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Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India.
Deval, Hirawati; Nyayanit, Dimpal A; Mishra, Shailendra Kumar; Yadav, Pragya D; Zaman, Kamran; Shankar, Prem; Misra, Brij R; Behera, Sthita Pragnya; Kumar, Niraj; Kumar, Abhinendra; Bhardwaj, Pooja; Dwivedi, Gaurav Raj; Singh, Rajeev; Shete, Anita M; Pandit, Priyanka; Pandey, Ashok K; Yadav, Girijesh Kumar; Gupta, Shashi; Kumar, Manoj; Kavathekar, Asif; Singh, Ravi Shankar; Prajapati, Sanjay; Kant, Rajni.
  • Deval H; Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India.
  • Nyayanit DA; Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, India.
  • Mishra SK; Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India.
  • Yadav PD; Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, India.
  • Zaman K; Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India.
  • Shankar P; All India Institute of Medical Sciences, Gorakhpur, India.
  • Misra BR; Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India.
  • Behera SP; Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India.
  • Kumar N; Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India.
  • Kumar A; Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, India.
  • Bhardwaj P; Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India.
  • Dwivedi GR; Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India.
  • Singh R; Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India.
  • Shete AM; Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, India.
  • Pandit P; Indian Council of Medical Research (ICMR)-National Institute of Virology, Pune, India.
  • Pandey AK; Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India.
  • Yadav GK; Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India.
  • Gupta S; Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India.
  • Kumar M; Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India.
  • Kavathekar A; Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India.
  • Singh RS; Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India.
  • Prajapati S; Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India.
  • Kant R; Indian Council of Medical Research (ICMR)-Regional Medical Research Centre, Gorakhpur, India.
Front Med (Lausanne) ; 8: 781287, 2021.
Article in English | MEDLINE | ID: covidwho-1649347
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 SL452R, SP681R, and SD614G were commonly detected in the Delta, Delta AY.1, and Kappa variants whereas ST19R and ST478K were confined to Delta and Delta AY.1 variants only. Vaccine breakthrough infections showed unique mutational changes at position SD574Y in the case of the Delta variant, whereas position ST95 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.
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Full text: Available Collection: International databases Database: MEDLINE Topics: Vaccines / Variants Language: English Journal: Front Med (Lausanne) Year: 2021 Document Type: Article Affiliation country: Fmed.2021.781287

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Full text: Available Collection: International databases Database: MEDLINE Topics: Vaccines / Variants Language: English Journal: Front Med (Lausanne) Year: 2021 Document Type: Article Affiliation country: Fmed.2021.781287