After its first description in Wuhan (China), SARS-CoV-2 the agent of coronavirus disease 2019 (COVID-19) rapidly spread worldwide. Previous studies suggested that pets could be susceptible to SARS-CoV-2. Here, we investigated the putative infection of SARS-CoV-2 in 22 cats and 11 dogs from owners previously infected or suspected of being infected by SARS-CoV-2. For each animal, rectal, nasopharyngeal swabs and serum were taken. Swabs were submitted to RT-qPCR assays targeting 2 genes of SARS-CoV-2. All dogs were tested SARS-CoV-2 negative. One cat was tested positive by RT-qPCR on rectal swab. Nasopharyngeal swabs from this animal were tested negative. This cat showed mild respiratory and digestive signs. Serological analysis confirm the presence of antibodies against the SARS-CoV-2 in the two serum samples taken 10 days apart. Genome sequence analysis revealed that the cat SARS-CoV-2 belongs to the phylogenetic clade A2a like most of the French human SARS-CoV-2. This study reports for the first time the natural infection of a cat in France (near Paris) probably through their owners. There is currently no evidence that cats can spread COVID-19 and owners should not abandon their pets or compromise their welfare.

Newcastle disease (ND), caused by avian orthoavulavirus type-1 (NDV), is endemic in poultry in the Middle East causing continuing outbreaks in poultry populations despite efforts to vaccinate. In the past, genotype 2.XXI (former 2.VI) was present in poultry in Egypt but has been replaced by genotype 2.VII. We investigated whether virus evolution contributed to superseding, and focused on the antigenic sites within the Heamagglutinin-Neuramindase (HN) spike protein. Full length sequences of a NDV genotype 2.VII isolate currently circulating in Egypt was compared to a genotype 2.XXI isolate that was present as co-infection with vaccine type viruses (2.II) in an historical isolate of the year 2011. Amino acid differences in the HN glycoprotein for both 2.XXI and 2.VII viruses amounted to 11,7% and 11,9 % compared to LaSota vaccine type. However, mutations within the globular head (aa 126-570), bearing relevant antigenic sites, were underrepresented (aa divergence of 8,8% and 8,1 % compared to 22,4% and 25,6% within the fragment encompassing cytoplasmic tail, transmembrane part and stalk regions (aa 1-125) for genotypes 2.XXI and 2.VII, respectively. Nevertheless, reaction patterns of HN-specific monoclonal antibodies revealed differences between vaccine type viruses and genotype 2.XXI and 2.VII viruses for specific epitopes. Accordingly, compared to Egyptian vaccine type isolates and the LaSota vaccine reference strain, single aa substitutions in 6 of 10 described neutralizing epitopes were found within the attachment protein. However, the same alterations in neutralization sensitive epitopes were present in old genotype 2.XXI as well as in newly emerged genotype 2.VII isolates. In addition, isolates were indistinguishable by polyclonal chicken sera raised against different genotypes including vaccine viruses. These findings suggest, that factors other than antigenic differences within the HN-protein account for facilitating spread of genotype 2.VII while displacing genotype 2.XXI viruses in Egypt.

The current COVID-19 pandemic highlights the need for zoonotic infectious disease surveillance. Avian influenza virus (AIV) poses a significant threat to animal and public health due to its pandemic potential. Virus-contaminated water has been suggested as an important AIV spread mechanism among multiple species. Nevertheless, few studies have characterized the global AIV subtype diversity and distribution in environmental water. Therefore, this study aims to provide an updated descriptive and phylogenetic analysis of AIVs isolated in water samples from high risk-sites for influenza outbreaks (i.e., live bird markets, poultry farms, and wild bird habitats) on a global scale. A total of 234 hemagglutinin (HA) gene sequences of 21 subtypes were reported from nine countries between 2003 – 2020. Fourteen AIV subtypes were solely reported from Asian countries. Most of the viral sequences were obtained in China and Bangladesh with 47.44% and 23.93%, respectively. Likewise, the greatest global AIV subtype diversity was observed in China with twelve subtypes. Live bird markets represented the main sampling site for AIV detection in water samples (64.10%), mostly from poultry cage water. Nevertheless, the highest subtype diversity was observed in water samples from wild bird habitats, especially from the Izumi plain and the Dongting Lake located in Japan and China, respectively. Water from drinking poultry troughs evidenced the greatest subtype diversity in live bird markets, meanwhile, environmental water used by ducks had the highest number of different subtypes in poultry farms. The maximum-likelihood phylogenetic tree showed that some HA sequences were closely related among different poultry/wild bird-related environments from different geographic origins. Therefore, the results suggest that even though the availability of HA gene sequences in public-access databases varies greatly among countries, environmental AIV surveillance represents a useful tool to elucidate potential viral diversity in wild and domestic bird populations.

