The objective of the study was to simulate New Zealand’s foot-and-mouth disease (FMD) operational plan to determine personnel requirements for a FMD response and understand how the numbers of frontline staff available could affect the size and duration of FMD outbreaks, when using stamping-out (SO) measures with or without vaccination. The model utilized a national dataset of all known livestock farms. Each simulation randomly seeded infection into a single farm. Transmission mechanisms included direct and indirect contacts, local and airborne spread. Prior to each simulation, the numbers of personnel for front-line tasks were set randomly. In a random subset of simulations, vaccination was allowed to be deployed as an adjunct to SO. Front-line tasks included contact tracing, surveillance of at-risk farms, depopulation and vaccination using teams comprising personnel of the different types required by New Zealand’s operational plans. The effect of personnel numbers on the size and duration of epidemics were explored using machine learning methods. In the second stage of the study, using a subset of iterations where numbers of personnel were unconstrained, the number of personnel used each day were quantified. When personnel resources were unconstrained, the 95 th percentile and maximum number of infected places (IPs) were 78 and 462 respectively, and the 95 th percentile and maximum duration were 69 and 217 days respectively. However, severe constraints on personnel resources allowed some outbreaks to exceed the size of the UK 2001 FMD epidemic which had 2026 IPs. The number of veterinarians available had a major influence on the size and duration of outbreaks, while the availability of other personnel types did not. A shortage of veterinarians was associated with an increase in time to detect and depopulate IPs, allowing for continued transmission. Emergency vaccination placed a short-term demand for additional staff at the start of the vaccination programme, but the overall number of person days used were similar to SO-only strategies. This study determined the optimal numbers of front-line personnel required to implement the current operational plans to support an FMD response in New Zealand. A shortage of veterinarians was identified as the most influential factor to impact disease control outcomes. Emergency vaccination led to earlier control of an FMD outbreak, but also resulted in a short-term spike in demand for personnel. A successful response needs to have access to sufficient personnel, particularly veterinarians, trained in response roles and available at short notice.

Ovine papillomavirus (OaPV) comprises four genotypes; OaPV1, OaPV2, and OaPV4 are fibropapillomaviruses within the genus Delta-papillomavirus ( Delta-PV ), whereas OaPV3 is an epitheliotropic virus that belongs to the genus Dyokappa-papillomavirus ( Dyokappa-PV ). To date, all of them have been known to infect sheep only. OaPV1, OaPV2, and OaPV4 have been associated with ovine cutaneous and mucosal fibropapillomas, while OaPV3 is a key factor in the squamous cell carcinoma (SCC) pathway of the sheep skin. Peripheral blood mononuclear cell (PBMC) samples obtained from 128 cattle at public slaughterhouses were investigated using droplet digital polymerase chain reaction (ddPCR). ddPCR is a new-generation PCR technique that enables accurate and absolute quantification of target molecules with high sensitivity and specificity. All OaPVs were detected by identification and quantification of nucleic acids using specific fluorescent probes. Of 128 PBMC samples, 100 (~78%) showed OaPV infections. Further, 42, 35, and 23 PBMC samples showed single, double, and triple OaPV infections, respectively. OaPV1 was responsible for 22 single infections, OaPV2 caused 16 single infections, and OaPV3 and OaPV4 caused two single infections each. OaPV1 and OaPV2 were the most frequent ovine viruses in dual and triple infections. In many PBMC samples, both ovine Delta-PV and Dyokappa-PV were found to be transcriptionally active, as shown by the detection and quantification of E5 oncogene transcripts for OaPV1, L1 transcripts for OaPV2, E6 and E7 transcripts for OaPV3, and E6 for OaPV4. OaPVs were found in the blood samples from cattle that shared grasslands rich in bracken ferns known to contain immunosuppressant substances. Furthermore, OaPVs were also found in cattle from intensive livestock farming without any contact with sheep. Because OaPV DNA was detected in both grass hay and corn silage, it is conceivable that these feed may be the viral sources.

