The genetic diversity of Nipah virus across spatial scales
Nipah virus (NiV), a highly lethal virus in humans, circulates silently in Pteropus bats throughout South and Southeast Asia. Difficulty in obtaining genomes from bats means we have a poor understanding of NiV diversity, including how many lineages circulate within a roost and the spread of NiV over increasing spatial scales. Here we develop phylogenetic approaches applied to the most comprehensive collection of genomes to date (N=257, 175 from bats, 73 from humans) from six countries over 22 years (1999-2020). In Bangladesh, where most human infections occur, we find evidence of increased spillover risk from one of the two co-circulating sublineages. We divide the four major NiV sublineages into 15 genetic clusters (emerged 20-44 years ago). Within any bat roost, there are an average of 2.4 co-circulating genetic clusters, rising to 5.5 clusters at areas of 1,500-2,000 km2. Using Approximate Bayesian Computation fit to a spatial signature of viral diversity, we estimate that each genetic cluster occupies an average area of 1.3 million km2 (95%CI: 0.6-2.3 million), with 14 clusters in an area of 100,000 km2 (95%CI: 6-24). In the few sites in Bangladesh and Cambodia where genomic surveillance has been concentrated, we estimate that most of the genetic clusters have been identified, but only ~15% of overall NiV diversity has been uncovered. Our findings are consistent with entrenched co-circulation of distinct lineages, even within individual roosts, coupled with slow migration over larger spatial scales.
| Medienart: |
E-Artikel |
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| Erscheinungsjahr: |
2023 |
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| Erschienen: |
2023 |
| Enthalten in: |
Zur Gesamtaufnahme - year:2023 |
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| Enthalten in: |
medRxiv : the preprint server for health sciences - (2023) vom: 04. Okt. |
| Sprache: |
Englisch |
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| Beteiligte Personen: |
Azuero, Oscar Cortés [VerfasserIn] |
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| Anmerkungen: |
Date Revised 20.10.2023 published: Electronic Citation Status PubMed-not-MEDLINE |
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| doi: |
10.1101/2023.07.14.23292668 |
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| funding: |
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| Förderinstitution / Projekttitel: |
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| PPN (Katalog-ID): |
NLM36002887X |
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| 245 | 1 | 4 | |a The genetic diversity of Nipah virus across spatial scales |
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| 520 | |a Nipah virus (NiV), a highly lethal virus in humans, circulates silently in Pteropus bats throughout South and Southeast Asia. Difficulty in obtaining genomes from bats means we have a poor understanding of NiV diversity, including how many lineages circulate within a roost and the spread of NiV over increasing spatial scales. Here we develop phylogenetic approaches applied to the most comprehensive collection of genomes to date (N=257, 175 from bats, 73 from humans) from six countries over 22 years (1999-2020). In Bangladesh, where most human infections occur, we find evidence of increased spillover risk from one of the two co-circulating sublineages. We divide the four major NiV sublineages into 15 genetic clusters (emerged 20-44 years ago). Within any bat roost, there are an average of 2.4 co-circulating genetic clusters, rising to 5.5 clusters at areas of 1,500-2,000 km2. Using Approximate Bayesian Computation fit to a spatial signature of viral diversity, we estimate that each genetic cluster occupies an average area of 1.3 million km2 (95%CI: 0.6-2.3 million), with 14 clusters in an area of 100,000 km2 (95%CI: 6-24). In the few sites in Bangladesh and Cambodia where genomic surveillance has been concentrated, we estimate that most of the genetic clusters have been identified, but only ~15% of overall NiV diversity has been uncovered. Our findings are consistent with entrenched co-circulation of distinct lineages, even within individual roosts, coupled with slow migration over larger spatial scales | ||
| 650 | 4 | |a Preprint | |
| 700 | 1 | |a Lefrancq, Noémie |e verfasserin |4 aut | |
| 700 | 1 | |a Nikolay, Birgit |e verfasserin |4 aut | |
| 700 | 1 | |a McKee, Clifton |e verfasserin |4 aut | |
| 700 | 1 | |a Cappelle, Julien |e verfasserin |4 aut | |
| 700 | 1 | |a Hul, Vibol |e verfasserin |4 aut | |
| 700 | 1 | |a Ou, Tey Putita |e verfasserin |4 aut | |
| 700 | 1 | |a Hoem, Thavry |e verfasserin |4 aut | |
| 700 | 1 | |a Lemey, Philippe |e verfasserin |4 aut | |
| 700 | 1 | |a Rahman, Mohammed Ziaur |e verfasserin |4 aut | |
| 700 | 1 | |a Islam, Ausraful |e verfasserin |4 aut | |
| 700 | 1 | |a Gurley, Emily S |e verfasserin |4 aut | |
| 700 | 1 | |a Duong, Veasna |e verfasserin |4 aut | |
| 700 | 1 | |a Salje, Henrik |e verfasserin |4 aut | |
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