Genomic analysis reveals dynamics of SARS-CoV-2 during the initial phases of the COVID-19 outbreak in the Dominican Republic

Abstract

Genomic sequencing of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been widely instituted during the coronavirus disease 2019 (COVID-19) pandemic to track the emergence and spread of new lineages. While this powerful tool can influence public health decisions and therapeutic development, not all regions of the world have had equal access to sequencing capacity, affecting surveillance. One such underrepresented region is the Caribbean islands, including the Dominican Republic (DR). To determine retrospectively what lineages were circulating in the DR in the first year of the pandemic, when there were strict travel restrictions imposed, we sequenced SARS-CoV-2 from nasal swab and saliva samples collected between July 2020 and February 2021. We investigated whether COVID-19 outbreaks were seeded by single or multiple introductions and established epidemiological linkages to other countries. Using 98 newly sequenced samples, we identified 16 SARS-CoV-2 lineages in the DR, indicating many independent introductions from diverse geographic areas. Further, we show that analyzing both globally prevalent and globally rare lineages within the DR highlights different aspects of international disease transmission.IMPORTANCEThis study uses genome sequencing of severe acute respiratory syndrome coronavirus 2 samples collected in an undersampled region of the world-the Caribbean, specifically the Dominican Republic-to make novel inferences about the dynamics of disease spread during a period of the coronavirus disease 2019 pandemic when many diverse lineages were co-circulating globally.

Keywords: COVID-19 pandemic; Dominican Republic; SARS-CoV-2 genomics; genomic epidemiology.