Tracking arboviruses, their transmission vectors and potential hosts by nanopore sequencing of mosquitoes.
Tracking arboviruses, their transmission vectors and potential hosts by nanopore sequencing of mosquitoes.
复制标题
通过蚊子纳米孔测序追踪虫媒病毒、其传播载体和潜在宿主。
DOI：
10.1099/mgen.0.001184
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发表时间：
2024
影响因子：
3.9
通讯作者：
Mirza JD
中科院分区：
文献类型：
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作者：
Mirza JD
由于人类扩张、森林砍伐和气候变化，登革热、基孔肯雅热和黄热病等蚊媒病毒对人类健康的风险正在增加。为了预测和预测蚊媒病毒的传播和传播，需要更好地了解蚊子种群的传播周期。我们提出了一种病原体不可知的组合测序方案，用于使用便携式牛津纳米孔测序来识别载体、病毒病原体及其宿主或储库。使用在巴西圣保罗收集的蚊子，我们提取了用于病毒鉴定的RNA和用于血粉和蚊子鉴定的DNA。通过将细胞色素c氧化酶I（COI）序列与策划的生命数据系统条形码（BOLD）进行比较来识别蚊子和血粉。使用SMART-9 N方案鉴定病毒，该方案允许用天然条形码制备扩增的DNA用于纳米孔测序。采用Kraken 2检测病毒病原体，Minimap 2和BOLD鉴定血粉的内容物。由于某些物种的高度相似性，使用RACON抛光产生共有COI序列后，使用blasting进行蚊子鉴定。该方案可以同时揭示病毒多样性、蚊子种类和蚊子的食性。它也有可能增加对蚊子遗传多样性和人畜共患蚊媒病毒传播动力学的了解。
The risk to human health from mosquito-borne viruses such as dengue, chikungunya and yellow fever is increasing due to increased human expansion, deforestation and climate change. To anticipate and predict the spread and transmission of mosquito-borne viruses, a better understanding of the transmission cycle in mosquito populations is needed. We present a pathogen-agnostic combined sequencing protocol for identifying vectors, viral pathogens and their hosts or reservoirs using portable Oxford Nanopore sequencing. Using mosquitoes collected in São Paulo, Brazil, we extracted RNA for virus identification and DNA for blood meal and mosquito identification. Mosquitoes and blood meals were identified by comparing cytochrome c oxidase I (COI) sequences against a curated Barcode of Life Data System (BOLD). Viruses were identified using the SMART-9N protocol, which allows amplified DNA to be prepared with native barcoding for nanopore sequencing. Kraken 2 was employed to detect viral pathogens and Minimap2 and BOLD identified the contents of the blood meal. Due to the high similarity of some species, mosquito identification was conducted usingblastafter generation of consensus COI sequences using RACON polishing. This protocol can simultaneously uncover viral diversity, mosquito species and mosquito feeding habits. It also has the potential to increase understanding of mosquito genetic diversity and transmission dynamics of zoonotic mosquito-borne viruses.