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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| Format: | Article |
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MDPI AG
2021-11-01
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| Series: | Genes |
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| Online Access: | https://www.mdpi.com/2073-4425/12/11/1803 |
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| 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 |
| collection | DOAJ |
| 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. |
| first_indexed | 2024-03-10T05:28:48Z |
| format | Article |
| id | doaj.art-ae4ac06836e94b6d8d2fea4f7442094a |
| institution | Directory Open Access Journal |
| issn | 2073-4425 |
| language | English |
| last_indexed | 2024-03-10T05:28:48Z |
| publishDate | 2021-11-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Genes |
| spelling | doaj.art-ae4ac06836e94b6d8d2fea4f7442094a2023-11-22T23:29:02ZengMDPI AGGenes2073-44252021-11-011211180310.3390/genes12111803Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in IndiaJitendra Singh0Anvita Gupta Malhotra1Debasis Biswas2Prem Shankar3Leena Lokhande4Ashvini Kumar Yadav5Arun Raghuvanshi6Dipesh Kale7Shashwati Nema8Saurabh Saigal9Sarman Singh10Translational Medicine Centre, All India Institute of Medical Sciences, Bhopal 462020, IndiaDepartment of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, IndiaDepartment of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, IndiaDepartment of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, IndiaDepartment of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, IndiaDepartment of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, IndiaDepartment of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, IndiaDepartment of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, IndiaDepartment of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, IndiaDepartment of Anesthesia and Critical Care, All India Institute of Medical Sciences, Bhopal 462020, IndiaDepartment of Microbiology, All India Institute of Medical Sciences, Bhopal 462020, IndiaIndia 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.https://www.mdpi.com/2073-4425/12/11/1803COVID-19SARS-CoV-2 genomenext generation sequencingion torrentalpha variantkappa variant and delta variant |
| spellingShingle | 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 Genes COVID-19 SARS-CoV-2 genome next generation sequencing ion torrent alpha variant kappa variant and delta variant |
| title | 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_short | 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 |
| topic | COVID-19 SARS-CoV-2 genome next generation sequencing ion torrent alpha variant kappa variant and delta variant |
| url | https://www.mdpi.com/2073-4425/12/11/1803 |
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