Performance comparison of probe-capture enrichment sequencing of viruses in wastewater influent and settled solids from the California Central Valley
- 1University of California, Davis
Abstract
Wastewater sequencing using probe-capture enrichment of public health-relevant viruses is a powerful, non-intrusive approach to monitor infectious diseases, but performance depends on sample type and processing approach. We compared two processing pipelines from wastewater influent samples collected at three timepoints across three wastewater treatment facilities. Each sample was split for parallel processing, with viruses concentrated (1) directly from whole influent using nano-sized affinity particles and (2) by settling and dewatering the solids fraction. Combined DNA/RNA extracts were prepared into libraries using a pre-commercial Illumina protocol, then probe-capture enrichment was performed with Illumina Viral Surveillance Panel (VSP) v1 (66 targets) and v2 (242 targets). Sequencing depth was increased for VSP v2 to accommodate the expanded target set. On average, 160 +/- 146 viral species were detected per sample, with wastewater fraction (sample type) explaining 19% of the variance in viral abundances. Solids contained a higher abundance of DNA viruses compared to RNA viruses, while influent exhibited the inverse. Metagenomic analysis of the VSP v2 sequencing data detected more viral species in influent (median 358) than in solids (median 184), but probe-capture enrichment produced more comparable target-virus readouts across fractions, supporting the use of either fraction for wastewater-based epidemiology.
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BibTeX
@misc{lavon2026performance,
title = {{Performance comparison of probe-capture enrichment sequencing of viruses in wastewater influent and settled solids from the California Central Valley}},
author = {A. Lavon and J. M. Pender and R. Olson and T. Chatterjee and C. C. Naughton and P. Prashar and S. Kuersten and J. A. Eisen and K. Whiteson and H. N. Bischel},
howpublished = {bioRxiv},
year = {2026},
month = oct,
doi = {10.64898/2026.10.02.756336},
url = {https://www.biorxiv.org/content/10.64898/2026.10.02.756336v1},
note = {CC BY-NC-ND},
}
RIS
TY - UNPB
TI - Performance comparison of probe-capture enrichment sequencing of viruses in wastewater influent and settled solids from the California Central Valley
AU - A. Lavon
AU - J. M. Pender
AU - R. Olson
AU - T. Chatterjee
AU - C. C. Naughton
AU - P. Prashar
AU - S. Kuersten
AU - J. A. Eisen
AU - K. Whiteson
AU - H. N. Bischel
PY - 2026
DA - 2026/10/02
PB - bioRxiv
DO - 10.64898/2026.10.02.756336
UR - https://www.biorxiv.org/content/10.64898/2026.10.02.756336v1
AB - Wastewater sequencing using probe-capture enrichment of public health-relevant viruses is a powerful, non-intrusive approach to monitor infectious diseases, but performance depends on sample type and processing approach. We compared two processing pipelines from wastewater influent samples collected at three timepoints across three wastewater treatment facilities. Each sample was split for parallel processing, with viruses concentrated (1) directly from whole influent using nano-sized affinity particles and (2) by settling and dewatering the solids fraction. Combined DNA/RNA extracts were prepared into libraries using a pre-commercial Illumina protocol, then probe-capture enrichment was performed with Illumina Viral Surveillance Panel (VSP) v1 (66 targets) and v2 (242 targets). Sequencing depth was increased for VSP v2 to accommodate the expanded target set. On average, 160 +/- 146 viral species were detected per sample, with wastewater fraction (sample type) explaining 19% of the variance in viral abundances. Solids contained a higher abundance of DNA viruses compared to RNA viruses, while influent exhibited the inverse. Metagenomic analysis of the VSP v2 sequencing data detected more viral species in influent (median 358) than in solids (median 184), but probe-capture enrichment produced more comparable target-virus readouts across fractions, supporting the use of either fraction for wastewater-based epidemiology.
ER -