Muskox (Ovibos moschatus, Zimmermann 1780), or Umingmak (in Inuktitut), is a critical component of the terrestrial Arctic ecosystem. In many regions, muskoxen are key to Inuit food security and important to cultural identity, while also providing economic opportunity. Although muskox populations in Greenland and part of Canada appear to be thriving, others are experiencing an uncertain future. A comprehensive understanding of factors driving demographic change, including Indigenous and western science-based knowledge of muskox biology and the Arctic ecosystem in which it lives, is necessary to safeguard populations in the crosshairs of climate change. The inclusion of genomic (or DNA-based) tools into management is predicated on Inuit needs and the amenability of such tools for co-development with Indigenous and scientific partners. The Muskox and Genomics in the Community (MAGIC) workshop was held in Cambridge Bay, Nunavut in January 2024, providing a cross-cultural grounding for discussion on the co-development of genomic tools for muskox conservation and management. Outcomes included forging opportunities for co-learning and knowledge exchange around genomics science and Inuit traditional ecological knowledge, identification of relevant species for whole genome sequencing, documentation of knowledge gaps in muskox biology, and laying conceptual foundations for the co-development of genomics tools based on Inuit Qaujimajatuqangit.

Sheep- and goatpox are highly contagious, transboundary viral diseases caused by capripoxviruses (CaPV), severely impacting small ruminant production and resulting in significant economic losses. Our study aimed to analyze the spatiotemporal SGP distribution using the available genome sequence data and to evaluate the recombination occurrence. For this, the WAHIS, WOAH and FAO databases were utilized for the epidemiological analysis of SGP outbreaks. The cross-correlation was calculated to assess the impact of massive animal movements associated with the Islamic holiday of Eid al-Adha on the SGP epizootic situation, and phylodynamic and phylogeographic analysis, as well as a recombination analysis were performed. A total of 1629 SGP outbreaks were reported to WAHIS during 2010-2024, with the majority occurring in Mongolia, the Balkan countries, Russia and the Middle East. Over 60% of all SGP outbreaks were associated with croplands or grasslands, with the highest proportion corresponding to animal densities of 10-50 head/km2. Statistically significant positive cross-correlation (p < 0.05) was identified between the month of the Eid al-Adha celebration and the number of SGP outbreaks in Russia, Mongolia, Bulgaria and Tajikistan, while in Greece and China no significant correlation was found. The inferred goat pox virus (GTPV) transmission pathways from China to Vietnam and from India to Bangladesh; for the sheeppox virus SPPV, the routes between Kazakhstan and Russia, Kazakhstan and India, as well as between Russia and China, had the strongest Bayes factor support. Intra-specific recombination events were not detected for the SSPV and GTPV datasets. However, inter-specific CaPV recombination analysis identified a single recombination event in GTPV. Therefore, the use of molecular epidemiological tools, along with the time-calibrated phylodynamic and phylogeographic analyses, has significant applications in the local and international surveillance of the occurrence of SGP outbreaks and for identification of potential recombination events.

Classical swine fever (CSF) remains endemic in the non-free zone (NFZ) of Brazil, posing a persistent threat to the country’s swine industry. Understanding the characteristics and the pathogenesis of endemic CSF virus (CSFV) in the NFZ is crucial for developing effective control and eradication strategies. This study provides a comprehensive molecular and pathological characterization of CSFV strains responsible for outbreaks in the northeastern states of Ceará and Piauí in the NFZ between 2018 and 2023. Phylogenetic analysis of full-length E2 and whole genome sequences confirmed that all isolates belonged to a distinct clade of CSFV sub-genotype 1.5, indicating ongoing viral evolution. When six weaned piglets were intranasally inoculated with CSFV Brazil 2019-0571, a representative isolate, they developed mild clinical signs and lesions. Despite mild clinical signs, the piglets developed viremia and shed virus throughout the study. At the conclusion of the study, three pigs had seroconverted and developed neutralizing antibodies. These findings suggest that the circulating CSFV sub-genotype 1.5 strains in the NFZ in Brazil are of low virulence, emphasizing the need for a continuous, multi-pronged approach including clinical, serological, and virological surveillance for the effective control and eradication of CSF in Brazil.