An adult male Kemp’s ridley was found dead on the coast of Kenedy County, Texas in August 2019 with bilateral severe, diffuse granulomatous nephritis. Pan-bacterial 16S rRNA gene PCR and amplicon sequencing of affected tissue indicated the presence of a Neorickettsia. Neorickettsia is a genus of obligate intracellular Alphaproteobacteria that are transmitted by digenean trematodes. For further characterization, primers were designed to amplify and sequence the groEL gene. Phylogenetic analysis found that the organism was distinct from other known species to a degree consistent with a novel species. Immunohistochemistry using an antibody directed against a Neorickettsia surface protein showed bacterial clusters within the renal granulomas. A species-specific quantitative PCR was designed, and detected the organism within the liver and colon of the index case. A qPCR survey of grossly normal kidneys opportunistically collected from additional stranded sea turtle kidneys detected this organism in five of 15 Kemp’s ridley turtles, two of nine green turtles, and neither of two loggerhead turtles. Recognition of this novel organism in an endangered species is concerning; additional work is underway to further characterize the potential of this organism as a pathogen of sea turtles.

African swine fever (ASF) is a high-consequence transboundary disease of domestic and wild swine often characterized by high case mortality rates. On July 29, 2021, the Dominican Republic announced the African swine fever virus (ASFV) had been detected in samples collected in early- to mid-July 2021. Retrospective testing of samples collected as part of a collaborative surveillance project between the United States and the Dominican Republic identified ASFV in samples collected as early as May 13, 2021. These detections represent a new outbreak of ASF in the Dominican Republic, which had been declared free of the disease since 1981. Overall, 73 whole genomes of ASFV were sequenced from clinical samples received during the outbreak across 18 provinces. The genomic sequence data have been deposited in public databases to support and expand global data sharing on this impactful disease. While the sequences show a high degree of nucleotide identity to publicly available ASFV genomes from Europe and Asia, they are genetically distant from genomes in the public repositories by at least 8 previously undescribed single nucleotide polymorphisms.

Crimean-Congo haemorrhagic fever (CCHF) is an emerging tick-borne human disease in Spain. Understanding the spatiotemporal dynamics and exposure risk determinants of CCHF virus (CCHFV) in animal models is essential to predict the time and areas of highest transmission risk. With this goal, we designed a longitudinal survey in two wild ungulate species, the red deer ( Cervus elaphus) and the Eurasian wild boar ( Sus scrofa), in Doñana National Park, a protected Mediterranean biodiversity hotspot with high ungulate and CCHFV vector abundance, and which is also one of the main stopover sites for migratory birds between Africa and western Europe. Both ungulates are hosts to the main CCHFV vector in Spain, Hyalomma lusitanicum. We sampled wild ungulates annually from 2005 to 2020 and analysed the frequency of exposure to CCHFV by a double-antigen ELISA. The annual exposure risk was modelled as a function of environmental traits in an approach to understand exposure risk determinants that allow us to predict the most likely places and years for CCHFV transmission. The main findings show that H. lusitanicum abundance is a major driver of the fine-scale spatial CCHFV transmission risk, while inter-annual variations in the risk are conditioned by virus/vector hosts, by host community structure and by weather variations. The most relevant conclusion of the study is that the emergence of CCHF in Spain might have been associated with recent wild ungulate population changes promoting higher vector abundance. Decreasing wild ungulate population densities could reduce vector abundance and thus virus prevalence and the risk of CCHFV transmission to humans.

Sarcoptic mange, a disease caused by the burrowing mite Sarcoptes scabiei, is globally endemic and an emerging threat to wildlife. Although many studies have shown that wildlife diseases play key roles in biodiversity conservation, knowledge about sarcoptic mange is still insufficient. In this study, we aim to improve the understanding of the impacts of sarcoptic mange on wildlife populations, the mechanisms involved in its ecoepidemiology, and the associated risks to public and ecosystem health by investigating mass death events in gorals and serows in the Qinling Mountains. We conducted interviews with practitioners and local people in the central Qinling Mountains. From the same locations, we collected 24 cutaneous samples from various animals and surveillance data from infrared cameras. Pathological, parasitological and microbiological examinations of the samples were performed. Mite-induced cutaneous lesions, mites and eggs were observed in samples from dead gorals and one dead serow, but not in other species. Molecular analysis confirmed the mites to be S. scabiei that originated from rabbits. The data obtained from the interviews and infrared cameras indicated that the death of wildlife was related to sarcoptic mange infection and that there had been a decrease in the goral population since the outbreak of the disease. We confirmed that sarcoptic mange was the major cause of the mass death events and may have spread from the western to eastern Qinling Mountains. Based on our findings, we propose several protection strategies to help preserve biodiversity in the Qinling Mountains.

