Surveillance of rhinovirus diversity among a university community identifies multiple types from all three species including an unassigned rhinovirus A genotype.

We determine the presence and diversity of rhinoviruses in nasopharyngeal swab samples from 248 individuals who presented with influenza-like illness (ILI) at a university clinic in the Southwest United States between October 1, 2020 and March 31, 2021. We identify at least 13 rhinovirus genotypes (A11, A22, A23, A25, A67, A101, B6, B79, C1, C17, C36, and C56, as well a new genotype [AZ88**]) and 16 variants that contributed to the burden of ILI in the community. We also describe the complete capsid protein gene of a member (AZ88**) of an unassigned rhinovirus A genotype.

Canine Parvovirus 2C Identified in Dog Feces from Poop Bags Collected from Outdoor Waste Bins in Arizona USA, June 2022.

Canine parvoviruses (CPVs) are a major cause of morbidity and mortality in dogs. However, surveillance has been largely limited to clinically manifest cases, resulting in a dearth of CPV genomic information on virus type, abundance, and diversity, limiting our understanding of its evolutionary dynamics. We tested the feasibility of using dog feces in poop bags collected from outdoor waste bins as a source for environmental surveillance of CPV. After polymerase chain reaction, long-read sequencing, and bioinformatics, we identified that CPV-2c was present in Arizona, USA, in June 2022 and documented variants with amino acid substitutions 530E and 101K in NS1 and NS2, respectively. Based on publicly available sequence data in GenBank as of January 2023, the CPV genome described here represents the only CPV genome described in the USA from the 2022 season, despite news of CPV outbreak-associated fatalities in dogs in the USA. This highlights the need for more studies that document CPV complete or near complete genomes, as well as experimental studies, to further our understanding of its evolutionary process.

Impact of sample clarification by size exclusion on virus detection and diversity in wastewater-based epidemiology.

The use of wastewater-based epidemiology (WBE) for early detection of virus circulation and response during the SARS-CoV-2 pandemic increased interest in and use of virus concentration protocols that are quick, scalable, and efficient. One such protocol involves sample clarification by size fractionation using either low-speed centrifugation to produce a clarified supernatant or membrane filtration to produce an initial filtrate depleted of solids, eukaryotes and bacterial present in wastewater (WW), followed by concentration of virus particles by ultrafiltration of the above. While this approach has been successful in identifying viruses from WW, it assumes that majority of the viruses of interest should be present in the fraction obtained by ultrafiltration of the initial filtrate, with negligible loss of viral particles and viral diversity. We used WW samples collected in a population of ~700,000 in southwest USA between October 2019 and March 2021, targeting three non-enveloped viruses (enteroviruses [EV], canine picornaviruses [CanPV], and human adenovirus 41 [Ad41]), to evaluate whether size fractionation of WW prior to ultrafiltration leads to appreciable differences in the virus presence and diversity determined. We showed that virus presence or absence in WW samples in both portions (filter trapped solids [FTS] and filtrate) are not consistent with each other. We also found that in cases where virus was detected in both fractions, virus diversity (or types) captured either in FTS or filtrate were not consistent with each other. Hence, preferring one fraction of WW over the other can undermine the capacity of WBE to function as an early warning system and negatively impact the accurate representation of virus presence and diversity in a population.

Genome Sequence of a Microvirus Recovered from Wastewater in Arizona, USA, in October 2020, Encodes a Previously Undescribed DNA-Binding Protein.

We describe the genome of Microvirus-AZ-2020, which was identified from wastewater in Arizona, USA, in October 2020. Microvirus-AZ-2020 belongs to subfamily Gokushovirinae and contains six (five known and one hypothetical) open reading frames (ORFs), each with >40 codons. HHPred analysis and Colabfold structure prediction suggest that the hypothetical ORF encodes a previously undescribed putative DNA-binding protein.

Canine picornaviruses detected in wastewater in Arizona, USA 2019 and 2021.

Virus surveillance by wastewater-based epidemiology (WBE) in two Arizona municipalities in Maricopa County, USA (~700,000 people), revealed the presence of six canine picornavirus (CanPV) variants: five in 2019 and one in 2021. Phylogenetic analysis suggests these viruses might be from domestic dog breeds living within or around the area. Phylogenetic and pairwise identity analyses suggest over 15 years of likely enzootic circulation of multiple lineages of CanPV in the USA and possibly globally. Considering <10 CanPV sequences are publicly available in GenBank as of June 2, 2022, the results provided here constitute an increase of current knowledge on CanPV diversity and highlight the need for increased surveillance.