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Background: Tick-borne encephalitis (TBE) is a severe human neuroinfection caused by TBE virus (TBEV). TBEV is transmitted by tick bites and by the consumption of unpasteurized dairy products from infected asymptomatic ruminants. In France, several food-borne transmission events have been reported since 2020, raising the question of the level of exposure of domestic ungulates to TBEV. In this study, our objectives were (i) to estimate TBEV seroprevalence and quantify antibodies titres in cattle in the historical endemic area of TBEV in France using the micro virus neutralisation test (MNT) and (ii) to compare the performance of two veterinary cELISA kits with MNT for detecting anti-TBEV antibodies in cattle in various epidemiological contexts. A total of 344 cattle sera from four grid cells of 100 km² in Alsace-Lorraine (endemic region) and 84 from western France, assumed to be TBEV-free, were investigated., Results: In Alsace-Lorraine, cattle were exposed to the virus with an overall estimated seroprevalence of 57.6% (95% CI: 52.1-62.8%, n = 344), varying locally from 29.9% (95% CI: 21.0-40.0%) to 92.1% (95% CI: 84.5-96.8%). Seroprevalence did not increase with age, with one- to three-year-old cattle being as highly exposed as older ones, suggesting a short-life duration of antibodies. The proportion of sera with MNT titres lower than 1:40 per grid cell decreased with increased seroprevalence. Both cELISA kits showed high specificity (> 90%) and low sensitivity (less than 78.1%) compared with MNT. Sensitivity was lower for sera with neutralising antibodies titres below 1:40, suggesting that sensitivity of these tests varied with local virus circulation intensity., Conclusions: Our results highlight that cattle were highly exposed to TBEV. Screening strategy and serological tests should be carefully chosen according to the purpose of the serological study and with regard to the limitations of each method., (© 2024. The Author(s).)

West Nile virus (WNV) is a single-stranded positive-sense RNA virus (+ssRNA) belonging to the genus Orthoflavivirus . Its enzootic cycle involves mosquito vectors, mainly Culex , and wild birds as reservoir hosts, while mammals, such as humans and equids, are incidental dead-end hosts. It was first discovered in 1934 in Uganda, and since 1999 has been responsible for frequent outbreaks in humans, horses and wild birds, mostly in America and in Europe. Virus spread, as well as outbreak severity, can be influenced by many ecological factors, such as reservoir host availability, biodiversity, movements and competence, mosquito abundance, distribution and vector competence, by environmental factors such as temperature, land use and precipitation, as well as by virus genetic factors influencing virulence or transmission. Former studies have investigated WNV factors of virulence, but few have compared viral genetic determinants of pathogenicity in different host species, and even fewer have considered the genetic drivers of virus invasiveness and excretion in Culex vector. In this study, we characterized WNV genetic factors implicated in the difference in virulence observed in two lineage 1 WNV strains from the Mediterranean Basin, the first isolated during a significant outbreak reported in Israel in 1998, and the second from a milder outbreak in Italy in 2008. We used an innovative and powerful reverse genetic tool, e.g., ISA ( infectious subgenomic amplicons ) to generate chimeras between Israel 1998 and Italy 2008 strains, focusing on non-structural (NS) proteins and the 3'UTR non-coding region. We analyzed the replication of these chimeras and their progenitors in mammals, in BALB/cByJ mice, and vector competence in Culex (Cx.) pipiens mosquitoes. Results obtained in BALB/cByJ mice suggest a role of the NS2B/NS3/NS4B/NS5 genomic region in viral attenuation in mammals, while NS4B/NS5/3'UTR regions are important in Cx. pipiens infection and possibly in vector competence., Competing Interests: The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Fiacre, Nougairède, Migné, Bayet, Cochin, Dumarest, Helle, Exbrayat, Pagès, Vitour, Richardson, Failloux, Vazeille, Albina, Lecollinet and Gonzalez.)

West Nile virus (WNV) is amplified in an enzootic cycle involving birds as amplifying hosts. Because they do not develop high levels of viremia, humans and horses are considered to be dead-end hosts. Mosquitoes, especially from the Culex genus, are vectors responsible for transmission between hosts. Consequently, understanding WNV epidemiology and infection requires comparative and integrated analyses in bird, mammalian, and insect hosts. So far, markers of WNV virulence have mainly been determined in mammalian model organisms (essentially mice), while data in avian models are still missing. WNV Israel 1998 (IS98) is a highly virulent strain that is closely genetically related to the strain introduced into North America in 1999, NY99 (genomic sequence homology > 99%). The latter probably entered the continent at New York City, generating the most impactful WNV outbreak ever documented in wild birds, horses, and humans. In contrast, the WNV Italy 2008 strain (IT08) induced only limited mortality in birds and mammals in Europe during the summer of 2008. To test whether genetic polymorphism between IS98 and IT08 could account for differences in disease spread and burden, we generated chimeric viruses between IS98 and IT08, focusing on the 3' end of the genome (NS4A, NS4B, NS5, and 3'UTR regions) where most of the non-synonymous mutations were detected. In vitro and in vivo comparative analyses of parental and chimeric viruses demonstrated a role for NS4A/NS4B/5'NS5 in the decreased virulence of IT08 in SPF chickens, possibly due to the NS4B-E249D mutation. Additionally, significant differences between the highly virulent strain IS98 and the other three viruses were observed in mice, implying the existence of additional molecular determinants of virulence in mammals, such as the amino acid changes NS5-V258A, NS5-N280K, NS5-A372V, and NS5-R422K. As previously shown, our work also suggests that genetic determinants of WNV virulence can be host-dependent.

Hepatitis E virus (HEV) is a zoonotic pathogen, in particular genotype 3 HEV is mainly transmitted to humans through the consumption of contaminated pork products. This study aimed at describing HEV infection patterns in pig farms and at assessing the impact of immunomodulating co-infections namely Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) and Porcine Circovirus Type 2 (PCV2), as well as other individual factors such as piglets' immunity and litters' characteristics on HEV dynamics. A longitudinal follow-up was conducted in three farrow-to-finish farms known to be HEV infected. Overall, 360 piglets were individually monitored from birth to slaughter with regular blood and faecal sampling as well as blood and liver samples collected at slaughterhouse. Virological and serological analyses were performed to detect HEV, PCV2 and PRRSV genome and antibodies. The links between 12 explanatory variables and four outcomes describing HEV dynamics were assessed using cox-proportional hazard models and logistic regression. HEV infection dynamics was found highly variable between farms and in a lower magnitude between batches. HEV positive livers were more likely related to short time-intervals between HEV infection and slaughter time (<40 days, OR = 4.1 [3.7-4.5]). In addition to an influence of piglets' sex and sows' parity, the sequence of co-infections was strongly associated with different HEV dynamics: a PRRSV or PCV2/PRRSV pre- or co-infection was associated with a higher age at HEV shedding (Hazard Ratio = 0.3 [0.2-0.5]), as well as a higher age at HEV seroconversion (HR = 0.5 [0.3-0.9] and HR = 0.4 [0.2-0.7] respectively). A PCV2/PRRSV pre- or co-infection was associated with a longer duration of shedding (HR = 0.5 [0.3-0.8]). Consequently, a PRRSV or PCV2/PRRSV pre- or co-infection was strongly associated with a higher risk of having positive livers at slaughter (OR = 4.1 [1.9-8.9] and OR = 6.5 [3.2-13.2] respectively). In conclusion, co-infections with immunomodulating viruses were found to affect HEV dynamics in the farrow-to-finish pig farms that were followed in this study., (© 2019 Blackwell Verlag GmbH.)

