Transboundary and Emerging Diseases

Bovine coronavirus (BCoV) is an important contributor to the respiratory disease complex in cattle; however, integrated genomic and epidemiological data describing currently circulating respiratory BCoV strains in the United States remain limited. The objective of this study was to monitor respiratory BCoV at the genomic level and analyze its epidemiological patterns over a five-year period. A total of 4,505 respiratory samples submitted to a diagnostic laboratory between January 2020 and November 2025 were analyzed, of which 693 (15.38%) tested positive for BCoV. Positivity was highest in young calves (0-40 days; 20.0%) and declined significantly with increasing age based on logistic regression analysis. Temporal trend analysis using LOESS smoothing and the Mann-Kendall test showed no significant monotonic change in BCoV detection during the study period. Co-infection analysis indicated that BCoV was commonly detected with other viral respiratory pathogens, while bacterial pathogens predominated in many samples. Lung tissues from infected cattle were screened by RT-PCR, and selected samples with high viral loads were subjected to next-generation sequencing. Complete genome sequencing identified four respiratory BCoV isolates ([~]31 kb), all clustering within genotype GIIb with recent U.S. strains. Comparative genomic analysis revealed several amino acid substitutions in structural and non-structural proteins that may influence viral attachment, replication, and tissue tropism. These findings provide updated epidemiological and genomic insights into respiratory BCoV circulating in U.S. cattle.

Johnes disease (JD), caused by Mycobacterium avium subsp. paratuberculosis (MAP), is an important livestock disease in Japan. We typed 48 field isolates from cattle feces collected on 13 farms in Kushiro Subprefecture during 2024-2025 and 62 MAP-positive cattle fecal samples collected in the same region during 2025-2026 using a real-time PCR assay targeting the Type S-specific arylsulfatase gene. No Type S strains were detected among the cultured isolates or fecal samples examined in this study, suggesting that the cattle cases analyzed were more consistent with Type C than with Type S strains. Broader surveys are needed to define MAP strain diversity in Japan and improve control strategies.

Foot-and-mouth disease (FMD) virus is one of the most feared and most consequential pathogens of livestock worldwide. It can be spread rapidly by the transboundary movement of animals, animal products and byproducts. In January 2025, Germany detected its first FMD outbreak since 1988 in extensively reared water buffalo on a small farm in the state of Brandenburg, directly outside Berlin, the federal capital. Immediate control measures including a standstill for movements of susceptible animals and pre-emptive culling were implemented by the veterinary authorities. Whole-genome sequencing identified the virus as serotype O, topotype ME-SA, lineage SA-2018 and revealed extensive recombination, but cross-neutralization assays suggested good heterologous protection by an O/PanAsia-2 vaccine strain. Epidemiological back-calculation placed the time of virus introduction in late December 2024. Although the entry route remains unresolved, human-associated introduction is most likely. Network analysis revealed minimal farm connectivity, and simulations predicted low potential for onward transmission, which is consistent with the outbreak being ultimately restricted to a single herd. This event underscores the constant and unpredictable risk of introduction of the virus. Early detection through increased awareness and comprehensive differential diagnostics as well as the international collaboration of veterinary services, laboratories and experts are essential in the face of the global presence of FMD.

Porcine Reproductive and Respiratory Syndrome Virus 2 (PRRSV-2) represents a major threat to the global swine industry. The epidemiological dynamics of PRRSV-2 are characterized by the recurrent annual emergence of dozens of variants. Long-distance spread of PRRSV-2 is largely driven by animal shipments. Spatiotemporal dynamics of PRRSV-2 in the USA have been explored; however, how fast variants spread to new regions after their emergence remains unclear, and this information could improve preparedness. To address this, we analyzed 14,835 sequences, retrieved from the Morrison Swine Health Monitoring Project (MSHMP), representing 156 variants sampled from 2015 to 2024, covering the five major swine-producing regions in the USA: the Upper Midwest (UM), Lower Midwest (LM), Atlantic Seaboard (AS), Northeast (NE), and Great Plains (GP). Time to spread was assessed using the time-to-dispersal event analysis and waiting time analyses. Genetic diversity was measured using Hill numbers. The UM had the highest variant richness (n=123), followed by the LM (n=47), AS (n=35), NE (n=45), and GP (n=38). Of the 62 variants that initially emerged in the UM, 17 later spread to other regions. The UM also received the highest number of variant introductions (n=24), followed by LM (n=14), NE (n=14), AS (n=4), and GP (n=7), highlighting regional differences in connectivity and risk. Our results suggest faster dispersal corridors among interior regions (e.g., GP to UM and LM to UM, [~]1.2-2.0 years) and slower for coast to interior pathways (AS to interior, [~]2-3 years). These findings may help anticipate the risk of PRRSV-2 variant introduction and provide more accurate dispersal time estimates, which are useful for improving epidemiological models and disease preparedness.

