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ORIGINAL RESEARCH article

Front. Public Health

Sec. Infectious Diseases: Epidemiology and Prevention

Volume 13 - 2025 | doi: 10.3389/fpubh.2025.1623413

This article is part of the Research TopicSARS-CoV-2: Virology, Epidemiology, Diagnosis, Pathogenesis and Control, Volume IIView all 13 articles

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

Provisionally accepted
Alfredo  BrunoAlfredo Bruno1Paola  RojasPaola Rojas2Carol  GuzmanCarol Guzman1Omar  CaceresOmar Caceres2Miguel Angel  Garcia BereguiainMiguel Angel Garcia Bereguiain3*
  • 1Instituto Nacional de Salud Publica, Guayaquil, Ecuador
  • 2Insituto Nacional de Salud, Bogota, Colombia
  • 3University of the Americas, Quito, Ecuador

The final, formatted version of the article will be published soon.

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. 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 16867 sequences from the GISAID database. From the initial lineages 19A and 19B, lineages 20A, 20B, and 20C emerged in 2020, followed by several variants such as 20J (Gamma), 21A (Delta), 21G (Lambda), and 21H (Mu) emergence along 2021; by the end of 2022, the highly transmissible Omicron variants (21K, 21L) emerged and have been evolving into multiple sub variants lineages like 22F, 23A, and 23I (JN.1), the latest dominant along 2024. 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.

Keywords: SARS-CoV-2, South America, Genomic surveillance, COVID-19, Andean Community

Received: 05 May 2025; Accepted: 12 Aug 2025.

Copyright: © 2025 Bruno, Rojas, Guzman, Caceres and Garcia Bereguiain. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

* Correspondence: Miguel Angel Garcia Bereguiain, University of the Americas, Quito, Ecuador

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