The objective of the study was to define and then evaluate an early decision indicator (EDI) trigger that operated within the first 5 weeks of a response that would indicate a large outbreak of FMD was developing, in order to be able to inform control options within an adaptive management framework. To define the trigger, a previous dataset of 10,000 simulated FMD outbreaks in New Zealand, controlled by the standard stamping-out approach, was re-analysed at various time points between days 11–35 of each response. The two predictive metrics adopted comprised the mean third quartiles of cumulative numbers of infected premises (IPs) at weekly time points, and estimated dissemination rate (EDR) values indicating sustained spread, specifically > 2.0 between days 11-14 or > 1.5 at any time point between days 15–35 of the response. To evaluate the trigger, the trigger was parameterized within the InterSpread Plus modelling framework, and a new series of simulation generated. The trigger was treated like a series of diagnostic tests that were applied during days 11–35 of each simulated outbreak, and its results recorded and then compared to the final size of each outbreak. The performance of the test was then evaluated across the population of outbreaks, and the sensitivity (Se), specificity (Sp), positive predictive value (PPV) and negative predictive value (NPV) calculated. The Se, Sp, PPV and NPV for predicting large outbreaks were 0.997, 0.513, 0.404 and 0.998 respectively. The study showed that the complex EDI incorporating both the cumulative number of IPs and EDR was very sensitive to detecting large outbreaks, although not all outbreaks predicted to be large were so, whereas outbreaks predicted to be small invariably were small. Therefore, it shows promise as a tool that could support an adaptive management approach to FMD control.

Ranaviruses can infect both captive and wild cold-blooded vertebrates, leading to significant economic and environmental losses. With the cases of ranavirus infection increasing, many ranavirus genomic sequences were published, but little is known about ranavirus taxonomy on a whole genome level. In this study, 44 ranaviruses core genes were identified in 32 ranaviruses genome suquences by using PanX. The Neighbor joining phylogenetic trees (NJ-tree) based on 44 ranaviruses core genes and 24 iridoviridae core genes and composition vector phylogenetic tree (CV-Tree) based on whole genome were constructed. The three of phylogenetic trees showed that 32 ranavirus isolates can be divided to 4 different subspecies including GIV-like, EHNV-like, FV3-like and CMTV-like, and subspecies taxonomic position of three phylogenetic trees were consistent. However, the phylogenetic position of ToRV could not be determined if it belongs to FV3-like or CMTV-like group. Subsequently, we carried out dot plot analysis and confirmed that ToRV should belong to CMTV-like group. Based on dot plot analysis and phylogenetic trees, taxonomic classification of ranaviruses were confirmed. Finally, 4 genes which are suitable for the construction of phylogenetic tree were selected from ranavirus core genes by recombination analysis, substitution saturation analysis and single-gene phylogenetic analysis. Phylogenetic tree based on concatenated sequences of the 4 selected genes showed that classification of subspecies was identical with 3 of the phylogenetic trees. Conclusion: our results confirmed taxonomic identification of ranaviruses, the 4 selected genes used in phylogenic analysis will make taxonomic identification more convenient and accurate.

Worldwide, Mycoplasma gallisepticum (MG) and M. synoviae (MS) are the main agents responsible for chronic respiratory disease in poultry. Therefore, we conducted a systematic review and meta-analysis to estimate their occurrence. We searched electronic databases to find peer-reviewed publications reporting the molecular detection of MG and MS in poultry and used meta-analysis to estimate their pooled occurrence (combined flock and individual), aggregating results at the regional and national levels. We performed a subgroup meta-analysis for subpopulations (broilers, layers, breeders, and diverse poultry including turkeys, ducks, and ostriches) and used meta-regression with categorical modifiers. We retrieved 2,294 publications from six electronic databases and included 85 publications from 33 countries that reported 62 studies with 22,162 samples for MG and 48 studies with 26,413 samples for MS. The pooled occurrence was 38.4% (95% CI: 23.5-54.5) for MS and 27.0% (20.4-34.2) for MG. Among regions, Europe and Central Asia had the lowest occurrence for both pathogens, while MG and MS were highly prevalent in South Asia and sub-Saharan Africa, respectively. MG occurrence was higher in Algeria, Saudi Arabia, and Sudan, whereas China, Egypt, and Ethiopia reported a higher occurrence of MS. MS and MG were more prevalent in the breeders and layers (62.6% and 31.2%, respectively) than in diverse poultry. The year of publication, the sample size, and the level of ambient air pollution (measured indirectly by PM2.5) were associated with the occurrence of both mycoplasmas. Our study revealed a high and heterogeneous occurrence of MG and MS and justifies the need for an early detection and improved control measures to reduce the spread of these pathogens.