Mycoplasmopsis [Mycoplasma] agassizii is one of the principal pathogens associated with upper respiratory tract disease (URTD) in tortoises, yet its epidemiology in European wild chelonian populations remains poorly understood. The pathogen has been linked to population declines in some wild tortoise populations and is frequently detected in captive tortoises, where infections may persist subclinically and prolonged contact can facilitate transmission. In this context, the pet trade and the release or escape of captive individuals represent potential pathways for pathogen exchange between captive and wild populations. We assessed the presence and prevalence of M. agassizii in wild Mediterranean tortoises in Spain and compared infection patterns with captive populations. A total of 259 tortoises were sampled between 2020 and 2025, including spur thighed tortoises (Testudo graeca; 127 wild; 63 captive) and Hermanns tortoises (Testudo hermanni; 46 wild; 23 captive). Detection of M. agassizii was performed using PCR. The pathogen was detected in both species, but prevalence patterns differed markedly between captivity status and species. High prevalence was consistently observed in captive individuals of both species. In contrast, wild populations showed species-specific patterns: T. graeca exhibited very low or absent prevalence across wild populations, whereas T. hermanni showed comparatively higher prevalence in the wild. These results provide the first baseline assessment of M. agassizii occurrence in Mediterranean tortoises in Spain and highlight the importance of incorporating pathogen surveillance into conservation and management strategies for European chelonian populations.

Red Mark Syndrome (RMS) is a widespread skin disease affecting rainbow trout (Onchorhynchus mykiss). It provokes substantial economic losses in aquaculture, and is putatively caused by a Rickettsiales bacterium named Midichloria-like organism (RMS-MLO), which is strongly associated with RMS lesions. However, RMS-MLO ecology and epidemiology in aquaculture systems remain poorly understood. In this study, we analysed environmental DNA to monitor the presence of RMS-MLO and its putative vector Ichthyophthirius multifiliis in a trout farm in Northern Italy over one year. Water and sediment samples were monthly collected from multiple water tanks. RMS-MLO was consistently detected by PCR throughout the study in all trout-containing tanks, both in water and sediment samples, but never in the trout-free inflow tank. We did not observe an increase in RMS-MLO abundance during the single RMS outbreak recorded nor in relation with the co-occurrence of I. multifiliis. Our findings indicate a long-term persistence of RMS-MLO in the aquaculture, possibly as a consequence of infections with low prevalence or abundance, rather than its entry from the external environment at the time of RMS outbreaks. Additionally, hints were recorded for a potential role of free-living aquatic microeukaryotes as additional occasional reservoirs. In contrast, I. multifiliis was negatively related with RMS-MLO, while it significantly increased in abundance during the RMS outbreak, particularly in the inflow tank. This supports that, rather than a stable reservoir, I. multifiliis may act as a facilitator of RMS outbreaks, which might indeed be triggered by the entry of this parasite in trout farms.

