A tale of two waves: Delineating diverse genomic and transmission landscapes driving the COVID-19 pandemic in Pune, India

Divya Niveditha; Soumen Khan; Ajinkya Khilari; Sanica Nadkarni; Unnati Bhalerao; Pradnya Kadam; Ritu Yadav; Jugal B. Kanekar; Nikita Shah; Bhagyashree Likhitkar; Rutuja Sawant; Shikha Thakur; Manisha Tupekar; Dhriti Nagar; Anjani G. Rao; Rutuja Jagtap; Shraddha Jogi; Madhuri Belekar; Maitreyee Pathak; Priyanki Shah; Shatakshi Ranade; Nikhil Phadke; Rashmita Das; Suvarna Joshi; Rajesh Karyakarte; Aurnab Ghose; Narendra Kadoo; L S Shashidhara; Joy Merwin Monteiro; Dhanasekaran Shanmugam; Anu Raghunathan; Krishanpal Karmodiya

doi:10.1016/j.jiph.2023.06.004

Retour

A tale of two waves: Delineating diverse genomic and transmission landscapes driving the COVID-19 pandemic in Pune, India

Article de revue

Avec comité de lecture

A tale of two waves: Delineating diverse genomic and transmission landscapes driving the COVID-19 pandemic in Pune, India

Divya Niveditha, Soumen Khan, Ajinkya Khilari, Sanica Nadkarni, Unnati Bhalerao, Pradnya Kadam, Ritu Yadav, Jugal B. Kanekar, Nikita Shah, Bhagyashree Likhitkar, …

Journal of infection and public health, Vol.16(8), pp.1290-1300

08/2023

DOI: https://doi.org/10.1016/j.jiph.2023.06.004

PMID: 37331277

Résumé

COVID-19

Delta

Omicron

SARS-CoV-2 genomic surveillance

Variant of concern

Whole Genome Sequencing (WGS)

Modern response to pandemics, critical for effective public health measures, is shaped by the availability and integration of diverse epidemiological outbreak data. Tracking variants of concern (VOC) is integral to understanding the evolution of SARS-CoV-2 in space and time, both at the local level and global context. This potentially generates actionable information when integrated with epidemiological outbreak data. A city-wide network of researchers, clinicians, and pathology diagnostic laboratories was formed for genome surveillance of COVID-19 in Pune, India. The genomic landscapes of 10,496 sequenced samples of SARS-CoV-2 driving peaks of infection in Pune between December-2020 to March-2022, were determined. As a modern response to the pandemic, a “band of five” outbreak data analytics approach was used. This integrated the genomic data (Band 1) of the virus through molecular phylogenetics with key outbreak data including sample collection dates and case numbers (Band 2), demographics like age and gender (Band 3–4), and geospatial mapping (Band 5). The transmission dynamics of VOCs in 10,496 sequenced samples identified B.1.617.2 (Delta) and BA(x) (Omicron formerly known as B.1.1.529) variants as drivers of the second and third peaks of infection in Pune. Spike Protein mutational profiling during pre and post-Omicron VOCs indicated differential rank ordering of high-frequency mutations in specific domains that increased the charge and binding properties of the protein. Time-resolved phylogenetic analysis of Omicron sub-lineages identified a highly divergent BA.1 from Pune in addition to recombinant X lineages, XZ, XQ, and XM. The band of five outbreak data analytics approach, which integrates five different types of data, highlights the importance of a strong surveillance system with high-quality meta-data for understanding the spatiotemporal evolution of the SARS-CoV-2 genome in Pune. These findings have important implications for pandemic preparedness and could be critical tools for understanding and responding to future outbreaks.

Indicateurs

1 Consultations de la notice

See more details

Détails

Titre: A tale of two waves: Delineating diverse genomic and transmission landscapes driving the COVID-19 pandemic in Pune, India
Créateurs - sans rôle: Divya Niveditha - Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
Soumen Khan - Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
Ajinkya Khilari - Biochemical Sciences Division, CSIR - National Chemical Laboratory, Dr. Homi Bhabha Road, 411008, Pune, India
Sanica Nadkarni - Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
Unnati Bhalerao - Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
Pradnya Kadam - Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
Ritu Yadav - Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
Jugal B. Kanekar - Biochemical Sciences Division, CSIR - National Chemical Laboratory, Dr. Homi Bhabha Road, 411008, Pune, India
Nikita Shah - Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
Bhagyashree Likhitkar - Biochemical Sciences Division, CSIR - National Chemical Laboratory, Dr. Homi Bhabha Road, 411008, Pune, India
Rutuja Sawant - Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
Shikha Thakur - Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
Manisha Tupekar - Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
Dhriti Nagar - Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
Anjani G. Rao - Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
Rutuja Jagtap - Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
Shraddha Jogi - Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
Madhuri Belekar - Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
Maitreyee Pathak - Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
Priyanki Shah - The Pune Knowledge Cluster (PKC), Savitribai Phule Pune University, Ganeshkhind Road, 411007 Pune, India
Shatakshi Ranade - GenePath Diagnostics India Private Limited, Pune 411004, India
Nikhil Phadke - GenePath Diagnostics India Private Limited, Pune 411004, India
Rashmita Das - Byramjee Jeejeebhoy Government Medical College (BJGMC), Jai Prakash Narayan Road, Pune 411001, India
Suvarna Joshi - Byramjee Jeejeebhoy Government Medical College (BJGMC), Jai Prakash Narayan Road, Pune 411001, India
Rajesh Karyakarte - Byramjee Jeejeebhoy Government Medical College (BJGMC), Jai Prakash Narayan Road, Pune 411001, India
Aurnab Ghose - Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
Narendra Kadoo - Biochemical Sciences Division, CSIR - National Chemical Laboratory, Dr. Homi Bhabha Road, 411008, Pune, India
L S Shashidhara - Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
Joy Merwin Monteiro - Department of Earth and Climate Science, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
Dhanasekaran Shanmugam - Biochemical Sciences Division, CSIR - National Chemical Laboratory, Dr. Homi Bhabha Road, 411008, Pune, India
Anu Raghunathan - Chemical Engineering & Process Development Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India
Krishanpal Karmodiya - Department of Biology, Indian Institute of Science Education and Research, Dr. Homi Bhabha Road, Pashan, Pune 411008, India
Détails de publication: Journal of infection and public health, Vol.16(8), pp.1290-1300
Éditeur: Elsevier Ltd
Nombre de pages: 11
Identifiants: 99155689409311
Unité académique: Laboratory of Pathogens and Host Immunity - LPHI
Langue: English
Type de ressource: Journal article