Based on analysis of available genome sequences, five gene lineages of MHC class I molecules (MHC I-U, -Z, -S, -L and -P) and one gene lineage of MHC class II molecules (MHC II-D) have been identified in Osteichthyes. In the latter lineage, three MHC II molecule sublineages have been identified (MHC II-A, -B and -E). As regards MHC class I molecules in Osteichthyes, it is important to take note of the fact that the lineages U and Z in MHC I genes have been identified in almost all fish species examined so far. Phylogenetic studies into MHC II molecule genes of sublineages A and B suggest that they may be descended from the genes of the sublineage named A/B that have been identified in spotted gar (Lepisosteus oculatus). The sublineage E genes of MHC II molecules, which represent the group of non-polymorphic genes with poor expression in the tissues connected with the immune system, are present in primitive fish, i.e. in paddlefish, sturgeons and spotted gar (Lepisosteus oculatus), as well as in cyprinids (Cyprinidae), Atlantic salmon (Salmo salar), and rainbow trout (Oncorhynchus mykiss). Full elucidation of the details relating to the organisation and functioning of the particular components of the major histocompatibility complex in Osteichthyes can advance the understanding of the evolution of the MHC molecule genes and the immune mechanism.

Carbapenem-resistant Pseudomonas aeruginosa (CRPA) has become the leading cause of health care-associated infections. Treatment is difficult due to the lack of an effective antimicrobial therapy, and mortality is high. This study investigated the occurrence of CRPA in farm animals (buffaloes and cattle), livestock drinking water, and humans in Egypt. A total of 180 samples were examined: 50 faecal each from buffaloes and cattle, 30 of livestock drinking water, and 50 stool from humans. The samples were cultured on cetrimide agar and the plates were incubated aerobically at 37°C for 24 h. The isolates were examined for the presence of the blaKPC, blaOXA₋₄₈, and blaNDM carbapenemase-encoding genes using PCR and investigated for the exotoxin A (toxA) gene. The toxA gene from carbapenem- group resistant isolates was phylogenetically analysed. P. aeruginosa was isolated from buffaloes, cattle, drinking water, and humans, with occurrences of 40%, 34%, 10%, and 20%, respectively. Carbapenem resistance genes were found in 60%, 59%, 67%, and 70% in buffalo, cattle, water and human samples, respectively. The toxA gene was detected in 80% of samples. The phylogenetic analysis showed that cattle and water sequences were in one cluster and more related to each other than to human isolates. Occurrence of CRPA among farm animals, drinking water, and humans was high, reflecting the environmental origin of P. aeruginosa and highlighting contaminated water as a potential transmitter of CRPA to livestock and next to humans.

Bovine Norovirus (BoNeV) which has been confirmed in Asia, America, and Europe, seems to be distributed worldwide, even though only reported from a number of countries. Bovine noroviruses are predominantly detected in diarrhoeic animals rather than neboviruses. The study reveals the importance of noro- and neboviruses in early age diarrhoea of calves. A total of 127 stool samples were collected from three provinces located in the central region of Turkey. Samples were subjected to nucleic acid isolation and reverse transcription and polymerase chain reaction (PCR). Positive samples were sequenced and analysed. According to PCR, five samples (3.93%) were found to be positive for bovine norovirus while 32 (25.19%) samples were found to be positive for bovine nebovirus. Phylogenetic analysis indicated that the novel Turkish norovirus strains were found to be of genotype III.2 and all novel neboviruses were substituted under Nebraska-like strains. Although predominantly bovine noroviruses are detected worldwide, the study indicated that bovine neboviruses were more prevalent in the studied area. We suggest that bovine neboviruses are more frequently responsible for calf diarrhoea than supposed by virologists. This is also the first report of neboviruses other than Kirklareli virus which is distantly related to neboviruses detected in Turkey.

