Division of Infectious Diseases, Department of Medicine 1, Medical University of Vienna, Spitalgasse 23, 1090, Vienna, Austria.
Department of Genomes & Genetics, Institut Pasteur, Paris, France.
Parasit Vectors. 2021 Jun 29;14(1):343. doi: 10.1186/s13071-021-04840-0.
The Zika virus (ZIKV) epidemic of 2015/2016 spread throughout numerous countries. It emerged in mainland Latin America and spread to neighboring islands, including the Caribbean island of Barbados. Recent studies have indicated that the virus must have already been circulating in local mosquito populations in Brazil for almost 2 years before it was identified by the World Health Organization in 2015. Metagenomic detection assays have the potential to detect emerging pathogens without prior knowledge of their genomic nucleic acid sequence. Yet their applicability as vector surveillance tools has been widely limited by the complexity of DNA populations from field-collected mosquito preparations. The aim of this study was to investigate local vector biology and characterize metagenomic arbovirus diversity in Aedes mosquitoes during the ongoing 2015/2016 ZIKV epidemic.
We performed a short-term vector screening study on the island of Barbados during the ongoing 2015/2016 ZIKV epidemic, where we sampled local Aedes mosquitoes. We reanalyzed mosquito viral microbiome data derived from standard Illumina MiSeq sequencing to detect arbovirus sequences. Additionally, we employed deep sequencing techniques (Illumina HiSeq) and designed a novel bait capture enrichment assay to increase sequencing efficiency for arbovirus sequences from complex DNA samples.
We found that Aedes aegypti seemed to be the most likely vector of ZIKV, although it prevailed at a low density during the observed time period. The number of detected viruses increased with sequencing depth. Arbovirus sequence enrichment of metagenomic DNA preparations allowed the detection of arbovirus sequences of two different ZIKV genotypes, including a novel one. To our knowledge, this is the first report of the S3116W mutation in the NS5 gene region of ZIKV polyprotein.
The metagenomic arbovirus detection approach presented here may serve as a useful tool for the identification of epidemic-causing arboviruses with the additional benefit of enabling the collection of phylogenetic information on the source. Apart from detecting more than 88 viruses using this approach, we also found evidence of novel ZIKV variants circulating in the local mosquito population during the observed time period.
2015/2016 年的寨卡病毒（ZIKV）疫情在众多国家蔓延。它起源于拉丁美洲大陆，并传播到包括加勒比海巴巴多斯岛在内的邻近岛屿。最近的研究表明，该病毒在 2015 年被世界卫生组织（WHO）发现之前，很可能已经在巴西当地蚊子种群中传播了将近 2 年。宏基因组检测方法具有在不知道其基因组核酸序列的情况下检测新出现病原体的潜力。然而，由于从现场采集的蚊子制剂中 DNA 种群的复杂性，它们作为媒介监测工具的适用性受到了广泛限制。本研究的目的是调查当地的媒介生物学，并在正在进行的 2015/2016 年寨卡病毒疫情期间，描述 Aedes 蚊子中的宏基因组虫媒病毒多样性。
在正在进行的 2015/2016 年寨卡病毒疫情期间，我们在巴巴多斯岛进行了一项短期的媒介筛选研究，对当地的 Aedes 蚊子进行了采样。我们重新分析了从标准 Illumina MiSeq 测序中获得的蚊子病毒微生物组数据，以检测虫媒病毒序列。此外，我们还采用了深度测序技术（Illumina HiSeq）和设计了一种新的诱饵捕获富集检测方法，以提高复杂 DNA 样本中虫媒病毒序列的测序效率。
我们发现，埃及伊蚊似乎是寨卡病毒的最可能媒介，尽管在观察期间它的密度很低。随着测序深度的增加，检测到的病毒数量也在增加。对宏基因组 DNA 制剂进行虫媒病毒序列富集，可以检测到两种不同的寨卡病毒基因型的病毒序列，包括一种新的病毒。据我们所知，这是首次报道寨卡病毒多蛋白 NS5 基因区域 S3116W 突变。
这里提出的宏基因组虫媒病毒检测方法可以作为一种有用的工具，用于识别引起疫情的虫媒病毒，此外还可以收集有关来源的系统发育信息。除了使用这种方法检测到 88 多种病毒外，我们还发现了在观察期间当地蚊子种群中循环的新型寨卡病毒变种的证据。
