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.

Ticks are involved in the transmission of various pathogens and some tick-borne diseases cause significant problems for the health of humans and livestock. Despite their obvious importance, the composition of viral communities in ticks, and their interactions with pathogens, is poorly understood, particularly in Eastern Europe that constitutes (via bird migrations for example) a major hub for animal-arthropod vectors exchanges. The aim of this study was first to describe the virome of Dermacentor sp., Rhipicephalus sp. and Haemaphysalis sp. ticks collected from poorly investigated regions of Romania (Iasi and Tulcea counties) located at the intersection of various biotopes, countries and routes of migrations. We then focused the study on viruses that could have potential relevance for human and animal health. More than 500 ticks were collected in 2019 from the environment and from small ruminants and analyzed by high-throughput transcriptome sequencing. Among the viral communities infecting Romanian ticks, viruses belonging to the Flaviviridae, Phenuiviridae and Nairoviridae families were identified and full genomes were derivedPhylogenetic analyses placed them in clades where mammalian isolates are found, suggesting that these viruses could constitute novel arboviruses. We also assessed the bacterial microbiome of the collected ticks. The characterization of these microbial communities increases the knowledge of the diversity of viruses in Eastern Europe and provide a basis for further studies on the relationship between ticks and tick-borne viruses.

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 this study, the digital droplet polymerase chain reaction (ddPCR) was used to quantify circulating bovine papillomavirus (BPV; genus: Deltapapillomavirus) levels in blood samples from 25 healthy cows and 15 cows with chronic enzootic hematuria due to papillomavirus-associated bladder tumors. ddPCR detected the BPV DNA in 95% of all the samples (i.e., in 24 of the healthy cows and 14 of the diseased animals), whereas quantitative real time PCR (qPCR) detected it in only 57.5% of the same blood samples, with the percentage differences between ddPCR and qPCR being statistically significant (P value  0.05), according to the 2 test of Campbell and Richardson. Furthermore, ddPCR detected BPV infections by a single genotype and by multiple genotypes in 37% and 63% of the cows, respectively, whereas qPCR detected these in 16% and 16%, respectively. Of the two assays, ddPCR was the more sensitive and accurate clinical diagnostic tool, allowing the detection of otherwise undetectable BPV genotypes, and consequently, a higher number of BPV co-infections. qPCR failed to detect many BPV co-infections by multiple genotypes. Therefore, ddPCR may be an essential tool for improving diagnostic procedures, allowing the identification of the genotypic distribution of BPV and a better understanding about the territorial divergence, if any, of the BPV prevalence in different areas. No significant differences in the blood viral load estimations were observed between the two animal groups, suggesting that the bloodstream could be a site of primary infection. Finally, as BPV DNA was detected in cows affected by noninvasive urothelial tumors, including papilloma and papillary urothelial neoplasms of low malignant potential, the circulating BPVs appeared to be independent of the status of urothelial neoplasms. Therefore, unlike in humans, circulating BPVs cannot be an actual prognostic marker of urothelial tumors in cows.

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.

Vectors of emerging infectious diseases have expanded their distributional ranges in recent decades due to increased global travel, trade connectivity, and climate change. Transboundary range shifts, arising from the continuous movement of humans and livestock across borders, are of particular disease control concern. Several tick-borne diseases are known to circulate between eastern Uganda and the western counties of Kenya, with one fatal case of Crimean-Congo haemorrhagic fever (CCHF) reported in 2000 in Western Kenya. Recent reports of CCHF in Uganda have highlighted the risk of cross-border disease translocation and the importance of establishing inter-epidemic, early warning systems to detect possible outbreaks. We therefore carried out surveillance of tick-borne zoonotic pathogens at livestock markets and slaughterhouses in three counties of western Kenya that neighbour Uganda. Ticks and other ectoparasites were collected from livestock and identified using morphological keys. The two most frequently sampled tick species were Rhipicephalus decoloratus (35%) and Amblyomma variegatum (30%), and Ctenocephalides felis fleas and Haematopinus suis lice were also present. In total 486 ticks, lice, and fleas were screened for pathogen presence using established molecular workflows incorporating high-resolution melting analysis and identified through PCR-sequencing of PCR products. We detected CCHF virus in Rh. decoloratus and Rhipicephalus sp. cattle ticks and 82 of 96 pools of Am. variegatum were positive for Rickettsia africae. Apicomplexan protozoa and bcteria of veterinary importance, such as Theileria parva, Babesia bigemina, and Anaplasma marginale, were primarily detected in rhipicephaline ticks. Our findings show the presence of several pathogens of public health and veterinary importance in ticks from livestock at livestock markets and slaughterhouses in western Kenya. Confirmation of CCHF virus, a Nairovirus that causes haemorrhagic fever with a high case fatality rate in humans, highlights the risk of under-diagnosed zoonotic diseases and calls for continuous surveillance and the development of preventative measures.

