The pigeon circovirus evolution, epidemiology and interaction with the host immune system under One Loft Race rearing conditions.

This study was aimed to investigate the frequency of PiCV recombination, the kinetics of PiCV viremia and shedding and the correlation between viral replication and host immune response in young pigeons subclinically infected with various PiCV variants and kept under conditions mimicking the OLR system. Fifteen racing pigeons originating from five breeding facilities were housed together for six weeks. Blood and cloacal swab samples were collected from birds every seven days to recover complete PiCV genomes and determine PiCV genetic diversity and recombination dynamics, as well as to assess virus shedding rate, level of viremia, expression of selected genes and level of anti-PiCV antibodies. Three hundred and eighty-eight complete PiCV genomes were obtained and thirteen genotypes were distinguished. Twenty-five recombination events were detected. Recombinants emerged during the first three weeks of the experiment which was consistent with the peak level of viremia and viral shedding. A further decrease in viremia and shedding partially corresponded with IFN-γ and MX1 gene expression and antibody dynamics. Considering the role of OLR pigeon rearing system in spreading infectious agents and allowing their recombination, it would be reasonable to reflect on the relevance of pigeon racing from both an animal welfare and epidemiological perspective.

Genome analysis of gyroviruses identified in waterfowl in Arizona (USA).

Gyroviruses are small single-stranded DNA (ssDNA) viruses that are largely associated with birds. Chicken anemia virus is the most extensively studied gyrovirus due to its disease impact on the poultry industry. However, we know much less about gyroviruses infecting other avian species. To investigate gyroviruses infecting waterfowl, we determined six complete genome sequences that fall into three gyrovirus groups, referred to as waterfowl gyrovirus 1 (n = 3), 2 (n = 2), and 3 (n = 1), in organs from hunter-harvested waterfowl from Arizona (USA). The waterfowl gyrovirus 1 variants were identified in multiple organs of a single American wigeon and represent a tentative new species. The waterfowl gyrovirus 2 variants were identified in the livers of two American wigeons and share >70% VP1 nucleotide sequence identity with gyrovirus 9, previously identified in the spleen of a Brazilian Pekin duck (MT318123) and a human fecal sample (KP742975). Waterfowl gyrovirus 3 was identified in a northern pintail spleen sample, and it shares >73% VP1 nucleotide sequence identity with two gyrovirus 13 sequences previously identified in Brazilian Pekin duck spleens (MT318125 and MT318127). These gyroviruses are the first to be identified in waterfowl in North America, as well as in American wigeons and northern pintails.

Two Lineages of Papillomaviruses Identified from Caracals (Caracal caracal) in South Africa.

Papillomaviruses (PV) infect epithelial cells and can cause hyperplastic or neoplastic lesions. In felids, most described PVs are from domestic cats (Felis catus; n = 7 types), with one type identified in each of the five wild felid species studied to date (Panthera uncia, Puma concolor, Leopardus wiedii, Panthera leo persica and Lynx rufus). PVs from domestic cats are highly diverse and are currently classified into three genera (Lambdapapillomavirus, Dyothetapapillomavirus, and Taupapillomavirus), whereas those from wild felids, although diverse, are all classified into the Lambdapapillomavirus genus. In this study, we used a metagenomic approach to identify ten novel PV genomes from rectal swabs of five deceased caracals (Caracal caracal) living in the greater Cape Town area, South Africa. These are the first PVs to be described from caracals, and represent six new PV types, i.e., Caracal caracal papillomavirus (CcarPV) 1-6. These CcarPV fall into two phylogenetically distinct genera: Lambdapapillomavirus, and Treisetapapillomavirus. Two or more PV types were identified in a single individual for three of the five caracals, and four caracals shared at least one of the same PV types with another caracal. This study broadens our understanding of wild felid PVs and provides evidence that there may be several wild felid PV lineages.

Genomes of cressdnaviruses, microviruses, a gyrovirus, and a caudovirus identified in the fecal samples of a mallard and double-crested cormorant.

Mallards and double-crested cormorants have a broad distribution across North America. In the fecal sample from two individual mallard and double-crested cormorant, we determined the genomes of a caudovirus, microviruses (n = 6), cressdnaviruses (n = 35), and a gyrovirus (chicken anemia virus, CAV). Here, we report double-crested cormorant as a CAV host.