The aim of this study was to detect and characterize foot-and-mouth disease virus (FMDV) serotypes circulating in cattle from Nigeria and to determine the genetic relationship with FMDV from previous studies in Nigeria. A cross-sectional study was undertaken between 2017 and 2020, during which a total of 234 epithelial tissue samples were collected from reported outbreaks in nine states across Nigeria over a four-year period. Serotypes O/EA-3 and SAT2/VII were identified in samples from 2017 and 2018, serotypes A/Africa/G-IV and SAT2/VII in 2019, and all three serotypes including O/EA-3 and O/WA were identified in samples from 2020. This study identified the presence of three FMDV serotypes (O/EA-3 and O/WA, A/Africa/G-IV and SAT2/VII) circulating in Nigeria. The three serotypes detected in this study can be recommended for production of the appropriate vaccines to control FMDV in Nigeria.

H5Nx clade 2.3.4.4b viruses are evolving rapidly, expanding host ranges and threatening animal and public health. In the US, genotype B3.13 dominates dairy outbreaks, while D1.1 is linked to fewer cases. In the UK, an asymptomatic ewe infected with genotype DI.2 raised concerns about ruminant susceptibility. We inoculated lactating and nonlactating sheep with D1.1 (H5N1) and A6 (H5N5) viruses. Intramammary inoculation in lactating sheep caused clinical mastitis, high viral loads in milk, and transmission to suckling lambs, which further spread infection to the uninoculated mammary glands. Both ewes and their lambs seroconverted. Aerosol exposure of nonlactating sheep led to transient respiratory infection, with low-level viral replication, and seroconversion. In vitro, both viruses replicated in sheep mammary epithelial cells. These findings establish sheep as a viable ruminant model for H5N1 and H5N5 infection and highlight previously unidentified transmission dynamics, including milk-mediated and lamb-to-ewe spread, relevant for surveillance and biosecurity in ruminant populations.

Diagnostic testing of foot-and-mouth disease virus (FMDV) currently utilizes reverse transcription quantitative PCR (RT-qPCR) to detect the presence of viral RNA and double antibody sandwich ELISAs (DAS-ELISAs) to determine viral serotype. Serotype identification is critical to support informed vaccine selection to combat outbreaks. While DAS-ELISAs are capable of serotype identification, the test suffers from low sensitivity and requires a viral isolate for successful detection. In this study, we developed FMDV-ONTAPS: an Oxford Nanopore Technologies Amplicon P1 Sequencing protocol involving reverse transcription-PCR to amplify P1 of the FMDV genome, and Nanopore sequencing of the amplicons to provide genetic data for serotype and subtype/topotype identification. FMDV isolates representing all seven serotypes were successfully sequenced with this method. Additionally, the protocol successfully provided serotype identification from a variety of specimen matrices obtained from experimentally infected animals that included milk, serum, oral and nasal swabs, tissue suspensions, vesicular fluid, and oral fluid. The limit of detection for FMDV cell culture isolates was comparable for both sequencing and RT-qPCR detection. RT-qPCR Cq values for clinical samples evaluated ranged from 8 to 28.21. Sequencing was successful for all samples except for a single tissue suspension sample (Cq of 28.21). Identification of FMDV serotype in clinical samples is critical for effective outbreak response, and Nanopore sequencing offers a timelier and more sensitive alternative to DAS-ELISAs.

Abstract Background Plasmids and viruses are two types of mobile genetic elements (ME), that rely on host cells to reproduce and propagate themselves. Recently, metagenomics has greatly facilitated the discovery and characterization of new plasmids and viruses, which relies on accurate identification of these reads in metagenomes. Some state-of-the-art tools can identify plasmid or viral reads, while others are able to identify the probable host or source species of these reads. Since the Minimizer-based Naïve Bayes Classifier (MNBC) tool accurately classifies chromosomal and viral reads to the species level, we extended it to develop the MNBC-ME tool that can also identify plasmid reads and their putative host species. Results A standard reference- and test-sequence framework using simulated variable-length reads was used to benchmark MNBC-ME with eleven other state-of-the-art tools for ME identification: DeepMicroClass, geNomad, PPR-Meta, viralVerify, Plasmer, PlasClass, PlasX, VIBRANT, DeepVirFinder, HOTSPOT, and MOSTPLAS. MNBC-ME was the most consistent tool at classifying chromosomal, viral and plasmid reads of variable lengths, in contrast to the other tools whose precision or recall dropped below 50% in some circumstances. MNBC-ME also exceeded 65% and 70% performance in predicting host genus and family of plasmid reads, respectively. Conclusions MNBC-ME is tool for identification of both short and long viral- and plasmid-originated reads across a wide variety of read types. It also identifies potential low-level host taxa for plasmid reads, and source taxa for chromosomal and viral reads. It is freely available at https://github.com/ComputationalPathogens/MNBC-ME and can be found as the ‘mnbc-me’ package in bioconda.