African horse sickness virus (AHSV) is an Orbivirus within the Reoviridae family, spread by Culicoides species of midges, which infects equids with high mortality, particularly in horses and has a considerable impact on the equine industry. In order to control the disease, we previously described Entry Competent Replication Abortive (ECRA) virus strains for each of the nine distinct AHSV serotypes and demonstrated their potential as vaccines, first in type I interferon receptor (IFNAR-/-) knockout mice, and then in ponies. In this report we have investigated whether or not a combination ECRA vaccine comprising nine vaccine strains as two different cocktails is as efficient in ponies and the duration of the immunity triggered by ECRA vaccines. In one study, a group of ponies were vaccinated with a cocktail of 4 vaccine strains, followed by a vaccination of the remaining 5 vaccine strains, mimicking the current live attenuated vaccine regimen. In the second study, ponies were vaccinated with a single ECRA-AHSV strain and monitored for 6 months. The first group of ponies developed neutralising antibody responses against all 9 serotypes, indicating that no cross-serotype interference occurred, while the second group developed robust neutralising antibody responses against the single serotype that were sustained at the same level throughout a 6-month study. The results support our previous data and further validate ECRA vaccines as a safe and efficacious replacement of current live vaccines., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 The Author(s). Published by Elsevier Ltd.. All rights reserved.)

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 by 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 confirms the presence of antibodies against the SARS-CoV-2 in both 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., (© 2020 Blackwell Verlag GmbH.)

Since 2015, annual West Nile virus (WNV) outbreaks of varying intensities have been reported in France. Recent intensification of enzootic WNV circulation was observed in the South of France with most horse cases detected in 2015 ( n = 49), 2018 ( n = 13), and 2019 ( n = 13). A WNV lineage 1 strain was isolated from a horse suffering from West Nile neuro-invasive disease (WNND) during the 2015 episode in the Camargue area. A breaking point in WNV epidemiology was achieved in 2018, when WNV lineage 2 emerged in Southeastern areas. This virus most probably originated from WNV spread from Northern Italy and caused WNND in humans and the death of diurnal raptors. WNV lineage 2 emergence was associated with the most important human WNV epidemics identified so far in France (n = 26, including seven WNND cases and two infections in blood and organ donors). Two other major findings were the detection of WNV in areas with no or limited history of WNV circulation (Alpes-Maritimes in 2018, Corsica in 2018-2019, and Var in 2019) and distinct spatial distribution of human and horse WNV cases. These new data reinforce the necessity to enhance French WNV surveillance to better anticipate future WNV epidemics and epizootics and to improve the safety of blood and organ donations.

Ticks can negatively affect their host by direct effects as blood feeding causing anaemia or discomfort, or by pathogen transmission. Consequently, ticks can have an important role in the population dynamics of their hosts. However, specific studies on the demographic effects of tick infestation on seabirds are still scarce. Seabird ticks have also the potential to be responsible for the circulation of little known tick-borne agents, which could have implications for non-seabird species. Here, we report the results of investigations on potential associations between soft tick Ornithodoros maritimus load and reproductive parameters of storm petrels Hydrobates pelagicus breeding in a large colony in a cave of Espartar Island, in the Balearic archipelago. We also investigated by molecular analyses the potential viral and bacterial pathogens associated with O. maritimus ticks present at the colony. Lower nestling survival was recorded in the most infested area, deep in the cave, compared to the area near the entrance. The parasite load was negatively associated with the body condition of the nestlings. One pool of ticks tested positive for West Nile virus and 4 pools tested positive for a Borrelia species which was determined by targeted nested PCR to have a 99% sequence identity with B. turicatae, a relapsing fever Borrelia. Overall, these results show that further investigations are needed to better understand the ecology and epidemiology of the interactions between ticks, pathogens and Procellariiform species., (Copyright © 2019 Elsevier GmbH. All rights reserved.)

Jingmenvirus is a recently identified group of segmented RNA viruses phylogenetically linked with unsegmented Flaviviridae viruses. Primarily identified in various tick genera originating in China, Jingmenvirus geographical distribution has rapidly expanded to cover Africa, South America, Caribbean, and Europe. The identification of Jingmen-related viruses in various mammals, including febrile humans, opens the possibility that Jingmenviruses may be novel tick-borne arboviruses. In this study, we aimed at increasing knowledge of the host range, genetic diversity, and geographical distribution of Jingmenviruses by reporting for the first time the identification of Jingmenviruses associated with Rhipicephalus microplus ticks originating in the French Antilles (Guadeloupe and Martinique islands), with Amblyomma testudinarium ticks in Lao PDR, and with Ixodes ricinus ticks in metropolitan France, and from urine of Pteropus lylei bats in Cambodia. Analyses of the relationships between the different Jingmenvirus genomes resulted in the identification of three main phylogenic subclades, each of them containing both tick-borne and mammal-borne strains, reinforcing the idea that Jingmenviruses may be considered as tick-borne arboviruses. Finally, we estimated the prevalence of Jingmenvirus-like infection using luciferase immunoprecipitation assay screening (LIPS) of asymptomatic humans and cattle highly exposed to tick bites. Among 70 French human, 153 Laotian human, and 200 Caribbean cattle sera tested, only one French human serum was found (slightly) positive, suggesting that the prevalence of Jingmenvirus human and cattle infections in these areas is probably low. IMPORTANCE Several arboviruses emerging as new pathogens for humans and domestic animals have recently raised public health concern and increased interest in the study of their host range and in detection of spillover events. Recently, a new group of segmented Flaviviridae -related viruses, the Jingmenviruses, has been identified worldwide in many invertebrate and vertebrate hosts, pointing out the issue of whether they belong to the arbovirus group. The study presented here combined whole-genome sequencing of three tick-borne Jingmenviruses and one bat-borne Jingmenvirus with comprehensive phylogenetic analyses and high-throughput serological screening of human and cattle populations exposed to these viruses to contribute to the knowledge of Jingmenvirus host range, geographical distribution, and mammalian exposure., (Copyright © 2019 Temmam et al.)

