SARS-CoV-2 sequencing: The technological initiative to strengthen early warning systems for public health emergencies in Latin America and the Caribbean

Abstract

The COVID-19 pandemic caused by SARS-CoV-2 is a public health problem on a scale unprecedented in the last 100 years, as has been the response focused on the rapid genomic characterization of SARS-CoV-2 in virtually all regions of the planet. This pandemic emerged during the era of genomic epidemiology, a science fueled by continued advances in next-generation sequencing. Since its recent appearance, genomic epidemiology included the precise identification of new lineages or species of pathogens and the reconstruction of their genetic variability in real time, evidenced in past outbreaks of influenza H1N1, MERS, and SARS. However, the global and uncontrolled scale of this pandemic created a scenario where genomic epidemiology was put into practice en masse, from the rapid identification of SARS-CoV-2 to the registration of new lineages and their active surveillance throughout the world. Prior to the COVID-19 pandemic, the availability of genomic data on circulating pathogens in several Latin America and the Caribbean countries was scarce or nil. With the arrival of SARS-CoV-2, this scenario changed significantly, although the amount of available information remains scarce and, in countries such as Colombia, Brazil, Argentina, and Chile, the genomic information of SARS-CoV-2 was obtained mainly by research groups in genomic epidemiology rather than the product of a public health surveillance policy or program. This indicates the need to establish public health policies aimed at implementing genomic epidemiology as a tool to strengthen surveillance and early warning systems against threats to public health in the region.

Keywords: Coronavirus infections; viral isolation severe acute respiratory syndrome; SARS virus; high-throughput nucleotide sequencing; epidemiological surveillance; public health policies.

Figura 1. Aplicaciones de los estudios genómicos de SARS-CoV-2

Figura 2. Distribución de los genomas del SARS-CoV-2 reportados en la base de datos GISAID originados en países de Latinoamérica y el Caribe

Figura 3. Distribución temporal de los reportes de genomas de SARS-CoV-2 en países de Latinoamériva y el Caribe utilizando la fecha de recolección de la muestra asociada con la secuencia reportada en GISAID