Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India

Hirawati Deval; Dimpal A Nyayanit; Shailendra Kumar Mishra; Pragya D Yadav; Kamran Zaman; Prem Shankar; Brij R Misra; Sthita Pragnya Behera; Niraj Kumar; Abhinendra Kumar; Pooja Bhardwaj; Gaurav Raj Dwivedi; Rajeev Singh; Anita M Shete; Priyanka Pandit; Ashok K Pandey; Girijesh Kumar Yadav; Shashi Gupta; Manoj Kumar; Asif Kavathekar; Ravi Shankar Singh; Sanjay Prajapati; Rajni Kant

doi:10.3389/fmed.2021.781287

Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India

Front Med (Lausanne). 2022 Jan 7:8:781287. doi: 10.3389/fmed.2021.781287. eCollection 2021.

Authors

Hirawati Deval¹, Dimpal A Nyayanit², Shailendra Kumar Mishra¹, Pragya D Yadav², Kamran Zaman¹, Prem Shankar³, Brij R Misra¹, Sthita Pragnya Behera¹, Niraj Kumar¹, Abhinendra Kumar², Pooja Bhardwaj¹, Gaurav Raj Dwivedi¹, Rajeev Singh¹, Anita M Shete², Priyanka Pandit², Ashok K Pandey¹, Girijesh Kumar Yadav¹, Shashi Gupta¹, Manoj Kumar¹, Asif Kavathekar¹, Ravi Shankar Singh¹, Sanjay Prajapati¹, Rajni Kant¹

Affiliations

¹ Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India.
² Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, India.
³ All India Institute of Medical Sciences, Gorakhpur, India.

Abstract

Uttar Pradesh is the densely populated state of India and is the sixth highest COVID-19 affected state with 22,904 deaths recorded on November 12, 2021. Whole-genome sequencing (WGS) is being used as a potential approach to investigate genomic evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus. In this study, a total of 87 SARS-CoV-2 genomes-49 genomes from the first wave (March 2020 to February 2021) and 38 genomes from the second wave (March 2021 to July 2021) from Eastern Uttar Pradesh (E-UP) were sequenced and analyzed to understand its evolutionary pattern and variants against publicaly available sequences. The complete genome analysis of SARS-CoV-2 during the first wave in E-UP largely reported transmission of G, GR, and GH clades with specific mutations. In contrast, variants of concerns (VOCs) such as Delta (71.0%) followed by Delta AY.1 (21.05%) and Kappa (7.9%) lineages belong to G clade with prominent signature amino acids were introduced in the second wave. Signature substitution at positions S:L452R, S:P681R, and S:D614G were commonly detected in the Delta, Delta AY.1, and Kappa variants whereas S:T19R and S:T478K were confined to Delta and Delta AY.1 variants only. Vaccine breakthrough infections showed unique mutational changes at position S:D574Y in the case of the Delta variant, whereas position S:T95 was conserved among Kappa variants compared to the Wuhan isolate. During the transition from the first to second waves, a shift in the predominant clade from GH to G clade was observed. The identified spike protein mutations in the SARS-CoV-2 genome could be used as the potential target for vaccine and drug development to combat the effects of the COVID-19 disease.

Keywords: COVID-19 breakthrough infection; Eastern Uttar Pradesh India; SARS-CoV-2; mutations; variant of concern; whole-genome sequencing.

Copyright © 2022 Deval, Nyayanit, Mishra, Yadav, Zaman, Shankar, Misra, Behera, Kumar, Kumar, Bhardwaj, Dwivedi, Singh, Shete, Pandit, Pandey, Yadav, Gupta, Kumar, Kavathekar, Singh, Prajapati and Kant.