Public Genomic Visibility of Lassa Virus in West Africa: Mapping Sequence Availability, Ecological Risk, and Surveillance Gaps

Abstract

Lassa fever is a major zoonotic infection in West Africa, but its true epidemiology is difficult to define because diagnostic access, reporting systems, and surveillance capacity vary across countries. Although substantial work has examined LASV ecology, epidemiology, diagnostics, and outbreak response, less is known about how regional burden/risk evidence aligns with publicly visible genomic data. This study distinguishes LASV transmission risk from public genomic visibility, viewing sequence availability as the product of ecology, laboratory systems, bioinformatics capacity, governance, research partnerships, and sustained financing. Public LASV sequence metadata were retrieved from NCBI Nucleotide and summarised across 16 West African countries. Countries were classified by sequence visibility, burden/risk evidence, ecological context, and public genomic surveillance gap category. CHIRPS rainfall data were included as contextual ecological descriptors. A systematic review of 31 studies identified structural, technical, and policy barriers to LASV genomic surveillance. Public LASV sequences were identified for 9 of 16 countries, totalling 1818 validated records. Sequence visibility was highly concentrated: Nigeria accounted for 71.3% of all records, while Nigeria, Sierra Leone, Guinea, and Liberia accounted for 94.3%. Seven countries had no publicly identifiable sequences despite documented, probable, or ecologically plausible risk. Public LASV genomic visibility does not reflect the broader regional risk landscape. Strengthening surveillance will require integrated genomic systems linked to diagnostics, One Health surveillance, local bioinformatics capacity, equitable data sharing, and sustained long-term investment.