Bacterial metatranscriptomes in wastewater can differentiate virally infected human populations

Salido, R. A.; Martino, C.; Karthikeyan, S.; Huang, S.; Rahman, G.; Gonzalez, A.; Zaramela, L. S.; Beck, K. L.; Bhute, S.; Cantrell, K.; Carrieri, A. P.; Farmer, S.; Haiminen, N.; Humphrey, G.; Kim, H.-C.; Parida, L.; Richter, R. A.; Vazquez-Baeza, Y.; Zengler, K.; Swafford, A.; Bartko, A.; Knight, R.

doi:10.1101/2022.02.23.481658

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bioRxiv · 10.1101/2022.02.23.481658

Bacterial metatranscriptomes in wastewater can differentiate virally infected human populations

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Abstract

Monitoring wastewater samples at building-level resolution screens large populations for SARS-CoV-2, prioritizing testing and isolation efforts. Here we perform untargeted metatranscriptomics on virally-enriched wastewater samples from 10 locations on the UC San Diego campus, demonstrating that resulting bacterial taxonomic and functional profiles discriminate SARS-CoV-2 status even without direct detection of viral transcripts. Our proof-of-principle reveals emergent threats through changes in the human microbiome, suggesting new approaches for untargeted wastewater-based epidemiology.

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Salido, R. A., Martino, C., Karthikeyan, S., Huang, S., Rahman, G., Gonzalez, A., Zaramela, L. S., Beck, K. L., Bhute, S., Cantrell, K., Carrieri, A. P., Farmer, S., Haiminen, N., Humphrey, G., Kim, H.-C., Parida, L., Richter, R. A., Vazquez-Baeza, Y., Zengler, K., Swafford, A., Bartko, A., Knight, R.. 2022-02-24. Bacterial metatranscriptomes in wastewater can differentiate virally infected human populations. https://doi.org/10.1101/2022.02.23.481658

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