Deciphering The Introduction And Transmission Of Sars-Cov-2 In The Colombian Amazon Basin

BackgroundThe SARS-CoV-2 pandemic has forced health authorities across the world to take important decisions to curtail its spread. Genomic epidemiology has emerged as a valuable tool to understand introductions and spread of the virus in a specific geographic location.Methodology/Principal findingsHere, we report the sequences of 59 SARS-CoV-2 samples from inhabitants of the Colombian Amazonas department. The viral genomes were distributed in two robust clusters within the distinct GISAID clades GH and G. Spatial-temporal analyses revealed two independent introductions of SARS-CoV-2 in the region, one around April 1, 2020 associated with a local transmission, and one around April 2, 2020 associated with other South American genomes (Uruguay and Brazil). We also identified ten lineages circulating in the Amazonas department including the P.1 variant of concern (VOC).Conclusions/SignificanceThis study represents the first genomic epidemiology investigation of SARS-CoV-2 in one of the territories with the highest report of indigenous community of the country. Such findings are essential to decipher viral transmission, inform on global spread and to direct implementation of infection prevention and control measures for this vulnerable population, especially, due to the recent circulation of one of the variants of concern (P.1) associated with major transmissibility and possible reinfections.Author summarySARS-CoV-2 has dramatically impacted Amerindian native communities across South America, particularly in the Amazonian basin. In order to unveil the introduction and initial spread of this pandemic virus into this region, we conducted a genomic epidemiology study in the Colombian Amazonas department where we sequenced 59 genomes from cases in the Amazonas department of Colombia. Our results showed two independent introductions of the virus into the department, one of these associated with asymptomatic cases. This represents the first genomic epidemiology study focused on the Colombian amazon where a great amount of native Amerindian indigenous communities inhabits. Our results provide insights of the transmission dynamic in this region and reported relevant information to pursue strategies to mitigate the spread of the virus in the Amazon population which currently are facing new risks due to the circulating new variant of concern P.1.