Deciphering the introduction and transmission of SARS-CoV-2 in the Colombian Amazon Basin

Abstract

Background The 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 findings Here, 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/Significance This 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.

MicroRNA-Mediated Regulation of the Virus Cycle and Pathogenesis in the SARS-CoV-2 Disease

“…They are defined by multiple convergent mutations that are hypothesized to have arisen either in the context of chronic infections or in previously infected individuals [ 16 , 17 ].…”

Direct and Indirect Proof of SARS-CoV-2 Infections in Indigenous Wiwa Communities in North-Eastern Colombia—A Cross-Sectional Assessment Providing Preliminary Surveillance Data

“…The regional SARS-CoV-2 spread suggests that—by chance—the assessment was performed while a local outbreak was ongoing. The finding of 30% active infections in assessed individuals from San Juan implies that local living conditions may facilitate SARS-CoV-2 transmission more easily than reported from over Colombian settings [ 22 , 23 , 24 ] in outbreak situations.…”

“…One Wiwa with PCR-confirmed SARS-CoV-2 infection reported previous COVID-19 half a year ago, and a second one a positive rapid antigen test three weeks prior to our assessment. Such hints in the medical history may indicate re-infections, either due to insufficient infection-induced immunity or emerging SARS-CoV-2 variants [ 24 ], or a prolonged shedding of SARS-CoV-2 in Wiwa individuals. In general, however, we did not record increased disease severity in participants with active infections, nor signs of relevant sequelae in convalescent individuals with detectable SARS-CoV-2-specific antibodies.…”

“…Probable reasons for this discrepancy have been summarized above. Second, in a previous study on COVID-19 in the Colombian indigenous population in the Amazon basin, a few SARS-CoV-2 introduction events into the local populations were sufficient to cause major outbreaks [ 24 ]. Due to the lack of molecular typing capacity in the present assessment, no comparable details on the local transmission chains within the Wiwa population can be provided.…”

“…The need to care for vulnerable indigenous populations had been already addressed in Columbia in the early stages of the pandemic [ 22 ], as it was soon recognized that indigenous communities with restricted health infrastructure were not only severely affected [ 23 ], but also particularly threated by the P.1 variant of concern (VOC) circulating in the Columbian Amazon basin [ 24 ]. In contrast, for indigenous populations such as the Wiwa, living in remote areas of the Sierra Nevada de Santa Marta in the north-east of Colombia, no information on the COVID-19 situation was available.…”