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

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...

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Autores principales:	Jitendra Singh, Anvita Gupta Malhotra, Debasis Biswas, Prem Shankar, Leena Lokhande, Ashvini Kumar Yadav, Arun Raghuvanshi, Dipesh Kale, Shashwati Nema, Saurabh Saigal, Sarman Singh
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	COVID-19 SARS-CoV-2 genome next generation sequencing ion torrent alpha variant kappa variant and delta variant Genetics QH426-470
Acceso en línea:	https://doaj.org/article/ae4ac06836e94b6d8d2fea4f7442094a
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spelling	oai:doaj.org-article:ae4ac06836e94b6d8d2fea4f7442094a2021-11-25T17:42:12ZRelative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India10.3390/genes121118032073-4425https://doaj.org/article/ae4ac06836e94b6d8d2fea4f7442094a2021-11-01T00:00:00Zhttps://www.mdpi.com/2073-4425/12/11/1803https://doaj.org/toc/2073-4425India 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.Jitendra SinghAnvita Gupta MalhotraDebasis BiswasPrem ShankarLeena LokhandeAshvini Kumar YadavArun RaghuvanshiDipesh KaleShashwati NemaSaurabh SaigalSarman SinghMDPI AGarticleCOVID-19SARS-CoV-2 genomenext generation sequencingion torrentalpha variantkappa variant and delta variantGeneticsQH426-470ENGenes, Vol 12, Iss 1803, p 1803 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	COVID-19 SARS-CoV-2 genome next generation sequencing ion torrent alpha variant kappa variant and delta variant Genetics QH426-470
spellingShingle	COVID-19 SARS-CoV-2 genome next generation sequencing ion torrent alpha variant kappa variant and delta variant Genetics QH426-470 Jitendra Singh Anvita Gupta Malhotra Debasis Biswas Prem Shankar Leena Lokhande Ashvini Kumar Yadav Arun Raghuvanshi Dipesh Kale Shashwati Nema Saurabh Saigal Sarman Singh Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India
description	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.
format	article
author	Jitendra Singh Anvita Gupta Malhotra Debasis Biswas Prem Shankar Leena Lokhande Ashvini Kumar Yadav Arun Raghuvanshi Dipesh Kale Shashwati Nema Saurabh Saigal Sarman Singh
author_facet	Jitendra Singh Anvita Gupta Malhotra Debasis Biswas Prem Shankar Leena Lokhande Ashvini Kumar Yadav Arun Raghuvanshi Dipesh Kale Shashwati Nema Saurabh Saigal Sarman Singh
author_sort	Jitendra Singh
title	Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India
title_short	Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India
title_full	Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India
title_fullStr	Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India
title_full_unstemmed	Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India
title_sort	relative consolidation of the kappa variant pre-dates the massive second wave of covid-19 in india
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/ae4ac06836e94b6d8d2fea4f7442094a
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Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India

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