Circulation and Evolution of SARS-CoV-2 in India: Let the Data Speak

The COVID-19 pandemic is a global challenge that impacted 200+ countries. India ranks in the second and third positions in terms of number of reported cases and deaths. Being a populous country with densely packed cities, SARS-CoV-2 spread exponentially. India sequenced ≈0.14% isolates from confirme...

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Autores principales:	Sanket Limaye, Sunitha M. Kasibhatla, Mukund Ramtirthkar, Meenal Kinikar, Mohan M. Kale, Urmila Kulkarni-Kale
Formato:	article
Lenguaje:	EN
Publicado:	MDPI AG 2021
Materias:	COVID-19 SARS-CoV-2 lineage diversity evolutionary dynamics virus bioinformatics India Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/0b7f9cc9a34844eca23f3dbbd5488226
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spelling	oai:doaj.org-article:0b7f9cc9a34844eca23f3dbbd54882262021-11-25T19:13:39ZCirculation and Evolution of SARS-CoV-2 in India: Let the Data Speak10.3390/v131122381999-4915https://doaj.org/article/0b7f9cc9a34844eca23f3dbbd54882262021-11-01T00:00:00Zhttps://www.mdpi.com/1999-4915/13/11/2238https://doaj.org/toc/1999-4915The COVID-19 pandemic is a global challenge that impacted 200+ countries. India ranks in the second and third positions in terms of number of reported cases and deaths. Being a populous country with densely packed cities, SARS-CoV-2 spread exponentially. India sequenced ≈0.14% isolates from confirmed cases for pandemic surveillance and contributed ≈1.58% of complete genomes sequenced globally. This study was designed to map the circulating lineage diversity and to understand the evolution of SARS-CoV-2 in India using comparative genomics and population genetics approaches. Despite varied sequencing coverage across Indian States and Union Territories, isolates belonging to variants of concern (VoC) and variants of interest (VoI) circulated, persisted, and diversified during the first seventeen months of the pandemic. Delta and Kappa lineages emerged in India and spread globally. The phylogenetic tree shows lineage-wise monophyletic clusters of VoCs/VoIs and diversified tree topologies for non-VoC/VoI lineages designated as ‘Others’ in this study. Evolutionary dynamics analyses substantiate a lack of spatio-temporal clustering, which is indicative of multiple global and local introductions. Sites under positive selection and significant variations in spike protein corroborate with the constellation of mutations to be monitored for VoC/VoI as well as substitutions that are characteristic of functions with implications in virus–host interactions, differential glycosylation, immune evasion, and escape from neutralization.Sanket LimayeSunitha M. KasibhatlaMukund RamtirthkarMeenal KinikarMohan M. KaleUrmila Kulkarni-KaleMDPI AGarticleCOVID-19SARS-CoV-2lineage diversityevolutionary dynamicsvirus bioinformaticsIndiaMicrobiologyQR1-502ENViruses, Vol 13, Iss 2238, p 2238 (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	COVID-19 SARS-CoV-2 lineage diversity evolutionary dynamics virus bioinformatics India Microbiology QR1-502
spellingShingle	COVID-19 SARS-CoV-2 lineage diversity evolutionary dynamics virus bioinformatics India Microbiology QR1-502 Sanket Limaye Sunitha M. Kasibhatla Mukund Ramtirthkar Meenal Kinikar Mohan M. Kale Urmila Kulkarni-Kale Circulation and Evolution of SARS-CoV-2 in India: Let the Data Speak
description	The COVID-19 pandemic is a global challenge that impacted 200+ countries. India ranks in the second and third positions in terms of number of reported cases and deaths. Being a populous country with densely packed cities, SARS-CoV-2 spread exponentially. India sequenced ≈0.14% isolates from confirmed cases for pandemic surveillance and contributed ≈1.58% of complete genomes sequenced globally. This study was designed to map the circulating lineage diversity and to understand the evolution of SARS-CoV-2 in India using comparative genomics and population genetics approaches. Despite varied sequencing coverage across Indian States and Union Territories, isolates belonging to variants of concern (VoC) and variants of interest (VoI) circulated, persisted, and diversified during the first seventeen months of the pandemic. Delta and Kappa lineages emerged in India and spread globally. The phylogenetic tree shows lineage-wise monophyletic clusters of VoCs/VoIs and diversified tree topologies for non-VoC/VoI lineages designated as ‘Others’ in this study. Evolutionary dynamics analyses substantiate a lack of spatio-temporal clustering, which is indicative of multiple global and local introductions. Sites under positive selection and significant variations in spike protein corroborate with the constellation of mutations to be monitored for VoC/VoI as well as substitutions that are characteristic of functions with implications in virus–host interactions, differential glycosylation, immune evasion, and escape from neutralization.
format	article
author	Sanket Limaye Sunitha M. Kasibhatla Mukund Ramtirthkar Meenal Kinikar Mohan M. Kale Urmila Kulkarni-Kale
author_facet	Sanket Limaye Sunitha M. Kasibhatla Mukund Ramtirthkar Meenal Kinikar Mohan M. Kale Urmila Kulkarni-Kale
author_sort	Sanket Limaye
title	Circulation and Evolution of SARS-CoV-2 in India: Let the Data Speak
title_short	Circulation and Evolution of SARS-CoV-2 in India: Let the Data Speak
title_full	Circulation and Evolution of SARS-CoV-2 in India: Let the Data Speak
title_fullStr	Circulation and Evolution of SARS-CoV-2 in India: Let the Data Speak
title_full_unstemmed	Circulation and Evolution of SARS-CoV-2 in India: Let the Data Speak
title_sort	circulation and evolution of sars-cov-2 in india: let the data speak
publisher	MDPI AG
publishDate	2021
url	https://doaj.org/article/0b7f9cc9a34844eca23f3dbbd5488226
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Circulation and Evolution of SARS-CoV-2 in India: Let the Data Speak

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