BackgroundThe emergence of the highly pathogenic avian influenza (HPAI) H5N1 clade 2.3.4.4b in North America, beginning in February 2022, has highlighted the dynamic, unpredictable, and regionally variable risk of infections. Studies are needed to assess the spatiotemporal clustering of HPAI H5 at the interface between wild waterfowl and commercial poultry to better understand and mitigate this risk. MethodsPublicly available data on HPAI H5 detections in wild birds and commercial poultry from January 2022 to January 2026 were analyzed at the county level. Retrospective space-time permutation models were used to identify and scan for clusters with higher than expected detection rates. ResultsA total of 17,091 HPAI H5 detections were reported in wild birds across 1,467 county-level locations. Four species, Mallard (Anas platyrhynchos) (2,848 detections, 16.66%), Canada goose (Branta canadensis) (1,496, 8.75%), Green-winged teal (Anas carolinensis) (1,364, 7.98%), and Snow goose (Anser caerulescens) (1,084, 6.34%), accounted for 39.73% of detections. In commercial poultry, 532 outbreaks in turkey operations, 148 outbreaks in table-egg layer operations, 99 outbreaks in broiler chicken operations, and 89 outbreaks in commercial duck operations were reported, respectively. Several spillover events followed an east-to-west expansion. In early 2022, mallard detections preceded outbreaks in Northeast egg-layer and duck farms, while snow goose detections in the Upper Midwest coincided with turkey farm outbreaks. In the Pacific and Mountain West during summer 2022, detections in Canada geese overlapped with turkey farm outbreaks. A resurgence occurred in the Midwest (2025), with snow and Canada goose detections overlapping severe outbreaks in turkey and layer flocks. Additionally, in the Upper Midwest, Canada goose and mallard detections overlapped with outbreaks in commercial duck farms during fall-winter 2025. ConclusionsThe study findings demonstrate distinct vector-based transmission dynamics of HPAI H5 at the wild waterfowl-poultry interface. Farm biosecurity strategies must adapt to these recurrent, vector-specific risks.

Avian influenza viruses (AIVs) are endemic in the Americas and responsible for outbreaks in both domestic and wild birds that occasionally spill over into humans. We report the first known outbreak of AIV H9N2 in lesser rhea (Rhea pennata), also known as Darwins rhea, in the region of Puno-Peru. The animals in this study lived in an isolated conservation center located in remote highlands above 4,000 m.a.s.l. Between June and July 2025, a total of 46/92 animals were recorded sick, with symptoms including greenish diarrhea (100%), hyporexia (24%), dyspnea (76%), nasal discharge (42%), drowsiness (18%) and isolation from the flock (73%), and 94% later died. Gross pathology exams revealed septicemia characterized by severe hepatitis, pneumonia, tracheitis, enteritis, and encephalitis. Swab and necropsy samples tested positive for Influenza A by PCR and were later identified as H9N2 through whole genome sequencing. We generated complete H9N2 genomes for two individuals. No additional pathogens were found. Phylogenetic analysis across all eight segments revealed that the viruses were low pathogenicity H9N2 AIV strains of North American origin, which indicated this outbreak was a new introduction of the virus into South America. We also performed a comparative mutational analysis and identified multiple mutations previously associated with mammalian host adaptation, increased virulence, increased pathogenicity, and increased virus binding to 2-6 receptors, which may explain the high mortality rates observed despite the supposedly low pathogenicity of the strain. We also identified novel mutations specific to rhea viruses that will need to be experimentally validated. This is the first report of a natural H9N2 systemic infection in an avian host, highlighting a need for increased surveillance efforts for zoonotic influenza viruses with pandemic potential. Author SummaryAvian influenza viruses (AIVs) are endemic in the Americas and cause more than 7,600 infections annually in domestic and wild birds worldwide each year. We report detection of AIV H9N2 in lesser rhea during an outbreak that occurred in June-July 2025 in the Andean highlands of Puno in Peru. Multiple sick animals were reported with symptoms of respiratory and gastrointestinal disease and 94% of them later died. Samples collected tested positive for Influenza A and they were subtyped as H9N2 of low pathogenic origin from North America. This is the third time H9N2 enters South America from North America, presumably through wild birds, some of which migrate along the Pacific Flyway. Comparison with other H9N2 sequences revealed a total of 44 mutations of interest that may explain the elevated death rates observed. Surveillance in wild birds remains patchy at best and needs to be strengthened in order to prevent spillover events into other animals, including humans.

Zoos may serve as sentinel sites for zoonotic vector-borne diseases. West Nile virus (WNV) and Usutu virus (USUV) are closely related orthoflaviviruses transmitted between Culex mosquitoes and a bird reservoir. Both viruses can also infect mammals, including humans, where they may cause symptoms and, more rarely, hospitalization and death. However, serological cross-reactivity between WNV and USUV complicates their differential diagnosis. Here, we aimed to reconstruct the dynamics of emergence of WNV in a zoo located in a newly affected area in Europe, using ELISA and Virus Neutralization Test (VNT) serological analysis of 1707 animal sera collected between 2015 and 2024. Combining this data in a model accounting for cross-reactivity with USUV, we estimated yearly forces of infection (FOI) by both viruses, and thus found that WNV likely circulated in the area one year prior to the first cases reported to the passive surveillance system. Our results also showed that, in the zoo, mammals and reptiles had a lower risk of infection than birds (relative risk of 0.14 [0.05; 0.28]), and that the exposure of birds to water (aquatic lifestyle or proximity to stagnant water) affected the risk. Finally, we estimated diagnosis parameters, including the sensitivity of the VNT (80.4% [76.5%; 84.3%]), the expected VNT titer value, and the level of serological cross-reactivity between viruses during the VNT. To conclude, our modelling framework allowed to disentangle the co-circulation of two closely related viruses, a crucial point in ensuring the reliable sentinel surveillance of these vector-borne zoonotic pathogens.