The Chinese pangolin ( Manis pentadactyla) is a critically endangered scale-covered mammal belonging to the order Pholidota. Wild pangolins are notably susceptible to pathogen infection and are typically characterized by impoverished health. However, little is currently known regarding the viruses prevalent among pangolins. In this study, we report the detection of two subtypes of canine parvovirus type 2 (CPV-2), namely, CPV-2a and CPV-2c, both of which caused severe diarrheal disease in two post-rescue pangolins with fatal consequences. As in CPV-2-infected dogs, intensive lesion of the mucosal layer of the small intestines is a prominent feature in infected pangolins. Phylogenetic analysis revealed that the VP2 viral protein sequences isolated from one pangolin were classified into the CPV-2c subclade, with 99.8% identities to a CPV-2c strain (MN832850) isolated from a Taiwanese pangolin found in Taiwan Province. In contrast, VP2 sequences obtained from the second pangolin were classified into the CPV-2a subclade, with 99.8% identities to a CPV-2a strain (KY386858) isolated from southern China. In this study, we thus confirmed the infection of pangolins with CPV-2c in mainland China and demonstrate that CPV-2a can also infect pangolins. Based on these findings, we recommend that further investigations should be conducted to establish the interspecies transmission of these viruses among wild pangolins, wild carnivores, and stray dogs.

The rustrela virus (RusV) was recently described as a novel pathogen in a circumscribed area of northern Germany close to the Baltic Sea. Up to now, the virus has been detected in cases of fatal non-suppurative meningoencephalitis in zoo animals of different species and a single wild carnivore as well as in apparently healthy yellow-necked field mice ( Apodemus flavicollis). Data regarding the background of this previously undiscovered pathogen, including clinical presentation of the disease, host range, and distribution of the virus, are still limited. Here, three euthanized red-necked wallabies ( Macropus rufogriseus) from zoos of different areas in northeastern Germany were submitted for necropsy after presenting with apathy and therapeutically unresponsive neurological symptoms. A moderate to severe, non-suppurative meningoencephalitis was diagnosed in all three cases. RusV was consistently detected via RT-qPCR and RNA in situ hybridization in the brains of all wallabies. Other, commonly known neuropathogens could not be detected. Overall, red-necked wallabies appear to be highly susceptible to RusV as novel neuropathogen, which is broader distributed in northeastern Germany.

A novel neurological disorder disease, shaking mink syndrome (SMS), emerged in Denmark and Sweden since 2000. The SMS has seldom been reported in China, and the causative agent is uncertain. SMS outbreaks occurred in multiple provinces in 2020, A total of 44 brain samples from minks associated with SMS were collected from Heilongjiang, Liaoning, and Shandong provinces, of which 28 samples (63.3%) were SMS-Astrovirus (SMS-AstV) positive by reverse transcription PCR. Moreover, the complete coding region sequences (CDS) of a sample collected from a two-month-old mink (termed SMS-Astv-H1) were amplified by PCR. The complete CDS and ORF2 sequences of SMS-AstV-H1 were 94.3% and 96.4% identical to an SMS-AstV strain (GenBank accession number: GU985458). Phylogenetically, SMS-Astv-H1 was closely related to an SMS-AstV strain (GU985458). Based on the above results, we describe the SMS-AstV infections related to SMS among farmed minks in China. Future studies need to focus on epidemiology, virus isolation, and potential interspecies transmission of SMS-AstV.

