用于近实时 HIV 和 HCV 分子流行病学的下一代测序方法。

IF 9 2区 医学 Q1 VIROLOGY Reviews in Medical Virology Pub Date : 2024-11-01 DOI:10.1002/rmv.70001
Bethany A Horsburgh, Gregory J Walker, Anthony Kelleher, Andrew R Lloyd, Rowena A Bull, Francesca Di Giallonardo
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引用次数: 0

摘要

世界卫生组织制定了到 2030 年将丙型肝炎(HCV)新感染传播率降低 90%,并终结人类免疫缺陷病毒-1(HIV)对公共卫生的威胁的目标。要实现这一目标,需要高效及时的病毒监测和有效的公共卫生干预措施。传统的流行病学方法在很大程度上依赖于对有症状病例的识别;HIV 和 HCV 急性感染通常无症状,这可能导致对此类新感染的识别延迟。相反,对于这些病毒,分子流行病学可提高对病毒传播群的检测和应对能力。利用历史数据集进行的分子流行病学分析突出了可能受益于及时干预的关键人群。要实现 2030 年的目标,还需要对当代样本进行类似的分析,但这需要近乎实时地生成一个完整的病毒基因组序列数据集。要生成这样的数据,应利用下一代测序(NGS)方法。在此,我们讨论了 NGS 为 HIV 和 HCV 的公共卫生监测带来的机遇,并讨论了可生成用于此类分析的序列的三种方法。这些方法包括全长基因组扩增法(用于研究领域的 HCV 分析)、平铺 PCR 法(SARS-CoV-2 大流行时许多诊断实验室选择的方法)和诱饵捕获杂交法(已用于当地 HIV 疫情爆发)。这些技术可用于近实时艾滋病病毒和丙型肝炎病毒监测,为公共卫生战略提供信息,这将是实现 2030 年目标的关键。
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Next-Generation Sequencing Methods for Near-Real-Time Molecular Epidemiology of HIV and HCV.

The World Health Organisation has set targets of reducing the transmission of new hepatitis C (HCV) infections by 90%, and ending human immunodeficiency virus-1 (HIV) as a public health threat, by 2030. To achieve this, efficient and timely viral surveillance, and effective public health interventions, are required. Traditional epidemiological methods are largely dependent on the recognition of incident cases with symptomatic illness; acute HIV and HCV infections are commonly asymptomatic, which may lead to delays in the recognition of such new infections. Instead, for these viruses, molecular epidemiology may improve the detection of, and response to, clusters of viral transmission. Molecular epidemiology using historical datasets has highlighted key populations that may have benefitted from a timely intervention. Similar analyses performed on contemporary samples are needed to underpin the 2030 targets, but this requires the generation of a cohesive dataset of viral genome sequences in near-real-time. To generate such data, methodologies harnessing next-generation sequencing (NGS) should be utilised. Here we discuss the opportunity presented by NGS for public health surveillance of HIV and HCV, and discuss three methods that can generate sequences for such analysis. These include full-length genome amplification, utilised for analysis of HCV in the research space; tiling PCR, which was the method of choice for many diagnostic laboratories in the SARS-CoV-2 pandemic; and bait-capture hybridisation, which has been utilised in local HIV outbreaks. These techniques could be applied for near-real-time HIV and HCV surveillance, informing public health strategies that will be key to achieving 2030 targets.

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来源期刊
Reviews in Medical Virology
Reviews in Medical Virology 医学-病毒学
CiteScore
21.40
自引率
0.90%
发文量
88
期刊介绍: Reviews in Medical Virology aims to provide articles reviewing conceptual or technological advances in diverse areas of virology. The journal covers topics such as molecular biology, cell biology, replication, pathogenesis, immunology, immunization, epidemiology, diagnosis, treatment of viruses of medical importance, and COVID-19 research. The journal has an Impact Factor of 6.989 for the year 2020. The readership of the journal includes clinicians, virologists, medical microbiologists, molecular biologists, infectious disease specialists, and immunologists. Reviews in Medical Virology is indexed and abstracted in databases such as CABI, Abstracts in Anthropology, ProQuest, Embase, MEDLINE/PubMed, ProQuest Central K-494, SCOPUS, and Web of Science et,al.
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