Lin Shang-Kuan, De Maio Nicola, Pedergnana Vincent, Wu Chieh-Hsi, Thézé Julien, Wilson Daniel J, Barnes Eleanor, Ansari M Azim
Nuffield Department of Population Health, Big Data Institute, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Old Road Campus, Oxford OX3 7LF, UK.
European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
Virus Evol. 2021 Jul 9;7(2):veab065. doi: 10.1093/ve/veab065. eCollection 2021.
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.
研究表明，丙型肝炎病毒3a型（HCV - 3a）在全球传播之前可能已在南亚传播。然而，这种传播的时间和途径仍不清楚。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。我们利用宿主基因组数据推断患者的血统，并利用这些信息研究HCV - 3a的流行病史。我们观察到，无论采样国家如何，来自南亚血统宿主的病毒在树的根部附近聚集在一起，并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感染，并利用推断出的宿主血统来区分感染获得的地点和样本采集的地点。接下来，我们推断三次独立的传播事件导致该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、北美和大洋洲之间又发生了许多独立的传播。利用宿主和病毒基因组信息在研究病毒流行病史方面可能具有很高的信息量，特别是在需要考虑迁移历史的慢性感染背景下。
