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Single mosquito metatranscriptomics recovers mosquito species, blood meal sources, and microbial cargo, including viral dark matter

View ORCID ProfileJoshua Batson, View ORCID ProfileGytis Dudas, Eric Haas-Stapleton, Amy L. Kistler, View ORCID ProfileLucy M. Li, Phoenix Logan, Kalani Ratnasiri, Hanna Retallack
doi: https://doi.org/10.1101/2020.02.10.942854
Joshua Batson
1Chan Zuckerberg Biohub, 499 Illinois St, San Francisco CA 94158
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  • ORCID record for Joshua Batson
Gytis Dudas
3Gothenburg Global Biodiversity Centre, Carl Skottsbergs gata 22B, 413 19, Gothenburg, Sweden
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Eric Haas-Stapleton
2Alameda County Mosquito Abatement District, 23187 Connecticut St., Hayward, CA 94545
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Amy L. Kistler
1Chan Zuckerberg Biohub, 499 Illinois St, San Francisco CA 94158
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  • For correspondence: amy.kistler@czbiohub.org
Lucy M. Li
1Chan Zuckerberg Biohub, 499 Illinois St, San Francisco CA 94158
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Phoenix Logan
1Chan Zuckerberg Biohub, 499 Illinois St, San Francisco CA 94158
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Kalani Ratnasiri
1Chan Zuckerberg Biohub, 499 Illinois St, San Francisco CA 94158
4Program in Immunology, Stanford University School of Medicine, Stanford CA 94305
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Hanna Retallack
5Department of Biochemistry and Biophysics, University of California San Francisco, San Francisco CA 94158
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Abstract

Mosquitoes are a disease vector with a complex ecology involving interactions between transmissible pathogens, endogenous microbiota, and human and animal blood meal sources. Unbiased metatranscriptomic sequencing of individual mosquitoes offers a straightforward and rapid way to characterize these dynamics. Here, we profile 148 diverse wild-caught mosquitoes collected in California, detecting sequences from eukaryotes, prokaryotes, and over 70 known and novel viral species. Because we sequenced singletons, it was possible to compute the prevalence of each microbe and recognize a high frequency of viral co-infection. By analyzing the pattern of co-occurrence of sequences across samples, we associated “dark matter” sequences with recognizable viral polymerases, and animal pathogens with specific blood meal sources. We were also able to detect frequent genetic reassortment events in a highly prevalent quaranjavirus undergoing a recent intercontinental sweep. In the context of an emerging disease, where knowledge about vectors, pathogens, and reservoirs is lacking, the approaches described here can provide actionable information for public health surveillance and intervention decisions.

Footnotes

  • https://dx.doi.org/10.6084/m9.figshare.11832999

  • https://github.com/czbiohub/california-mosquito-study

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY 4.0 International license.
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Posted February 13, 2020.
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Single mosquito metatranscriptomics recovers mosquito species, blood meal sources, and microbial cargo, including viral dark matter
Joshua Batson, Gytis Dudas, Eric Haas-Stapleton, Amy L. Kistler, Lucy M. Li, Phoenix Logan, Kalani Ratnasiri, Hanna Retallack
bioRxiv 2020.02.10.942854; doi: https://doi.org/10.1101/2020.02.10.942854
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Single mosquito metatranscriptomics recovers mosquito species, blood meal sources, and microbial cargo, including viral dark matter
Joshua Batson, Gytis Dudas, Eric Haas-Stapleton, Amy L. Kistler, Lucy M. Li, Phoenix Logan, Kalani Ratnasiri, Hanna Retallack
bioRxiv 2020.02.10.942854; doi: https://doi.org/10.1101/2020.02.10.942854

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