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Genomic epidemiology of SARS-CoV-2 in Peru from 2020 to 2024
Author(s)
Sobkowiak, Benjamin
Simon Fraser University
Langdon, Amy E.
Simon Fraser University
Romero, Pedro E.
National University of San Marcos
Carrasco-Escobar, Gabriel
Universidad Peruana Cayetano Heredia
Villa, Diego
Universidad Peruana Cayetano Heredia
Cava Miller, Renato
Universidad Peruana Cayetano Heredia
Cornejo, Victor G.
Universidad Peruana Cayetano Heredia
Dávila-Barclay, Alejandra
Universidad Peruana Cayetano Heredia
Cuicapuza, Diego
Universidad Peruana Cayetano Heredia
Salvatierra, Guillermo R.
Universidad Peruana Cayetano Heredia
González, Luis
Universidad Peruana Cayetano Heredia
Ayzanoa, Brenda
Universidad Peruana Cayetano Heredia
Huancachoque, Janet
Universidad Peruana Cayetano Heredia
Gómez De La Torre, Juan Carlos
Barletta, Claudia
Chenet, Stella M.
National University Toribio Rodríguez de Mendoza
Tapia-Limonchi, Rafael
National University Toribio Rodríguez de Mendoza
Ballon, Jorge Andres
Universidad Nacional de San Agustin de Arequipa
Fernández, Patrick
Universidad Nacional de San Agustin de Arequipa
Valderrama, Rosario
Universidad Nacional de San Agustin de Arequipa
Leguia, Mariana
Pontificia Universidad Católica del Perú
Delgado-Ratto, Christopher
University of Antwerp
Gotuzzo, Eduardo H.
Universidad Peruana Cayetano Heredia
Zamudio, Carlos Caicedo
Universidad Peruana Cayetano Heredia
Lescano, Willy
Universidad Peruana Cayetano Heredia
Cárcamo, Cesar P.
Universidad Peruana Cayetano Heredia
Hurtado, Verónica
Instituto Nacional de Salud
Lope-Pari, Priscila
Instituto Nacional de Salud
Padilla-Rojas, Carlos P.
Instituto Nacional de Salud
Jiménez-Vásquez, Víctor Alberto
Instituto Nacional de Salud
Escalante-Maldonado, Oscar Roberto
Instituto Nacional de Salud
Araujo-Castillo, Roger V.
Instituto Nacional de Salud
Cabezas-Sánchez, César Augusto
Instituto Nacional de Salud
Colijn, Caroline
Simon Fraser University
Tsukayama, Pablo
Universidad Peruana Cayetano Heredia
Date Issued
9 de enero de 2026
Type
Article
Publisher
Springer Nature
Volume
6
Issue
1
Series/Report No.
Communications Medicine
Contained in
Communications Medicine
ISSN
2730-664X
Abstract
Background: Peru recorded one of the world’s highest COVID-19 mortality rates, with nearly 4.5 million reported cases and 220,000 deaths by March 2024. Understanding the emergence and spread of SARS-CoV-2 variants in this context is key to informing effective public health responses. This study describes the genomic diversity, transmission dynamics, and geographic spread of SARS-CoV-2 in Peru from 2020 to 2024. Methods: We analyzed nearly 50,000 high-quality public SARS-CoV-2 genome sequences collected nationwide between March 2020 and March 2024. Phylogeographic and mutational analyses were performed to identify variant lineages, trace their origins, and map viral movements within and beyond Peru. Results: We show that Peru’s epidemic waves were shaped by the emergence of locally evolved variants, including Lambda (C.37), Gamma (P.1.12), and Omicron (XBB.2.6 and DJ.1) sub-lineages. The city of Lima acted as the primary hub for inter-regional spread, accounting for 47.3% of inferred viral movements to other departments, notably Ancash, Cusco, and Piura. Peru was the source of various lineages that spread internationally, primarily to Chile, the USA, and Europe. Mutational analysis highlighted critical mutations in the spike protein, including L452Q and F490S in Lambda, associated with immune evasion and increased transmissibility. Conclusions: This work demonstrates the capacity of genomic surveillance in Peru to detect and track emerging SARS-CoV-2 variants, providing insights into regional and global transmission dynamics in a high-transmission, middle-income country setting. Sustained, cost-effective genomic monitoring, combined with strengthened bioinformatics and laboratory capacity, is essential for pandemic preparedness in resource-limited settings.
Financiamiento(s)
PE501086419-2024
Sponsor(s)
We thank all the researchers, healthcare workers, laboratory technicians, patients, and individuals who contributed to generating the genomic sequences analyzed in this study. This work was funded by (1) Peru\u2019s National Program for Scientific Research and Advanced Studies (PROCIENCIA \u2013 CONCYTEC) Contract PE501086419-2024-PROCIENCIA, (2) D43 TW007393 training grant awarded to UPCH by the Fogarty International Center of the U.S. National Institutes of Health, (3) US Centers for Disease Control and Prevention cooperative agreement award GH00266, (4) VLIRUOS JOINT project \u201CImproved infectious diseases control in Peru through sustainable capacity building for bioinformatics and genome sequencing\u201D (PE2019JOI018A102), and (5) Wellcome Sanger Institute International Fellowship awarded to P.T.