Emerging zoonoses caused by previously unknown agents are one of the most important challenges for human health because of their inherent inability to be predictable, conversely to emergences caused by previously known agents that could be targeted by routine surveillance programs. Emerging zoonotic infections either originate from increasing contacts between wildlife and human populations, or from the geographical expansion of hematophagous arthropods that act as vectors, this latter being more capable to impact large-scale human populations. While characterizing the viral communities from candidate vectors in high-risk geographical areas is a necessary initial step, the need to identify which viruses are able to spill over and those restricted to their hosts has recently emerged. We hypothesized that currently unknown tick-borne arboviruses could silently circulate in specific biotopes where mammals are highly exposed to tick bites, and implemented a strategy that combined high-throughput sequencing with broad-range serological techniques to both identify novel arboviruses and tick-specific viruses in a ticks/mammals interface in Thailand. The virome of Thai ticks belonging to the Rhipicephalus, Amblyomma, Dermacentor, Hyalomma , and Haemaphysalis genera identified numerous viruses, among which several viruses could be candidates for future emergence as regards to their phylogenetic relatedness with known tick-borne arboviruses. Luciferase immunoprecipitation system targeting external viral proteins of viruses identified among the Orthomyxoviridae, Phenuiviridae, Flaviviridae, Rhabdoviridae , and Chuviridae families was used to screen human and cattle Thai populations highly exposed to tick bites. Although no positive serum was detected for any of the six viruses selected, suggesting that these viruses are not infecting these vertebrates, or at very low prevalence (upper estimate 0.017% and 0.047% in humans and cattle, respectively), the virome of Thai ticks presents an extremely rich viral diversity, among which novel tick-borne arboviruses are probably hidden and could pose a public health concern if they emerge. The strategy developed in this pilot study, starting from the inventory of viral communities of hematophagous arthropods to end by the identification of viruses able (or likely unable) to infect vertebrates, is the first step in the prediction of putative new emergences and could easily be transposed to other reservoirs/vectors/susceptible hosts interfaces., (Copyright © 2019 Temmam, Chrétien, Bigot, Dufour, Petres, Desquesnes, Devillers, Dumarest, Yousfi, Jittapalapong, Karnchanabanthoeng, Chaisiri, Gagnieur, Cosson, Vayssier-Taussat, Morand, Moutailler and Eloit.)

New Caledonia and French Polynesia are areas in which arboviruses circulate extensively. A large serological survey among horses from New Caledonia and French Polynesia was carried out to investigate the seroprevalence of flaviviruses in the horse population. Here, 293 equine sera samples were screened for flaviviruses using a competitive enzyme-linked immunosorbent assay (cELISA). The positive sera were then confirmed using a flavivirus-specific microsphere immunoassay (MIA) and seroneutralization tests. This serosurvey showed that 16.6% (27/163) and 30.8% (40/130) of horses were positive for cELISA tests in New Caledonia and French Polynesia, respectively, but the MIA technique, targeting only flaviviruses causing neuro-invasive infections in humans and horses (i.e. West Nile virus [WNV], Japanese encephalitis virus [JEV] and tick-borne encephalitis virus [TBEV]), showed negative results for more than 85% (57/67) of the cELISA-positive animals. Seroneutralization tests with the main flaviviruses circulating in the South Pacific revealed that 6.1% (10/163; confidence interval [95% CI] 3.0%-11.0%) of sera in New Caledonia and 7.7% (10/130; 95% CI 3.8%-13.7%) in French Polynesia were positive for dengue virus serotype 1 (DENV1) and 4.3% (7/163; 95% CI 1.7%-8.6%) in New Caledonia and 15.4% (20/130, 95% CI 9.7%-22.8%) in French Polynesia were found positive for Zika virus (ZIKV). Seroprevalence of the JEV and WNV flaviviruses on the 293 samples from both island groups were comparatively much lower (less than 2%). This seroprevalence study in the horse population shows that horses can be infected with dengue and Zika viruses and that these infections lead to seroconversions in horses. The consequences of these infections in horses and their role in ZIKV and DENV epidemiological cycles are two issues that deserve further investigation., Competing Interests: The authors have declared that no competing interests exist.

We conducted the first survey of zoonotic risk of Hepatitis E virus (HEV) transmissions in Ouagadougou, Burkina Faso, through the direct contact with pork meat during professional activity. Anti-HEV antibodies were more prevalent in pork butchers, 76% than in the general population, which was 47.8% in 2013 (odds ratio = 3.46, 95% CI = 2.85-4.21, P < 0.001). Among slaughter-aged swine, HEV seroprevalence was of 80%, and HEV RNA was detected in 1% of pork livers. Phylogenetic analysis pointed out HEV genotype 3. Thus, in addition to possible HEV contamination through the water source, as in endemic region, zoonotic transmissions of HEV probably occur in west Africa., (© The American Society of Tropical Medicine and Hygiene.)

Recent studies show that human skin at homeostasis is a complex ecosystem whose virome include circular DNA viruses, especially papillomaviruses and polyomaviruses. To determine the chicken skin virome in comparison with human skin virome, a chicken swabs pool sample from fifteen indoor healthy chickens of five genetic backgrounds was examined for the presence of DNA viruses by high-throughput sequencing (HTS). The results indicate a predominance of herpesviruses from the Mardivirus genus, coming from either vaccinal origin or presumably asymptomatic infection. Despite the high sensitivity of the HTS method used herein to detect small circular DNA viruses, we did not detect any papillomaviruses, polyomaviruses, or circoviruses, indicating that these viruses may not be resident of the chicken skin. The results suggest that the turkey herpesvirus is a resident of chicken skin in vaccinated chickens. This study indicates major differences between the skin viromes of chickens and humans. The origin of this difference remains to be further studied in relation with skin physiology, environment, or virus population dynamics.

Background: Swine pasivirus (SPaV1) is a recently described enteric virus close to human parechoviruses and highly prevalent in pigs. Antibodies to Escherichia coli-expressed VP1 of SpaV1 have been found in a majority of humans in China., Objectives: The objectives were to estimate the antibody prevalence in a European country, to test if exposure to the virus was linked to pig products and if this exposure was a risk factor for the development of diabetes type 1., Study Design: An ELISA test was developed and used to screen 842 healthy subjects with known exposure to pig products, 39 patients with diabetes type 1 and 20 controls., Results: We identified a high seroprevalence (15.6%) reacting to VP1 of SPaV1 among healthy human subjects. Analysis of risk factors argues against cross-species transmission from pigs as the source of infection. Data also indicate that the presence of SPaV1 VP1-binding antibodies is not associated with diabetes type 1 in humans., Conclusion: Our results suggest that the seroreactivity frequently found in humans against SpaV1 is due to cross-reactivity with related antigen, perhaps a picornavirus, and that SpaV1 is not a zoonotic virus., (Copyright © 2015 Elsevier B.V. All rights reserved.)

