The genetic diversity of nipah virus across spatial scales

Cortes-Azuero Oscar, Lefrancq Noémie, Nikolay Birgit, McKee Clifton, Cappelle Julien, Hul Vibol, Putita Ou Tey, Hoem Thavry, Lemey Philippe, Ziaur Rahman Mohammed, Islam Ausraful, Gurley Emily S., Duong Veasna, Salje Henrik. 2024. The genetic diversity of nipah virus across spatial scales. Journal of Infectious Diseases:jiae221, 11 p.

https://doi.org/10.1093/infdis/jiae221

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Liste HCERES des revues (en SHS) : oui

Thème(s) HCERES des revues (en SHS) : Psychologie-éthologie-ergonomie

Résumé : Background: Nipah virus (NiV), a highly lethal virus in humans, circulates in Pteropus bats throughout South and Southeast Asia. Difficulty in obtaining viral genomes from bats means we have a poor understanding of NiV diversity. Methods: We develop phylogenetic approaches applied to the most comprehensive collection of genomes to date (N = 257, 175 from bats, 73 from humans) from 6 countries over 22 years (1999–2020). We divide the 4 major NiV sublineages into 15 genetic clusters. Using Approximate Bayesian Computation fit to a spatial signature of viral diversity, we estimate the presence and the average size of genetic clusters per area. Results: We find that, within any bat roost, there are an average of 2.4 co-circulating genetic clusters, rising to 5.5 clusters at areas of 1500–2000 km2. We estimate that each genetic cluster occupies an average area of 1.3 million km2 (95% confidence interval [CI], .6–2.3 million km2), with 14 clusters in an area of 100 000 km2 (95% CI, 6–24 km2). In the few sites in Bangladesh and Cambodia where genomic surveillance has been concentrated, we estimate that most clusters have been identified, but only approximately 15% of overall NiV diversity has been uncovered. Conclusions: Our findings are consistent with entrenched co-circulation of distinct lineages, even within roosts, coupled with slow migration over larger spatial scales.

Mots-clés Agrovoc : Nipah henipavirus, transmission des maladies, Pteropus, variation génétique, surveillance épidémiologique, phylogénie, Chiroptera, modélisation, maladie infectieuse

Mots-clés géographiques Agrovoc : Cambodge, Bangladesh, Thaïlande, Inde, Indonésie, Malaisie, Asie du Sud, Asie du Sud-Est

Mots-clés libres : Nipah virus, Phylogenetics, Disease modeling, Pteropus, Emerging pathogens

Classification Agris : L73 - Maladies des animaux
U10 - Informatique, mathématiques et statistiques

Champ stratégique Cirad : CTS 4 (2019-) - Santé des plantes, des animaux et des écosystèmes

Agences de financement européennes : European Research Council, European Commission

Agences de financement hors UE : National Institutes of Health

Programme de financement européen : H2020

Projets sur financement : (EU) Coupling dynamic population immunity profiles and host behaviours to arboviral spread

Auteurs et affiliations