Local genomic epidemiology investigations of SARS-CoV-2 during the early pandemic response: A global systematic review

Genomic epidemiology was essential for characterizing SARS-CoV-2 transmission during the early COVID-19 pandemic. This systematic review examined how whole-genome sequencing was used in local outbreak investigations published between March 2020 and March 2021. 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.