Abstract Background Influenza A virus (IAV) is a major public health burden, causing seasonal epidemics and occasional pandemics. Its transmission from avian species to mammals and subsequent spread requires adaptive changes in the viral genome. Understanding these molecular adaptations is essential for pandemic preparedness, and machine learning offers a powerful approach to uncover the evolution and biology of IAV. Results This study established a well-calibrated WaveSeekerNet model that accurately predicted the host source across all 8 IAV segments (macro F1-score: 0.9728), significantly improving the reliability of predicted probabilities with calibration errors approaching zero. Model interpretation revealed that avian-adapted IAVs consistently activated G/C content, whereas mammalian-adapted IAVs generally activated A/T content. This distinction was confirmed by codon-level analysis, in which G/C-rich codons were rewarded for the avian hosts and A/T-rich codons for the mammalian hosts. In the feature space learned by WaveSeekerNet, we defined host-adaptive distance to quantify species barriers and proposed it as a risk-assessment metric. We hypothesized the Mammalian Adaptation Zone (MAZ), a zone where the virus is expected to adjust its host-adaptive distance to reach, thereby helping it establish persistent mammalian lineages. The analysis also revealed the Hard Distance of avian-origin viruses (e.g., H5Nx, H9N2), indicating they have not yet established persistent mammalian lineages. Finally, analysis of human H7N9 (2013, China) and non-human mammalian H5Nx (North America) viruses showed that WaveSeekerNet accurately identified key mammalian-adaptive mutations, including PB2-E627K and PB2-D701N. Conclusions WaveSeekerNet elucidated IAV host-adaptation mechanisms in silico, providing insights into the underlying mechanisms of host adaptation and informing improved surveillance and intervention strategies.

The 2021 discovery of a divergent lineage (B.1.641) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in free-ranging white-tailed deer (Odocoileus virginianus) in Ontario raised concerns that deer were a potential reservoir. To assess whether B.1.641 was still circulating in deer and to test for cross-species spillover, we established a surveillance program in Ontario by sampling wildlife via existing ecological projects and through active surveillance of captive and wild animals. Between 2022 and 2024, we tested 2839 animals, identifying one active SARS-CoV-2 infection in a deer (likely a spillover event involving a recombinant XBB.2.3.11.3 lineage), but no cases of B.1.641. Overall, 93 wild animals (6.8%) tested positive for antibodies, including 89 white-tailed deer, two Virginia opossums (Didelphis virginiana), one American mink (Neogale vison), and one river otter (Lontra canadensis). In southwestern Ontario, where B.1.641 was originally detected, 15.2% of deer samples were seropositive. Generalized Linear Models demonstrated that seropositive deer were more likely to be in areas with a higher fall deer harvest and human population, and closer to previous B.1.641 cases. Our data suggest that deer-associated B.1.641 may have caused a relatively localized epizootic without forming a stable reservoir. This study underscores the importance of One Health-focused surveillance.

Amphibians in agricultural drainage ditches may be exposed to contaminants through runoff and subsurface drainage, which can result in toxicity. Understanding the agroecosystem management activities that can sustain healthy amphibian populations will support biodiversity and ecosystem services within intensive agricultural areas. This study examined how woody vegetation within agricultural areas is associated with water quality and amphibian health metrics. Cages containing northern leopard frog (Lithobates [Rana] pipiens) tadpoles were placed within nine agricultural ditches differing in their riparian vegetation height and percentage of surrounding forest cover for eight weeks (May-July) in an agriculturally dominated watershed in eastern Canada. Physicochemical water quality measurements and pesticide concentrations indicated that sites higher in percent forest cover (within 1 km radius) had lower specific conductance, atrazine, nitrate, and potassium concentrations. Percent forest cover was positively associated with tadpole growth (snout-to-vent length, tail length, mass) and riparian vegetation height positively related to tadpole development. Furthermore, glucose levels increased with forest cover, while corticosterone and hepatosomatic index remained unchanged, suggesting that elevated glucose was not strongly associated with chronic stress in this study. Finally, tested tadpoles were negative for Batrachochytrium dendrobatidis, B. salamandrivorans and Frog Virus 3, suggesting these pathogens are not currently a threat to these organisms at the sites tested. Collectively, our findings suggest forested habitats within intensive agroecosystems are critical landscape elements for reducing agrochemical exposure and improving tadpole health in drainage ditches, whereas woody riparian buffers provide limited additional benefits for aquatic stages, highlighting the importance of considering life-stage-specific responses.

