The genetic diversity of nipah virus across spatial scales

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.

Bibliographic Details

Main Authors:	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
Format:	article biblioteca
Language:	eng
Published:	Oxford University Press
Subjects:	L73 - Maladies des animaux, U10 - Informatique, mathématiques et statistiques, Nipah henipavirus, transmission des maladies, Pteropus, variation génétique, surveillance épidémiologique, phylogénie, Chiroptera, modélisation, maladie infectieuse, http://aims.fao.org/aos/agrovoc/c_a5e259a2, http://aims.fao.org/aos/agrovoc/c_2329, http://aims.fao.org/aos/agrovoc/c_331406, http://aims.fao.org/aos/agrovoc/c_15975, http://aims.fao.org/aos/agrovoc/c_16411, http://aims.fao.org/aos/agrovoc/c_13325, http://aims.fao.org/aos/agrovoc/c_1560, http://aims.fao.org/aos/agrovoc/c_230ab86c, http://aims.fao.org/aos/agrovoc/c_34024, http://aims.fao.org/aos/agrovoc/c_4073, http://aims.fao.org/aos/agrovoc/c_810, http://aims.fao.org/aos/agrovoc/c_7701, http://aims.fao.org/aos/agrovoc/c_3825, http://aims.fao.org/aos/agrovoc/c_3840, http://aims.fao.org/aos/agrovoc/c_4533, http://aims.fao.org/aos/agrovoc/c_29172, http://aims.fao.org/aos/agrovoc/c_7260,
Online Access:	http://agritrop.cirad.fr/609601/ http://agritrop.cirad.fr/609601/1/Cortes-Azuero%20et%20al%202024%20-%20Nipah%20phylogeny.pdf
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