Phylogeography and reassortment patterns of human influenza A viruses in sub-Saharan Africa

The role of sub-Saharan Africa in the global spread of influenza viruses remains unclear due to insufficient spatiotemporal sequence data. Here, we analyzed 222 codon-complete sequences of influenza A viruses (IAVs) sampled between 2011 and 2013 from five countries across sub-Saharan Africa (Kenya,...

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Vydáno v:Scientific reports Ročník 14; číslo 1; s. 18987 - 11
Hlavní autoři: Owuor, D. Collins, de Laurent, Zaydah R., Oketch, John W., Murunga, Nickson, Otieno, James R., Nabakooza, Grace, Chaves, Sandra S., Nokes, D. James, Agoti, Charles N.
Médium: Journal Article
Jazyk:angličtina
Vydáno: London Nature Publishing Group UK 16.08.2024
Nature Publishing Group
Nature Portfolio
Témata:
631/181
631/181/735
A(H1N1)pdm09
A(H3N2)
Africa South of the Sahara - epidemiology
Genome, Viral
Genomes
Humanities and Social Sciences
Humans
Influenza
Influenza A
Influenza A virus - genetics
Influenza, Human - epidemiology
Influenza, Human - virology
Metapopulations
multidisciplinary
Orthomyxoviridae
PERCH study
Phylogeny
Phylogeography
Reassortant Viruses - genetics
Reassortment
Science
Science (multidisciplinary)
Sub-Saharan Africa
Vaccination
Viruses
Africa South of the Sahara
Sub-Saharan Africa
Africa
A(H1N1)pdm09
Reassortment
A(H3N2)
Sub-Saharan Africa
PERCH study
ISSN:2045-2322, 2045-2322
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Shrnutí:The role of sub-Saharan Africa in the global spread of influenza viruses remains unclear due to insufficient spatiotemporal sequence data. Here, we analyzed 222 codon-complete sequences of influenza A viruses (IAVs) sampled between 2011 and 2013 from five countries across sub-Saharan Africa (Kenya, Zambia, Mali, Gambia, and South Africa); these genomes were compared with 1209 contemporaneous global genomes using phylogeographical approaches. The spread of influenza in sub-Saharan Africa was characterized by (i) multiple introductions of IAVs into the region over consecutive influenza seasons, with viral importations originating from multiple global geographical regions, some of which persisted in circulation as intra-subtype reassortants for multiple seasons, (ii) virus transfer between sub-Saharan African countries, and (iii) virus export from sub-Saharan Africa to other geographical regions. Despite sparse data from influenza surveillance in sub-Saharan Africa, our findings support the notion that influenza viruses persist as temporally structured migrating metapopulations in which new virus strains can emerge in any geographical region, including in sub-Saharan Africa; these lineages may have been capable of dissemination to other continents through a globally migrating virus population. Further knowledge of the viral lineages that circulate within understudied sub-Saharan Africa regions is required to inform vaccination strategies in those regions.
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ISSN:2045-2322
2045-2322
DOI:10.1038/s41598-024-70023-3