Recently, a wound dressing formulation, (Tri-Solfen®, Medical Ethics Pty Ltd, Australia; TS) registered for use in ruminant husbandry in Australia, was registered for Foot-and-Mouth Disease (FMD) therapy in large ruminants in Laos, following clinical observations of improved welfare and healing following treatment of FMD lesions. In November 2019, an FMD outbreak in Cameroon provided an opportunity for a field trial, comparing clinical responses and recoveries to treatments on a sample of cattle (n = 36) comprising three equal groups of animals (n = 12), comparing responses to three treatments:(i) the application to lesions of TS, (ii) the administration of parenteral oxytetraycline commonly used for FMD in Cameroon; and (iii) an untreated control group (C). Appetite scores, lesion healing scores, and changes in dimensions of lesions, were recorded over a 15-day study period. Cattle treated with TS achieved both superior appetite and lesion healing scores with more rapid reduction in dimensions of lesions than other groups. Farmer observations indicated the TS treatment group had a more rapid return to eating with cessation of excessive salivation, and more rapid return of mobility (walking) with absence of overt lameness. The findings indicate that although mortality is usually low in FMD outbreaks, the disease is a debilitating and painful disorder with negative animal welfare impacts that should be addressed. All farmers expressed their desire that the product be made available for use in their region and modelling indicates that TS therapy imposes no additional financial burden on farmers, with the treatment likely to be provided at a similar or reduced cost to current treatment choices. As use of antibiotics for treatment of a viral disease potentially increases pressures for development of antimicrobial resistance and residues in the food chain, TS as an alternative non-antimicrobial therapy should be promoted for wider use in FMD outbreaks.

The current COVID-19 pandemic offers a unique opportunity to examine the utility of Internet search data in disease modelling across multiple countries. Google Trends data (GTD) indicating the volume of Internet searching on ‘Coronavirus’ were obtained for a range of European countries along with corresponding incident case numbers. Significant positive correlations between GTD with incident case numbers occurred across European countries, with the strongest correlations being obtained using contemporaneous data for most countries. GTD was then integrated into a lag distributed model; this improved model quality for both the increasing and decreasing epidemic phases.

In the present study one hundred and sixteen partial G gene sequences of Avian metapneumovirus (aMPV) subtype B, obtained during routine diagnostics in different European Countries in the last few years (2014-2019), were analysed by sequence and phylogenetic analyses in order to draw an updated picture of the molecular characteristics of circulating strains. Nucleotide sequences were compared with other sequences of European and extra-European aMPV-Bs collected prior to that period or retrieved from GenBank. Phylogenetic relationships among the aMPV-B strains, reconstructed using the Maximum Likelihood method implemented in MEGA X, demonstrated that aMPV-B has evolved in Europe from its first appearance, frequently displaying a clear relation with the geographic area of detection. The 40% of aMPV-B viruses analysed were classified as vaccine-derived strains, being phylogenetically related, and showing high nucleotide identity with live commercial vaccine strains licensed in Europe. The remaining 60% were classified as field strains since they clustered separately and showed a low nucleotide identity with vaccines and vaccine-derived strains. The phylogenetic tree showed that the virus has continued to evolve from its first appearance in the ’80s since more recently detected strains belonged to clades phylogenetically distant from the older strains. Unlike vaccine-derived strains, field strains tended to cluster according to their geographic origin and irrespective of the host species where the viruses had been detected. In conclusion, the molecular characterization of aMPV-B and the differentiation between vaccines and field strains through G gene sequence analysis can be a useful tool towards correct diagnosis and should be routinely applied in order to better address the control strategies.

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.