Sea otters are a keystone species with cultural significance to Indigenous populations. The increased mortality of Northern sea otters (E. lutris kenyoni) near Kachemak Bay, Alaska, led to a surveillance study to determine the cause of the increased deaths. Samples EL1562 and EL1411 were obtained from two dead-stranded sea otters. Whole genomes of two different orthoreoviruses with all ten segments were obtained. All EL1562 genome segments show the highest similarity to Phocid orthoreovirus 1, a new species isolated from harbor seals. However, the σ1 protein exhibits high divergence (34% amino acid identity) that warrants re-evaluation of the species demarcation criteria. Cell culture and microscopy are consistent with EL1562 being similar to Phocid orthoreovirus 1. Based on binomial naming conventions, we suggest the species name Orthoreovirus marinarum, which encompasses both EL1562 and PhRV1. Characterization of EL1411 sequences shows that it belongs to the species Orthoreovirus mammalis, which includes members from terrestrial mammals. This study represents the first orthoreovirus cultured and genome sequenced from sea otters, and is only the second report of a mammalian orthoreovirus in marine mammals. This study provides new insights into the genetic diversity of orthoreovirus in marine mammals and the evolutionary linkage between terrestrial and marine orthoreoviruses.

Bats are reservoir hosts for a number of coronaviruses, some of which may pose spillover risks for humans and other animals. We detected two alphacoronaviruses in big brown bats (Eptesicus fuscus) and little brown myotis (Myotis lucifugus) in Ontario, Canada. These viruses are closely related to other coronaviruses circulating in bats in North America and also distantly related to human and swine coronaviruses. We found high similarity in the receptor-binding domain (RBD) in viruses derived from the same species of bat, but markedly lower in those derived from other species. We also functionally characterized the accessory protein ORF3 finding that ORF3 inhibited both IFN beta production and signaling. Our study provides insights into coronavirus diversity in bats in a previously under-sampled region. This work provides a baseline for in-depth surveillance to characterize the transmission dynamics of endemic coronaviruses in free-ranging wildlife, and for exploring the evolutionary relationships between coronaviruses and their hosts.

BACKGROUND:Influenza A virus (IAV) poses a significant threat to animal health globally, with its ability to overcome species barriers and cause pandemics. Rapid and accurate IAV subtypes and host source prediction is crucial for effective surveillance and pandemic preparedness. Deep learning has emerged as a powerful tool for analyzing viral genomic sequences, offering new ways to uncover hidden patterns associated with viral characteristics and host adaptation. FINDINGS:We introduce WaveSeekerNet, a novel deep learning model for accurate and rapid prediction of IAV subtypes and host source. The model leverages attention-based mechanisms and efficient token mixing schemes, including the Fourier Transform and the Wavelet Transform, to capture intricate patterns within viral RNA and protein sequences. Extensive experiments on diverse datasets demonstrate WaveSeekerNet's superior performance to existing models that use the traditional self-attention mechanism. Notably, WaveSeekerNet rivals VADR (Viral Annotation DefineR) in subtype prediction using the high-quality RNA sequences, achieving the maximum score of 1.0 on metrics, including the Balanced Accuracy, F1-score (Macro Average), and Matthews Correlation Coefficient. Our approach to subtype and host source prediction also exceeds the pretrained ESM-2 (Evolutionary Scale Modeling) models with respect to generalization performance and computational cost. Furthermore, WaveSeekerNet exhibits remarkable accuracy in distinguishing between human, avian, and other mammalian hosts. The ability of WaveSeekerNet to flag potential cross-species transmission events underscores its significant value for real-time surveillance and proactive pandemic preparedness efforts. CONCLUSIONS:WaveSeekerNet's superior performance, efficiency, and ability to flag potential cross-species transmission events highlight its potential for real-time surveillance and pandemic preparedness. This model represents a significant advancement in applying deep learning for IAV classification and holds promise for future epidemiological, veterinary studies, and public health interventions.

Two near full-length sequences of vesicular stomatitis Indiana virus (VSIV), representing endemic VSIV lineages circulating in cattle in Mexico, are reported. These sequences will allow us to gain more insight into the genetic relationship between endemic viruses in Mexico and the emergence of epizootic lineages in the United States.