BackgroundInfectious bovine keratoconjunctivitis is the most important cattle ocular disease worldwide. The infection is primarily caused by Moraxella bovis and is a highly contagious disease that significantly affects cattle welfare. Currently, antibiotic medication is the primary treatment for infectious bovine keratoconjunctivitis. However, with rising concerns over antibiotic resistance, we propose developing a more targeted therapeutic strategy using bacteriophages (phages). Materials and MethodsWe have isolated the first known Moraxella bovis phages, characterised them according to their genome sequence, local virulence index and with transmission electron microscopy. The host ranges were assessed using 41 clinical M. bovis strains isolated from infected cows. ResultsFour phages were isolated and characterised. Comparative analysis identified a high degree of genomic similarity between the phages MB15, MB16, MB26 and MB43. MB43 was the most distinct, with the smallest host range phenotype. ConclusionsThe isolated phages show therapeutic potential for further development against Moraxella infections.

BackgroundIn 2021, the Los Angeles County (LAC) Department of Public Health suspected a leptospirosis outbreak in LAC affecting over 200 client-owned dogs. ObjectiveTo characterize the outbreak and describe microbiologic findings, risk factors, diagnostic test performance, and outcomes in dogs diagnosed with leptospirosis at two specialty practices. MethodsLeptospira culture isolates from four cases were subjected to serotyping and whole genome sequencing (WGS); WGS was also performed on one enriched genome isolate. After the outbreak, data were gathered on 59 cases through record review and compared to the background hospital population (controls, n=15,536). ResultsAll isolates were Leptospira interrogans serovar Canicola, but each was distinct based on WGS. Cases clustered in space and in time. Cases evaluated during the outbreak peak had increased odds of exposure to indoor congregate facilities (ICFs). None of 47 dogs with known leptospirosis vaccination history were completely vaccinated. Leptospira real-time PCR on blood and urine and initial serologic testing using the microscopic agglutination test and point-of-care tests were positive in 15/56 (27%), 49/54 (91%) dogs, 22/29 (76%), and 27/35 (77%) dogs respectively. Fifty-four (92%) of 59 dogs survived to discharge; some remained azotemic. No associated human cases were identified. Conclusions and Clinical ImportanceL. interrogans serovar Canicola was associated with a leptospirosis outbreak in unvaccinated dogs from LAC, which had public health implications given widespread dog ownership rates. Data analysis suggested multiple infection sources, including ICFs. Urine PCR was the most sensitive diagnostic test. Such outbreaks might be prevented through more widespread vaccination.

Human leptospirosis is a disease of public health importance in Thailand, but the animal species involved in the transmission cycle have not been fully uncovered. This study investigated Leptospira infection in dogs and terrestrial micromammals in rural Nan Province, Thailand, and the pathogen diversity. Sera from 95 seemingly healthy dogs and kidney samples from 399 micromammals were analyzed using real-time PCR for Leptospira detection, followed by conventional PCR and sequencing of infecting Leptospira. We investigated environmental factors associated with Leptospira infection in micromammals, using data collected during trapping. Real-time PCR revealed ongoing infection in 8.4% (8/95) of dogs and 10.0% (40/399) of terrestrial micromammals, with 12 infected species including Bandicota indica, Berylmys berdmorei, Berylmys bowersi, Mus cervicolor, Mus cookii, and Hylomys suillus. In this qPCR-positive micromammals, three pathogenic Leptospira species were identified: L. interrogans, L. weilii, and L. borgpetersenii. This represents the first confirmed detection of L. weilii in rodents in Thailand. Infected micromammals were found in agricultural and forest habitats but not in human settlements. Our study demonstrates potential complex leptospirosis epidemiology in rural Thailand, with multiple species serving as pathogenic Leptospira reservoirs across diverse habitats, and some shared pathogen diversity with human leptospirosis cases in Thailand. Free-roaming dogs may serve as bridge hosts, transmitting zoonotic Leptospira from micromammals to humans by visiting both animal habitats and human settlements. These findings emphasize the need for integrated One Health surveillance approaches to control leptospirosis in rural communities.