African swine fever virus variants with different numbers of a 10-bp tandem repeat were isolated in South Korea soon after being identified in wild boar. The short emergence periods and sympatric distributions within a narrow geographical region suggest that the variants were sporadically generated in the pre-existing viral population.

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.

In Southern Africa, the African Swine Fever (ASF) sylvatic cycle presents a permanent threat for the development of the pig farming industry. Warthogs (Phacochoerus africanus) and bushpigs (Potamochoerus larvatus), wild reservoirs of ASF are present in Ndumo Game Reserve (NGR), located in Northern KwaZulu Natal Province in South Africa and within 30 km of the locations of endemic ASF outbreaks in Mozambique where sylvatic disease transmission has been implicated. To assess if wild suids represent a risk of ASF virus spillover to domestic pigs in the neighbouring community, transect counts and fence patrols were conducted and camera traps were deployed in NGR to estimate wild suid abundance and incursions outside NGR boundaries. We searched for Ornithodoros ticks in 35 warthog burrows distributed across different NGR areas. Pig farmers (n=254) surrounding Mathenjwa Community were interviewed to gather information on interactions between domestic and wild suids and the occurrence of ASF. We conclude that NGR has established populations of bushpigs and warthogs, estimated at 5 and 3-5 individuals/km2 respectively. Both species move out of the reserve regularly (15.4 warthogs/day and 6.35 bushpigs/day), with a significant increase of movements during the dry season. Some farmers observed warthogs and bushpigs as far as 8 and 19 km from the reserve respectively, but no direct wild-domestic suids interactions nor any ASF outbreaks were reported. In addition, no soft ticks were found among the 35 warthog burrows. The absence of ticks in warthog burrows from NGR and the absence of reported outbreaks and familiarity with ASF in the surrounding farming area, suggest that a sylvatic cycle of ASF is at present unlikely in NGR. However, further research should be undertaken to confirm this by surveying a larger number of warthog burrows and monitoring potential antibodies in warthogs from NGR and domestic pigs in the neighbouring community.

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.

We report on a 15-year-long outbreak of bovine tuberculosis (bTB) in wildlife from a Brazilian safari park. A timeline of diagnostic events and whole-genome sequencing (WGS) of 21 Mycobacterium bovis isolates from deer and llamas were analyzed. Accordingly, from 2003 to 2018, at least 16 animals, from 8 species, died due to TB, which is likely an underestimated number. In three occasions since 2013, the deer presented positive tuberculin tests, leading to the park closure and culling of all deer. WGS indicated that multiple M. bovis strains were circulating, with at least three founding introductions since the park inauguration in 1977. Recent transmission events between nearby farms and the park were not found based on WGS. Lastly, by discussing socio-economic and environmental factors escaping current regulatory gaps that were determinant of this outbreak, we pledge for the development of a plan to report and control bTB in wildlife in Brazil.

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.

Bovine tuberculosis (bTB), caused by Mycobacterium bovis (M. bovis) infection, is a multi-host disease which negatively affects the wildlife industry, with adverse consequences for conservation, ecotourism, and game/wildlife sales. Although interspecies transmission has been reported between some wildlife hosts, the risk of spread in complex ecosystems is largely unknown. As a controlled disease, tools for accurate detection of M. bovis infection is crucial for effective surveillance and management, especially in wildlife populations. There are however, limited species-specific diagnostic tests available for wildlife. Hippopotamuses are rarely tested for M. bovis infection and infection has not previously been confirmed in these species. In this study, blood and tissue samples collected from common hippopotamus (Hippopotamus amphibius) residing in a bTB endemic area, the Greater Kruger Protected area (GKPA), were retrospectively screened to determine whether there was evidence for interspecies transmission of M. bovis, and to identify tools for M. bovis detection in this species. Using the multi-species DPP® VetTB serological assay, a bTB seroprevelance of 8% was found in hippopotamus from GKPA. In addition, the first confirmed case of M. bovis infection in a free-ranging common hippopotamus is reported, based on the isolation in mycobacterial culture, genetic speciation, and detection of DNA in tissue samples. Importantly, the M. bovis spoligotype (SB0121) isolated from this common hippopotamus is shared with other M. bovis-infected hosts in GKPA, suggesting interspecies transmission. These results support the hypothesis that M. bovis infection may be under recognized in hippopotamus. Further investigation is needed to determine the risk of interspecies transmission of M. bovis to common hippopotamus in bTB endemic ecosystems and evaluate serological and other diagnostic tools in this species.