Widespread Horizontal Gene Transfer Among Animal Viruses.

The initial objective of this study was to shed light on the evolution of small DNA tumor viruses by analyzing de novo assemblies of publicly available deep sequencing datasets. The survey generated a searchable database of contig snapshots representing more than 100,000 Sequence Read Archive records. Using modern structure-aware search tools, we iteratively broadened the search to include an increasingly wide range of other virus families. The analysis revealed a surprisingly diverse range of chimeras involving different virus groups. In some instances, genes resembling known DNA-replication modules or known virion protein operons were paired with unrecognizable sequences that structural predictions suggest may represent previously unknown replicases and novel virion architectures. Discrete clades of an emerging group called adintoviruses were discovered in datasets representing humans and other primates. As a proof of concept, we show that the contig database is also useful for discovering RNA viruses and candidate archaeal phages. The ancillary searches revealed additional examples of chimerization between different virus groups. The observations support a gene-centric taxonomic framework that should be useful for future virus-hunting efforts.

Two Novel Geminiviruses Identified in Bees (Apis mellifera and Nomia sp.).

Members of the Geminviridae family are circular single-stranded DNA plant-infecting viruses, some of which impact global food production. Geminiviruses are vectored by sap-feeding insects such as leafhoppers, treehoppers, aphids, and whiteflies. Additionally, geminivirus sequences have also been identified in other insects such as dragonflies, mosquitoes, and stingless bees. As part of a viral metagenomics study on honeybees and solitary bees (Nomia sp.), two geminivirus genomes were identified. These represent a novel citlodavirus (from honeybees collected from Westmoreland, Jamaica) and a mastrevirus-like genome (from a solitary bee collected from Tempe, Arizona, USA). The novel honeybee-derived citlodavirus genome shares ~61 to 69% genome-wide nucleotide pairwise identity with other citlodavirus genome sequences and is most closely related to the passion fruit chlorotic mottle virus identified in Brazil. Whereas the novel solitary bee-derived mastrevirus-like genome shares ~55 to 61% genome-wide nucleotide identity with other mastreviruses and is most closely related to tobacco yellow dwarf virus identified in Australia, based on pairwise identity scores of the full genome, replication-associated protein, and capsid protein sequences. Previously, two geminiviruses in the Begomovirus genus were identified in samples of stingless bee (Trigona spp.) samples. Here, we identify viruses that represent two new species of geminiviruses from a honeybee and a solitary bee, which continues to demonstrate that plant pollinators can be utilized for the identification of plant-infecting DNA viruses in ecosystems.

Virome release of an invasive exotic plant species in southern France.

The increase in human-mediated introduction of plant species to new regions has resulted in a rise of invasive exotic plant species (IEPS) that has had significant effects on biodiversity and ecosystem processes. One commonly accepted mechanism of invasions is that proposed by the enemy release hypothesis (ERH), which states that IEPS free from their native herbivores and natural enemies in new environments can outcompete indigenous species and become invasive. We here propose the virome release hypothesis (VRH) as a virus-centered variant of the conventional ERH that is only focused on enemies. The VRH predicts that vertically transmitted plant-associated viruses (PAV, encompassing phytoviruses and mycoviruses) should be co-introduced during the dissemination of the IEPS, while horizontally transmitted PAV of IEPS should be left behind or should not be locally transmitted in the introduced area due to a maladaptation of local vectors. To document the VRH, virome richness and composition as well as PAV prevalence, co-infection, host range, and transmission modes were compared between indigenous plant species and an invasive grass, cane bluestem (Bothriochloa barbinodis), in both its introduced range (southern France) and one area of its native range (Sonoran Desert, Arizona, USA). Contrary to the VRH, we show that invasive populations of B. barbinodis in France were not associated with a lower PAV prevalence or richness than native populations of B. barbinodis from the USA. However, comparison of virome compositions and network analyses further revealed more diverse and complex plant-virus interactions in the French ecosystem, with a significant richness of mycoviruses. Setting mycoviruses apart, only one putatively vertically transmitted phytovirus (belonging to the Amalgaviridae family) and one putatively horizontally transmitted phytovirus (belonging to the Geminiviridae family) were identified from B. barbinodis plants in the introduced area. Collectively, these characteristics of the B. barbinodis-associated PAV community in southern France suggest that a virome release phase may have immediately followed the introduction of B. barbinodis to France in the 1960s or 1970s, and that, since then, the invasive populations of this IEPS have already transitioned out of this virome release phase, and have started interacting with several local mycoviruses and a few local plant viruses.