Heparin is one of the main pharmaceutical products manufactured from raw animal material. In order to describe the viral burden associated with this raw material, we performed high-throughput sequencing (HTS) on mucus samples destined for heparin manufacturing, which were collected from European pigs. We identified Circoviridae and Parvoviridae members as the most prevalent contaminating viruses, together with viruses from the Picornaviridae, Astroviridae, Reoviridae, Caliciviridae, Adenoviridae, Birnaviridae, and Anelloviridae families. Putative new viral species were also identified. The load of several known or novel small non-enveloped viruses, which are particularly difficult to inactivate or eliminate during heparin processing, was quantified by qPCR. Analysis of the combined HTS and specific qPCR results will influence the refining and validation of inactivation procedures, as well as aiding in risk analysis of viral heparin contamination., (Copyright © 2014 The International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.)

Minks, cats, and some other species of carnivores are susceptible of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and have a high risk of transmitting SARS-CoV-2 to humans. The development of animal vaccines can be an effective measure to protect animals against SARS-CoV-2 and reduce the potential risk of human infection. We previously developed a messenger ribonucleic acid (mRNA) vaccine SYS6006 that has been proven to be an efficient coronavirus disease 2019 (COVID-19) vaccine widely used in humans. Here, we further evaluated the safety and immunogenicity of SYS6006 as an animal COVID-19 vaccine candidate for SARS-CoV-2 susceptible animals or wild animals. SYS6006 was safe and immunogenic in mice and completely protected mice against mouse-adapted SARS-CoV-2 infection in the upper and lower respiratory tracts. SYS6006 was able to induce neutralizing antibodies against the SARS-CoV-2 wild-type, Delta, and Omicron BA.2 strain on day 7 after prime immunization, and two doses of immunization could enhance the neutralizing antibody responses and produce long-lasting potent antibodies for more than 8 months in minks and cats, blue foxes, and raccoon dogs, while all immunized animals had no abnormal clinical signs during immunization. These results provided here warrant further development of this safe and efficacious mRNA vaccine platform against animal COVID-19. [ABSTRACT FROM AUTHOR]

Studies have demonstrated the susceptibility of companion animals to natural infection with SARS-CoV-2. Using quantitative reverse transcription polymerase chain reaction and sequencing analyses, this study investigated SARS-CoV-2 RNA excretion in pets in households with infected owners. Oropharyngeal and rectal swabs were collected from dogs and cats in Parana, Southern Brazil, between October 2020 and April 2021. Viral RNA was detected in 25% of cats and 0.98% of dog oropharyngeal swabs; however, systemic, respiratory, and gastrointestinal signs were absent. Complete viral genomes belonged to the Gamma lineage. Phylogenetic analyses indicated that pet samples were probably derived from human-positive cases in Parana. Viral excretion in the oropharynx was more frequent in cats than in dogs. Mutations in the S protein characteristic of Gamma strains were present in all sequenced SARS-CoV-2 strains. The receptor-binding domain of these Brazilian strains did not show any additional mutations not reported in the Gamma strains. Mutations in NSP6, NSP12, and N proteins previously mapped to strains that infect deer or minks were detected. This study highlights the importance of actively monitoring the SARS-CoV-2 strains that infect pets with continued viral exposure. Monitoring genetic changes is crucial because new variants adapted to animals may pose human health risks. [ABSTRACT FROM AUTHOR]

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Specific Pathogen Free (SPF) embryonated eggs are used for the production of many veterinary and human vaccines. We have used High Throughput Sequencing to screen allantoic fluids and embryos for the presence of encapsidated viral genomes and viral transcripts, respectively. SPF eggs from two different producers were tested. We evidenced sequences corresponding to known endogenous retroviruses and sequences of Avian Leukosis Virus, but no sequence that might suggest a productive infection of eggs with a virus even distant from known viruses. Our results strongly suggest that SPF eggs such as those used for this study represent a safe substrate for the production of vaccines., (Copyright © 2014 The International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.)

Fetal bovine serum (FBS) and trypsin are reagents used in cell culture and have been the source of viral contamination of pharmaceutical products. We performed high throughput sequencing (HTS) of two pools of commercial batches of FBS and three commercial batches of trypsin. Taxonomies were assigned by comparing sequences of contigs and singletons to the entire NCBI nucleic acid and protein databases. The same major viral species were evidenced between batches of a given reagent but the proportion of viral reads among total reads varied markedly between samples (from 0.002% to 22.7%). In FBS, the sequences found were mainly from bovine viral diarrhea virus (BVDV) 1 to 3 and bovine parvovirus 3 (BPV3). The BVDV sequences derived from FBS showed only minor discrepancies with primers generally used for the screening of BVDV. Viral sequences in trypsin were mainly from porcine circovirus type 2. Other known viral sequences at lower read counts and potential new viral species (bovine parvovirus and bovine pegivirus) were evidenced. The load of some known and new viruses detected by HTS could be quantified by qPCR. Results of HTS provide a framework for evaluating the pertinence of control measures including the design of PCRs, bioassays and inactivation procedures., (Copyright © 2014 The International Alliance for Biological Standardization. Published by Elsevier Ltd. All rights reserved.)

Hepatitis E virus (HEV) can cause enterically-transmitted hepatitis in humans. The zoonotic nature of Hepatitis E infections has been established in industrialized areas and domestic pigs are considered as the main reservoir. The dynamics of transmission in pig herds therefore needs to be understood to reduce the prevalence of viremic pigs at slaughter and prevent contaminated pig products from entering the food chain. An experimental trial was carried out to study the main characteristics of HEV transmission between orally inoculated pigs and naïve animals. A mathematical model was used to investigate three transmission routes, namely direct contact between pigs and two environmental components to represent within-and between-group oro-fecal transmission. A large inter-individual variability was observed in response to infection with an average latent period lasting 6.9 days (5.8; 7.9) in inoculated animals and an average infectious period of 9.7 days (8.2; 11.2). Our results show that direct transmission alone, with a partial reproduction number of 1.41 (0.21; 3.02), can be considered as a factor of persistence of infection within a population. However, the quantity of virus present in the environment was found to play an essential role in the transmission process strongly influencing the probability of infection with a within pen transmission rate estimated to 2 · 10(-6)g ge(-1)d(-1)(1 · 10(-7); 7 · 10(-6)). Between-pen environmental transmission occurred to a lesser extent (transmission rate: 7 · 10(-8)g ge(-1) d(-1)(5 · 10(-9); 3 · 10(-7)) but could further generate a within-group process. The combination of these transmission routes could explain the persistence and high prevalence of HEV in pig populations.

