Biology subjects

Kantor, R. S.

Publications and source records attributed to Kantor, R. S..

4 recordsLinked to original sources

bioRxiv2025

Developing and Benchmarking One Health Genomic Surveillance Tools for Influenza A Virus in Wastewater

Influenza A viruses (IAV) remain a persistent One Health threat, and whole-genome sequencing from wastewater offers a promising surveillance tool. However, IAV is at low abundance in wastewater, making it difficult to sequence. We benchmarked four targeted enrichment methods suited for whole-genome sequencing including custom and off-the-shelf amplicon and probe-based methods. Our custom HA tiled-amplicon panel was sensitive, fast, and cost-effective, making it suitable for monitoring low-abundance seasonal variants of known subtypes. However, its reliance on conserved and intact primer-binding sites limited primer design to fewer subtypes. A previously published universal amplicon method targeted all IAV subtypes, but it performed poorly in wastewater due to its reliance on intact genome segments. Probe-capture methods were resilient to RNA degradation and mismatches, potentially enabling broader surveillance and detection of emerging strains. However, probes were costly, labor-intensive, and less sensitive than tiled-amplicon. When testing compatibility of sequencing methods with upstream virus concentration and extraction methods, ultrafiltration-based virus concentration outperformed large-volume direct extraction with all four sequencing methods. This set of benchmarking comparisons and custom panels provides needed information for the translation of IAV genomic sequencing into a routine component of wastewater surveillance.

microbiology↗

bioRxiv2024

Benchmarking concentration and direct extraction methods for wastewater-based surveillance of eight human respiratory viruses: implications for rapid application to novel pathogens

Wastewater monitoring is rapidly expanding to provide surveillance for a growing number of epidemic and endemic pathogens. To provide early warning and support rapid response to a novel virus through wastewater surveillance, it would be ideal to understand in advance which concentration and extraction methods are likely to be effective for dPCR-based methods, depending on virus characteristics. In this study, we spiked wastewater samples with eight human respiratory viruses and processed them with four commercial methods that concentrate and/or extract nucleic acids from both liquid and solid fractions (Promega, Nanotrap, InnovaPrep), or only the solid fraction of wastewater (Solids). Our findings provide encouraging evidence that all four concentration/extraction methods combined with dPCR could detect an emerging virus in wastewater, although they differed in sensitivity. The pattern of recovery efficiency for adenoviruses, coronaviruses, and influenza A viruses was consistent across methods, while distinct patterns were observed for coxsackieviruses. Promega produced higher median recovery efficiencies based on dPCR for all viruses except for coxsackieviruses, even though it had the highest dPCR inhibition. We suggest caution in applying Nanotrap to new targets, based on the low recovery of coxsackievirus B5 compared to the other viruses. We also quantified the endogenous indicators PMMoV and Carjivirus (formerly crAssphage), illustrating how normalization could either improve or worsen the comparison of virus concentrations measured by different methods. These findings can guide the selection of concentration and extraction methods for wastewater monitoring based on the properties of target viruses, thus enhancing pandemic preparedness. Synopsis StatementBenchmarking scalable concentration and extraction methods on respiratory viruses with diverse properties facilitates the rapid application of wastewater-based surveillance to emerging viruses.

microbiology↗

bioRxiv2024

In silico analysis reveals differential targeting of enterovirus species by commonly used PCR assays

Quantitative polymerase chain reaction (qPCR) assays are sensitive molecular tools commonly used to quantify pathogens in environmental samples. These assays have become a staple of wastewater-based surveillance and often form the basis of quantitative microbial risk assessments. However, PCR assays may fail to capture all of their intended targets due to signature erosion over time. Here, we performed an in silico analysis of four human enterovirus PCR assays to assess signature erosion against the NCBI virus database. The predicted number of genomes hit by each assay rose alongside total genomes in the database through 2010 but the proportion of predicted hits began to level off with the emergence of the clinically important enterovirus D-68. We found that although all assays captured a majority of enterovirus species, only one recently developed assay adequately captured enterovirus D species. Some assays also appeared more likely to capture non-human enteroviruses than others, an important consideration for data interpretation. We conclude that broad-spectrum virus assays applied to environmental samples should be regularly checked against expanding sequence databases and provide methods to do so.

microbiology↗

bioRxiv2017

Dramatic expansion of microbial groups that shape the global sulfur cycle

The biogeochemical cycle of sulfur on Earth is driven by microbial sulfate reduction, yet organisms from relatively few lineages have been implicated in this process. Recent studies using functional marker genes have detected abundant, novel dissimilatory sulfite reductases that confer the capacity for microbial sulfate reduction and could do not be affiliated with known organisms. Thus, the identity of a significant fraction of sulfate reducing microbes has remained elusive. Here we report the discovery of the capacity for sulfate reduction in the genomes of organisms from twelve bacterial and archaeal phyla, thereby doubling the number of microbial phyla associated with this process. Eight of the twelve newly identified groups are candidate phyla that lack isolated representatives, a finding only possible given genomes from metagenomes. Two candidate phyla, Candidatus Rokubacteria and Candidatus Hydrothermarchaeota contain the earliest evolved genes. The capacity for sulfate reduction has been laterally transferred in multiple events within some phyla, and a key gene potentially capable of switching sulfur oxidation to sulfate reduction in associated cells has been acquired by putatively symbiotic bacteria. We conclude that functional predictions based on phylogeny will significantly underestimate the extent of sulfate reduction across Earths ecosystems. Understanding the prevalence of this capacity is integral to interpreting the carbon cycle because sulfate reduction is often coupled to turnover of buried organic carbon. Our findings expand the diversity of microbial groups associated with sulfur transformations in the environment and motivate revision of biogeochemical process models based on microbial community composition.

microbiology↗