Diverse papillomaviruses identified from Antarctic fur seals, leopard seals and Weddell seals from the Antarctic.

Papillomaviruses (family Papillomaviridae) are non-enveloped, circular, double-stranded DNA viruses known to infect squamous and mucosal epithelial cells. In the family Papillomaviridae there are 53 genera and 133 viral species whose members infect a variety of mammalian, avian, reptilian, and fish species. Within the Antarctic context, papillomaviruses (PVs) have been identified in Adélie penguins (Pygoscelis adeliae, 2 PVs), Weddell seals (Leptonychotes weddellii, 7 PVs), and emerald notothen (Trematomus bernacchii, 1 PV) in McMurdo Sound and Ross Island in eastern Antarctica. Here we identified 13 diverse PVs from buccal swabs of Antarctic fur seals (Arctocephalus gazella, 2 PVs) and leopard seal (Hydrurga leptonyx, 3 PVs) in western Antarctica (Antarctic Peninsula), and vaginal and nasal swabs of Weddell seals (8 PVs) in McMurdo Sound. These PV genomes group into four genera representing 11 new papillomavirus types, of which five are from two Antarctic fur seals and a leopard seal and six from Weddell seals.

New duck papillomavirus type identified in a mallard in Missouri, USA.

Papillomaviruses are small circular DNA viruses that infect epithelial and mucosal cells and have co-evolved with their hosts. Some papillomaviruses in mammals are well studied (especially those associated with disease). However, there is limited information on papillomaviruses associated with avian hosts. From a cloacal swab sample of a mallard (Anas platyrhynchos) sampled in Missouri, USA (6 Jan 2023), we identified a papillomavirus (7839 nt) that shares ~68% genome-wide nucleotide sequence identity with Anas platyrhynchos papillomavirus 1 (AplaPV1) from a mallard sampled in Newfoundland (Canada) and ~40% with AplaPV2 from a mallard sampled in Minnesota (USA) with mesenchymal dermal tumors. The papillomavirus we identified shares 73.6% nucleotide sequence identity in the L1 gene with that of AplaPV1 and thus represents a new AplaPV type (AplaPV3). The genome sequence of AplaPV3 shares >97% identity with three partial PV genome sequences (1316, 1997, and 4241 nt) identified in a mallard in India, indicating that that virus was also AplaPV3.

Sex-specific recruitment rates contribute to male-biased sex ratio in Adélie penguins.

Sex-related differences in vital rates that drive population change reflect the basic life history of a species. However, for visually monomorphic bird species, determining the effect of sex on demographics can be a challenge. In this study, we investigated the effect of sex on apparent survival, recruitment, and breeding propensity in the Adélie penguin (Pygoscelis adeliae), a monochromatic, slightly size dimorphic species with known age, known sex, and known breeding history data collected during 1996-2019 (n = 2127 birds) from three breeding colonies on Ross Island, Antarctica. Using a multistate capture-mark-recapture maximum-likelihood model, we estimated apparent survival (S^), recapture (resighting) probability (p^), and the probability of transitioning among breeding states and moving between colonies (ψ^; colony-specific non-juvenile pre-breeders, breeders, and non-breeders). Survival rate varied by breeding status and colony, but not sex, and pre-breeders had higher survival rates than breeders and non-breeders. Females had a higher probability of recruiting into the breeding population each year and may enter the breeding pool at younger ages. In contrast, both sexes had the same probability of breeding from year to year once they had recruited. Although we detected no direct sex effects on survival, the variation in recruitment probability and age-at-first reproduction, along with lower survival rates of breeders compared to pre-breeders, likely leads to shorter lifespans for females. This is supported by our findings of a male-biased mean adult sex ratio (ASR) of 1.4 males for every female (x^ proportion of males = 0.57, SD = 0.07) across all colonies and years in this metapopulation. Our study illustrates how important it can be to disentangle sex-related variation in population vital rates, particularly for species with complex life histories and demographic dynamics.

