Genomic Epidemiology of Early SARS-CoV-2 Transmission Dynamics, Gujarat, India

Raghwani, J; du Plessis, L; McCrone, JT; Hill, SC; Parag, KV; Theze, J; Kumar, D; Puvar, A; Pandit, R; Pybus, OG; Fournie, G; Joshi, M; Joshi, C

Abstract

Limited genomic sampling in many high-incidence countries has impeded studies of severe respiratory syndrome coronavirus 2 (SARS-CoV-2) genomic epidemiology. Consequently, critical questions remain about the generation and global distribution of virus genetic diversity. We investigated SARS-CoV-2 transmission dynamics in Gujarat, India, during the state's first epidemic wave to shed light on spread of the virus in one of the regions hardest hit by the pandemic. By integrating case data and 434 whole-genome sequences sampled across 20 districts, we reconstructed the epidemic dynamics and spatial spread of SARS-CoV-2 in Gujarat. Our findings indicate global and regional connectivity and population density were major drivers of the Gujarat outbreak. We detected >100 virus lineage introductions, most of which appear to be associated with international travel. Within Gujarat, virus dissemination occurred predominantly from densely populated regions to geographically proximate locations that had low population density, suggesting that urban centers contributed disproportionately to virus spread.

Citation

Raghwani, J., du Plessis, L., McCrone, J., Hill, S., Parag, K., Theze, J., Kumar, D., Puvar, A., Pandit, R., Pybus, O., Fournie, G., Joshi, M., & Joshi, C. (2022). Genomic Epidemiology of Early SARS-CoV-2 Transmission Dynamics, Gujarat, India. Emerging Infectious Disease, 28(4), 751-758. https://doi.org/10.3201/eid2804.212053

• Journal Article Type: Article
• Acceptance Date: Feb 23, 2022
• Publication Date: Feb 24, 2022
• Deposit Date: Aug 23, 2022
• Publicly Available Date: Aug 23, 2022
• Journal: Emerging Infectious Disease
• Print ISSN: 1080-6040
• Electronic ISSN: 1080-6059
• Publisher: Centers for Disease Control and Prevention
• Peer Reviewed: Peer Reviewed
• Volume: 28
• Issue: 4
• Pages: 751-758
• DOI: https://doi.org/10.3201/eid2804.212053