Genomic epidemiology of SARS-CoV-2 in Peru from 2020 to 2024
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 desc...
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| Formato: | Artículo |
| Lenguaje: | inglés |
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Nature Portfolio
2026
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| _version_ | 1881510600232665088 |
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| author | Sobkowiak, Benjamin Langdon, Amy Romero, Pedro E. Carrasco-Escobar, Gabriel Villa, Diego Cava Miller, Renato Cornejo Villanueva, Víctor Dávila-Barclay, Alejandra Cuicapuza, Diego Salvatierra, Guillermo González, Luis Ayzanoa, Brenda Huancachoque, Janet Marcos-Carbajal, Pool Gómez de la Torre, Juan Carlos Barletta, Claudia M. Chenet, Stella Tapia-Limonchi, Rafael Ballón, Jorge Fernández, Patrick Valderrama, Rosario Leguía, Mariana Delgado-Ratto, Christopher Gotuzzo, Eduardo Zamudio, Carlos Lescano, Willy Cárcamo, César Hurtado, Verónica Lope-Pari, Priscila Padilla-Rojas, Carlos Jiménez-Vásquez, Víctor Escalante-Maldonado, Oscar Araujo-Castillo, Roger V. Cabezas, César Colijn, Caroline Tsukayama, Pablo |
| author_browse | Araujo-Castillo, Roger V. Ayzanoa, Brenda Ballón, Jorge Barletta, Claudia Cabezas, César Carrasco-Escobar, Gabriel Cava Miller, Renato Colijn, Caroline Cornejo Villanueva, Víctor Cuicapuza, Diego Cárcamo, César Delgado-Ratto, Christopher Dávila-Barclay, Alejandra Escalante-Maldonado, Oscar Fernández, Patrick González, Luis Gotuzzo, Eduardo Gómez de la Torre, Juan Carlos Huancachoque, Janet Hurtado, Verónica Jiménez-Vásquez, Víctor Langdon, Amy Leguía, Mariana Lescano, Willy Lope-Pari, Priscila M. Chenet, Stella Marcos-Carbajal, Pool Padilla-Rojas, Carlos Romero, Pedro E. Salvatierra, Guillermo Sobkowiak, Benjamin Tapia-Limonchi, Rafael Tsukayama, Pablo Valderrama, Rosario Villa, Diego Zamudio, Carlos |
| author_facet | Sobkowiak, Benjamin Langdon, Amy Romero, Pedro E. Carrasco-Escobar, Gabriel Villa, Diego Cava Miller, Renato Cornejo Villanueva, Víctor Dávila-Barclay, Alejandra Cuicapuza, Diego Salvatierra, Guillermo González, Luis Ayzanoa, Brenda Huancachoque, Janet Marcos-Carbajal, Pool Gómez de la Torre, Juan Carlos Barletta, Claudia M. Chenet, Stella Tapia-Limonchi, Rafael Ballón, Jorge Fernández, Patrick Valderrama, Rosario Leguía, Mariana Delgado-Ratto, Christopher Gotuzzo, Eduardo Zamudio, Carlos Lescano, Willy Cárcamo, César Hurtado, Verónica Lope-Pari, Priscila Padilla-Rojas, Carlos Jiménez-Vásquez, Víctor Escalante-Maldonado, Oscar Araujo-Castillo, Roger V. Cabezas, César Colijn, Caroline Tsukayama, Pablo |
| author_sort | Sobkowiak, Benjamin |
| collection | Repositorio institucional |
| description | 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 ioinformatics and
laboratory capacity, is essential for pandemic preparedness in resource-limited settings. |
| format | info:eu-repo/semantics/article |
| id | oai:repositorio.upeu.edu.pe:20.500.12840/9881 |
| institution | UPeU |
| language | English |
| ocde_area_str_mv | Ciencias médicas y de la salud |
| ocde_disciplina_str_mv | Ciencias médicas y de la salud (general) |
| ocde_str_mv | 3.00.00 |