Understanding hobby beekeepers’ perception of risks affecting bee health and mortality is essential to analyse the reasons for adopting or rejecting good management practices. A perception survey on how beekeepers perceive and manage risks related to climate change, Varroa infestation, management practices, and pesticide exposure was designed and launched online. This unpreceded sociological survey involved 355 beekeepers spread all over Belgium. A two-sample t-test with unequal variances comparing beekeepers with colony mortality rates below or exceeding the acceptable level, i.e. <10% and ≥10%, indicates that beekeepers (N=213), with colony mortality rates <10% generally have greater levels of perceived risk and the benefits of action that lead to increased motivation to act in better ways. The results of this survey highlight the importance of taking socio-economic determinants into account in any risk mitigation strategy associated with bee mortality when dealing with hobby beekeepers.

Advanced and accurate forecasting of COVID-19 cases plays a crucial role in planning and supplying resources effectively. Artificial Intelligence (AI) techniques have proved its capability in time series forecasting of the non-linear problems. In the present study, the relationship between weather factor and COVID-19 cases was assessed and also developed a forecasting model using long short term memory (LSTM), a deep learning model. The study found that the specific humidity has a strong positive correlation, whereas there is a negative correlation with maximum temperature and positive correlation with minimum temperature was observed in various geographic locations of India. The weather data and COVID-19 confirmed cases data (1st April-30th June 2020) was used to optimize univariate and multivariate LSTM time series forecast models. The optimized models were utilized to forecast the COVID-19 cases for the period 1st July 2020 to 31st July 2020 with 1 to 14 days of lead time. The results showed that the univariate LSTM model was reasonably good for the short term (1day lead) forecast of COVID-19 cases (relative error < 20%). Moreover, the multivariate LSTM model improved the medium-range forecast skill (1-7days) after including the weather factors. The study observed that the specific humidity played a crucial role in improving the forecast skill majorly in the West and northwest region of India. Similarly, the temperature played a significant role in model enhancement in the Southern and Eastern regions of India.

Bovine tuberculosis (bTB) prevalence substantially increased over the past two decades with relatively high impact on large dairy herds, raising the concern of regulatory authorities and industry stakeholders, and threatening animal and public health. Lack of resources, together with the economic and social consequences of whole-herd stamping-out, makes depopulation an impractical disease control alternative in these herds. The increase in bTB-prevalence was associated with demographic and management changes in the dairy industry in Uruguay, reducing the efficacy of the current control program (i.e. status quo) based on intradermal serial testing with caudal fold- and comparative cervical- tuberculin test-and slaughter of reactors (CFT-CCT). Here, we aimed to assess the epidemiological effectiveness of six alternative control scenarios based on test-and-slaughter of positive animals, using mathematical modeling to infer bTB-within-herd dynamics. We simulated six alternative control strategies consisting of testing adult cattle (>1 year) in the herd every three months using one test (in-vivo or in-vitro) or a combination in parallel of two tests (CFT, interferon-gamma release assay –IGRA- or Enzyme-linked immunosorbent assay). Results showed no significant differences overall in the time needed to reach bTB-eradication (median ranging between 61 to 82 months) or official bovine tuberculosis-free status (two consecutive negative herd-tests) between any of the alternative strategies and the status quo (median ranging between 50 and 59 months). However, we demonstrate how alternative strategies can significantly reduce bTB-prevalence when applied for restricted periods (6, 12, or 24 months), and in the case of IGRAc (IGRA using peptide-cocktail antigens), without incurring on higher unnecessary slaughter of animals (false-positives) than the status quo in the first 6 months of the program (P-value <0.05). Enhanced understanding bTB-within-herd dynamics with the application of different control strategies help to identify optimal strategies to ultimately improve bTB-control and -eradication from dairies in Uruguay and similar endemic settings.

