Transmission Dynamics of the COVID-19 Epidemic at the District Level in India: Prospective Observational Study

Abstract

Background: On March 9, 2020, the first COVID-19 case was reported in Jodhpur, Rajasthan, in the northwestern part of India. Understanding the epidemiology of COVID-19 at a local level is becoming increasingly important to guide measures to control the pandemic.

Objective: The aim of this study was to estimate the serial interval and basic reproduction number (R₀) to understand the transmission dynamics of the COVID-19 outbreak at a district level. We used standard mathematical modeling approaches to assess the utility of these factors in determining the effectiveness of COVID-19 responses and projecting the size of the epidemic.

Methods: Contact tracing of individuals infected with SARS-CoV-2 was performed to obtain the serial intervals. The median and 95th percentile values of the SARS-CoV-2 serial interval were obtained from the best fits with the weibull, log-normal, log-logistic, gamma, and generalized gamma distributions. Aggregate and instantaneous R₀ values were derived with different methods using the EarlyR and EpiEstim packages in R software.

Results: The median and 95th percentile values of the serial interval were 5.23 days (95% CI 4.72-5.79) and 13.20 days (95% CI 10.90-18.18), respectively. R₀ during the first 30 days of the outbreak was 1.62 (95% CI 1.07-2.17), which subsequently decreased to 1.15 (95% CI 1.09-1.21). The peak instantaneous R₀ values obtained using a Poisson process developed by Jombert et al were 6.53 (95% CI 2.12-13.38) and 3.43 (95% CI 1.71-5.74) for sliding time windows of 7 and 14 days, respectively. The peak R₀ values obtained using the method by Wallinga and Teunis were 2.96 (95% CI 2.52-3.36) and 2.92 (95% CI 2.65-3.22) for sliding time windows of 7 and 14 days, respectively. R₀ values of 1.21 (95% CI 1.09-1.34) and 1.12 (95% CI 1.03-1.21) for the 7- and 14-day sliding time windows, respectively, were obtained on July 6, 2020, using method by Jombert et al. Using the method by Wallinga and Teunis, values of 0.32 (95% CI 0.27-0.36) and 0.61 (95% CI 0.58-0.63) were obtained for the 7- and 14-day sliding time windows, respectively. The projection of cases over the next month was 2131 (95% CI 1799-2462). Reductions of transmission by 25% and 50% corresponding to reasonable and aggressive control measures could lead to 58.7% and 84.0% reductions in epidemic size, respectively.

Conclusions: The projected transmission reductions indicate that strengthening control measures could lead to proportionate reductions of the size of the COVID-19 epidemic. Time-dependent instantaneous R₀ estimation based on the process by Jombart et al was found to be better suited for guiding COVID-19 response at the district level than overall R₀ or instantaneous R₀ estimation by the Wallinga and Teunis method. A data-driven approach at the local level is proposed to be useful in guiding public health strategy and surge capacity planning.

Keywords: COVID-19; Epidemiology; India; SARS-CoV-2; basic reproduction number; infectious disease; mathematical modeling; outbreak response; projection; serial interval.