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The high biodiversity and the differing transmission pathways require the use of highly sensitive methods to track the emergence and spread of these diseases. High-throughput sequencing technologies have become a critical resource for the field of infectious disease monitoring, specifically for tracking pathogen evolution, antimicrobial resistance, and transmission. This review provides an overview of the implementation of genomics-informed infectious disease surveillance conducted by the U.S. Naval Medical Research Unit SOUTH, focusing on operational, infrastructural, and logistical challenges in resource-limited settings and outlining strategies for building sustainable regional capacity. Selected case studies focused on prominent biothreats including dengue, Oropouche, malaria, and antimicrobial resistance demonstrate the significance and applicability of targeted and agnostic sequencing approaches to elucidate transmission pathways, pathogen discovery, and guide public health responses and field-deployable applications.<\/jats:p>","DOI":"10.3390\/tropicalmed11090245","type":"journal-article","created":{"date-parts":[[2026,8,28]],"date-time":"2026-08-28T12:27:46Z","timestamp":1787920066000},"page":"245","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Application of Genomics to Prevent and Combat Emerging Infectious Disease Threats in Latin America: Perspectives from an Overseas U.S. Navy Research Command"],"prefix":"10.3390","volume":"11","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-2159-5667","authenticated-orcid":false,"given":"Hugo 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Peru"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuliya S.","family":"Johnson","sequence":"additional","affiliation":[{"name":"U.S. Naval Medical Research Unit SOUTH, Lima 07006, Peru"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8281-3229","authenticated-orcid":false,"given":"Alden S.","family":"Estep","sequence":"additional","affiliation":[{"name":"Center for Medical, Agricultural and Veterinary Entomology, United States Department of Agriculture\u2019s Agricultural Research Service, Gainesville, FL 32608, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5455-2423","authenticated-orcid":false,"given":"Steev","family":"Loyola","sequence":"additional","affiliation":[{"name":"U.S. Naval Medical Research Unit SOUTH, Lima 07006, Peru"},{"name":"Culmen Inc., Alexandria, VA 22314, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0091-1272","authenticated-orcid":false,"given":"Carmen","family":"Flores-Mendoza","sequence":"additional","affiliation":[{"name":"U.S. Naval Medical Research Unit SOUTH, Lima 07006, Peru"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0009-0007-0594-8852","authenticated-orcid":false,"given":"Gissella M.","family":"Vasquez","sequence":"additional","affiliation":[{"name":"U.S. Naval Medical Research Unit SOUTH, Lima 07006, Peru"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jose A.","family":"Garcia-Rivera","sequence":"additional","affiliation":[{"name":"U.S. Naval Medical Research Unit SOUTH, Lima 07006, Peru"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Henju","family":"Marjuki","sequence":"additional","affiliation":[{"name":"U.S. Naval Medical Research Unit SOUTH, Lima 07006, 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