TY - JOUR
T1 - Genome Sequencing Reveals a Mixed Picture of SARS-CoV-2 Variant of Concern Circulation in Eastern Uttar Pradesh, India
AU - Deval, Hirawati
AU - Nyayanit, Dimpal A.
AU - Mishra, Shailendra Kumar
AU - Yadav, Pragya D.
AU - Zaman, Kamran
AU - Shankar, Prem
AU - Misra, Brij R.
AU - Behera, Sthita Pragnya
AU - Kumar, Niraj
AU - Kumar, Abhinendra
AU - Bhardwaj, Pooja
AU - Dwivedi, Gaurav Raj
AU - Singh, Rajeev
AU - Shete, Anita M.
AU - Pandit, Priyanka
AU - Pandey, Ashok K.
AU - Yadav, Girijesh Kumar
AU - Gupta, Shashi
AU - Kumar, Manoj
AU - Kavathekar, Asif
AU - Singh, Ravi Shankar
AU - Prajapati, Sanjay
AU - Kant, Rajni
N1 - Publisher Copyright:
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.
PY - 2022/1/7
Y1 - 2022/1/7
N2 - 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.
AB - 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.
KW - COVID-19 breakthrough infection
KW - Eastern Uttar Pradesh India
KW - SARS-CoV-2
KW - mutations
KW - variant of concern
KW - whole-genome sequencing
UR - https://www.scopus.com/pages/publications/85123186558
UR - https://www.scopus.com/pages/publications/85123186558#tab=citedBy
U2 - 10.3389/fmed.2021.781287
DO - 10.3389/fmed.2021.781287
M3 - Article
AN - SCOPUS:85123186558
SN - 2296-858X
VL - 8
JO - Frontiers in Medicine
JF - Frontiers in Medicine
M1 - 781287
ER -