Direct detection of canine picornavirus complete coding sequence in wastewater using long-range reverse-transcriptase polymerase chain reaction and long-read sequencing.

We describe four complete coding sequence (cCDS) of canine picornavirus from wastewater in Arizona, USA detected by coupling cCDS single-contig (∼7.5 kb) reverse-transcriptase polymerase chain reaction (RT-PCR) and low-cost long-read high-throughput sequencing. For viruses of medical/veterinary importance, this workflow expands possibilities of wastewater based genomic epidemiology for exploring virus evolutionary dynamics especially in low-resource settings.

Diverse Small Circular DNA Viruses Identified in an American Wigeon Fecal Sample.

American wigeons (Mareca americana) are waterfowls that are widely distributed throughout North America. Research of viruses associated with American wigeons has been limited to orthomyxoviruses, coronaviruses, and circoviruses. To address this poor knowledge of viruses associated with American wigeons, we undertook a pilot study to identify small circular DNA viruses in a fecal sample collected in January 2021 in the city of Tempe, Arizona (USA). We identified 64 diverse circular DNA viral genomes using a viral metagenomic workflow biased towards circular DNA viruses. Of these, 45 belong to the phylum Cressdnaviricota based on their replication-associated protein sequence, with 3 from the Genomoviridae family and the remaining 42 which currently cannot be assigned to any established virus group. It is most likely that these 45 viruses infect various organisms that are associated with their diet or environment. The remaining 19 virus genomes are part of the Microviridae family and likely associated with the gut enterobacteria of American wigeons.

Identification of small circular DNA viruses in coyote fecal samples from Arizona (USA).

Coyotes (Canis latrans) have a broad geographic distribution across North and Central America. Despite their widespread presence in urban environments in the USA, there is limited information regarding viruses associated with coyotes in the USA and in particular the state of Arizona. To explore viruses associated with coyotes, particularly small DNA viruses, 44 scat samples were collected (April-June 2021 and November 2021-January 2022) along the Salt River near Phoenix, Arizona (USA), along 43 transects (500 m). From these samples, we identified 11 viral genomes: two novel circoviruses, six unclassified cressdnaviruses, and two anelloviruses. One of the circoviruses is most closely related to a circovirus sequence identified from an aerosolized dust sample in Arizona, USA. The second circovirus is most closely related to a rodent-associated circovirus and canine circovirus. Of the unclassified cressdnaviruses, three encode replication-associated proteins that are similar to those found in protists (Histomonas meleagridis and Monocercomonoides exilis), implying an evolutionary relationship with or a connection to similar unidentified protist hosts. The two anelloviruses are most closely related to those found in rodents, and this suggests a diet-related identification.

Anelloviridae taxonomy update 2023.

The family Anelloviridae comprises negative single-stranded circular DNA viruses. Within this family, there are 30 established genera. Anelloviruses in the genus Gyrovirus have been identified infecting various avian species, whereas those in the remaining 29 genera have been found primarily infecting various mammal species. We renamed the 146 anellovirus species with binomial species names, as required by the International Committee on Taxonomy of Viruses (ICTV) using a "genus + freeform epithet" format.

Identification of a novel polyomavirus in wild Sonoran Desert rodents of the family Heteromyidae.

Rodents are the largest and most diverse group of mammals. Covering a wide range of structural and functional adaptations, rodents successfully occupy virtually every terrestrial habitat, and they are often found in close association with humans, domestic animals, and wildlife. Although a significant amount of research has focused on rodents' prominence as known reservoirs of zoonotic viruses, there has been less emphasis on the viral ecology of rodents in general. Here, we utilized a viral metagenomics approach to investigate polyomaviruses in wild rodents from the Baja California peninsula, Mexico, using fecal samples. We identified a novel polyomavirus in fecal samples from two rodent species, a spiny pocket mouse (Chaetodipus spinatus) and a Dulzura kangaroo rat (Dipodomys simulans). These two polyomaviruses represent a new species in the genus Betapolyomavirus. Sequences of this polyomavirus cluster phylogenetically with those of other rodent polyomaviruses and two other non-rodent polyomaviruses (WU and KI) that have been identified in the human respiratory tract. Through our continued work on seven species of rodents, we endeavor to explore the viral diversity associated with wild rodents on the Baja California peninsula and expand on current knowledge of rodent viral ecology and evolution.

