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Emerging and reemerging viruses are responsible for a number of recent epidemic outbreaks. A crucial step in predicting and controlling outbreaks is the timely and accurate characterization of emerging virus strains. We present a portable microfluidic platform containing carbon nanotube arrays with differential filtration porosity for the rapid enrichment and optical identification of viruses. Different emerging strains (or unknown viruses) can be enriched and identified in real time through a multivirus capture component in conjunction with surface-enhanced Raman spectroscopy. More importantly, after viral capture and detection on a chip, viruses remain viable and get purified in a microdevice that permits subsequent in-depth characterizations by various conventional methods. We validated this platform using different subtypes of avian influenza A viruses and human samples with respiratory infections. This technology successfully enriched rhinovirus, influenza virus, and parainfluenza viruses, and maintained the stoichiometric viral proportions when the samples contained more than one type of virus, thus emulating coinfection. Viral capture and detection took only a few minutes with a 70-fold enrichment enhancement; detection could be achieved with as little as 10 2 EID 50 /mL (50% egg infective dose per microliter), with a virus specificity of 90%. After enrichment using the device, we demonstrated by sequencing that the abundance of viral-specific reads significantly increased from 4.1 to 31.8% for parainfluenza and from 0.08 to 0.44% for influenza virus. This enrichment method coupled to Raman virus identification constitutes an innovative system that could be used to quickly track and monitor viral outbreaks in real time.
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This content will become publicly available on April 16, 2026
Quantifying virus load and characterising virus diversity in wildlife samples with target enrichment sequencing
ABSTRACT Metagenomics is a powerful tool for characterising viruses, with broad applications across diverse disciplines, from understanding the ecology and evolutionary history of viruses to identifying causative agents of emerging outbreaks with unknown aetiology. Additionally, metagenomic data contains valuable information about the amount of virus present within samples. However, we have yet to leverage metagenomics to assess viral load, which is a key epidemiological parameter. To effectively use sequencing outputs to inform transmission, we need to understand the relationship between read depth and viral load across a diverse set of viruses. Here, using target enrichment sequencing, we investigated the detection and recovery of virus genomes by spiking known concentrations of DNA and RNA viruses into wild rodent faecal samples. In total, 15 experimental replicates were sequenced with target enrichment sequencing and compared to shotgun sequencing of the same background samples. Target enriched sequencing recovered all spike-in viruses at every concentration (102, 103, and 105± 1 log genome copies) and showed a log-linear relationship between spike-in concentration and mean read depth. Background viruses (includingKobuvirusandCardiovirus) were recovered consistently across all biological and technical replicates, but genome coverage was variable between virus genera and likely reflected the composition of target enrichment probe panel. Overall, our study highlights the strengths and weaknesses of using commercially available panels to quantify and characterise wildlife viromes, and underscores the importance of probe panel design for accurately interpreting coverage and read depth. To advance the use of metagenomics for understanding virus transmission, further research will be needed to elucidate how sequencing strategy (e.g. library depth, pooling), virome composition, and probe design influence viral read counts and genome coverage.
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- Award ID(s):
- 2308273
- PAR ID:
- 10600396
- Publisher / Repository:
- bioRxiv
- Date Published:
- Format(s):
- Medium: X
- Institution:
- bioRxiv
- Sponsoring Org:
- National Science Foundation
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