| publishDate | 2026 |
| publishDateRange | 2026 |
| publishDateSort | 2026 |
| publisher | Nature Portfolio |
| publisherStr | Nature Portfolio |
| record_format | dspace |
| spelling | Genomic epidemiology of SARS-CoV-2 in Peru from 2020 to 2024 Sobkowiak, Benjamin Langdon, Amy Romero, Pedro E. Carrasco-Escobar, Gabriel Villa, Diego Cava Miller, Renato Cornejo Villanueva, Víctor Dávila-Barclay, Alejandra Cuicapuza, Diego Salvatierra, Guillermo González, Luis Ayzanoa, Brenda Huancachoque, Janet Marcos-Carbajal, Pool Gómez de la Torre, Juan Carlos Barletta, Claudia M. Chenet, Stella Tapia-Limonchi, Rafael Ballón, Jorge Fernández, Patrick Valderrama, Rosario Leguía, Mariana Delgado-Ratto, Christopher Gotuzzo, Eduardo Zamudio, Carlos Lescano, Willy Cárcamo, César Hurtado, Verónica Lope-Pari, Priscila Padilla-Rojas, Carlos Jiménez-Vásquez, Víctor Escalante-Maldonado, Oscar Araujo-Castillo, Roger V. Cabezas, César Colijn, Caroline Tsukayama, Pablo Medicina SARS-CoV-2 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 ioinformatics and laboratory capacity, is essential for pandemic preparedness in resource-limited settings. Programa Nacional de Investigación Científica y de Estudios Avanzados del Perú (PROCIENCIA \u2013 CONCYTEC) Contrato PE501086419-2024-PROCIENCIA 2026-01-09 2026-03-10T16:58:50Z 2026-03-10T16:58:50Z info:eu-repo/semantics/article info:eu-repo/semantics/publishedVersion https://hdl.handle.net/20.500.12840/9881 eng urn:issn:2730-664X https://doi.org/10.1038/s43856-025-01273-z info:eu-repo/semantics/openAccess http://creativecommons.org/licenses/by-nc-sa/4.0/ application/pdf Nature Portfolio PE oai:repositorio.upeu.edu.pe:20.500.12840/9881 2026-06-11T10:52:07Z |
| spellingShingle | Medicina SARS-CoV-2 Sobkowiak, Benjamin Langdon, Amy Romero, Pedro E. Carrasco-Escobar, Gabriel Villa, Diego Cava Miller, Renato Cornejo Villanueva, Víctor Dávila-Barclay, Alejandra Cuicapuza, Diego Salvatierra, Guillermo González, Luis Ayzanoa, Brenda Huancachoque, Janet Marcos-Carbajal, Pool Gómez de la Torre, Juan Carlos Barletta, Claudia M. Chenet, Stella Tapia-Limonchi, Rafael Ballón, Jorge Fernández, Patrick Valderrama, Rosario Leguía, Mariana Delgado-Ratto, Christopher Gotuzzo, Eduardo Zamudio, Carlos Lescano, Willy Cárcamo, César Hurtado, Verónica Lope-Pari, Priscila Padilla-Rojas, Carlos Jiménez-Vásquez, Víctor Escalante-Maldonado, Oscar Araujo-Castillo, Roger V. Cabezas, César Colijn, Caroline Tsukayama, Pablo Genomic epidemiology of SARS-CoV-2 in Peru from 2020 to 2024 |
| title | Genomic epidemiology of SARS-CoV-2 in Peru from 2020 to 2024 |
| title_full | Genomic epidemiology of SARS-CoV-2 in Peru from 2020 to 2024 |
| title_fullStr | Genomic epidemiology of SARS-CoV-2 in Peru from 2020 to 2024 |
| title_full_unstemmed | Genomic epidemiology of SARS-CoV-2 in Peru from 2020 to 2024 |
| title_short | Genomic epidemiology of SARS-CoV-2 in Peru from 2020 to 2024 |
| title_sort | genomic epidemiology of sars cov 2 in peru from 2020 to 2024 |
| topic | Medicina SARS-CoV-2 |
| topic_facet | Medicina SARS-CoV-2 |
| url | https://hdl.handle.net/20.500.12840/9881 |
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