Numerous unknown factors influence anthrax epidemiology in multi-host systems, especially at wildlife/livestock/human interfaces. Serology tests for anti-anthrax antibodies in carnivores are useful tools in identifying the presence or absence of Bacillus anthracis in a range. These were employed to ascertain if the disease pattern followed the recognized high and low risk anthrax zonation in Zimbabwe and also to establish if anthrax was absent from Hwange National Park in which there has been no reported outbreaks. African lions (Panthera leo) (n= 114) drawn from -free-range protected areas and captive game parks located in recognized high and low risk zones across Zimbabwe were tested for antibodies to anthrax PA antigen using the ELISA immunoassay. A random selection of 27 lion sera samples comprising 17 sero-positive and 10 sero-negative sera were further tested in the species-independent toxin neutralization assay (TNA) in order to validate the former as a surveillance tool for anthrax in African lions. Using the ELISA-PA immunoassay, 21.9% (25/114) of the lions tested positive for antibodies to anthrax. Seropositivity was recorded in all study areas and there was no significant difference (p= 0.852) in seropositivity between lions in high and low risk anthrax zones. Also, there was no significant difference (McNemar’s χ2 = 0.9, p = 0.343) in the proportion of lions testing positive to anti-PA anthrax antibodies on ELISA-PA immunoassay compared to the TNA, with fair agreement between the two tests [Kappa (K) statistic = 0.30; 0.08

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.

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.

Emerging and reemerging viral diseases can lead to devastating effects on human lives and at times also lead to economic crises. The ongoing COVID-19 pandemic due to the novel coronavirus (nCoV), severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), which originated in Wuhan, China, has caused a global public health emergency. Still, the molecular mechanism of transmission of SARS-CoV-2, its clinical manifestations and pathogenesis is not completely understood. The global scientific community has intensified their efforts to understand the biology of SARS-CoV-2 to develop vaccines and therapeutic interventions to prevent the rapid spread of the virus and to control mortality and morbidity associated with COVID-19. To understand the pathophysiology of SARS-CoV-2, appropriate animal models that mimic the biology of human SARS-COV-2 infection is urgently needed. In this review, we outline animal models that have been used to study previous human coronaviruses (HCoVs), that includes severe acute respiratory syndrome coronavirus (SARS-CoV) and Middle East respiratory syndrome coronavirus (MERS-CoV). Importantly, we discuss which model is appropriate for SARS-CoV-2 as well as the advantages and disadvantages of each.

In this study, we introduce the vulnerability index to measure the regional ASF epidemic and present the ASF severity ratings of 31 provincial regions of China. The index is defined based on the data from investigation, national statistical yearbook and reports. The data to be used includes pig breeding, financial resources, human resources, epidemic information of ASF and price fluctuation from the 31 regions. Then we use the data envelopment analysis (DEA) model to define the vulnerability index, the relative severity values for each region which quantitatively reflect the damage degree caused by the epidemic of ASF. The method allows us to provide a systematic classification for regional vulnerability level of ASF in China. Using the index, we find that the vulnerability of the whole country is at a high level, and there is no regional aggregation phenomenon. The vulnerability level of the 31 provinces are quite different and the provinces with high vulnerability level are dispersive geographically. For the five major prevention and control zones for ASF in China, the northern region has the highest vulnerability level, while the level of eastern zoon is the lowest.

Landscape anthropization has been identified as one of the main drivers of pathogen emergence worldwide, facilitating pathogen spillover between domestic species and wildlife. The present study investigated Carnivore protoparvovirus-1 (CPPV) infection using molecular methods in 98 free-ranging wild guignas (Leopardus guigna) and 262 co-occurring owned, free-roaming rural domestic cats. We also assessed landscape anthropization variables as potential drivers of infection. CPPV DNA was detected in guignas across their entire distribution range, with observed prevalence of 13.3% (real-time PCR) and 9% (conventional PCR) in guignas, and 6.1% (conventional PCR) in cats. Prevalence in guigna did not vary depending on age, sex, study area or landscape variables. Prevalence was higher in juvenile cats (16.7%) than in adults (4.4%). Molecular characterization of the virus by amplification and sequencing of almost the entire vp2 gene (1746 bp) from one guigna and five domestic cats was achieved, showing genetic similarities to canine parvovirus 2c (CPV-2c) (one guigna and one cat), feline panleukopenia virus (FPV) (one cat), CPV-2 (no subtype identified) (two cats), CPV-2a (one cat). The CVP-2c-like sequence found in a guigna clustered together with domestic cat and dog CPV-2c sequences from South America, suggesting possible spillover from a domestic to a wild species as the origin of infection in guigna. No clinical signs of disease were found in PCR-positive animals except for the CPV-2c-infected guigna, which had hemorrhagic diarrhea and died a few days after arrival at a wildlife rescue center. Our findings reveal widespread presence of Carnivore protoparvovirus-1 across the guigna distribution in Chile and suggest that virus transmission potentially occurs from domestic to wild carnivores, causing severe disease and death in susceptible wild guignas.

