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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


J Raghwani

L du Plessis

JT McCrone

SC Hill

KV Parag

J Theze

D Kumar

A Puvar

R Pandit

OG Pybus

G Fournie

M Joshi

C Joshi


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.


Raghwani, J., du Plessis, L., McCrone, J., Hill, S., Parag, K., Theze, J., …Joshi, C. (2022). Genomic Epidemiology of Early SARS-CoV-2 Transmission Dynamics, Gujarat, India. Emerging Infectious Diseases, 28(4), 751-758.

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
Print ISSN 1080-6040
Publisher Centers for Disease Control and Prevention
Peer Reviewed Peer Reviewed
Volume 28
Issue 4
Pages 751-758


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