The incidence of bovine tuberculosis (TB, caused by Mycobacterium bovis) in cattle has been associated with TB in badgers ( Meles meles) in parts of England. The aim was to identify badger associated M. bovis reservoirs in the Edge Area, between the High and Low Risk Areas for cattle TB. Data from badger TB surveys were sparse. Therefore, a definition for a local M. bovis reservoir potentially shared by cattle and badgers was developed using cattle TB surveillance data. The performance of the definition was estimated through Latent Class Analysis using badger TB survey data. Spatial units (25 km 2 ) in the Edge Area were classified as having a reservoir if they had i) at least one OTF-W (Officially Tuberculosis Free – Withdrawn) incident in a cattle herd not attributed to cattle movement in the previous two years, ii) more OTF-W incidents than Officially Tuberculosis Free – Suspended (OTF-S) incidents in the previous two years and iii) at least one TB incident (OTF-S or OTF-W) in at least three of the previous seven years. Approximately twenty percent of the Edge Area was classified as having a local M. bovis reservoir using the cattle-based definition. Assuming 15% TB prevalence in Edge Area badgers, sensitivity for the local M. bovis reservoir definition varied from 25.7% (95% Credible Interval (CrI) 10.7 to 85.1 %) to 64.8 % (95% CrI 48.1 to 88.0 %). Specificity was 91.9% (CrI 83.6 to 97.4 %). Over ninety percent of the local reservoir was in stable endemic TB areas identified through previous work and its spatial distribution was largely consistent with local veterinary knowledge. Uncertainty in the reservoir spatial distribution was explored through its recalculation in spatial units shifted in different directions. We recommend that the definition is re-evaluated as further data on badger infection with M. bovis becomes available.

Hirudo nipponia is not only an important economic pillar for farmers, but is also a precious raw material for medicinal materials. However, in recent years, H. nipponia suffered from diseases with symptoms including systemic edema and hyperemia. It has not yet been demonstrated which pathogen causes this disease and whether this could be transmitted to humans. In this study, Klebsiella pneumoniae was isolated and identified from diseased H. nipponia and the pathogenicity of the isolated strain was confirmed. Furthermore, by comparing the sequence of the pathogen isolated from leeches to the same pathogen infecting humans, we identified that the isolated strain is a threat to human health. This work emphasizes the importance of the first discovery of pathogenic bacteria from leeches similar to human pathogens, as well as the need for identifying comorbidities for both humans and aquatic animals.

During the current COVID-19 pandemic, different methods have been used to evaluate patients suspected with infection of SARS-CoV-2. In this study, we evaluate the longevity of saliva and dry swab samples to retain SARS-CoV-2 for storage and transport at different environmental settings. Our results show that at ambient temperature of 20°C, SARS-CoV-2 RNA remains stable for up to 9 days giving a long span of time for transport and storage without compromising clinical results. Additionally, this study demonstrates that sali­­­va and dry swabs specimens can also be stored at -20°C and +4°C for up to 26 days without affecting RT-qPCR results. Our data is relevant for low-and middle-income countries, which have limited access to rapid refrigerated transport and storage of samples representing an economical alternative. Finally, our study demonstrates that dry swabs provide clear advantages over using transport medium.