Global emergence and re-emergence of Porcine epidemic diarrhea virus (PEDV), an Alphacoronavirus which causes a highly contagious enteric disease, have led to several studies addressing its variability. The aim of this study was to characterize the infection of weaned pigs with Swine enteric coronavirus (SeCoV) -a chimeric virus most likely originated from a recombination event between PEDV and Transmissible gastroenteritis virus, or its mutant Porcine respiratory coronavirus-, and two PEDV G1b variants, including a recently described recombinant PEDV-SeCoV (rPEDV-SeCoV), as well as to determine the degree of cross-protection achieved against the rPEDV-SeCoV. For this purpose, forty-eight 4-week-old weaned pigs were randomly allocated into four groups of 12 animals; piglets in groups B, C and D were orally inoculated with a PEDV variant (B and D) or SeCoV (C), while piglets in group A were mock inoculated and maintained as controls. At day 20 post-infection all groups were exposed to rPEDV-SeCoV; thus, group D was subjected to a homologous re-challenge, groups B and C to a heterologous re-challenge (PEDV/rPEDV-SeCoV and SeCoV/rPEDV-SeCoV, respectively) and group A was primary challenged (-/rPEDV-SeCoV). Clinical signs, viral shedding, microscopic lesions and specific humoral and cellular immune responses (IgG, IgA, neutralizing antibodies and IgA and IFN-γ-secreting cells) were monitored. After primo-infection all three viral strains induced an undistinguishable mild-to-moderate clinical disease with diarrhea as the main sign and villus shortening lesions in the small intestine. In homologous re-challenged pigs, no clinical signs or lesions were observed, and viral shedding was only detected in a single animal. This fact may be explained by the significant high level of rPEDV-SeCoV-specific neutralizing antibodies found in these pigs before the challenge. In contrast, prior exposition to a different PEDV G1b variant or SeCoV only provided partial cross-protection, allowing rPEDV-SeCoV replication and shedding in feces.

The H9N2 subtype of avian influenza virus (H9N2 AIV) has caused significant losses in chicken flocks throughout China. Our previous research has showed that field isolates of H9N2 underwent antigenic drift to evolve into distinct groups with significant antigenic divergence from the commercially available vaccines. The present study sought to identify which single mutations that have naturally appeared in isolates from the past 5 years has driven antigenic drift. Six high-frequency mutation sites in/near the receptor binding site (RBS) region were screened by comparing amino acid alignments of the H9N2 AIVs isolated from China between 2014 and 2019. Two substitutions, (A168N and D201G) were demonstrated to have a significant impact on the antigenicity, but did not change the growth kinetics and cell tropism of the virus. It is worth noting that the D201G substitution not only significantly changed the antigenicity, but also caused immune escape of the parental virus. In conclusion, A168N and D201G substitution are newly discovered determinants that can significantly change the antigenicity of H9N2 AIV, which should be tracked during outbreaks.

The analysis of domestic pig movements have became useful in the understanding of disease spread patterns and epidemiology, which facilitates the development of more effective animal diseases control strategies. The aim of this work was to analyse the static and spatial characteristics of the pig network, to identify its trading communities and to analyse the contribution of the network to the transmission of classical swine fever. Pig movement data were extracted from the national veterinary service database (2017-2019), using social network analysis and spatial analysis we constructed a network with registered premises as nodes and their movements as edges, and also a network of parishes as its nodes aggregating their premises movements as edges. The annual network metrics showed in average a diameter of 20.33, a number of neighbours of 2.61, a shortest path length of 4.39 and a clustering coefficient of 0.38 (small-world structure). The most frequent movements were to or from markets (57%). Backyard producers made up 89% of the network premises, and the top 2% of parishes (highest degree) contributed to 50% of the movements. The highest frequencies of movements between parishes were in the centre of the country, while the highest frequency of movements to abattoirs was in the south-west. Finally, the pattern of CSF disease outbreaks within the Ecuador network was likely the result of network transmission processes. In conclusion, our results represent the first exploratory analysis of domestic pig movements at premise and parish levels. These results could be taken into account by the surveillance system to improve its procedures and update the disease control and management policy, allowing the implementation of targeted or risk-based surveillance.

