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SARS-CoV-2 Lineage Tracking, and Evolving Trends Seen During Three Consecutive Peaks of Infection in Delhi, India – A Clinico-Genomic Study
47 Pages Posted: 17 Dec 2021
More...Abstract
Background: Since its advent, the pandemic has caused havoc in multiple waves due partly to amplified transmissibility and immune escape to vaccines. Delhi also witnessed brutal multiple peaks causing exponential rise in cases. Here we had retrospectively investigated clade variation, emergence of new lineages and varied clinical characteristics during those three peaks in order to understand the trajectory of the ongoing pandemic.
Methods: In this study a total of 1,23,378 samples were collected for a time span of fourteen months (1st June 2020, to 3rd August, 2021) encompassing three different peaks in Delhi. A subset of 747 samples was processed for sequencing. Complete clinical and demographic details of all the enrolled cases were also collected.
Findings: We detected 26 lineages across three peaks non-uniformly from 612 quality passed samples. The first peak was driven by diverse early variants, while the second one by B.1.36 and B.1.617.2, unlike third peak caused entirely by B.1.617.2. A total of 18316 mutations with median of 34 were reported. Majority of mutations were present in less than 1% of samples. Differences in clinical characteristics across three peaks was also reported.
Interpretation: In order to be ahead of the frequently changing course of the ongoing pandemic, it is of utmost importance that novel lineages to be tracked continuously. Prioritized sequencing of sudden local outburst and community hotspots must be done in order to swiftly detect a novel mutation/lineage of potential clinical importance.
Funding Information: WGS laboratory at our institute is funded by the Government of NCT, Delhi.
Declaration of Interests: The authors declare no conflict of interest.
Ethics Approval Statement: The present study was approved by Institutional Ethics Committee (IEC) at Institute of Liver and Biliary Sciences, New Delhi (Ethical no. IEC/2020/77/MA07). In this study de-identified and anonymised archived samples were subjected to whole genome sequencing. No personal details except clinically relevant information (age, sex, symptoms and outcome) were used for the purpose of the study. Hence individual consent form was waived off by the IEC.
Keywords: SARS-CoV-2 variants, COVID-19, pandemic, Lineage tracking, Delhi, India
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