Current sampling and sequencing biases of Lassa mammarenavirus limit inference from phylogeography and molecular epidemiology in Lassa fever endemic regions

Bibliographic Data

ID19593531
AuthorsLiã Bárbara Arruda (0000-0003-3539-8154, University College London, corresponding author), Hayley Beth Free (University of London, corresponding author), David Simons (0000-0001-9655-1656, University of London, corresponding author), Rashid Ansumana (0000-0002-1973-7200, Njala University, corresponding author), Linzy Elton (0000-0003-4270-1553, University College London, corresponding author), Najmul Haider (0000-0002-5980-3460, University of London, corresponding author), Isobella Honeyborne (0000-0003-0596-758X, University College London, corresponding author), Danny Asogun (0000-0001-6811-9268, Irrua Specialist Teaching Hospital, corresponding author), Timothy D McHugh (0000-0003-4658-8594, University College London, corresponding author), Francine Ntoumi (0000-0003-4748-050X, Fondation Congolaise Pour La Recherche Médicale, corresponding author), Alimuddin Zumla (0000-0002-5111-5735, UCL Biomedical Research Centre, corresponding author), Richard Kock (0000-0002-6561-3209, University of London, corresponding author)
EditorsVijaykrishna Dhanasekaran
Year2023
Volume3
Issue11
Pagese0002159
Publication date2023-11-08
Open AccessYes
TypeARTICLE
VenuePLOS Global Public Health (JOURNAL)
Journal identifiersISSN: 2767-3375 • E-ISSN: 2767-3375
PublisherPublic Library of Science (PLoS) (PUBLISHER)
DOI10.1371/journal.pgph.0002159
PMID37939051
OpenAlexW4388501181
LanguageEN
Citations received1
References cited20

Lassa fever (LF) is a potentially lethal viral haemorrhagic infection of humans caused by Lassa mammarenavirus (LASV). It is an important endemic zoonotic disease in West Africa with growing evidence for increasing frequency and sizes of outbreaks. Phylogeographic and molecular epidemiology methods have projected expansion of the Lassa fever endemic zone in the context of future global change. The Natal multimammate mouse ( Mastomys natalensis ) is the predominant LASV reservoir, with few studies investigating the role of other animal species. To explore host sequencing biases, all LASV nucleotide sequences and associated metadata available on GenBank (n = 2,298) were retrieved. Most data originated from Nigeria (54%), Guinea (20%) and Sierra Leone (14%). Data from non-human hosts (n = 703) were limited and only 69 sequences encompassed complete genes. We found a strong positive correlation between the number of confirmed human cases and sequences at the country level ( r = 0.93 (95% Confidence Interval = 0.71–0.98), p r = -0.019 (95% C.I. -0.71–0.69), p = 0.96). Spatial modelling of sequencing effort highlighted current biases in locations of available sequences, with increased sequencing effort observed in Southern Guinea and Southern Nigeria. Phylogenetic analyses showed geographic clustering of LASV lineages, suggestive of isolated events of human-to-rodent transmission and the emergence of currently circulating strains of LASV from the year 1498 in Nigeria. Overall, the current study highlights significant geographic limitations in LASV surveillance, particularly, in non-human hosts. Further investigation of the non-human reservoir of LASV, alongside expanded surveillance, are required for precise characterisation of the emergence and dispersal of LASV. Accurate surveillance of LASV circulation in non-human hosts is vital to guide early detection and initiation of public health interventions for future Lassa fever outbreaks

Biology · Evolutionary biology · Gene · Genotype · Lassa fever · Lassa virus · Molecular epidemiology · Outbreak · Phylogenetic tree · Phylogeography · Sierra leone · Socioeconomics · Virus · Hepatitis B Virus Studies · Viral Infections and Outbreaks Research · Viral Infections and Vectors · Genetics · Virology

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