Genomic surveillance of SARS-CoV-2 in the Andean Community (2020–2024): integrating regional sequencing efforts from Colombia, Ecuador, Peru, and Bolivia through “ORAS-CONHU” program

Introduction The COVID-19 pandemic has deeply affected Latin American countries, with countless COVID-19 cases and deaths. In countries like Peru, Colombia, Ecuador and Bolivia there was a collapse of the public health system, and the lack of testing capacity did not allow to control the spread of SARS-CoV-2 during the first year of the COVID-19 pandemic. After these dramatic beginnings, regional efforts focused on improving testing capacity and massive vaccinations campaigns, but also implementing a sustained SARS-CoV-2 genomic surveillance program to follow up the evolution of the virus. Methods This study examines the regional efforts in the Andean Community in terms of SARS-CoV-2 genomic surveillance for Colombia, Ecuador, Peru, and Bolivia in coordination with “Organismo Andino de Salud-Convenio Hipólito Unanue” (ORAS-CONHU). Moreover, SARS-CoV-2 emerging lineages distribution, clade determination and phylogenetic analysis in those countries for the period 2020–2024 was done by retrieving 16,867 sequences from the GISAID database. Results From the initial lineages 19A and 19B, lineages 20A, 20B, and 20C emerged in 2020, followed by several variants such as 20 J (Gamma), 21A (Delta), 21G (Lambda), and 21H (Mu) emergence along 2021; by the end of 2022, the highly transmissible Omicron variants (21 K, 21 L) emerged and have been evolving into multiple sub variants lineages like 22F, 23A, and 23I (JN.1), the latest dominant along 2024. Discussion While each country exhibits some specific characteristics, the phylogenetic analysis underscored a common pattern in the lineage evolution of SARS-CoV-2 in the Andean Community supporting a rapid transnational transmission of the virus. This study was part of a regional effort to develop an integrative transnational genomic surveillance network for SARS-CoV-2 as a proxy for a more ambitious regional infectious diseases genomic surveillance program.