Infections with Tuberculosis (TB)-causing agents of the Mycobacterium tuberculosis complex threaten human, livestock, and wildlife health globally due to the high capacity to cross trans-species boundaries. Tuberculosis is a cryptic disease characterized by prolonged, sometimes lifelong subclinical infections, complicating disease monitoring. Consequently, our understanding of infection risk, disease progression, and mortality across species affected by TB remains limited. The TB agent Mycobacterium suricattae was first recorded in the late 1990s in a wild population of meerkats inhabiting the Kalahari in South Africa and has since spread considerably, becoming a common cause of meerkat mortality. This offers an opportunity to document the epidemiology of naturally spreading TB in a wild population. Here, we synthesize more than 25 years-worth of TB reporting and social interaction data across 3,420 individuals to track disease spread, and quantify rates of TB social exposure, progression, and mortality. We found that most meerkats had been exposed to the pathogen within eight years of first detection in the study area, with exposure reaching up to 95% of the population. Approximately one quarter of exposed individuals progressed to clinical TB stages, followed by physical deterioration and death within a few months. Since emergence, 11.6% of deaths were attributed to TB, although the true toll of TB-related mortality is likely higher. Lastly, we observed marked variation in disease progression among individuals, suggesting inter-individual differences in both TB susceptibility and resistance. Our results highlight that TB prevalence and mortality could be higher than previously reported, particularly in species or populations with complex social group dynamics. Long-term studies, such as the present one, allow us to assess temporal variation in disease prevalence and progression and quantify exposure, which is rarely measured in wildlife. Long-term studies are highly valuable tools to explore disease emergence and ecology, and study host-pathogen co-evolutionary dynamics in general, and its impact on social mammals.

The last influenza pandemic in 2009 emerged from swine and surveillance of swine influenza is important for pandemic preparedness. Movement of swine during husbandry, trade or marketing for slaughter provide opportunities for transfer and possible genetic reassortment of swine influenza viruses. Over 90% of the swine slaughtered at the central swine abattoir in Hong Kong are imported from farms located in multiple provinces in mainland China. There is opportunity for virus cross-infection during this transport and slaughter process. Of the 26,980 swabs collected in the slaughterhouse in Hong Kong from 5 th January 2012 to 15 th December 2016, we analyzed sequence data on influenza A (H3N2) virus isolates (n = 174) in conjunction with date of sampling and originating farm. Molecular epidemiology provided evidence of virus cross-infection between swine originating from different farms during transport and also evidence of a virus lineage persisting in a swine farm for over 2 years. We used virus serology and isolation data from 4,226 paired pig serum and nasal swabs collected from swine originating from Guangdong Province to compare the force of infection (FOI) during transport and within farms. The mean weekly FOI during transport was λ t = 0.0286 (95% CI = 0.0211-0.0391) while the weekly FOI in farms was λ f = 0.0089 (95% CI = 0.0084-0.0095), assuming a duration of stay in farm of 28 weeks, suggesting increased force of infection during the transport process. Potential risk factors for infection including the duration in transport, length of stay at slaughterhouse and farm-level seroprevalence were also assessed by multivariable logistic regression analysis. Transport may increase virus cross-infection rates and provide opportunities for virus reassortment potentially increasing zoonotic risk to those involved in the transportation and slaughtering processes.

Background: Mites represent the second largest group with diverse niches and feeding habits, except for insects. Scabies mites are the causative agents of highly contagious skin disease in humans and more than 100 mammals. Although several versions of Sarcoptes scabiei genome have been published, i.e. var. suis, var. canis and var. hominis, the chromosome-level genome and population divergence is still desired for the community. Besides, the molecular mechanisms that scabies mites adapt to a parasitic lifestyle remains unclear. The taxonomy and ancestral origin of the scabies mite is unknown. Results: Here, we reported the first chromosome-level reference genome of S. scabiei, which was isolated from rabbits. The genome has a contig N50 size of 5.92 Mb, a total assembled length of 57.30 Mb, and ~12.65% of repetitive sequences and 9,333 protein‑coding genes were predicted. Population genetics analysis supported that scabies mites isolated from different hosts can be subdivided by hosts, and humans are likely the primary hosts of scabies mites, followed by pigs, dogs, and rabbits. However, phylogeny results suggested that rabbit was infected with scabies long before they were domesticated by humans, contradicting previous hypothesis that humans transmitted scabies mites to animals through domestication. Comparative genomics between scabies mites and mites of other feeding habits provided clues concerning the mechanisms of adaptation to permanent parasitic life from morphology, detoxification, and metabolism. Conclusions: Together, the first chromosome-level S. scabiei genome and population genetics analysis indicated its genetic subdivisions and within-host species divergence, which also provide evidence for further control of this highly contagious skin disease.