Consumption of raw or undercooked wild boar (WB) meat is considered an important risk factor for hepatitis E virus (HEV) infection in humans. The possibility of HEV contamination during the slaughtering practices may pose an additional risk. Based on these assumptions, we evaluated HEV contamination of WB meat hunted in Umbria (central Italy) during the 2022–2023 hunting season by real-time RT-PCR. Herein, we show that 10.8% of livers from slaughtered WB were positive for HEV RNA, thus providing an estimate of HEV infection in WB in the Umbria region. Then, by evaluating paired liver–muscle samples from both HEV-positive and HEV-negative animals, we found evidence of muscle HEV contamination in 33% and 14% of cases, respectively. This is the first report on the detection of HEV in WB meat in Umbria, an Italian region with diffuse WB hunting and consumption. The evidence of contamination provided by our study underscores the importance of adopting good hygienic practices in the processing stages of hunted WB carcasses to significantly reduce meat contamination and the risk posed for the final consumer. [ABSTRACT FROM AUTHOR]

The genus Borrelia has been divided into Borreliella spp., which can cause Lyme Disease (LD), and Borrelia spp., which can cause Relapsing Fever (RF). The distribution of genus Borrelia has broadened due to factors such as climate change, alterations in land use, and enhanced human and animal mobility. Consequently, there is an increasing necessity for a One Health strategy to identify the key components in the Borrelia transmission cycle by monitoring the human-animal-environment interactions. The aim of this study is to summarize all accessible data to increase our understanding and provide a comprehensive overview of Borrelia distribution in the Mediterranean region. Databases including PubMed, Google Scholar, and Google were searched to determine the presence of Borreliella and Borrelia spp. in vectors, animals, and humans in countries around the Mediterranean Sea. A total of 3026 were identified and screened and after exclusion of papers that did not fulfill the including criteria, 429 were used. After examination of the available literature, it was revealed that various species associated with LD and RF are prevalent in vectors, animals, and humans in Mediterranean countries and should be monitored in order to effectively manage and prevent potential infections. [ABSTRACT FROM AUTHOR]

Marek's disease virus (MDV) vaccines were the first vaccines that protected against cancer. The avirulent turkey herpesvirus (HVT) was widely employed and protected billions of chickens from a deadly MDV infection. It is also among the most common vaccine vectors providing protection against a plethora of pathogens. HVT establishes latency in T-cells, allowing the vaccine virus to persist in the host for life. Intriguingly, the HVT genome contains telomeric repeat arrays (TMRs) at both ends; however, their role in the HVT life cycle remains elusive. We have previously shown that similar TMRs in the MDV genome facilitate its integration into host telomeres, which ensures efficient maintenance of the virus genome during latency and tumorigenesis. In this study, we investigated the role of the TMRs in HVT genome integration, latency, and reactivation in vitro and in vivo. Additionally, we examined HVT infection of feather follicles. We generated an HVT mutant lacking both TMRs (vΔTMR) that efficiently replicated in cell culture. We could demonstrate that wild type HVT integrates at the ends of chromosomes containing the telomeres in T-cells, while integration was severely impaired in the absence of the TMRs. To assess the role of TMRs in vivo, we infected one-day-old chickens with HVT or vΔTMR. vΔTMR loads were significantly reduced in the blood and hardly any virus was transported to the feather follicle epithelium where the virus is commonly shed. Strikingly, latency in the spleen and reactivation of the virus were severely impaired in the absence of the TMRs, indicating that the TMRs are crucial for the establishment of latency and reactivation of HVT. Our findings revealed that the TMRs facilitate integration of the HVT genome into host chromosomes, which ensures efficient persistence in the host, reactivation, and transport of the virus to the skin. Author summary: Several herpesviruses harbor telomeric repeats (TMRs) at the ends of their genomes. These TMRs are identical to the host telomeres, which protect the ends of host chromosomes from deterioration. One of these viruses is the herpesvirus of turkey (HVT), which is commonly used as a live-attenuated vaccine against MDV but also as a vaccine vector. Our study revealed that HVT efficiently integrates into the ends of host chromosomes containing the telomeres. Removal of the TMRs from the virus genome did not affect virus replication but severely impaired integration. In addition, persistence of the vaccine virus was drastically reduced in the host. Our data also revealed that integration and/or persistence of the virus is crucial for the transport of the virus to the skin of infected animals, where HVT replicates and is shed into the environment. Our study provides important insights into HVT biology and sheds light on the role of the TMRs in virus integration, persistence and shedding. [ABSTRACT FROM AUTHOR]

Hepatitis E virus (HEV) is one of the emerging zoonotic diseases in Sub-Saharan Africa. Domestic pigs are considered to be the main reservoir for this infectious disease. A third of the world's population is thought to have been exposed to the virus. The zoonotic transmission of the HEV raises serious zoonotic and food safety concerns for the general public. This is a major public health issue in both developed and developing countries. The World Health Organization (WHO) estimated that 44,000 people died in 2015 as a result of HEV infection. East and South Asia have the highest prevalence of this disease overall. In this study, we proposed, developed, and analyzed the transmission routes of the infection using a fractional-order derivative approach. The existence, stability, and uniqueness of solutions were established using the approach and concept in Banach space. Local and global stability was determined using the Hyers–Ulam (HU) stability approach. Numerical simulation was conducted using existing parameter values, and it was established that, as the susceptible human population declines, the number of infected human populations rises with a change in fractional order θ ^. When the susceptible pig population increases, the number of infected pig populations rises with a change in θ ^. It was observed that a few variations in the fractional derivative order did not alter the function's overall behavior with the results of numerical simulations. Moreover, as the number of recovered human populations increases, there is a corresponding increase in the population of recovered pigs with a change in θ ^. The exponential increase in the infected pig population can be controlled by treatment of the infected pigs and prevention of the susceptible pigs. The authors recommend policymakers, and stakeholders prioritize the fight against the virus by enforcing the prevention of humans and treatment of infected pigs. The model can be extended to optimal control and cost-effectiveness analysis to determine the most effective control strategy that comes with less cost in the combat of the disease. [ABSTRACT FROM AUTHOR]

This article reviews the avian viruses that infect the skin of domestic farm birds of primary economic importance: chicken, duck, turkey, and goose. Many avian viruses (e.g., poxviruses, herpesviruses, Influenza viruses, retroviruses) leading to pathologies infect the skin and the appendages of these birds. Some of these viruses (e.g., Marek's disease virus, avian influenza viruses) have had and/or still have a devasting impact on the poultry economy. The skin tropism of these viruses is key to the pathology and virus life cycle, in particular for virus entry, shedding, and/or transmission. In addition, for some emergent arboviruses, such as flaviviruses, the skin is often the entry gate of the virus after mosquito bites, whether or not the host develops symptoms (e.g., West Nile virus). Various avian skin models, from primary cells to three-dimensional models, are currently available to better understand virus-skin interactions (such as replication, pathogenesis, cell response, and co-infection). These models may be key to finding solutions to prevent or halt viral infection in poultry. [ABSTRACT FROM AUTHOR]