The recent COVID-19 pandemic has demonstrated again the global threat posed by emerging zoonotic coronaviruses. During the past two decades alone, humans have experienced the emergence of several coronaviruses, such as SARS-CoV in 2003, MERS-CoV in 2012, and SARS-CoV-2 in 2019. To date, MERS-CoV has been detected in 27 countries, with a case fatality ratio of approximately 34.5 %. Similar to other coronaviruses, MERS-CoV presumably originated from bats; however, the main reservoir and primary source of human infections are dromedary camels. Other species within the Camelidae family, such as Bactrian camels, alpacas, and llamas, seem to be susceptible to the infection as well, although to a lesser extent. In contrast, susceptibility studies on sheep, goats, cattle, pigs, chickens, and horses obtained divergent results. In the present study, we tested nasal swabs and/or sera from 55 sheep, 45 goats, and 52 cattle, collected at the largest livestock market in the United Arab Emirates, where dromedaries are also traded, for the presence of MERS-CoV nucleic acid by RT-qPCR, and for specific antibodies by immunofluorescence assay (IFA). All sera were negative for MERS-CoV-reactive antibodies, but the nasal swab of one sheep (1.8 %) was positive for MERS-CoV nucleic acid. Next generation sequencing (NGS) of the complete N gene of the sheep-derived MERS-CoV revealed >99 % nucleotide identity to MERS-CoV sequences of five dromedaries in nearby pens and to three reference sequences. The NGS sequence of the sheep-derived MERS-CoV was confirmed by conventional RT-PCR of a part of the N gene and subsequent Sanger sequencing. All MERS-CoV sequences clustered within clade B, lineage 5. In conclusion, our study shows that non-camelid livestock, such as sheep, goats, and cattle do not play a major role in MERS-CoV epidemiology. The one sheep that tested positive most likely reflects an accidental viral spillover event from infected dromedaries in nearby pens.

Summary: The unusual genetic diversity of the Omicron strain has led to speculation about its origin. The mathematical modeling platform developed for the Stockholm Paradigm (SP) indicates strongly that it has retro-colonized humans from an unidentified animal reservoir originally infected by humans. The relationship between Omicron and all other SARS-CoV-2 variants indicates oscillations among hosts, a core part of the SP. Such oscillations result from the emergence of novel variants following colonization of new hosts, replenishing and expanding the risk space for disease emergence. The SP predicts that pathogens colonize new hosts using pre-existing capacities. Those events are thus predictable to a certain extent. Novel variants emerge after a colonization and are not predictable. This makes it imperative to take proactive measures for anticipating emerging infectious diseases (EID) and mitigating their impact. The SP suggests a policy protocol to accomplish this goal. This is the DAMA Protocol: comprising DOCUMENT to detect pathogens before they emerge in new places or colonize new hosts; ASSESS to determine risk; MONITOR to detect changes in pathogen populations that increase the risk of outbreaks; and ACT to prevent outbreaks when possible and minimize their impact when they occur.

For the first time we built a correlative model for predicting the distribution of H. marginatum, one of the main vector of Crimean-Congo Haemorrhagic fever virus (CCHFV), at high resolution in a recently colonized area, namely south of France. Field tick collections were conducted on horses from 2016 to 2021 in 14 French southern departments, which resulted in a first map of H. marginatum on the national territory. Such updated presence/absence data, as well as the mean number of H. marginatum per examined animal (mean parasitic load) as a proxy of the tick abundance, were correlated to multiple parameters that described the climate and habitats characterizing each collection site, as well as movements of horses as a possible source of tick diffusion and new establishment. Our model highlighted the importance of warm temperatures all along the year, as well as dry conditions during summer and moderate annual humidity for the establishment of H. marginatum. A predominance of open natural habitats in the environment was also identified as a supporting factor, in opposition to artificial and humid habitats that were determined as unsuitable. Based on this model, we predicted the current suitable areas for the establishment of the tick H. marginatum in South of France, with a relatively good accuracy using internal and external validation methods. Concerning tick abundance, some correlative relationships were similar than in the occurrence model but the type of horse movements were also pointed out as an important factor explaining the mean parasitic load, leading to differential exposure to ticks. The limitations of estimating and modelling H. marginatum abundance in a correlative model are discussed.