tetano
Editor, Senior Moderator
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[SUP] 1 [/SUP], Dimpal A Nyayanit[SUP] 2 [/SUP], Shailendra Kumar Mishra[SUP] 1 [/SUP], Pragya D Yadav[SUP] 2 [/SUP], Kamran Zaman[SUP] 1 [/SUP], Prem Shankar[SUP] 3 [/SUP], Brij R Misra[SUP] 1 [/SUP], Sthita Pragnya Behera[SUP] 1 [/SUP], Niraj Kumar[SUP] 1 [/SUP], Abhinendra Kumar[SUP] 2 [/SUP], Pooja Bhardwaj[SUP] 1 [/SUP], Gaurav Raj Dwivedi[SUP] 1 [/SUP], Rajeev Singh[SUP] 1 [/SUP], Anita M Shete[SUP] 2 [/SUP], Priyanka Pandit[SUP] 2 [/SUP], Ashok K Pandey[SUP] 1 [/SUP], Girijesh Kumar Yadav[SUP] 1 [/SUP], Shashi Gupta[SUP] 1 [/SUP], Manoj Kumar[SUP] 1 [/SUP], Asif Kavathekar[SUP] 1 [/SUP], Ravi Shankar Singh[SUP] 1 [/SUP], Sanjay Prajapati[SUP] 1 [/SUP], Rajni Kant[SUP] 1 [/SUP]
Affiliations
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
681R, and S
614G 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.
. 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[SUP] 1 [/SUP], Dimpal A Nyayanit[SUP] 2 [/SUP], Shailendra Kumar Mishra[SUP] 1 [/SUP], Pragya D Yadav[SUP] 2 [/SUP], Kamran Zaman[SUP] 1 [/SUP], Prem Shankar[SUP] 3 [/SUP], Brij R Misra[SUP] 1 [/SUP], Sthita Pragnya Behera[SUP] 1 [/SUP], Niraj Kumar[SUP] 1 [/SUP], Abhinendra Kumar[SUP] 2 [/SUP], Pooja Bhardwaj[SUP] 1 [/SUP], Gaurav Raj Dwivedi[SUP] 1 [/SUP], Rajeev Singh[SUP] 1 [/SUP], Anita M Shete[SUP] 2 [/SUP], Priyanka Pandit[SUP] 2 [/SUP], Ashok K Pandey[SUP] 1 [/SUP], Girijesh Kumar Yadav[SUP] 1 [/SUP], Shashi Gupta[SUP] 1 [/SUP], Manoj Kumar[SUP] 1 [/SUP], Asif Kavathekar[SUP] 1 [/SUP], Ravi Shankar Singh[SUP] 1 [/SUP], Sanjay Prajapati[SUP] 1 [/SUP], Rajni Kant[SUP] 1 [/SUP]
Affiliations
- PMID: 35071267
- PMCID: PMC8777020
- DOI: 10.3389/fmed.2021.781287
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
681R, 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.