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Haemaphysalis longicornis ticks, commonly found in East Asia, can transmit various pathogenic viruses, including the severe fever with thrombocytopenia syndrome virus (SFTSV) that has caused febrile diseases among humans in Hubei Province. However, understanding of the viromes of H. longicornis was limited, and the prevalence of viruses among H. longicornis ticks in Hubei was not well clarified. This study investigates the viromes of both engorged (fed) and free (unfed) H. longicornis ticks across three mountainous regions in Hubei Province from 2019 to 2020. RNA-sequencing analysis identified viral sequences that were related to 39 reference viruses belonging to unclassified viruses and seven RNA viral families, namely Chuviridae, Nairoviridae, Orthomyxoviridae, Parvoviridae, Phenuiviridae, Rhabdoviridae, and Totiviridae. Viral abundance and diversity in these ticks were analysed, and phylogenetic characteristics of the Henan tick virus (HNTV), Dabieshan tick virus (DBSTV), Okutama tick virus (OKTV), and Jingmen tick virus (JMTV) were elucidated based on their full genomic sequences. Prevalence analysis demonstrated that DBSTV was the most common virus found in individual H. longicornis ticks (12.59%), followed by HNTV (0.35%), whereas JMTV and OKTV were not detected. These results improve our understanding of H. longicornis tick viromes in central China and highlight the role of tick feeding status and geography in shaping the viral community. The findings of new viral strains and their potential impact on public health raise the need to strengthen surveillance efforts for comprehensively assessing their spillover potentials. [ABSTRACT FROM AUTHOR]

West Nile Virus (WNV) and Usutu Virus (USUV) are both neurotropic mosquito-borne viruses belonging to the Flaviviridae family. These closely related viruses mainly follow an enzootic cycle involving mosquitoes as vectors and birds as amplifying hosts, but humans and other mammals can also be infected through mosquito bites. WNV was first identified in Uganda in 1937 and has since spread globally, notably in Europe, causing periodic outbreaks associated with severe cases of neuroinvasive diseases such as meningitis and encephalitis. USUV was initially isolated in 1959 in Swaziland and has also spread to Europe, primarily affecting birds and having a limited impact on human health. There has been a recent expansion of these viruses' geographic range in Europe, facilitated by factors such as climate change, leading to increased human exposure. While sharing similar biological traits, ecology, and epidemiology, there are significant distinctions in their pathogenicity and their impact on both human and animal health. While WNV has been more extensively studied and is a significant public health concern in many regions, USUV has recently been gaining attention due to its emergence in Europe and the diversity of its circulating lineages. Understanding the pathophysiology, ecology, and transmission dynamics of these viruses is important to the implementation of effective surveillance and control measures. This perspective provides a brief overview of the current situation of these two viruses in Europe and outlines the significant challenges that need to be addressed in the coming years. [ABSTRACT FROM AUTHOR]

Hepatitis E virus (HEV) is the main cause of acute hepatitis in humans worldwide and is responsible for a large number of outbreaks especially in Africa. Human infections are mainly caused by genotypes 1 and 2 of the genus Paslahepevirus, which are exclusively associated with humans. In contrast, viruses of genotypes 3 and 4 are zoonotic and have their main reservoir in domestic and wild pigs, from which they can be transmitted to humans primarily through the consumption of meat products. Both genotypes 3 and 4 are widespread in Europe, Asia, and North America and lead to sporadic cases of hepatitis E. However, there is little information available on the prevalence of these genotypes and possible transmission routes from animal reservoirs to humans in African countries. We therefore analysed 1086 pig sera collected in 2016/2017 in four districts in Sierra Leone for antibodies against HEV using a newly designed in-house ELISA. In addition, the samples were also analysed for HEV RNA by quantitative real-time RT-PCR. The overall seroprevalence in Sierra Leone was low with only 44 positive sera and a prevalence of 4.0%. Two serum pools were RT-PCR-positive and recovered partial sequences clustered into the genotype 3 (HEV-3) of the order Paslahepevirus, species Paslahepevirus balayani. The results are the first evidence of HEV-3 infection in pigs from Sierra Leone and demonstrate a low circulation of the virus in these animals to date. Further studies should include an examination of humans, especially those with close contact with pigs and porcine products, as well as environmental sampling to evaluate public health effects within the framework of a One Health approach. [ABSTRACT FROM AUTHOR]

The hepatitis E virus (HEV) is a zoonotic pathogen with various hosts, including pigs, which act as reservoirs. In industrialized countries, sporadic cases caused by genotype 3, contracted by ingesting contaminated uncooked or undercooked meat, have been reported. However, in developing countries, HEV infection is mainly dominated by genotype 2 and often associated with poor hygiene conditions and drinking water supplies. HEV infection and its circulation in domestic fauna in West Africa are poorly documented. This study aimed to assess the presence of HEV in pork sold in Saint-Louis, Senegal. Meat products (250 g samples, n = 74) were purchased in August 2022 from three locations. Then, 2 g/sample was minced to extract total nucleic acids using the Purelink™ Viral DNA/RNA kit. RT-PCR reactions were performed using the One-Taq™ One-Step RT-PCR kit targeting the HEV ORF2 genomic region. The products obtained were visualized on a 1% agarose gel. Of a total of 74 samples, divided into pork meat (n = 65) and pork liver (n = 9), 5.4% (n = 4) tested positive for HEV. In both cases, two samples were positive, representing a rate of 3.1% and 22.2% for meat and pork liver, respectively. All new viral sequences were obtained from a monophyletic group within HEV genotype 3. This study is the first to report the presence of HEV in pork sold in Senegal and the results reveal a potential circulation of HEV in the pig population. The high proportion of contamination in the pork liver samples highlights a major risk associated with their consumption. [ABSTRACT FROM AUTHOR]