We report the detection of a clade 2.3.4.4b A(H5N1) reassortant virus with a neuraminidase surface protein derived from a North American lineage low-pathogenic avian influenza virus. This virus caused a widespread and ongoing outbreak across 45 poultry farms in British Columbia, Canada. Isolates from 8 farms reveal a mutation in the neuraminidase protein (H275Y) that is exceptionally rare among clade 2.3.4.4b viruses (present in 0.045% of publicly available clade 2.3.4.4b isolates). NA-H275Y is a well-known marker of resistance to the neuraminidase inhibitor oseltamivir. We demonstrate that this substitution maintains its resistance phenotype on the genetic background of H5N1 clade 2.3.4.4b viruses.

Domestic pigs are a vital component of the global food supply, with a population nearing 780 million worldwide, making them one of the most commonly raised livestock. As pig production intensifies, the associated practices and environmental conditions may elevate the risk of emergence and spread of zoonotic agents, including ebolaviruses. Previously, we demonstrated that experimentall infection with Orthoebolavirus bundibugyoense and Orthoebolavirus restonense in pigs caused sub-clinical signs, with only a few animals exhibiting elevated temperatures and limited signs of acute respiratory distress. In this study, we sought to describe immune-related gene exression changes following those viral infections in pigs. Our findings revealed no significant changes in infection- and inflammation-related cytokines, but a strong adaptive immune response was observed in the lungs and tracheobronchial lymph nodes. Comparative analysis with a study in which non-human primates were experimentally infected with Orthoebolavirus bundibugyoense, where the virus is lethal, revealed molecular similarities in gene expression. This may suggest that certain viral processes may be conserved across species. These results highlight the potential role of pigs in ebolavirus spillover dynamics and underscore the importance of understanding the role of livestock in the emergence of these pathogens to guide prevention and mitigation strategies.

The emergence of highly pathogenic avian influenza (HPAI) H5N1 clade 2.3.4.4b has led to unprecedented spillover and spread among US dairy cows, raising concerns about transmission to other ruminants. We inoculated two groups of lactating goats via intramammary and respiratory routes with Cow-H5N1 (genotype B3.13) or avian-H5N1 (genotype B1.2) virus. Both groups developed severe clinical mastitis and shed viruses in milk, resulting in transmission to suckling kids. Viral RNA was detected in nasal and oral swabs and various tissues, and virus-neutralizing antibodies were present in serum, milk, and bronchoalveolar lavage fluid. In vitro, both viruses replicated efficiently in goat respiratory and mammary epithelial cells. Mammary tissue expresses both α2,3- and α2,6-linked sialic acid receptors. These findings demonstrate that goats are highly susceptible to H5N1 infection, with mammary tropism facilitating transmission to offspring, and underscore the need for increased surveillance in ruminant livestock.

Crimean-Congo hemorrhagic fever orthonairovirus (CCHFV) is a tick-borne RNA virus that can cause a severe hemorrhagic disease in humans. In animals, CCHFV infection is known to produce a transient viremia followed by host recovery and thus a short window in which animals can serve as potential intermediate hosts. Here we report that, in domestic sheep experimentally infected with CCHFV Kosovo Hoti, viral whole genome sequences were recovered from tissues long after the clearance of viremia. While viral RNA persistence in tissues was largely characterized by a lack of continuous and extensive viral replication, the sporadic presence of replication products (RNA transcripts and proteins) was detected. These findings suggest that the biology of CCHFV in animals goes far beyond an acute infection. A possibility of viral reactivation from a dormant state, akin to that observed in other RNA viruses, warrants further investigation. ### Competing Interest Statement The authors have declared no competing interest. Canadian Safety and Security Program, CSSP-2018-CP-2341 Canadian Food Inspection Agency

Senecavirus A (SVA) continues to cause vesicular lesions in swine in Canada and many regions worldwide. Since the vesicular lesions caused by SVA are similar to those caused by foot and mouth disease virus, swine vesicular disease virus and vesicular stomatitis virus, a foreign animal disease investigation must be initiated to rule out these diseases. SVA isolates from pigs displaying vesicular lesions in Canada from 2015 to 2023 were sequenced, and phylogeographic analysis was performed using the complete genome sequences. The results infer that SVA has spread between the United States and Canada several times. In addition, the results suggest that SVA spreads from different regions. SVA spread was inferred from Canada into Thailand, India and Mexico and inferred from the United States to Brazil, Columbia, Chile and China with ten separate introductions. Furthermore, recombination was observed in SVA genomes from Canada, the United States and China.

We sequenced a novel rhabdovirus, Tupavirus delphini (dolphin tupavirus), from the brain of a stranded dead Atlantic white-sided dolphin with severe encephalitis in Canada. In situ hybridization linked presence of the virus to the animal's brain pathology and death. Our findings underscore the importance of monitoring marine mammals for unexpected pathogens.