Novel polyomaviruses identified in fecal samples from four carnivore species.

Polyomaviruses are oncogenic viruses that are generally thought to have co-evolved with their hosts. While primate and rodent polyomaviruses are increasingly well-studied, less is known about polyomaviruses that infect other mammals. In an effort to gain insight into polyomaviruses associated with carnivores, we surveyed fecal samples collected in the USA from bobcats (Lynx rufus), pumas (Puma concolor), Canada lynxes (Lynx canadensis), and grizzly bears (Ursus arctos). Using a viral metagenomic approach, we identified six novel polyomavirus genomes. Surprisingly, four of the six genomes showed a phylogenetic relationship to polyomaviruses found in prey animals. These included a putative rabbit polyomavirus from a bobcat fecal sample and two possible deer-trophic polyomaviruses from Canada lynx feces. One polyomavirus found in a grizzly bear sample was found to be phylogenetically distant from previously identified polyomaviruses. Further analysis of the grizzly bear fecal sample showed that it contained anelloviruses that are known to infect pigs, suggesting that the bear might have preyed on a wild or domestic pig. Interestingly, a polyomavirus genome identified in a puma fecal sample was found to be closely related both to raccoon polyomavirus 1 and to Lyon-IARC polyomavirus, the latter of which was originally identified in human saliva and skin swab specimens but has since been found in samples from domestic cats (Felis catus).

Complex evolutionary history of felid anelloviruses.

Anellovirus infections are highly prevalent in mammals, however, prior to this study only a handful of anellovirus genomes had been identified in members of the Felidae family. Here we characterise anelloviruses in pumas (Puma concolor), bobcats (Lynx rufus), Canada lynx (Lynx canadensis), caracals (Caracal caracal) and domestic cats (Felis catus). The complete anellovirus genomes (n = 220) recovered from 149 individuals were diverse. ORF1 protein sequence similarity network analysis coupled with phylogenetic analysis, revealed two distinct clusters that are populated by felid-derived anellovirus sequences, a pattern mirroring that observed for the porcine anelloviruses. Of the two-felid dominant anellovirus groups, one includes sequences from bobcats, pumas, domestic cats and an ocelot, and the other includes sequences from caracals, Canada lynx, domestic cats and pumas. Coinfections of diverse anelloviruses appear to be common among the felids. Evidence of recombination, both within and between felid-specific anellovirus groups, supports a long coevolution history between host and virus.

Identification of novel circovirus and anelloviruses from wolverines using a non-invasive faecal sampling approach.

Viruses in the families Circoviridae and Anelloviridae have circular single-stranded DNA genomes and have been identified in various animal species. Some members of the Circoviridae family such as beak and feather disease and porcine circovirus have been found to cause disease in their host animals. Anelloviruses on the other hand have not been identified to cause disease in their hosts but are highly prevalent in mammalian species. Using a non-invasive sampling approach, we identified novel circovirus and anelloviruses from faecal samples of wolverines dwelling in Montana, USA. Wolverines are forest carnivores that feed on a wide variety of carrion and other prey species, and they occupy diverse habitats across northern Europe to North America. Little is known about viruses associated with wild wolverines. Our investigation of the faecal samples resulted in the identification of a novel circovirus from three out of four wolverine samples, two collected in 2018 and one in 2019. Comparison with other circoviruses shows it is most closely related to a porcine circovirus 3, sharing ~69% identity. Additionally, three anellovirus genomes were recovered from two wolverine faecal samples which share 68--69% ORF1 nucleotide similarity with an anellovirus from another mustelid species, pine martens. Here we identify novel single-stranded DNA viruses associated with wolverine and open up new avenues for research.

Improving the accessibility and transferability of machine learning algorithms for identification of animals in camera trap images: MLWIC2.

Motion-activated wildlife cameras (or "camera traps") are frequently used to remotely and noninvasively observe animals. The vast number of images collected from camera trap projects has prompted some biologists to employ machine learning algorithms to automatically recognize species in these images, or at least filter-out images that do not contain animals. These approaches are often limited by model transferability, as a model trained to recognize species from one location might not work as well for the same species in different locations. Furthermore, these methods often require advanced computational skills, making them inaccessible to many biologists. We used 3 million camera trap images from 18 studies in 10 states across the United States of America to train two deep neural networks, one that recognizes 58 species, the "species model," and one that determines if an image is empty or if it contains an animal, the "empty-animal model." Our species model and empty-animal model had accuracies of 96.8% and 97.3%, respectively. Furthermore, the models performed well on some out-of-sample datasets, as the species model had 91% accuracy on species from Canada (accuracy range 36%-91% across all out-of-sample datasets) and the empty-animal model achieved an accuracy of 91%-94% on out-of-sample datasets from different continents. Our software addresses some of the limitations of using machine learning to classify images from camera traps. By including many species from several locations, our species model is potentially applicable to many camera trap studies in North America. We also found that our empty-animal model can facilitate removal of images without animals globally. We provide the trained models in an R package (MLWIC2: Machine Learning for Wildlife Image Classification in R), which contains Shiny Applications that allow scientists with minimal programming experience to use trained models and train new models in six neural network architectures with varying depths.

Identification of circular single-stranded DNA viruses in faecal samples of Canada lynx (Lynx canadensis), moose (Alces alces) and snowshoe hare (Lepus americanus) inhabiting the Colorado San Juan Mountains.

The San Juan Mountains of southern Colorado provide subalpine habitat for a suite of mammalian species including Canada lynx (Lynx canadensis), moose (Alces alces) and snowshoe hare (Lepus americanus). In the winter field season of 2016 five faecal samples from lynx, and one each from moose and snowshoe hare were collected to identify small single-stranded DNA viruses associated with these three prominent species. Thirty-two novel viruses were identified and classified as members of two well established ssDNA families Genomoviridae (n = 22) and Microviridae (n = 10) and one recently proposed new family, Smacoviridae (n = 1). In addition one highly novel circular ssDNA virus was identified which at present does not group with any known family. A high level of genomovirus diversity was identified from faeces collected between and across the three mammal species, with full genome-wide pairwise comparisons showing 57%-97% identity. Twenty genomoviruses can be assigned to the genus Gemycircularvirus and represent 11 species, and two into a distinct species in the genus Gemykolovirus. The single smacovirus identified from moose also represents a distinct smacovirus species. Ten microviruses, seven from moose, one from snowshoe hare and two from lynx, all are part of the Gokushovirinae subfamily. The two from lynx are highly similar to a microvirus previously detected in domestic cat (sharing 88%-90% genome-wide identity), indicating this may be a common felid gut microbiome associated virus. Our findings highlight the broad range of diverse ssDNA viruses present in three mammals inhabiting the San Juan Mountains.