Transmission dynamics and molecular epidemiology of arboviruses in Indonesia

印度尼西亚虫媒病毒的传播动力学和分子流行病学

• 批准号: MR/P017541/1
• 负责人: Simon Frost
• 金额: $ 33.98万
• 依托单位: University of Cambridge
• 依托单位国家: 英国
• 项目类别: Research Grant
• 财政年份: 2017
• 资助国家: 英国
• 起止时间: 2017 至 无数据
• 项目状态: 已结题
• 来源: https://gtr.ukri.org/projects?ref=MR%2FP017541%2F1
• 关键词: Transmission; dynamics; molecular; epidemiology; arboviruses

Large scale outbreaks of dengue virus (DENV) and dengue haemorrhagic fever are reported every year in Indonesia. In addition, Chikungunya virus (CHIKV) is endemic in parts of Indonesia, and two positive cases of Zika virus (ZIKV) have been described, one from an Australian who travelled to Indonesia, a second from Jambi province. DENV, CHIKV, and ZIKV are all transmitted by the mosquito Aedes aegypti, and are co-circulating in the same population. They also cause overlapping symptoms in adults, and hence are difficult to differentiate by symptoms alone. Indonesia has a large population - around 250 million people - with around 90% of the population living in areas suitable for the transmission of 'arboviruses' (short for arthropod-borne viruses), and collectively, arboviruses represent a major public health concern in Indonesia. The number of cases varies both geographically and over time, and relatively little is known about the drivers of this variation in Indonesia.DENV, CHIKV, and ZIKV are all RNA viruses, which evolve at a high rate. Consequently, these viruses are genetically variable, and through the application of statistical models to viral sequence data, information on the dynamics of transmission, both over time and space, can be obtained. However, although the number of arbovirus infections per year is high, the number of viral sequences from Indonesia is relatively low, and often, these sequences only span a small part of the viral genome.This project aims to characterise the transmission dynamics of DENV, CHIKV, and ZIKV through viral sequencing of clinical samples from humans. We will harness a network of collaborators to provide archived samples, and prospective studies in locations representing west (Sumatra - Palembang City), central (Kalimantan - Banjarmasin city), and east (Maluku - Ambon city) Indonesia. In addition, we will study outbreaks that may occur during the study period. Using next-generation sequencing platforms, we aim to generate a large dataset of full-length viral genomes that will significantly add to the existing body of viral sequence data currently available.Sequences of DENV and CHIKV (and potentially ZIKV) will be analysed using a 'phylodynamic' approach, integrating the sequence data with epidemiological data using mathematical models in order to gain a more complete understanding of the transmission dynamics of these arboviruses.

印度尼西亚每年都有登革热病毒和登革出血热大规模暴发的报告。此外，基孔肯雅病毒（CHIKV）在印度尼西亚部分地区流行，已描述了两例寨卡病毒（ZIKV）阳性病例，一例来自前往印度尼西亚的澳大利亚人，第二例来自詹比省。DENV、CHIKV和ZIKV都是由埃及伊蚊传播的，并且在同一种群中共同传播。它们也会在成人中引起重叠的症状，因此很难单独通过症状来区分。印度尼西亚人口众多-约2.5亿人-约90%的人口生活在适合“虫媒病毒”（节肢动物传播病毒的简称）传播的地区，虫媒病毒是印度尼西亚主要的公共卫生问题。病例数量在地理上和时间上都有差异，对印度尼西亚这种变化的驱动因素知之甚少。DENV，CHIKV和ZIKV都是RNA病毒，它们以很高的速度进化。因此，这些病毒在遗传上是可变的，通过将统计模型应用于病毒序列数据，可以获得关于传播动态的信息，包括时间和空间。然而，尽管每年虫媒病毒感染的数量很高，但来自印度尼西亚的病毒序列数量相对较低，而且这些序列通常只跨越病毒基因组的一小部分。本项目旨在通过对人类临床样本进行病毒测序，来确定DENV、CHIKV和ZIKV的传播动态。我们将利用合作者网络提供存档样本，并在代表印度尼西亚西部（苏门答腊-帕伦邦市）、中部（加里曼丹-班加马辛市）和东部（马鲁古-安汶市）的地点进行前瞻性研究。此外，我们将研究研究期间可能发生的疫情。使用下一代测序平台，我们的目标是生成一个大型的全长病毒基因组数据集，这将大大增加现有的病毒序列数据。DENV和CHIKV的序列（以及潜在的ZIKV）将使用“动态”方法进行分析，使用数学模型将序列数据与流行病学数据相结合，以便更全面地了解传播动态这些虫媒病毒的。

项目成果

Assessment of a multiplex PCR and Nanopore-based method for dengue virus sequencing in Indonesia

在印度尼西亚对多重 PCR 和基于纳米孔的登革热病毒测序方法进行评估

• DOI: 10.17863/cam.64681
• 发表时间: 2020
• 作者: Stubbs S

A Nanopore-based method for generating complete coding region sequences of dengue virus in resource-limited settings

一种基于纳米孔的方法，用于在资源有限的环境中生成登革热病毒的完整编码区序列

• DOI: 10.1101/499111
• 发表时间: 2018
• 作者: Stubbs S

An investig-ation into the epidemiology of chikungunya virus across neglected regions of Indonesia.

对印度尼西亚被忽视地区基孔肯雅病毒流行病学的调查。

• DOI: 10.17863/cam.59441
• 发表时间: 2020
• 作者: Stubbs S

Molecular epidemiology of dengue in a setting of low reported endemicity: Kupang, East Nusa Tenggara province, Indonesia.

低度报告流行地区登革热的分子流行病学：印度尼西亚东努沙登加拉省古邦。

• DOI: 10.1093/trstmh/trab138
• 发表时间: 2021
• 期刊: Transactions of the Royal Society of Tropical Medicine and Hygiene
• 影响因子: 2.2
• 作者: Hayati RF

Distinct Dengue Disease Epidemiology, Clinical, and Diagnosis Features in Western, Central, and Eastern Regions of Indonesia, 2017-2019.

• DOI: 10.3389/fmed.2020.582235
• 发表时间: 2020
• 期刊: Frontiers in medicine
• 影响因子: 3.9
• 作者: Sasmono RT;Santoso MS;Pamai YWB;Yohan B;Afida AM;Denis D;Hutagalung IA;Johar E;Hayati RF;Yudhaputri FA;Haryanto S;Stubbs SCB;Blacklaws BA;Myint KSA;Frost SDW
• 通讯作者: Frost SDW