Introduction: Leptospirosis affects a wide range of mammals, humans, and even a few poikilothermic animal species. In Pakistan, serological studies of equine leptospirosis have reported a prevalence of over 40%, but no study has ever been conducted towards molecular detection of Leptospira in horses. Material and Methods: Blood samples from 128 horses were screened using ELISA and 41 positive samples were examined for the presence of leptospiral DNA using specific primers for 16S rRNA gene. Results: Out of 41 tested samples, 20 samples were found to be PCR-positive, revealing a fragment of 306 bp after gel electrophoresis. Sequencing and phylogenetic analysis of positive samples revealed circulation of pathogenic Leptospira spp. in Pakistani horses. No evidence of circulation of intermediate species was found in this study. Conclusion: This study reports the first molecular evidence of equine leptospirosis in Pakistan and lays ground for further research in this area. It also confirms the efficiency of 16S rRNA for the diagnosis of equine leptospirosis.

Introduction: Bovine viral diarrhoea (BVD), caused by the bovine viral diarrhoea virus (BVDV), is one of the most important diseases of cattle worldwide. The purpose of the study was to determine the BVDV infection status in a dairy herd vaccinated against BVD. Before vaccination started in 2008, there had been no prior identification or the removal of the possible source of infection (persistently infected animals). It was expected that vaccination itself would enable the elimination of viral shedders on a long term basis. Material and Methods: Serological screening for antibodies against BVDV with determination for antibodies titres, BVDV antigen, and the presence of the viral genome with phylogenetic analysis of positive samples in the herd were performed, despite the lack of any clinical problems indicating possible presence of BVDV infection. Results: 19 individuals persistently infected with BVDV were identified among calves and heifers but not in adult cattle. All virus shedders were antibody negative and the genotype of isolated virus was BVDV-1b, indicating a single source of infection. The vaccine used in the herd was composed of BVDV-1a strain. In each of the tested cowsheds, antibody titres against BVDV-1b were higher than against BVDV-1a (median values). Conclusion: Despite a long-lasting vaccination programme and relatively high sequence homology of vaccinal and field strains of BVDV (83.6%), it was not possible to avoid transplacental infections of foetuses and the birth of persistently infected calves from vaccinated heifers although the protection against clinical disease was accomplished.

Fasciola hepatica is a trematode infecting ruminants worldwide and occasionally affecting other animal species, including humans. It causes significant economic losses. Geographic distribution and patterns of infection must be considered before control and management measures are developed for this parasite. DNA molecular markers are useful for the identification of flukes and elucidation of their genetic evolution. Therefore, the population structure of F. hepatica was studied using this method in sheep in Xinjiang, China. The molecular characteristics, genetic relationships within the population and dispersal patterns of F. hepatica isolates were analysed based on the cox1 and nad1 genes. The population structure of F. hepatica from three regions of Xinjiang was explored and a neutrality test was conducted. The cox1 and nad1 genes have 21 and 42 variable sites, respectively, which can be classified into 34 and 33 haplotypes. Median-joining network and phylogenetic tree analyses showed that there was no significant variation in F. hepatica isolates between the three geographical regions. Analysis of variance revealed that the genetic variation of F. hepatica was mainly present within the populations. The neutrality test indicated that the populations were relatively stable but the Hami population may have undergone short-term expansion. This study revealed for the first time the molecular characteristics, genetic diversity and dispersal patterns of F. hepatica isolates from sheep in Xinjiang, thus providing new insights into the genetic variation and haplotype diversity of F. hepatica from indigenous sheep.

Although ovine cysticercosis is not a zoonotic problem, it results in substantial economic losses due to the condemnation of infected tissues or entire carcasses. This study aimed to record preliminary data on the prevalence, and phylogenetic diversity of Cysticercus ovis isolates from slaughtered sheep in the province of Sulaymaniyah, Iraq. From January to September 2020, 6, 411 slaughtered sheep were examined for C. ovis by routine meat inspection. The amplification and sequence analysis of the COX1 gene for up to 35 specimens of C. ovis was performed using conventional PCR. The overall prevalence rate was 1.3%, and the prevalence was significantly higher in older sheep (>1 year) than younger ones (<1 year) (P< 0.05). The cardiac muscle showed a higher tendency to carry C. ovis infection compared to other examined muscles. Sequence analysis of the COX1 gene revealed six haplotypes, and the level of pairwise nucleotide diversity between individual haplotypes was 1–2%. Five out of six of the Taenia ovis haplotypes recovered could have been recorded for the first time globally. Phylogenetic interpretation indicated that all the T. ovis haplotypes clustered in a single clade, and it also indicated an extremely close similarity to Iranian and New Zealand isolates. Globally, this report adds new data on C. ovis genetic diversity, which provide an extremely useful molecular background with regard to future preventive as well as control strategies.

