Front Med (Lausanne) . Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India

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Front Med (Lausanne)


. 2022 Jan 7;8:781287.
doi: 10.3389/fmed.2021.781287. eCollection 2021.
Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India


Hirawati Deval ¹ , Dimpal A Nyayanit ² , Shailendra Kumar Mishra ¹ , Pragya D Yadav ² , Kamran Zaman ¹ , Prem Shankar ³ , Brij R Misra ¹ , Sthita Pragnya Behera ¹ , Niraj Kumar ¹ , Abhinendra Kumar ² , Pooja Bhardwaj ¹ , Gaurav Raj Dwivedi ¹ , Rajeev Singh ¹ , Anita M Shete ² , Priyanka Pandit ² , Ashok K Pandey ¹ , Girijesh Kumar Yadav ¹ , Shashi Gupta ¹ , Manoj Kumar ¹ , Asif Kavathekar ¹ , Ravi Shankar Singh ¹ , Sanjay Prajapati ¹ , Rajni Kant ¹



Affiliations

• PMID: 35071267
• PMCID: PMC8777020
• DOI: 10.3389/fmed.2021.781287

Free PMC article

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 S614G 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 S574Y 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.