Cross-sectional genomic perspective of epidemic waves of SARS-CoV-2 : A pan India study
Copyright © 2021. Published by Elsevier B.V..
BACKGROUND: COVID-19 has posed unforeseen circumstances and throttled major economies worldwide. India has witnessed two waves affecting around 31 million people representing 16% of the cases globally. To date, the epidemic waves have not been comprehensively investigated to understand pandemic progress in India.
OBJECTIVE: Here, we aim for pan Indian cross-sectional evolutionary analysis since inception of SARS-CoV-2.
METHODS: High quality genomes, along with their collection date till 26th July 2021, were downloaded. Whole genome-based phylogeny was obtained. Further, the mutational analysis was performed using SARS-CoV-2 first reported from Wuhan (NC_045512.2) as reference.
RESULTS: Based on reported cases and mutation rates, we could divide the Indian epidemic into seven phases. The average mutation rate for the pre-first wave was <11, which elevated to 17 in the first wave and doubled in the second wave (∼34). In accordance with mutation rate, VOCs and VOIs started appearing in the first wave (1.5%), which dominated the second (∼96%) and post-second wave (100%). Nation-wide mutational analysis depicted >0.5 million mutation events with four major mutations in >19,300 genomes, including two mutations in coding (spike (D614G), and NSP 12b (P314L) of rdrp), one silent mutation (NSP3 F106F) and one extragenic mutation (5' UTR 241).
CONCLUSION: Whole genome-based phylogeny could demarcate post-first wave isolates from previous ones by point of diversification leading to incidences of VOCs and VOIs in India. Such analysis is crucial in the timely management of pandemic.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2022 |
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| Erschienen: |
2022 |
| Enthalten in: |
Zur Gesamtaufnahme - volume:308 |
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| Enthalten in: |
Virus research - 308(2022) vom: 15. Jan., Seite 198642 |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Kumar, Sanjeet [VerfasserIn] |
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| Links: |
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| Anmerkungen: |
Date Completed 01.02.2022 Date Revised 21.12.2022 published: Print-Electronic Citation Status MEDLINE |
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| doi: |
10.1016/j.virusres.2021.198642 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| 520 | |a Copyright © 2021. Published by Elsevier B.V. | ||
| 520 | |a BACKGROUND: COVID-19 has posed unforeseen circumstances and throttled major economies worldwide. India has witnessed two waves affecting around 31 million people representing 16% of the cases globally. To date, the epidemic waves have not been comprehensively investigated to understand pandemic progress in India | ||
| 520 | |a OBJECTIVE: Here, we aim for pan Indian cross-sectional evolutionary analysis since inception of SARS-CoV-2 | ||
| 520 | |a METHODS: High quality genomes, along with their collection date till 26th July 2021, were downloaded. Whole genome-based phylogeny was obtained. Further, the mutational analysis was performed using SARS-CoV-2 first reported from Wuhan (NC_045512.2) as reference | ||
| 520 | |a RESULTS: Based on reported cases and mutation rates, we could divide the Indian epidemic into seven phases. The average mutation rate for the pre-first wave was <11, which elevated to 17 in the first wave and doubled in the second wave (∼34). In accordance with mutation rate, VOCs and VOIs started appearing in the first wave (1.5%), which dominated the second (∼96%) and post-second wave (100%). Nation-wide mutational analysis depicted >0.5 million mutation events with four major mutations in >19,300 genomes, including two mutations in coding (spike (D614G), and NSP 12b (P314L) of rdrp), one silent mutation (NSP3 F106F) and one extragenic mutation (5' UTR 241) | ||
| 520 | |a CONCLUSION: Whole genome-based phylogeny could demarcate post-first wave isolates from previous ones by point of diversification leading to incidences of VOCs and VOIs in India. Such analysis is crucial in the timely management of pandemic | ||
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