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 KavathekarRavi Shankar Singh, Sanjay Prajapati, Rajni Kant

Research output: Contribution to journalArticlepeer-review

6 Scopus citations


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.

Original languageEnglish (US)
Article number781287
JournalFrontiers in Medicine
StatePublished - Jan 7 2022
Externally publishedYes


  • COVID-19 breakthrough infection
  • Eastern Uttar Pradesh India
  • SARS-CoV-2
  • mutations
  • variant of concern
  • whole-genome sequencing

ASJC Scopus subject areas

  • General Medicine


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