Characterization of Diverse Anelloviruses, Cressdnaviruses, and Bacteriophages in the Human Oral DNA Virome from North Carolina (USA).

The diversity of viruses identified from the various niches of the human oral cavity-from saliva to dental plaques to the surface of the tongue-has accelerated in the age of metagenomics. This rapid expansion demonstrates that our understanding of oral viral diversity is incomplete, with only a few studies utilizing passive drool collection in conjunction with metagenomic sequencing methods. For this pilot study, we obtained 14 samples from healthy staff members working at the Duke Lemur Center (Durham, NC, USA) to determine the viral diversity that can be identified in passive drool samples from humans. The complete genomes of 3 anelloviruses, 9 cressdnaviruses, 4 Caudoviricetes large bacteriophages, 29 microviruses, and 19 inoviruses were identified in this study using high-throughput sequencing and viral metagenomic workflows. The results presented here expand our understanding of the vertebrate-infecting and microbe-infecting viral diversity of the human oral virome in North Carolina (USA).

Identification and characterization of a polyomavirus in the thornback skate (Raja clavata).

Members of the family Polyomaviridae have a circular double-stranded DNA genome that have been identified in various hosts ranging from mammals to arachnids. Here we report the identification and analysis of a complete genome sequence of a novel polyomavirus, Raja clavata polyomavirus (RcPyV1), from a cartilaginous fish, the thornback skate (Raja clavata). The genome sequence was determined using a metagenomics approach with an aim to provide baseline viral data in cartilaginous fish in different ecosystems. The RcPyV1 genome (4,195 nucleotides) had typical organization of polyomavirus, including early antigens (small T; Large T) encoded on one strand and late viral proteins (VP1; VP2) on the complementary strand. Maximum-likelihood phylogenetic analysis of the large T-antigen revealed that RcPyV1 clusters with a polyomavirus obtained from another cartilaginous fish, the guitarfish polyomavirus 1 (GfPyV1). These two share ~ 56% pairwise identity in LT and VP1 protein sequences. These analyses support the hypothesis that cartilaginous fishes have a specific lineage of polyomaviruses.

Enhanced detection of mpox virus in wastewater using a pre-amplification approach: A pilot study informing population-level monitoring of low-titer pathogens.

A recent outbreak of the mpox virus (MPXV) occurred in non-endemic regions of the world beginning in May 2022. Pathogen surveillance systems faced pressure to quickly establish response protocols, offering an opportunity to employ wastewater-based epidemiology (WBE) for population-level monitoring. The pilot study reported herein aimed to: (i) develop a reliable protocol for MPXV DNA detection in wastewater which would reduce false negative reporting, (ii) test this protocol on wastewater from various regions across the United States, and (iii) conduct a state of the science review of the current literature reporting on experimental methods for MPXV detection using WBE. Twenty-four-hour composite samples of untreated municipal wastewater were collected from the states of New Jersey, Georgia, Illinois, Texas, Arizona, and Washington beginning July 3rd, 2022 through October 16th, 2022 (n = 60). Samples underwent vacuum filtration, DNA extraction from captured solids, MPXV DNA pre-amplification, and qPCR analysis. Of the 60 samples analyzed, a total of eight (13%) tested positive for MPXV in the states of Washington, Texas, New Jersey, and Illinois. The presence of clade IIb MPXV DNA in these samples was confirmed via Sanger sequencing and integration of pre-amplification prior to qPCR decreased the rate of false negative detections by 87% as compared to qPCR analysis alone. Wastewater-derived detections of MPXV were compared to clinical datasets, with 50% of detections occurring as clinical cases were increasing/peaking and 50% occurring as clinical cases waned. Results from the literature review (n = 9 studies) revealed successful strategies for the detection of MPXV DNA in wastewater, however also emphasized a need for further method optimization and standardization. Overall, this work highlights the use of pre-amplification prior to qPCR detection as a means to capture the presence of MPXV DNA in community wastewater and offers guidance for monitoring low-titer pathogens via WBE.