Introduction Nontyphoidal Salmonella enterica (NTS) is a major zoonotic enteric pathogen. Animal contact-related NTS outbreaks have increased in the United States of America (U.S.) over the last decade. Geospatial analysis can identify locations with elevated risk of NTS outbreaks where public health authorities can focus their NTS prevention and intervention efforts. Methods We analyzed NTS outbreak data reported from individual states to the Centers for Disease Control via the National Outbreak Reporting System between 2009 and 2022 across the continental contiguous U.S. A geospatial analytical framework that included disease mapping, spatial interpolation, and global and local clustering methods was applied to identify regions with high NTS outbreak rates. Results A total of 104 NTS single-state outbreaks were reported to the National Outbreak Reporting System (NORS) during the study period. The mean annual incidence rate was 0.02 NTS outbreaks per million person-years. The primary animal contact categories associated with these outbreaks were mammals (cattle, pigs, sheep, and horses), birds (backyard chickens, ducklings, and turkeys), and reptiles (turtles and lizards). Exposure settings included farms, fairgrounds, agricultural feed stores, veterinary clinics, dairy/agricultural settings, and residential settings. The local cluster detection methods consistently identified areas with significantly high NTS animal contact-related outbreak rates in the Mountain West, Midwest, and Northeast of the US. Conclusion NTS animal contact-related single-state outbreaks revealed distinct spatial clustering across the United States, with potentially higher risks in the Mountain West, Midwest, and Northeast. Diversity of animal-contact sources and exposure settings depicted complex transmission dynamics of NTS. Focused prevention and control programs in these areas are needed to mitigate the burden of NTS outbreaks.

Human sapovirus is increasingly recognized as a significant cause of acute viral gastroenteritis, but in vitro studies have been limited due to the previous lack of cell models. In this study, we optimized two novel in vitro models for sapovirus infection: the human enteroendocrine cell (EEC) line GOT1 and apical-out 3D human enteroids. Using 31 sapovirus-positive fecal samples, we compared these models with the EEC-derived HuTu80, and human enteroid monolayers, both previously used for sapovirus infection. Among the analyzed samples, genotypes GI.1 (36%), GII.1 (32%), and GII.3 (26%) were identified, with GI.1 exhibiting the highest fecal viral load. We demonstrated that GOT1 cells supported replication of more of the samples containing GI.1 sapovirus (9 of 11) compared to HuTu80 (8 of 11) and with a generally higher replication fold change. Moreover, GOT1 cells were able to support the replication of several GII.1 (3 of 10) and GII.3 (5 of 8) samples, unlike HuTu80 cells that only supported replication of one sample with GII.3 and none of the GII.1 sapoviruses. Given that organoids are considered a more physiologically relevant model than transformed cell lines, we established a sapovirus infection model using human apical-out 3D enteroids. Compared to previously used enteroid monolayers, the apical-out model supported replication of a higher number of samples with GI.1 and with higher replication fold change. In conclusion, these findings provide valuable insights for future in vitro studies of sapovirus infection and replication, which may contribute to a better understanding of sapovirus cell tropism and pathogenesis. ImportanceUnderstanding sapovirus biology requires efficient, reliable, and physiologically relevant in vitro models. By systematically comparing four infection models using clinical samples from three common sapovirus genotypes, this study contributes to important information about differences in cellular susceptibility between these in vitro models. We identified the GOT1 cell line as an efficient model for sapovirus replication and introduced apical-out enteroids as a sensitive organoid-based system for studying sapovirus GI.1. Together, the introduced models provide complementary platforms that can contribute to knowledge about sapovirus pathogenesis and cell tropism as well as provide guidance in selecting suitable in vitro models for future sapovirus research.

