Single mosquito metatranscriptomics identifies vectors, emerging pathogens and reservoirs in one assay
- Chan Zuckerberg Biohub, United States
- Gothenburg Global Biodiversity Centre, Sweden
- Alameda County Mosquito Abatement District, United States
- Stanford University, United States
- University of California, San Francisco, United States
Abstract
Mosquitoes are major infectious disease-carrying vectors. Assessment of current and future risks associated with the mosquito population requires knowledge of the full repertoire of pathogens they carry, including novel viruses, as well as their blood meal sources. Unbiased metatranscriptomic sequencing of individual mosquitoes offers a straightforward, rapid and quantitative means to acquire this information. Here, we profile 148 diverse wild-caught mosquitoes collected in California and detect sequences from eukaryotes, prokaryotes, 24 known and 46 novel viral species. Importantly, sequencing individuals greatly enhanced the value of the biological information obtained. It allowed us to a) speciate host mosquito, b) compute the prevalence of each microbe and recognize a high frequency of viral co-infections, c) associate animal pathogens with specific blood meal sources, and d) apply simple co-occurrence methods to recover previously undetected components of highly prevalent segmented viruses. In the context of emerging diseases, where knowledge about vectors, pathogens, and reservoirs is lacking, the approaches described here can provide actionable information for public health surveillance and intervention decisions.
Data availability
Raw and assembled sequencing data are deposited in NCBI Bioproject PRJNA605178. Code is available on Github at https://github.com/czbiohub/california-mosquito-study. Derived data (including all contigs) and supplementary data are available on Figshare at dx.doi.org/10.6084/m9.figshare.11832999 .
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Genome survey of RNA viruses within arthropodsNCBI BioProjectPRJNA271540.
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Mosquitoes (mosquitoes raw sequence reads)NCBI Short read archive (SRA) PRJNA388696.
Article and author information
Author details
Funding
Chan Zuckerberg Initiative
- Joshua Batson
UCSF Medical Science Training Program
- Hanna Retallack
National Science Foundation
- Kalani Ratnasiri
The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.
Copyright
© 2021, Batson et al.
This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.
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Single mosquito metatranscriptomics identifies vectors, emerging pathogens and reservoirs in one assay
eLife 10:e68353.
https://doi.org/10.7554/eLife.68353