Despite the recognized role of wild waterfowl in the potential dispersal and transmission of highly pathogenic avian influenza (HPAI) virus, little is known about how infection affects these birds. This lack of information limits our ability to estimate viral spread in the event of an HPAI outbreak, thereby limiting our abilities to estimate and communicate risk. Here we present telemetry data from a wild Lesser Scaup ( Aythya affinis), captured during a separate ecology study in the Chesapeake Bay, Maryland. This bird tested positive for infection with clade 2.3.4.4 HPAI virus of the A/goose/Guangdong/1/1996 (Gs/GD) H5N1 lineage (results received post-release) during the 2021-22 ongoing outbreaks in North America. While the infected bird was somewhat lighter than other adult males surgically implanted with transmitters (790g, mean=868g, n=11), it showed no clinical signs of infection at capture, during surgery, nor upon release. The bird died 3d later, pathology undetermined as the specimen was not able to be recovered. Analysis of movement data within the 3d window showed that the infected individual’s maximum and average hourly movements (3894.3m, 428.8m respectively) were noticeably lower than noninfected conspecifics tagged and released the same day (mean =21594.5m, mean =1097.9m, respectively; n=4). We identified four instances where the infected bird had direct contact (fixes located within 25m and 15 min) with another marked bird during this time. Collectively, these data suggest that the HPAI positive bird observed in this study may have been shedding virus for some period prior to death, with opportunities for direct bird to bird or environmental transmission. Although limited by low sample size and proximity to the time of tagging, we hope that these data will provide useful information as managers continue to respond to this ongoing outbreak event.

Feline panleukopenia (FPL) is a severe, often fatal disease caused by feline parvovirus (FPV). How infection with FPV might impact the composition of the entire eukaryotic enteric virome in cats has not been characterized. We used metatranscriptomic and viral particle enrichment metagenomic approaches to characterize the enteric viromes of 23 cats naturally infected with FPV (FPV-cases) and 36 age-matched healthy shelter cats (healthy controls). Sequencing reads were detected from 11 mammalian infecting viral families mostly belonging to Coronaviridae, Parvoviridae and Astroviridae. Among the healthy control cats the most abundant viruses were Feline coronavirus, Mamastrovirus 2 and Carnivore bocaparvovirus 3 (Feline bocavirus 1) with frequent co-infections of all three. Feline chaphamaparvovirus was only detected in healthy controls (6/36, 16.7%). Among the FPV-cases, in addition to FPV, the most abundant viruses were Mamastrovirus 2, Feline coronavirus and Carnivore bocaparvovirus 4 (Feline bocaparvovirus 2). The latter and Feline bocaparvovirus 3 were detected significantly more frequently in FPV-cases than in healthy controls. Feline calicivirus was present in a high proportion of FPV-cases (11/23, 47.8%) compared to healthy controls (5/36, 13.9%, p=0.0067). Feline kobuvirus infections were also common among FPV-cases (9/23, 39.1%) and were not detected in any healthy control cats (p<0.0001). While abundant in both groups, astroviruses were more frequently present in FPV-cases (19/23, 82.6%) than in healthy controls (18/36, p=0.0142). The differences in eukaryotic virome composition found in this study indicate that further investigations to determine associations between enteric viral co-infections on clinical disease severity in cats with FPL are warranted.

Tenacibaculum maritimum is a devastating bacterial pathogen affecting a large variety of marine fish species. It is responsible for significant economic losses in aquaculture farms worldwide. Different typing methods have been proposed to analyze bacterial diversity and population structure. Serological heterogeneity has been observed and up to four different serotypes have been described so far. However, the underlying molecular factors remain unknown. By combining conventional serotyping and genome-wide association study, we identified the genomic loci likely involved in the O-antigen biosynthesis. This finding allowed the development of a robust multiplex PCR-based serotyping scheme able to detect subgroups within each serotype and therefore performs better than conventional serotyping. This scheme was successfully applied to a large number of isolates from worldwide origin and retrieved from a large variety of fish species. No obvious correlations were observed between the mPCR-based serotype and the host species or the geographic origin of the isolates. Strikingly, the distribution of mPCR-based serotypes does not follow the core-genome phylogeny. Nevertheless, this simple and cost-effective mPCR-based serotyping method could be useful for different applications such as population structure analysis, disease surveillance, vaccine formulation and efficacy follow-up.