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 six countries over 22 years (1999-2020). We divide the four 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 1500-2000km2. We estimate that each genetic cluster occupies an average area of 1.3million km2 (95%CI: 0.6-2.3 million), with 14 clusters in an area of 100,000km2 (95%CI: 6-24). In the few sites in Bangladesh and Cambodia where genomic surveillance has been concentrated, we estimate that most clusters have been identified, but only ∼15% of overall NiV diversity has been uncovered. Conclusion Our findings are consistent with entrenched co-circulation of distinct lineages, even within roosts, coupled with slow migration over larger spatial scales.

中文翻译：

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尼帕病毒在空间尺度上的遗传多样性

背景尼帕病毒（NiV）是一种对人类高度致命的病毒，在整个南亚和东南亚的翼蝠中传播。从蝙蝠中获取病毒基因组的困难意味着我们对 NiV 多样性了解甚少。方法 我们开发了系统发育方法，应用于 22 年来（1999-2020 年）来自 6 个国家的迄今为止最全面的基因组集合（N = 257，其中 175 个来自蝙蝠，73 个来自人类）。我们将 4 个主要 NiV 亚系分为 15 个遗传簇。使用近似贝叶斯计算拟合病毒多样性的空间特征，我们估计每个区域的遗传簇的存在和平均大小。结果我们发现，在任何蝙蝠栖息地内，平均有2.4个共循环遗传簇，在1500-2000平方公里的区域增加到5.5个簇。我们估计每个遗传簇的平均面积为130万平方公里（95%CI：0.6-230万），其中14个簇的面积为10万平方公里（95%CI：6-24）。在孟加拉国和柬埔寨集中进行基因组监测的少数地点，我们估计大多数簇已被识别，但仅发现了总体 NiV 多样性的约 15%。结论 我们的研究结果与不同谱系根深蒂固的共循环一致，即使在栖息地内，加上在更大空间尺度上的缓慢迁移。