Foodborne illness is a significant public health concern worldwide. Shiga toxin-producing Escherichia coli and Campylobacter species are recognized as important zoonotic bacterial pathogens contributing to human infections through the food chain, particularly via foods of animal origin. Although goat meat is in high demand in the southern region of Thailand, studies on foodborne pathogens in this livestock species remain limited. The current study aimed to (i) determine the antimicrobial susceptibility of Campylobacter spp. and STEC isolated from goats, and (ii) analyze the genetic relationships among Campylobacter spp. And E. coli O157 isolates obtained from different sources. Campylobacter jejuni and C. coli isolates were characterized based on sequences of seven housekeeping genes using the Achtman multilocus sequence typing scheme. For E. coli O157:H7, core genome multilocus sequence typing analysis was performed using whole-genome sequencing data. Genetic diversity was observed among C. jejuni, whereas a clonal population structure was detected in C. coli and E. coli O157:H7. Overlapping genetic characteristics were observed between C. jejuni isolates from goats and those previously reported in livestock and humans in Thailand. Among Campylobacter species, resistance to fluoroquinolones, including ciprofloxacin and nalidixic acid, was observed, whereas resistance to fosfomycin was most frequently detected in Shiga toxin-producing E. coli. Tetracycline-resistant isolates were identified in both Campylobacter species and Shiga toxin-producing E. coli at moderate levels. A multidrug-resistant pattern was observed only in C. coli, whereas no multidrug-resistant C. jejuni or Shiga toxin-producing E. coli isolates were detected. These findings indicate that healthy goats may serve as potential reservoirs of zoonotic pathogens and antimicrobial resistance in southern Thailand, where goat meat is frequently consumed.

Cetacean pathology is a cornerstone for population and marine ecosystem health monitoring, allowing clear differentiation among natural and anthropogenic threats. Previous studies in the Canary Islands reported natural causes of death in 59.4% (1999-2005) and 81% (2006-2012) of stranded cetaceans, versus anthropogenic causes in 33.3% and 19%, respectively. This study aimed to determine the causes of death (CD), pathologic findings, and epidemiological patterns of 316 cetaceans stranded in the Canary Islands between 2013 and 2018. The CDs were classified in pathologic entities (PEs) emphasizing natural versus anthropic origins. Of 316 animals, 224 (70.9%) from 18 species were suitable for pathological investigations. Among natural PEE, natural pathology associated with good nutritional status (NP-GNS) and natural pathology associated with significant loss of nutritional status (NP-LNS) represented 43/224 (19.2%) and 36/224 (16%) cases, respectively. Natural pathology with undetermined nutritional status (NP-UNS) occurred in 19/224 (8.5%) animals. Intra- and interspecific traumatic interactions (ITI) represented 30/224 (13.4%) cases, followed by neonatal/perinatal pathology (NPN) 19/224 (8.5%) and live-stranding stress and/or capture myopathy (LS-CM) 18/224 (8%). Infectious and parasitic diseases predominated in natural PEs. Anthropogenic PEs included interaction with fishing activities (IFA) in 17/224 (7.6%) cases, vessel collisions (VC) in 9/22 (4%) cases, and foreign body-associated pathology (FBAP) in 3/224 (1.3%) animals. Overall, anthropogenic causes accounted for 12.9% of deaths, natural causes for 73.6%, and the CD could not be established in 30/194 (13.4%) cases. This study reaffirms the trends concerning recognized PEs (NP-GNS, NP-LNS, NP-UNS, ITI, NPN, LS-CM, IFA, VC, and FBAP), expands the body of knowledge on cetacean pathology in the Canary Islands, and reports novel findings including mixed infections, clostridiosis in uncommon species, uremic syndrome secondary to urethral nematodiasis, gas embolism in unusual species, epibiont stomatitis, congenital musculo-skeletal malformations, or neoplastic processes. These findings advance understanding of cetacean mortality patterns and support conservation and management strategies.

This study aimed to evaluate DARO Systems detection of Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) against serum and oral fluid surveillance methods within a controlled study consisting of one PRRSV infected seeder pig and 46 naive nursery pigs. Findings showed DARO Systems comprehensive herd-level surveillance approach detected PRRSV earlier than traditional testing methods.