Human astrovirus (HAstV) is a known cause of viral gastroenteritis in children worldwide, but HAstV can cause also severe and systemic infections in immunocompromised patients. There are three clades of HAstV: classical, MLB, and VA/HMO. While all three clades are found in gastrointestinal samples, HAstV-VA/HMO is the main clade associated with meningitis and encephalitis in immunocompromised patients. To understand how the HAstV-VA/HMO can infect the central nervous system, we investigated its sequence-divergent capsid spike, which functions in cell attachment and may influence viral tropism. Here we report the high-resolution crystal structures of the HAstV-VA1 capsid spike from strains isolated from patients with gastrointestinal and neuronal disease. The HAstV-VA1 spike forms a dimer and shares a core beta-barrel structure with other astrovirus capsid spikes but is otherwise strikingly different, suggesting that HAstV-VA1 may utilize a different cell receptor, and an infection competition assay supports this hypothesis. Furthermore, by mapping the capsid protease cleavage site onto the structure, the maturation and assembly of the HAstV-VA1 capsid is revealed. Finally, comparison of gastrointestinal and neuronal HAstV-VA1 sequences, structures, and antigenicity suggests that neuronal HAstV-VA1 strains may have acquired immune escape mutations. Overall, our studies on the HAstV-VA1 capsid spike lay a foundation to further investigate the biology of HAstV-VA/HMO and to develop vaccines and therapeutics targeting it. Author summary: Human astroviruses, well-established as a leading cause of viral diarrhea, are increasingly associated with viral encephalitis in immunocompromised patients, with the sequence-divergent VA1 strains being the most common in these cases. Our study presents the high-resolution capsid spike structures from VA1 strains isolated from patients with both gastrointestinal and neuronal manifestations. Compared to the classical human astrovirus capsid spike structure, the VA1 capsid spike structure has striking differences in size, shape, and surface features, suggesting that the divergent VA1 strains may have evolved a different mechanism to attach to host cells, which in turn may influence their ability to infect the central nervous system. On the other hand, comparison of the gastrointestinal and neuronal VA1 spike structures reveals few differences. Instead, sequence and antigenic studies suggest that neuronal VA1 strains isolated from immunocompromised patients may have acquired mutations to escape immunoglobulin therapy. Altogether, this work provides a structural basis to investigate the mechanism of infection by the divergent human astrovirus VA1 strains and to develop tailored diagnostics, vaccines, and therapeutics against them. [ABSTRACT FROM AUTHOR]

Simple Summary: In surveillance studies conducted in industrialized EU nations, a rise has been noted in hepatitis E infections that are unrelated to travel. According to previous research studies, eating undercooked or uncooked meat and organs, as well as products from pigs or other wild animals (wild boars and deer), was predominantly linked to human hepatitis caused by the hepatitis E virus genotype 3. Furthermore, domestic pigs and wild boars represent nature's primary reservoirs of this virus, and the liver is the main organ for hosting this virus. The goal of this study conducted in Serbia was to detect HEV in pig liver samples from slaughterhouses, retail outlets, and environmental swabs over the course of a year. All positive HEV samples were measured and expressed as HEV gene copy numbers per gram of sample, and a representative number of samples were sequenced using the Sanger approach. A total of 45 HEV-positive samples were re-amplified using nested RT-PCR employing CODEHOP primers targeting ORF2 (493 nucleotides). The average prevalence of the HEV genotype 3 in all pig liver samples from the slaughterhouses was 29%, while HEV prevalence was 44% in liver samples from animals younger than 3 months. HEV RNA was found in thirteen out of sixty (22%) environmental swab samples that were taken from different surfaces along the slaughter line. Our findings confirmed seasonal patterns in HEV prevalence, with two picks (summer and winter periods) during the one-year examination. Among HEV-positive samples, the average viral particles for all positive liver samples was 4.41 ± 1.69 log10 genome copies per gram. Phylogenetic analysis revealed the majority of HEV strains (43/45) from Serbia were grouped in the HEV-3a subtype, while two strains were classified into the HEV-3c subtype, and one strain could not be classified into any of the HEV-3 subtypes. [ABSTRACT FROM AUTHOR]

Since the outbreak of SARS‐CoV‐2 was first identified in 2019, it has been reported that the virus could infect a variety of animals either naturally or experimentally. This review discusses the occurrence SARS‐CoV‐2 in dogs and cats and the role of these animals in transmitting coronavirus disease 2019 (COVID‐19) to their owners. The data were collected from epidemiological studies and case reports that focused on studying the occurrence of SARS‐CoV‐2 in pet animals and their owners. Epidemiological studies and case reports indicate that dogs and cats are infected with SARS‐CoV‐2 either naturally or experimentally; however, the global number of naturally infected animals is far lower than the number of people who have COVID‐19. These studies demonstrate that pet animals acquire the infection from direct contact with COVID‐19‐infected owners. Currently, there are no studies reporting that dogs and cats can transmit SARS‐CoV‐2 to other animals and humans, under natural conditions. The emergence of SARS‐CoV‐2 infection in companion animals (dogs and cats) in different countries worldwide raises concerns that pets are at higher risk for spreading and transmitting SARS‐CoV‐2 to humans and other animals, which poses a hazard to the public health. Therefore, investigating the role of dogs and cats in the transmission and epidemiology of SARS‐CoV‐2 will help us to design and implement appropriate preventive measures against the further transmission of SARS‐CoV‐2. [ABSTRACT FROM AUTHOR]

Tick‐associated viruses remain a substantial zoonotic risk worldwide, so knowledge of the diversity of tick viruses has potential health consequences. Despite their importance, large amounts of sequences in public data sets from tick meta‐genomic and ‐transcriptomic projects remain unannotated, sequence data that could contain undocumented viruses. Through data mining and bioinformatic analysis of more than 37,800 public meta‐genomic and ‐transcriptomic data sets, we found 83 unannotated contigs exhibiting high identity with known tick viruses. These putative viral contigs were classified into three RNA viral families (Alphatetraviridae, Orthomyxoviridae and Chuviridae) and one DNA viral family (Asfarviridae). After manual checking of quality and dissimilarity towards other sequences in the data set, these 83 contigs were reduced to five contigs in the Alphatetraviridae from four putative viruses, four in the Orthomyxoviridae from two putative viruses and one in the Chuviridae which clustered with known tick‐associated viruses, forming a separate clade within the viral families. We further attempted to assess which previously known tick viruses likely represent zoonotic risks and thus deserve further investigation. We ranked the human infection potential of 133 known tick‐associated viruses using a genome composition‐based machine learning model. We found five high‐risk tick‐associated viruses (Langat virus, Lonestar tick chuvirus 1, Grotenhout virus, Taggert virus and Johnston Atoll virus) that have not been known to infect human and two viral families (Nairoviridae and Phenuiviridae) that contain a large proportion of potential zoonotic tick‐associated viruses. This adds to the knowledge of tick virus diversity and highlights the importance of surveillance of newly emerging tick‐associated diseases. [ABSTRACT FROM AUTHOR]

Many studies have been conducted to explore outbreaks of SARS-CoV-2 in farmed mink and their intra-/inter-species spread and spillover to provide data to the scientific community, protecting human and animal health. Studies report anthropozoonotic introduction, which was initially documented in April 2020 in the Netherlands, and subsequent inter-/intra-species spread of SARS-CoV-2 in farmed mink, likely due to SARS-CoV-2 host tropism capable of establishing efficient interactions with host ACE2 and the mink hosts' ability to enhance swift viral transmission due to their density, housing status, and occupational contacts. Despite the rigorous prevention and control measures adopted, transmission of the virus within and between animal species was efficient, resulting in the development of mink-associated strains able to jump back and forth among the mink hosts and other animal/human contacts. Current knowledge recognizes the mink as a highly susceptible animal host harboring the virus with or without clinical manifestations, furthering infection transmission as a hidden animal reservoir. A One Health approach is, thus, recommended in SARS-CoV-2 surveillance and monitoring on mink farms and of their susceptible contact animals to identify and better understand these potential animal hosts. [ABSTRACT FROM AUTHOR]