Current results do not provide conclusive evidence on the effect of BCG vaccination on COVID-19 alone or in combination with other factors. To address this limitation, in this study we used a citizen science initiative on the COVID-19 pandemic to collect data worldwide during October 2-30, 2020 (1,233 individuals) in a structured way for analyzing factors and characteristics of affected individuals in relation to BCG vaccination. For the first time, the results of our study suggested that vaccination with BCG may increase the risk for COVID-19 at certain age, particularly in individuals vaccinated at childhood. A reasonable explanation for this effect is the activation of certain innate immunity mechanisms associated with inflammatory reactions, which should be considered when analyzing the risks associated with this global pandemic. These factors should be considered when analyzing the risks associated with this global pandemic.

The raw case fatality rate (CFR, reported number of COVID-19 deaths divided by the number of cases) is a useful indicator to quantify the severity or treatment efficacy in a locality. In many countries, the pandemic showed a two-wave pattern now, namely the daily reported cases once reached a low level and now went up. To our knowledge, no study has compared the CFR for the two waves. In this work, we report that in 53 countries or regions with the highest deaths, the CFR is reduced in 43 countries or regions in the on-going second wave. We discussed the possible reasons. Also, we compare the two-wave pattern of COVID-19 with the weekly influenza positive tests. The influenza activity in pre-pandemic era provided an indicator for climate in a country, since it is well-known that influenza is driven by weather. The sharp drop in 2020 influenza activity is an indicator of the effects of social distancing.

This systematic review and meta-analysis aimed to recalculate the efficacy of these two vaccine strains, and to discuss the main variables associated with controlled trials to evaluate bovine brucellosis vaccines efficacy. The most used vaccine strain was S19, at the dose of 10 10 colony forming units (CFU), followed by the vaccine strain RB51 at 10 10 CFU. The most used challenge strain was B. abortus 2308, at the dose of 10 7 CFU by intraconjunctival route. For the meta-analysis, trials were grouped according to the vaccine strain and dose to recalculate protection against abortion (four groups) or infection (five groups), using pooled risk ratio (RR) and vaccine efficacy (VE). For protection against abortion (n = 15 trials), S19 vaccine at 10 9 CFU exhibited the highest protection rate (RR = 0.25, 95% CI: 0.12 to 0.52; VE = 75.09%, 95% CI: 48.08 – 88.05), followed by RB51 10 10 (RR = 0.31, 95% CI: 0.16 to 0.61; VE = 69.25%, 95% CI: 39.48 – 84.38). For protection against infection (n = 23 trials), only two subgroups exhibited significant protection: S19 at 10 9 CFU (RR = 0.28, 95% CI: 0.14 to 0.55; VE = 72.03%, 95% CI: 57.70 – 81.50) and RB51 at 10 10 CFU dose (RR = 0.43, 95% CI: 0.22 to 0.84; VE = 57.05%, 95% CI: 30.90 – 73.30). In conclusion, our results suggest that the dose of 10 9 CFU for S19 and 10 10 CFU for RB51 are the most suitable for the prevention of abortion and infection caused by B. abortus.

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.

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.

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.

During the European emergence of Schmallenberg virus (SBV) in 2011, examination of Culicoides spp. showed that SBV infected midges were present across Denmark. However, SBV associated malformations in ruminant species have not been reported in Denmark. In April 2021, seven calves with severe congenital generalized arthrogryposis and reduced body weight originating from a narrow region of the Jutlandic peninsula were submitted for examination. Analysis of fetal brain tissue for SBV viral RNA and pleural effusion for fetal anti-SBV antibodies identified SBV as the cause of the congenital syndrome. Backwards calculation from the calving dates indicated the occurrence of an unnoticed emergence of SBV in Denmark from early August 2020 and during the late summer and autumn. As SBV associated malformations may lead to dystocia urging for fetotomy or Cesarean section, veterinarians performing obstetric intervention are first line personnel in recognition of SBV emergence in domestic ruminants.