Mycoplasma bovis was first detected in cattle in New Zealand in 2017, prompting an eradication programme that incorporated extensive surveillance and a test-and-cull policy. Genome sequence data and phylodynamic models were used to inform decision making throughout the eradication programme. Isolates from 697 cattle on 126 farms were collected and sequenced between July 2017 and December 2023. Phylodynamic models were used to estimate the time of most recent common ancestor, the effective reproduction number (Reff) and effective population size, and long-range and local between-farm transmission dynamics. The analysis revealed the dramatic impact of movement restrictions and culling up to early 2020, with a sharp reduction in the Reff to less than 1 in 2018/9 and the extinction of two of three major lineages in 2020. This was followed by three-years of residual infection in farms in the South Island, associated with persistent infection of a large feedlot farm and nearby farms. The comprehensive dataset of genomic and epidemiological data provided a unique opportunity to study the dynamics of a country-wide outbreak of a single-host pathogen from first detection to potential eradication, underlining the utility of integrated genomic surveillance during an outbreak response. Author summaryThe economically important cattle pathogen, Mycoplasma bovis, was first detected in New Zealand in 2017. This led to a large-scale, successful control programme aimed at eradication of the pathogen. The decision to undertake an eradication programme was informed by initial analyses of whole genome sequences from isolates collected as part of the surveillance programme. The analysis showed that the bacteria had entered New Zealand relatively recently and was unlikely to be widespread. Over the subsequent years, genome sequencing and modelling of transmission dynamics informed important policy decisions made by the New Zealand Government and the cattle industry, and helped to monitor progress of the eradication programme. The impact of the detection, movement control and culling programme was profound, with sharp reductions in transmission between 2018 and 2020. This was followed by a long tail of localised infection in the South Island, involving transmission from a large feedlot farm. Provisional eradication was achieved after depopulation of this feedlot. This analysis highlights the role of genomic surveillance and modelling to inform decision making during an infectious disease outbreak.

Borealpox virus (BRPV; formerly Alaskapox) is an orthopoxvirus that has caused seven reported human infections in Alaska since 2015, including a fatal case in 2023. The natural reservoir of BRPV is unknown, although previous investigations have raised the possibility of wild small mammals transmitting the virus to humans, either through direct contact or via domestic cats and dogs. To understand which species may be involved in the maintenance and/or spillover of BRPV in Alaska, we trapped and sampled wild small mammals (including voles, shrews, and squirrels) in 2021 and 2024 near reported human case locations in Fairbanks and the Kenai Peninsula, respectively. We found evidence of previous exposure to orthopoxviruses in five species (including the House Mouse, Mus musculus) and detected BRPV DNA as well as viable virus in Northern Red-backed Voles (Clethrionomys rutilus). Further, screening of tissues from historical museum specimens revealed BRPV DNA in C. rutilus specimens collected in Denali National Park and Preserve in 1998 and 1999, 17 years before the first reported human case of BRPV. Phylogenomic analysis of all human and animal BRPV isolates strongly supports the hypothesis of local human infections through multiple spillover events. These findings suggest C. rutilus as a possible reservoir species for BRPV and indicate that BRPV has been present in Alaskan wild small-mammal populations for at least 25 years. Our study highlights the potential of museum collections to elucidate the temporal, spatial, and host ranges of emerging pathogens. Further museum- and field-based sampling will clarify the true geographic range of BRPV, which is closely related to Old World orthopoxviruses and may be circulating beyond North America.

Rickettsia senegalensis is a novel Rickettsia species isolated from cat fleas, Ctenocephalides felis, in Senegal. Genomic analysis confirmed its status as a distinct species, placing it within the transitional Rickettsia group, within a R. felis cluster. Furthermore, rickettsial genes identical to those of Rickettsia senegalensis had been already identified in several hematophagous arthropods, including fleas and ticks parasitizing various hosts such as cats, dogs, opossums, and rodents in tropical and subtropical regions all over the world. It has also been detected in cat tissues, suggesting a potential host-pathogen association. Here we formally propose Rickettsia senegalensis sp. nov. as a new species. The type strain of this species is strain PU01-02T (= CSUR R184T = DSM 28250T). Strain PU01-02T grows aerobically in XTC-2, SF9, and LD652 cell lines at 28 {degrees}C in a CO2-free atmosphere. The genome of strain PU01-02T has a size of 1.62 Mb and a G+C content of 33.2%. RepositoriesThe genome sequence of Rickettsia senegalensis sp. nov. strain PU01-02T has been deposited in GenBank under accession number JBVYTQ000000000, and the rrs, gltA, ompB and sca4 gene sequences under accession numbers KF666476, KF666472, KF666470, KF666474, respectively. The plasmid accession numbers are PZ272915, PZ272916, and PZ272917, for pRS01, pRS02 and pRS03, respectively.