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Genome surveillance of SARS-CoV-2 variants and their role in pathogenesis focusing on second wave of COVID-19 in India.
Sci Rep. 2023 Mar 22; 13(1):4692.SR

Abstract

India had witnessed unprecedented surge in SARS-CoV-2 infections and its dire consequences during the second wave of COVID-19, but the detailed report of the epidemiological based spatiotemporal incidences of the disease is missing. In the manuscript, we have applied various statistical approaches (correlation, hierarchical clustering) to decipher the pattern of pathogenesis of the circulating VoCs responsible for surge in the incidences. B.1.617.1 (Kappa) was the predominant VoC during the early phase of the second wave, whereas, Delta (B.1.617.2) or Delta-like (AY.x) VoC constitutes majority ([Formula: see text]%) of the cases during the peak of the second wave. The correlation plot of Delta/Delta-like lineage demonstrates inverse correlation with other lineages including B.1.617.1, B.1.1.7, B.1, B.1.36.29 and B.1.36. The spatiotemporal analysis shows that most of the Indian states were affected during the peak of the second wave due to the Delta surge, and fall under the same cluster. The second cluster populated mostly by north-eastern states and the islands of India were minimally affected. The presence of signature mutations (T478K, D950N, E156G) along with L452K, D614G and P681R within the spike protein of Delta or Delta-like might cause elevation in the host cell attachment, increased transmission and altered antigenicity which in due course of time has replaced the other circulating variants.The timely assessment of new VoCs including Delta-like will provide a rationale for updating the diagnostic, vaccine development by medical industries and decision making by various agencies including government, educational institutions, and corporate industries.

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Authors+Show Affiliations

Sarkar P
CSIR-Indian Institute of Chemical Biology (IICB), Calcutta, WB, 700032, India. IICB-Translational Research Unit of Excellence, Cancer Biology and Inflammatory Disorder, Salt Lake, WB, 700091, India.
Banerjee S
CSIR-Indian Institute of Chemical Biology (IICB), Calcutta, WB, 700032, India. IICB-Translational Research Unit of Excellence, Cancer Biology and Inflammatory Disorder, Salt Lake, WB, 700091, India.
Saha SA
CSIR-Indian Institute of Chemical Biology (IICB), Calcutta, WB, 700032, India. IICB-Translational Research Unit of Excellence, Cancer Biology and Inflammatory Disorder, Salt Lake, WB, 700091, India.
Mitra P
Indian Institute of Technology (IIT) Kharagpur, Computer Science and Engineering, Kharagpur, WB, 721302, India.
Sarkar S
CSIR-Indian Institute of Chemical Biology (IICB), Calcutta, WB, 700032, India. siddik.sarkar@iicb.res.in. IICB-Translational Research Unit of Excellence, Cancer Biology and Inflammatory Disorder, Salt Lake, WB, 700091, India. siddik.sarkar@iicb.res.in.

MeSH

HumansAsian PeopleCOVID-19IndiaMutationSARS-CoV-2

Pub Type(s)

Journal Article

Language

eng

PubMed ID

36949118

Citation

Sarkar, Poulomi, et al. "Genome Surveillance of SARS-CoV-2 Variants and Their Role in Pathogenesis Focusing On Second Wave of COVID-19 in India." Scientific Reports, vol. 13, no. 1, 2023, p. 4692.
Sarkar P, Banerjee S, Saha SA, et al. Genome surveillance of SARS-CoV-2 variants and their role in pathogenesis focusing on second wave of COVID-19 in India. Sci Rep. 2023;13(1):4692.
Sarkar, P., Banerjee, S., Saha, S. A., Mitra, P., & Sarkar, S. (2023). Genome surveillance of SARS-CoV-2 variants and their role in pathogenesis focusing on second wave of COVID-19 in India. Scientific Reports, 13(1), 4692. https://doi.org/10.1038/s41598-023-30815-5
Sarkar P, et al. Genome Surveillance of SARS-CoV-2 Variants and Their Role in Pathogenesis Focusing On Second Wave of COVID-19 in India. Sci Rep. 2023 Mar 22;13(1):4692. PubMed PMID: 36949118.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Genome surveillance of SARS-CoV-2 variants and their role in pathogenesis focusing on second wave of COVID-19 in India. AU - Sarkar,Poulomi, AU - Banerjee,Sarthak, AU - Saha,Sarbar Ali, AU - Mitra,Pralay, AU - Sarkar,Siddik, Y1 - 2023/03/22/ PY - 2022/03/02/received PY - 2023/03/01/accepted PY - 2023/3/23/entrez PY - 2023/3/24/pubmed PY - 2023/3/25/medline SP - 4692 EP - 4692 JF - Scientific reports JO - Sci Rep VL - 13 IS - 1 N2 - India had witnessed unprecedented surge in SARS-CoV-2 infections and its dire consequences during the second wave of COVID-19, but the detailed report of the epidemiological based spatiotemporal incidences of the disease is missing. In the manuscript, we have applied various statistical approaches (correlation, hierarchical clustering) to decipher the pattern of pathogenesis of the circulating VoCs responsible for surge in the incidences. B.1.617.1 (Kappa) was the predominant VoC during the early phase of the second wave, whereas, Delta (B.1.617.2) or Delta-like (AY.x) VoC constitutes majority ([Formula: see text]%) of the cases during the peak of the second wave. The correlation plot of Delta/Delta-like lineage demonstrates inverse correlation with other lineages including B.1.617.1, B.1.1.7, B.1, B.1.36.29 and B.1.36. The spatiotemporal analysis shows that most of the Indian states were affected during the peak of the second wave due to the Delta surge, and fall under the same cluster. The second cluster populated mostly by north-eastern states and the islands of India were minimally affected. The presence of signature mutations (T478K, D950N, E156G) along with L452K, D614G and P681R within the spike protein of Delta or Delta-like might cause elevation in the host cell attachment, increased transmission and altered antigenicity which in due course of time has replaced the other circulating variants.The timely assessment of new VoCs including Delta-like will provide a rationale for updating the diagnostic, vaccine development by medical industries and decision making by various agencies including government, educational institutions, and corporate industries. SN - 2045-2322 UR - https://www.unboundmedicine.com/medline/citation/36949118/Genome_surveillance_of_SARS_CoV_2_variants_and_their_role_in_pathogenesis_focusing_on_second_wave_of_COVID_19_in_India_ DB - PRIME DP - Unbound Medicine ER -