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Searches of PubMed, Scopus, and Web of Science identified 32 studies from 18 countries that integrated genomic and epidemiological data for local outbreak investigations. Most studies were conducted in healthcare settings or in high-income countries. A limited number of studies were conducted in low- and middle-income countries, except for China and Vietnam. Illumina or Oxford Nanopore platforms and tiled-amplicon protocols were the most common sequencing methods. Phylogenetic trees were the most common genomic epidemiology analytical approach. Genomic data enabled confirmation of suspected transmission links, detection of multiple introductions, and identification of asymptomatic or presymptomatic transmission. Important enablers of early implementation included open-access genomics databases, standardized protocols (e.g. ARTIC), open-source tools (e.g. Nextstrain), and cross-sector partnerships and funding. Study quality and adherence to common observational study reporting guidelines varied widely. Familiarity with the STROME-ID guidelines for molecular epidemiology studies would have improved overall quality. These findings highlight the utility of genomic epidemiology in outbreak response and support its continued integration into public health surveillance systems.<\/jats:p>","DOI":"10.1017\/s0950268826101381","type":"journal-article","created":{"date-parts":[[2026,4,10]],"date-time":"2026-04-10T08:59:42Z","timestamp":1775811582000},"update-policy":"https:\/\/doi.org\/10.1017\/policypage","source":"Crossref","is-referenced-by-count":0,"title":["Local genomic epidemiology investigations of SARS-CoV-2 during the early pandemic response: A global systematic review"],"prefix":"10.1017","volume":"154","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-7295-8475","authenticated-orcid":false,"given":"Lindsay C.","family":"Morton","sequence":"first","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00y4zzh67","id-type":"ROR","asserted-by":"publisher"}],"name":"The George Washington University Milken Institute of Public Health"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brett M.","family":"Forshey","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05xf94514","id-type":"ROR","asserted-by":"publisher"}],"name":"US Public Health Service Commissioned Corps"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Katharina E.","family":"Klinkhammer","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00y4zzh67","id-type":"ROR","asserted-by":"publisher"}],"name":"The George Washington University Milken Institute School of Public Health"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Andrew","family":"Romaner","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05xf94514","id-type":"ROR","asserted-by":"publisher"}],"name":"US Public Health Service Commissioned Corps"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zoumanna","family":"Traore","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/05vzafd60","id-type":"ROR","asserted-by":"publisher"}],"name":"Georgetown University"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laurie J.","family":"Hartman","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00p23dy23","id-type":"ROR","asserted-by":"publisher"}],"name":"Cherokee Nation Businesses"},{"id":[{"id":"https:\/\/ror.org\/03df8gj37","id-type":"ROR","asserted-by":"publisher"}],"name":"Global Emerging Infections Surveillance"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Claire J.","family":"Standley","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/00p23dy23","id-type":"ROR","asserted-by":"publisher"}],"name":"Cherokee Nation Businesses"},{"id":[{"id":"https:\/\/ror.org\/01t08q012","id-type":"ROR","asserted-by":"publisher"}],"name":"Coalition for Epidemic Preparedness Innovations"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amira A.","family":"Roess","sequence":"additional","affiliation":[{"id":[{"id":"https:\/\/ror.org\/02jqj7156","id-type":"ROR","asserted-by":"publisher"}],"name":"George Mason University"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"56","published-online":{"date-parts":[[2026,4,10]]},"reference":[{"key":"S0950268826101381_r32","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciaa1935"},{"key":"S0950268826101381_r36","doi-asserted-by":"publisher","DOI":"10.3389\/fmicb.2020.01316"},{"key":"S0950268826101381_r19","doi-asserted-by":"publisher","DOI":"10.15585\/mmwr.mm6947e1"},{"key":"S0950268826101381_r35","doi-asserted-by":"publisher","DOI":"10.1093\/cid\/ciaa1180"},{"key":"S0950268826101381_r11","unstructured":"[11] National Heart, Lung, and Blood Institute (2021) Study Quality Assessment Tools. 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