Since 2007, African swine fever virus (ASFV) has spread to countries in Europe, Asia and Oceania, and has caused devastating impacts on pigs and the pork industry. Transmission can be direct or indirect, and epidemiologic scenarios have been described in which spread occurs between free-living and domestic pigs. The purpose of this scoping review was to identify primary research in which authors made statements to support ASFV transmission between free-living and domestic pigs and assess the circumstances in which transmission events occurred. A search was conducted in five bibliographic databases and the grey literature. Two reviewers (from a team of ten) independently screened each record and charted data (demographics of the pig populations, their husbandry [domestic pigs] and habitat [free-living pigs], the spatial and temporal distribution of ASF, the occurrence or burden of ASF in the populations, and whether ticks were present in the geographic range of the pig populations). Data synthesis included statistics and a narrative summary. From 1,349 records screened, data were charted from 46 individual studies published from 1985 to 2020. Outbreak investigations revealed that whilst poor biosecurity of domestic pig operations was often reported, direct contact resulting in transmission between free-living and domestic pigs was rarely reported. Studies in which quantitative associations were made generally found that spread within populations was more important than spread between populations, although this was not always the case, particularly when domestic pigs were free-ranging. We conclude that there is limited evidence that transmission of ASFV between free-living and domestic pigs is an important feature of ASF epidemiology, especially in the current ASF epidemic in Europe and the Russian Federation. If ASFV elimination cannot be achieved in free-living pigs, compartmentalisation of free-living and domestic pig populations via biosecurity strategies could be used to support trade of domestic pigs.

Being able to link clinical outcomes to SARS-CoV-2 virus strains is a critical component of understanding COVID-19. Here we discuss how current processes hamper sustainable data collection to enable meaningful analysis and insights. Following ‘Fast Healthcare Interoperable Resource’ implementation guide, we introduce an ontology-based standard questionnaire to overcome these shortcomings and describe patient “journeys” in coordination with the World Health Organization. We identify steps in the clinical health data acquisition cycle and workflows that likely have the biggest impact in the data-driven understanding of this virus.

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.

Level and duration of protective immunity against SARS-CoV-2 after primary infection is of crucial importance for preventive approaches. In order to provide evidence for the longevity of specific antibodies, we investigated the generation and maintenance of neutralizing antibodies of convalescent SARS-CoV-2-afflicted patients over a five month period post primary infection using an immunofluorescence assay, a commercial chemiluminescent immunoassay and an in-house enzyme-linked plaque-reduction neutralization assay. We present the successful application of an improved version of the plaque-reduction neutralization assay, which can be analyzed optometrically, significantly simplifying the interpretation of the results. Based on the results of the plaque-reduction neutralization assay, neutralizing antibodies were maintained in 85.3% of convalescent individuals without significant decay over five months. Furthermore, a positive correlation between severity of infection and neutralizing titer was shown. In conclusion, SARS-CoV-2-afflicted individuals have been proven to be able to establish and maintain neutralizing antibodies over a five months’ period after primary infection which allows to hope for long-lasting presumably protective humoral immunity after wild-type infection or even after vaccination.

From 2003 onwards, three pandemics have been caused by coronaviruses: severe acute respiratory syndrome coronavirus (SARS-CoV); middle east respiratory syndrome coronavirus (MERS-CoV); and, most recently, SARS-CoV-2. Notably, all three were transmitted from animals to humans. This would suggest that animals are potential sources of epidemics for humans. The emerging porcine delta-coronavirus was reported to infect children. This is a red flag that marks the ability of PDCoV to break barriers of cross-species transmission to humans. Therefore, we conducted molecular genetic analysis of global clade PDCoV to characterize spatio-temporal patterns of viral diffusion and genetic diversity. PDCoV was classified into three major lineages, according to distribution and phylogenetic analysis of PDCoV. It can be determined that PDCoV originated in Asia—most likely in Southeast Asia—through inference of migration rate and transmission routes. We also selected six special spike amino acid sequences to align and analyze to find seven significant mutation sites. The accumulation of these mutations may enhance dynamic movements, accelerating spike protein membrane fusion events and transmission. Altogether, our study offers a novel insight into the diversification, evolution, and interspecies transmission and origin of PDCoV and emphasizes the need to study the zoonotic potential of the PDCoV and comprehensive surveillance and enhanced biosecurity precautions for PDCoV.