The prevalence of West Nile virus (WNV) is increasing across Europe, with cases emerging in previously unaffected countries. Kosovo is situated in a WNV-endemic region where the seroepidemiological data on WNV in humans remains absent. To address this issue, we have conducted a seroepidemiological investigation of 453 randomly selected sera from a hospital in Kosovo, revealing a 1.55% anti-WNV IgG seroprevalence. Comparative and phylogeographic analyses of the WNV genomes obtained by sequencing archived samples from patients with West Nile fever indicate at least two recent and distinct introductions of WNV lineage 2 into Kosovo from neighboring countries. These findings confirm the eco-epidemiological status of WNV in southeast Europe, where long- and short-range dispersion of lineage 2 strains contributes to a wider circulation via central Europe. Our results suggest an increasing risk for WNV spreading in Kosovo, underscoring the need for an integrated national surveillance program targeting vectors and avian populations for early epidemic detection, as well as the screening of blood donors to gauge the impact of virus circulation on the human population. [ABSTRACT FROM AUTHOR]

Introduction: Metagenomic next-generation sequencing (mNGS) has emerged as a powerful tool for rapid pathogen identification in clinical practice. However, the parameters used to interpret mNGS data, such as read count, genus rank, and coverage, lack explicit performance evaluation. In this study, the developed indicators as well as novel parameters were assessed for their performance in bacterium detection. Methods: We developed several relevant parameters, including 10M normalized reads, double-discard reads, Genus Rank Ratio, King Genus Rank Ratio, Genus Rank Ratio*Genus Rank, and King Genus Rank Ratio*Genus Rank. These parameters, together with frequently used read indicators including raw reads, reads per million mapped reads (RPM), transcript per kilobase per million mapped reads (TPM), Genus Rank, and coverage were analyzed for their diagnostic efficiency in bronchoalveolar lavage fluid (BALF), a common source for detecting eight bacterium pathogens: Acinetobacter baumannii, Klebsiella pneumoniae, Streptococcus pneumoniae, Staphylococcus aureus, Hemophilus influenzae, Stenotrophomonas maltophilia, Pseudomonas aeruginosa, and Aspergillus fumigatus. Results: The results demonstrated that these indicators exhibited good diagnostic efficacy for the eight pathogens. The AUC values of all indicators were almost greater than 0.9, and the corresponding sensitivity and specificity values were almost greater than 0.8, excepted coverage. The negative predictive value of all indicators was greater than 0.9. The results showed that the use of double-discarded reads, Genus Rank Ratio*Genus Rank, and King Genus Rank Ratio*Genus Rank exhibited better diagnostic efficiency than that of raw reads, RPM, TPM, and in Genus Rank. These parameters can serve as a reference for interpreting mNGS data of BALF. Moreover, precision filters integrating our novel parameters were built to detect the eight bacterium pathogens in BALF samples through machine learning. Summary: In this study, we developed a set of novel parameters for pathogen identification in clinical mNGS based on reads and ranking. These parameters were found to be more effective in diagnosing pathogens than traditional approaches. The findings provide valuable insights for improving the interpretation of mNGS reports in clinical settings, specifically in BALF analysis. [ABSTRACT FROM AUTHOR]

West Nile Virus (WNV) is a mosquito vector-borne zoonosis with an increasing incidence in Europe that has become a public health concern. In Spain, although local circulation has been known for decades, until 2020, when a large outbreak occurred, West Nile Virus cases were scarce and mostly occurred in southern Spain. Since then, there have been new cases every year and the pathogen has spread to new regions. Thus, monitoring of circulating variants and lineages plays a fundamental role in understanding WNV evolution, spread and dynamics. In this study, we sequenced WNV consensus genomes from mosquito pools captured in 2022 as part of a newly implemented surveillance program in southern Spain and compared it to other European, African and Spanish sequences. Characterization of WNV genomes in mosquitoes captured in 2022 reveals the co-circulation of two WNV lineage 1 variants, the one that caused the outbreak in 2020 and another variant that is closely related to variants reported in Spain in 2012, France in 2015, Italy in 2021–2022 and Senegal in 2012–2018. The geographic distribution of these variants indicates that WNV L1 dynamics in southern Europe include an alternating dominance of variants in some territories. [ABSTRACT FROM AUTHOR]

This report by the European Food Safety Authority and the European Centre for Disease Prevention and Control presents the results of the zoonoses monitoring and surveillance activities carried out in 2022 in 27 Member States (MSs), the United Kingdom (Northern Ireland) and 11 non‐MSs. Key statistics on zoonoses and zoonotic agents in humans, food, animals and feed are provided and interpreted historically. In 2022, the first and second most reported zoonoses in humans were campylobacteriosis and salmonellosis, respectively. The number of cases of campylobacteriosis and salmonellosis remained stable in comparison with 2021. Nineteen MSs and the United Kingdom (Northern Ireland) achieved all the established targets in poultry populations for the reduction of Salmonella prevalence for the relevant serovars. Salmonella samples from carcases of various animal species, and samples for Campylobacter quantification from broiler carcases, were more frequently positive when performed by the competent authorities than when own checks were conducted. Yersiniosis was the third most reported zoonosis in humans, followed by Shiga toxin‐producing Escherichia coli (STEC) and Listeria monocytogenes infections. L. monocytogenes and West Nile virus infections were the most severe zoonotic diseases, with the most hospitalisations and highest case fatality rates. In 2022, reporting showed an increase of more than 600% compared with 2021 in locally acquired cases of human West Nile virus infection, which is a mosquito‐borne disease. In the EU, the number of reported foodborne outbreaks and cases, hospitalisations and deaths was higher in 2022 than in 2021. The number of deaths from outbreaks was the highest ever reported in the EU in the last 10 years, mainly caused by L. monocytogenes and to a lesser degree by Salmonella. Salmonella and in particular S. Enteritidis remained the most frequently reported causative agent for foodborne outbreaks. Norovirus (and other calicivirus) was the agent associated with the highest number of outbreak human cases. This report also provides updates on brucellosis, Coxiella burnetii (Q fever), echinococcosis, rabies, toxoplasmosis, trichinellosis, infection with Mycobacterium tuberculosis complex (focusing on Mycobacterium bovis and Mycobacterium caprae) and tularaemia. This publication is linked to the following EFSA Journal article: https://efsa.onlinelibrary.wiley.com/doi/10.2903/j.efsa.2023.p211202 [ABSTRACT FROM AUTHOR]