Studies have shown that hepatitis C virus subtype 3a (HCV-3a) is likely to have been circulating in South Asia before its global spread. However, the time and route of this dissemination remain unclear. For the first time, we generated host and virus genome-wide data for more than 500 patients infected with HCV-3a from the UK, North America, Australia, and New Zealand. We used the host genomic data to infer the ancestry of the patients and used this information to investigate the epidemic history of HCV-3a. We observed that viruses from hosts of South Asian ancestry clustered together near the root of the tree, irrespective of the sampling country, and that they were more diverse than viruses from other host ancestries. We hypothesized that South Asian hosts are more likely to have been infected in South Asia and used the inferred host ancestries to distinguish between the location where the infection was acquired and where the sample was taken. Next, we inferred that three independent transmission events resulted in the spread of the virus from South Asia to the UK, North America, and Oceania. This initial spread happened during or soon after the end of World War II. This was subsequently followed by many independent transmissions between the UK, North America, and Oceania. Using both host and virus genomic information can be highly informative in studying the virus epidemic history, especially in the context of chronic infections where migration histories need to be accounted for.

中文翻译：

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利用宿主遗传学推断 HCV 亚型 3a 的全球传播和进化史

研究表明，丙型肝炎病毒 3a 亚型 (HCV-3a) 很可能在全球传播之前就已经在南亚传播。但是，这种传播的时间和途径尚不清楚。我们首次为来自英国、北美、澳大利亚和新西兰的 500 多名感染 HCV-3a 的患者生成了宿主和病毒全基因组数据。我们使用宿主基因组数据推断患者的血统，并使用此信息调查 HCV-3a 的流行史。我们观察到，来自南亚血统宿主的病毒聚集在树的根部附近，与采样国家无关，而且它们比来自其他宿主血统的病毒更加多样化。我们假设南亚宿主更有可能在南亚被感染，并使用推断的宿主血统来区分获得感染的位置和采集样本的位置。接下来，我们推断三个独立的传播事件导致病毒从南亚传播到英国、北美和大洋洲。这种最初的传播发生在第二次世界大战期间或结束后不久。随后在英国、北美和大洋洲之间进行了许多独立传输。使用宿主和病毒基因组信息可以为研究病毒流行历史提供大量信息，特别是在需要考虑迁移历史的慢性感染的情况下。