a corresponding decrease in the α variant

Summary

Introduction

As of 1 August 2021, the ongoing COVID-19 pandemic had infected more than 200 million individuals and resulted in more than 4 million deaths globally. This relentless progression has been marked by periodic waves of extensive transmission, catalyzed by the emergence of novel viral variants, which have been controlled through implementation of medical and social countermeasures like vaccination, lockdown, social distancing and masking Consistent with this pattern of alternating peaks and troughs of viral spread, India experienced the peak of its first wave in the month of September 2020, and, in the four months, the country witnessed >80% drop in cases with the daily number of new cases dropping from 83,809 to 21,822 cases between 15 September and 31 December 2020 [1]. Considering the reports of novel variants of the SARS-CoV-2 virus driving new waves of the pandemic in the UK, Brazil, and South Africa, we were interested in exploring if the second wave in India was orchestrated by the emergence of a new viral variant [3,4,5,6]

Methods

Results

Discussion

Conclusion