Repeated incursions of highly pathogenic avian influenza virus (HPAIV) H5 subtype of Gs/GD lineage pose a serious threat to poultry worldwide. We provide a detailed analysis of the spatio-temporal spread and genetic characteristics of HPAIV Gs/GD H5N8 from the 2019/20 epidemic in Poland. Samples from poultry and free-living birds were tested by real-time RT-PCR. Whole genome sequences from 24 (out of 35) outbreaks were generated and genetic relatedness was established. The clinical status of birds and possible pathways of spread were analysed based on the information provided by veterinary inspections combined with the results of phylogenetic studies. Between 31 December 2019 and 31 March 2020, 35 outbreaks in commercial and backyard poultry holdings and 1 case in a wild bird were confirmed in nine provinces of Poland. Most of the outbreaks were detected in meat turkeys and ducks. All characterised viruses were closely related and belonged to a previously unrecognised genotype of HPAIV H5N8 clade 2.3.4.4b. Wild birds and human activity were identified as the major modes of HPAIV spread. The unprecedentedly late introduction of the HPAI virus urges for re-evaluation of current risk assessments. Continuous vigilance, strengthening biosecurity and intensifying surveillance in wild birds are needed to better manage the risk of HPAI occurrence in the future.

Bovine tuberculosis, caused by M. bovis, is endemic in Mexico and has had a big impact on public health. Jalisco is considered to be an important dairy region in the country, accounting for approximately 19% of the total milk production. Within Jalisco, the region of Altos Sur holds the largest proportion of the cattle inventory of the state. To determine the frequency of bovine tuberculosis in Altos Sur, Jalisco, as well as M. bovis genetic diversity, sampling of tissue (lymph nodes, lungs, and liver) from Holstein cattle was performed in four abattoirs belonging to three municipalities of this region (Tepatitlán de Morelos, San Miguel el Alto, and Arandas). Spoligotyping and whole-genome sequencing were carried out to assess the genetic relationships of M. bovis strains circulating in this area, as well as a comparison to isolates from other places in Mexico. Prevalence was 15.06%, and distribution similar among the three municipalities. The most frequent spoligotypes were SB0673, SB121, and SB0145. Whole-genome sequencing revealed three main clades (I, II, III), but isolates did not show clustering by region. Phylogenetic analysis suggested ongoing transmission between herds of the different regions, and no unique source of infection was determined. This hinders efforts under the national program for the control and eradication of the disease, so serious attention must be paid to rural regions such as Altos Sur in order to improve its success.

Malignant catarrhal fever (MCF) is a rare, under-explored lethal viral infection of cattle with gammaherpesvirus aetiological agents. Most often, the disease occurs on farms where cattle and sheep are kept together. However, other trigger mechanisms and environmental factors contribute. This study investigates the causation of MCF. An outbreak of MCF occurred in June - August 2017 in Kharchev village in Irkutsk Oblast, Russia. In this paper, we provide epidemiological (sanitary status of pastures, watering places, and premises) and weather data during the outbreak, and descriptions of the clinical signs and post-mortem changes in cattle. The virus was detected and isolated from pathological material samples and identified by molecular methods. Extreme weather conditions, mixed-herd cattle and sheep farming, and unsatisfactory feed quality contributed to the outbreak. A virus related to herpesvirus OvHV2 was isolated and typed (MCF/Irkutsk/2017). Phylogenetic analysis showed its close genetic relationship to isolates from cattle and sheep in Germany, USA, and the Netherlands. Sporadic outbreaks of MCF caused by biotic and abiotic factors together are typical for the Russian Federation, and the Irkutsk outbreak epitomised this. Temperature anomalies caused pasture depletion, resulting in feed and water deficiency for grazing animals and dehydration and acidosis. Heat stress in animals ultimately led to the occurrence of MCF in the herd.