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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Springer Nature
2026
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| author | Sobkowiak, Benjamin Langdon, Amy E. Romero, Pedro E. Carrasco-Escobar, Gabriel Villa, Diego Cava Miller, Renato Cornejo, Victor G. Dávila-Barclay, Alejandra Cuicapuza, Diego Salvatierra, Guillermo R. González, Luis Ayzanoa, Brenda Huancachoque, Janet Marcos Carbajal, Pool Gómez De La Torre, Juan Carlos Barletta, Claudia Chenet, Stella M. Tapia-Limonchi, Rafael Ballon, Jorge Andres Fernández, Patrick Valderrama, Rosario Leguia, Mariana Delgado-Ratto, Christopher Gotuzzo, Eduardo H. Zamudio, Carlos Caicedo Lescano, Willy Cárcamo, Cesar P. Hurtado, Verónica Lope-Pari, Priscila Padilla-Rojas, Carlos P. Jiménez-Vásquez, Víctor Alberto Escalante-Maldonado, Oscar Roberto Araujo-Castillo, Roger V. Cabezas-Sánchez, César Augusto Colijn, Caroline Tsukayama, Pablo |
| author_browse | Araujo-Castillo, Roger V. Ayzanoa, Brenda Ballon, Jorge Andres Barletta, Claudia Cabezas-Sánchez, César Augusto Carrasco-Escobar, Gabriel Cava Miller, Renato Chenet, Stella M. Colijn, Caroline Cornejo, Victor G. Cuicapuza, Diego Cárcamo, Cesar P. Delgado-Ratto, Christopher Dávila-Barclay, Alejandra Escalante-Maldonado, Oscar Roberto Fernández, Patrick González, Luis Gotuzzo, Eduardo H. Gómez De La Torre, Juan Carlos Huancachoque, Janet Hurtado, Verónica Jiménez-Vásquez, Víctor Alberto Langdon, Amy E. Leguia, Mariana Lescano, Willy Lope-Pari, Priscila Marcos Carbajal, Pool Padilla-Rojas, Carlos P. Romero, Pedro E. Salvatierra, Guillermo R. Sobkowiak, Benjamin Tapia-Limonchi, Rafael Tsukayama, Pablo Valderrama, Rosario Villa, Diego Zamudio, Carlos Caicedo |
| author_facet | Sobkowiak, Benjamin Langdon, Amy E. Romero, Pedro E. Carrasco-Escobar, Gabriel Villa, Diego Cava Miller, Renato Cornejo, Victor G. Dávila-Barclay, Alejandra Cuicapuza, Diego Salvatierra, Guillermo R. González, Luis Ayzanoa, Brenda Huancachoque, Janet Marcos Carbajal, Pool Gómez De La Torre, Juan Carlos Barletta, Claudia Chenet, Stella M. Tapia-Limonchi, Rafael Ballon, Jorge Andres Fernández, Patrick Valderrama, Rosario Leguia, Mariana Delgado-Ratto, Christopher Gotuzzo, Eduardo H. Zamudio, Carlos Caicedo Lescano, Willy Cárcamo, Cesar P. Hurtado, Verónica Lope-Pari, Priscila Padilla-Rojas, Carlos P. Jiménez-Vásquez, Víctor Alberto Escalante-Maldonado, Oscar Roberto Araujo-Castillo, Roger V. Cabezas-Sánchez, César Augusto Colijn, Caroline Tsukayama, Pablo |
| author_sort | Sobkowiak, Benjamin |
| collection | Producción científica |
| 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 bioinformatics and laboratory capacity, is essential for pandemic preparedness in resource-limited settings. |
| format | Article |
| id | oai:cris.upeu.edu.pe:20.500.15037/2369 |
| institution | UPeU |
| language | English |
| publishDate | 2026 |
| publishDateRange | 2026 |
| publishDateSort | 2026 |
| publisher | Springer Nature |
| publisherStr | Springer Nature |
| record_format | dspace |
| spelling | oai:cris.upeu.edu.pe:20.500.15037/23692026-11-02T12:57:04ZGenomic epidemiology of SARS-CoV-2 in Peru from 2020 to 2024Sobkowiak, BenjaminLangdon, Amy E.Romero, Pedro E.Carrasco-Escobar, GabrielVilla, DiegoCava Miller, RenatoCornejo, Victor G.Dávila-Barclay, AlejandraCuicapuza, DiegoSalvatierra, Guillermo R.González, LuisAyzanoa, BrendaHuancachoque, JanetMarcos Carbajal, PoolGómez De La Torre, Juan CarlosBarletta, ClaudiaChenet, Stella M.Tapia-Limonchi, RafaelBallon, Jorge AndresFernández, PatrickValderrama, RosarioLeguia, MarianaDelgado-Ratto, ChristopherGotuzzo, Eduardo H.Zamudio, Carlos CaicedoLescano, WillyCárcamo, Cesar P.Hurtado, VerónicaLope-Pari, PriscilaPadilla-Rojas, Carlos P.Jiménez-Vásquez, Víctor AlbertoEscalante-Maldonado, Oscar RobertoAraujo-Castillo, Roger V.Cabezas-Sánchez, César AugustoColijn, CarolineTsukayama, PabloSARS-CoV-2Computational biology and bioinformaticsEpidemiologyBackground: 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.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.Article10.1038/s43856-025-01273-z2-s2.0-105027066356https://hdl.handle.net/20.500.15037/2369enCommunications MedicineCommunications Medicine2730-664XPE501086419-2024PE501086419-2024Springer Nature2026-01-092026-06-27T00:58:52Z2026-06-27T00:58:52Z |
| spellingShingle | SARS-CoV-2 Computational biology and bioinformatics Epidemiology Sobkowiak, Benjamin Langdon, Amy E. Romero, Pedro E. Carrasco-Escobar, Gabriel Villa, Diego Cava Miller, Renato Cornejo, Victor G. Dávila-Barclay, Alejandra Cuicapuza, Diego Salvatierra, Guillermo R. González, Luis Ayzanoa, Brenda Huancachoque, Janet Marcos Carbajal, Pool Gómez De La Torre, Juan Carlos Barletta, Claudia Chenet, Stella M. Tapia-Limonchi, Rafael Ballon, Jorge Andres Fernández, Patrick Valderrama, Rosario Leguia, Mariana Delgado-Ratto, Christopher Gotuzzo, Eduardo H. Zamudio, Carlos Caicedo Lescano, Willy Cárcamo, Cesar P. Hurtado, Verónica Lope-Pari, Priscila Padilla-Rojas, Carlos P. Jiménez-Vásquez, Víctor Alberto Escalante-Maldonado, Oscar Roberto Araujo-Castillo, Roger V. Cabezas-Sánchez, César Augusto 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 | SARS-CoV-2 Computational biology and bioinformatics Epidemiology |
| topic_facet | SARS-CoV-2 Computational biology and bioinformatics Epidemiology |
| url | https://hdl.handle.net/20.500.15037/2369 |
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