Rabbit Haemorrhagic Disease (RHD) is a significant viral disease affecting lagomorphs. The first documented cases of RHD in Singapore occurred in adult pet European rabbits in September 2020. Singapore subsequently declared the outbreak resolved in December 2020. Epidemiological investigations ruled out introductions via importation of infected rabbits and contaminated feed. The source could not be definitively determined. However, the findings suggest that the incident involved both inter- and intra-household transmission and veterinary clinic-household transmission. This incident demonstrated the importance of sustained application of biosecurity measures, epidemiological investigations, and control, including active case finding, expedient vaccine dissemination, and risk communications. It shows that Singapore, an urbanised city-state, without a significant lagomorph population, could still encounter emerging diseases such as rabbit haemorrhagic disease. Given its social impact on rabbit owners, the National Parks Board Singapore and the private veterinarians worked together to communicate and urge the adoption of biosecurity measures and assuage the concerns of rabbit owners.

Toxoplasmosis is a zoonotic disease caused by the ubiquitous coccidia Toxoplasma gondii. Rodents play an important role in maintaining its life cycle, as they are one of the main diet sources for felids (wild and domestic), the unique definitive hosts. However, reports of toxoplasmosis in porcupines (Rodentia Order) are uncommon, with gaps concerning its pathophysiology. South America is the continent with the greatest genetic diversity of rodents and T. gondii. A free-ranging hairy dwarf porcupine was admitted to a wildlife rescue center with a history of trauma. During rehabilitation, the animal presented neurological symptoms (sporadic episodes of hind limbs paresis) and died five months later. The main findings during necropsy were brain congestion and severe incisor overgrowth associated with maxillary perforation. The histopathological exam showed moderate encephalitis, with variable-sized round cysts, positive for PAS stain and immunohistochemistry for T. gondii. Additionally, two cysts were observed in the medulla of the adrenal gland. Molecular techniques were performed to characterize the parasite load by qPCR (Cq=30) and the genotype by PCR-RFLP with 11 markers, which revealed a new genotype. This case adds to the body of knowledge in comparative pathology of Neotropical Rodentia and reports a new genotype circulating in South America.

There are several routes of African swine fever (ASF) introduction into a country. Among the possible routes of entry, quarantine policies determine the possibility of introduction by legal import of live pigs and pig products. This study aimed at assessing the probability of ASF introduction through legal import of live pigs and pig products during the high risk period (HRP) using a quantitative stochastic approach during 2009-2018. The result indicates that the mean annual probability of ASF introduction by legal import of live pig was 1.58×10-7 (1.52~1.67×10-7 95% CI). The mean annual probability by legal import of pig products was 1.59×10-10 (1.55~1.64×10-10 95% CI), of which Poland assumed 87.9% of the mean annual risk. The current import quarantine policy of Korean government may be enough to block the release of the virus via legal import of live pigs and pig products, and it should be continually enforced. This result can help to elucidate source of infection and minimize the catastrophic consequences of the potential ASF reintroduction into South Korea by designing risk mitigation strategies such as risk-based selection of routes to be assessed and prevented and decreased exposure possibility by increased control of food waste and swill feeding practices.

Since 2014, highly pathogenic avian influenza H5N6 viruses have been responsible for outbreaks in poultry. In this study, four H5N6 virus strains were isolated from fecal samples of sick white ducks and dead chickens in Shandong in 2019. These H5N6 viruses were triple-reassortant viruses that have not been previously characterized. Their HA genes were derived from the H5 viruses and were closely related to the vaccine strain Re-11. Their NA genes all fell into the N6-like lineage and the internal gene were derived from H5N1 and H9N2 viruses. They all showed high pathogenicity in mice and caused lethal infection with high rates of transmission in chickens. Moreover, the SPF chickens inoculated with the current used vaccine in China were completely protected from these four H5N6 viruses. Our study indicated the necessity of continued surveillance for H5 IAV and the importance of timely update of vaccine strains in poultry industry.