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

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.

Keywords: COVID-19; Gujarat; India; SARS-CoV-2; coronavirus disease; coronaviruses; genomic epidemiology; phylogeography; respiratory infections; severe acute respiratory syndrome coronavirus 2; transmission dynamics; virus; virus transmission; zoonoses.

Figure 1

COVID-19 epidemiology during the first epidemic wave, Gujarat, India, 2020. A) Gujarat, highlighting the 3 most populous districts. Purple indicates Ahmedabad, blue indicates Surat, green indicates Vadodara, and yellow indicates all other districts. Inset map shows location of Gujarat in India. B) Weekly counts of newly reported cases of infection with COVID-19 for Ahmedabad, Surat, Vadodara, and other districts during April‒July 2020. C) Estimates of R_t for 4 locations on the basis of daily incidence data using 7-day averaging (see Methods). The black line indicates the median estimate, the blue shaded region indicates 95% equal-tailed Bayesian credible intervals, and the gray shaded region indicates the period of national lockdown. The dotted line indicates R_t = 1. COVID-19, coronavirus disease; R_t, epidemic instantaneous reproduction number.

Figure 2

Size, duration, and importation of severe acute respiratory syndrome coronavirus 2 transmission lineages, Gujarat, India. A) Tree map summarizing the 113 detected transmission lineages by size. Colors indicate the duration of persistence of the lineage, and areas indicate the size of the transmission lineages. Lineage duration corresponds to time between the lineage’s oldest and most recently sampled genomes. B) Strong log‒linear relationship between size and mean tMRCA of each transmission lineages. Gray shading indicates time of testing; dashed line indicates slope. C) Breakdown of virus importations into Gujarat from other states in India or other countries. The number of location state transitions were estimated by using a robust counting approach (21) and a 3-location discrete trait phylogeographic analysis. tMRCA, time to most recent common ancestor.

Figure 3

Determinants of SARS-CoV-2 lineage spread, Gujarat, India. A) Choropleth maps of key predictors (left, no. cases; middle, population size; right, population density, persons per square kilometer) that were evaluated in the phylogeographic generalized linear model analysis along with geographic distance. B) tMRCA and sample distribution of the 7 largest transmission lineages. For each lineage, circles correspond to the estimated lineage tMRCA, and horizontal bars indicate the 95% highest posterior density interval of the tMRCA. Box indicates date range of the samples from Gujarat for each lineage. Total number of samples and duration of each lineage are shown on the right. C) Predictors of SARS-CoV-2 lineage movement in Gujarat on the basis of 20 sampled districts. The contribution of each predictor is indicated by the mean coefficient value (points) and 95% highest posterior density interval (horizontal bars). tMRCA, time to most recent common ancestor. SARS-CoV-2, severe acute respiratory syndrome coronavirus 2.

Figure 4

Timing of exportation of severe acute respiratory syndrome coronavirus 2 from Gujarat, India. Maximum clade credibility trees are for the 2 largest transmission lineages identified in this study: A) DTA_MCC_4; B) DTA_MCC_5. UAE, United Arab Emirates.