Abstract
Globally, SARS-CoV-2 has moved from one tide to another with ebbs in between. Genomic surveillance has greatly aided the detection and tracking of the virus and the identification of the variants of concern (VOC). The knowledge and understanding from genomic surveillance is important for a populous country like India for public health and healthcare officials for advance planning. An integrative analysis of the publicly available datasets in GISAID from India reveals the differential distribution of clades, lineages, gender, and age over a year (Apr 2020–Mar 2021). The significant insights include the early evidence towards B.1.617 and B.1.1.7 lineages in the specific states of India. Pan-India longitudinal data highlighted that B.1.36* was the predominant clade in India until January–February 2021 after which it has gradually been replaced by the B.1.617.1 lineage, from December 2020 onward. Regional analysis of the spread of SARS-CoV-2 indicated that B.1.617.3 was first seen in India in the month of October in the state of Maharashtra, while the now most prevalent strain B.1.617.2 was first seen in Bihar and subsequently spread to the states of Maharashtra, Gujarat, and West Bengal. To enable a real time understanding of the transmission and evolution of the SARS-CoV-2 genomes, we built a transmission map available on https://covid19-indiana.soic.iupui.edu/India/EmergingLineages/April2020/to/March2021. Based on our analysis, the rate estimate for divergence in our dataset was 9.48 e-4 substitutions per site/year for SARS-CoV-2. This would enable pandemic preparedness with the addition of future sequencing data from India available in the public repositories for tracking and monitoring the VOCs and variants of interest (VOI). This would help aid decision making from the public health perspective.
Highlights
RNA viruses such as SARS-CoV-2 exist as a swarm of genetically related variants and not as a single genotype
We addressed several of these limitations from smaller scale studies focusing on Indian SARS-CoV-2 genomes in recent times, including i) panIndia representation, ii) longitudinal view from April 2020–March 2021, iii) SARS-CoV-2 genome sequences deposited in GISAID, iv) more than 99% genome coverage, v) sample metadata, vi) nucleotide substitution rate, and vii) transmission dynamics within India
By filtering out sequences related to patients’ metadata lacking date of sample collection, sampling location, age, and gender information, we retrieved a final set of 7631 sequences used for analysis presented in this study and Auspice data visualization
Summary
RNA viruses such as SARS-CoV-2 exist as a swarm of genetically related variants and not as a single genotype This property enables the virus to change hosts and adapt to changing environmental conditions. This is achieved through polymerase fidelity and genomic recombination that regulate this feature of RNA viruses (Barr and Fearns, 2016). In a pandemic, these features lead to generation of strains with modified epidemiological characteristics such as changing transmissibility, virulence, and varying immunological characteristics leading to altered vaccine, drug, and detection efficacy (Davies et al, 2021a; Becker et al, 2021; U.S, Food and Grug Administration, 2021). The VOC—alpha, beta, gamma, and delta—have been shown to have increased transmissibility or virulence and suggested to have increased immune evasion (WHO., 2021)
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