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.
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.
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 22.214.171.124 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.
Wild boar is the main sylvatic reservoir of the genotype 3 of hepatitis E virus (HEV). The occurrence of HEV-3 human cases has been linked to the consumption of raw or undercooked pig and wild boar meat and liver. The zoonotic transmission of HEV-3 has been confirmed by sequencing identical or strictly related viral strains in humans, wild boar, and derived food. The HEV sequences classified within the HEV-3 genotype are highly variable, and although only one serotype has been identified so far, the observed differences allow for the further classification of the HEV-3 genotype into subtypes, named in alphabetical order. Compared to human and pig strains, an even higher heterogeneity is observed among strains infecting wild boar. In the present study, the genetic variability of eight HEV-3 strains detected in wild boars living in a small geographical area in central Italy (Lazio and Umbria regions) was investigated by full genome sequencing and phylogenetic analysis. The strains were classified within the HEV-3a, HEV-3c, HEV-3f subtypes and within two new recently proposed subtypes. Results demonstrate – despite the relatively small geographic area of origin – an unexpected divergence within HEV-3 strains hosted by the investigated wild boar population and highlights the need for extensive sequencing of HEV in reservoirs to fully understand diversity, geographical distribution and evolution of this group of viruses.
Schistosomiasis is a tropical neglected disease commonly associated with rural areas; however, urban schistosomiasis has been reported world-wide, and increasing urbanization is one of the most important demographic shifts of the 20 th and now 21 st centuries. The pattern of urbanization is not uniform so that within the same city the rates and sources of population increase vary. Here we report on the parasite composition in one neighborhood in the metropolitan area of Salvador, Bahia, Brazil. Using epidemiological data and population genetics we find evidence for local transmission and maintenance of Schistosoma mansoni infection within an urban population and little contribution from rural-urban migration. Our findings provide direction for local mitigation strategies and to assist the public living in this neighborhood to interrupt the local transmission cycle.
Hyalomma ticks are important vectors of Crimean-Congo Haemorrhagic Fever Virus (CCHFV) and other pathogens. They are frequently carried as immatures from Africa, the Middle East and Mediterranean areas to temperate Europe via migratory birds and emergence of its adults has been reported in many countries where it has so far been non-endemic. Our aim was to implement the first steps of the DAMA (Document, Assess, Monitor, Act) protocol by monitoring the potential arrival of adult Hyalomma ticks in Hungary applying citizen-science methods. Ticks were collected from April-December 2021 by asking volunteer participants through a self-made website to look for unusual hard ticks on themselves, their pets and livestock. Owing to the intensive media campaign, the project website had over 31 thousand visitors within seven months and 137 specimens and several hundreds of photos of hard ticks were submitted by citizen scientists from all over the country. Beside Ixodes ricinus, Dermacentor reticulatus, Dermacentor marginatus and Haemaphysalis inermis, a specimen from a dog was morphologically identified as a male Hyalomma marginatum and another removed from a cattle as a male Hyalomma rufipes. The dog and the cattle had never been abroad, they were approximately 280 km apart, thus the two Hyalomma observations can be considered as separate introductions. Amplification of the partial mitochondrial cytochrome C oxidase subunit I gene was successful for both specimens. Sequencing verified the previous morphological identification for both ticks. Based on the phylogenetic analyses the Hy. marginatum individual most likely belongs to the Eurasian population and the Hy. rufipes to a clade of mixed sequences from Europe and Africa. We summarize the scattered historical reports about the occurrence of Hyalomma ticks and CCHFV in Hungary. Our data highlight the effectiveness of citizens science programmes in the monitoring and risk assessment of CCHFV emergence and preparedness in our region.
Successful prevention of epidemics depends on vaccine compliance and the resultant maintenance of high vaccination coverage for long periods. However, to the best of our knowledge, a study of the temporal dynamics of compliance in voluntary vaccination campaigns and of the factors which influence them was never published. In this study, we investigated the factors influencing the dynamics of vaccination compliance against lumpy skin disease (LSD) after the occurrence of LSD epidemics in Israel in 2012-2013 and 2019. From 2016 to 2019, we followed voluntary LSD annual vaccination among a cohort of 566 farmers and used questionnaires based on the theory of planned behaviour to investigate the incentives influencing vaccine compliance among 90 farmers. The results showed a reduction in vaccination against LSD from 61% in 2016 to 27% in 2019 and a very strong association between prior vaccination and vaccination compliance. The actual vaccination by farmers who stated a positive intention to vaccinate was 4.5 times higher than farmers who did not (p-value=0.007). However, half of the highly intended farmers eventually didn’t vaccinate their herd. These farmers were significantly more concerned by manpower and vaccine price compared to their vaccinating counterparts, pointing to vaccination effort perceptions as a major factor influencing compliance. In addition, we found that farmers who answered the questionnaires before the epidemic of 2019 perceived significantly less pressure to vaccinate imposed by veterinary organizations (private and governmental) than farmers answering them during or after the epidemic. We conclude that the veterinarian-associated social pressure is a major compliance-enhancing factor, influenced by the occurrence of an epidemic. Our findings suggest that the deterioration of vaccination compliance after an epidemic can be mitigated by maintenance of pressure to vaccinate by veterinarians. Manpower support and vaccine discounts may be advocated to promote vaccine compliance.