BACKGROUND: This study was conducted to characterize two fowlpox viruses isolated in Iran and study their phylogenic relationship. OBJECTIVES: The aim of this study was to determine the identity of two pox viruses recovered from a tissue sample with typical lesions of fowl pox and red mites from a laying farm. Fowl pox in poultry industry causes significant economic losses associated with decreased egg production, reduced growth, blindness and increased mortality. The pox virus, by direct or indirect contact, may also be transmitted through vectors such as mites and fleas. Dermanyssus gallinae also known as the poultry red mite is the most important blood feeder ectoparasite affecting poultry, in particular, laying hens. In addition to its significant economic losses, it is considered as a potential vector for a number of important avian pathogens. METHODS: Both isolates were inoculated to chorioallantoic membrane (CAM) of embryonated chicken eggs, detected by specific PCR for pox virus 4b gene and characterized by sequencing and phylogentic analysis. RESULTS: Both isolates developed pock lesions in CAM of embryonated eggs. A 578 bp fragment of the poxvirus 4b gene was amplified in both isolates by PCR. The sequence analyses revealed that the two isolates were 100% identical and placed in the same branch. The nucleotide sequence of these two isolates showed a similarity of 73 to 100% to the other selected avian pox sequences available in the GenBank. CONCLUSIONS: These results confirmed that Dermanyssus gallinae are considered to be an important vector for the spread of fowl pox virus in the flocks. Therefore, controlling the red mites in poultry farms will not only inhibit problems such as blood feeding, decreased production and reduced growth rate, it can reduce the transmission of diseases and pathogenic agents in the farms.

Porcine epidemic diarrhoea virus (PEDV) is an enteric pathogen causing porcine epidemic diarrhoea and acute gastroenteritis in pigs of all ages. Previous analysis of the viral genome of PEDV in Poland was only based on the spike protein (S) gene sequences and no analysis of other genes has been performed. The aim of this study was to analyse the envelope (E), membrane (M) and nucleocapsid (N) protein and open reading frame 3 (ORF3) gene sequences.

Akabane virus (AKAV) has been detected in a variety of host species in China, but there are only limited records of its occurrence in goats. However, more attention needs to be paid to understanding the diversity of viruses in this species. The aim of the study was to explore the genotype characteristics and variation trend of AKAV and their relationship with virulence in Yunnan, China.

Ornithobacterium rhinotracheale (ORT) causes significant economic losses to the poultry industry around the world. The bacterium often affects poultry as part of multiple infections causing very serious clinical signs that are usually not limited only to the respiratory system. This study’s main objective was the retrospective detection and identification of ORT in turkey flocks.

Nematodes of the Trichuris genus are commonly reported parasites that can cause trichuriasis in many animals, which leads to inflammation, intestinal bleeding and reductions of productivity in livestock. Knowledge of the prevalence of Trichuris infestation in the Tianshan ovine population and of the nematode species parasitising the population is not exhaustive, and this study aimed to expand the knowledge.

Newcastle disease (ND) is regarded as a highly contagious and economically important disease in poultry and has a worldwide distribution. Viral determinants for Newcastle disease virus (NDV) virulence are not completely understood and viruses of different pathotypes can be found at live-bird markets in different geographical areas. The prevalence of Newcastle disease in village poultry in Mozambique is not well documented and strains of NDV involved in yearly outbreaks are unknown. The fusion (F) protein is an important determinant of pathogenicity of the virus and is used commonly for phylogenetic analysis. Newcastle disease viruses from various geographical regions of Mozambique were sequenced and compared genetically to published sequences obtained from GenBank. Samples were collected in three different areas of Mozambique and NDV was isolated by infection of embryonated chicken eggs. Sequence analysis of the F-protein encoding gene was used to classify 28 isolates from Mozambique into genotypes and compare these genotypes phylogenetically with existing genotypes found in GenBank. The isolates obtained from Mozambique grouped mainly into two clades. In the first clade, 12 isolates grouped together with sequences of isolates representing genotypes from Mozambique that were previously described. In the second clade, 16 isolates group together with sequences obtained from GenBank originating from Australia, China, South Africa and the USA. Eleven of these isolates showed a high similarity with sequences from South Africa. The number of samples sequenced (<em>n</em> = 28), as well as the relatively small geographical collection area used in this study, are too small to be a representation of the circulating viruses in Mozambique in 2005. Viruses characterised in this study belonged to lineage 5b, a similar finding of a previous study 10 years ago. From this data, it merely can be concluded that no new introduction of the virus occurred from 1995 to 2005 in Mozambique.

Lotmaria passim (L. passim) is a single-celled flagellate which colonises the bee gastrointestinal tract and is highly prevalent in honey bees. This parasite is associated with colony losses. Honey bee (Apis mellifera) colonies were sampled from five apiaries in the north-eastern part of Poland for the phylogenetic analysis of L. passim.

Ornithobacterium rhinotracheale (ORT) causes significant economic losses to the poultry industry around the world. The bacterium often affects poultry as part of multiple infections causing very serious clinical signs that are usually not limited only to the respiratory system. This study’s main objective was the retrospective detection and identification of ORT in turkey flocks. ORT identification was performed in 6,225 samples taken from 133 different flocks between 2015 and 2020. Molecular methods were used, specifically real-time PCR and traditional PCR. We focused on partial 16S rRNA gene sequences of isolates, which were compared with sequences obtained from GenBank. The reaction products were analysed phylogenetically. Molecular methods indicating secondary infections was carried out, and the bacterial composition of the upper respiratory tract was 16S metasequenced for selected flocks to identify any other pathogens. The presence of ORT was detected in 30.83% of samples by real-time PCR and 28.57% by PCR. Phylogenetic analysis of the PCR products from the turkeys samples showed that their sequences resolved into two main genetic groups. Tests for the occurrence of secondary infections showed the presence of Mycoplasma gallisepticum and M. synoviae in some samples but the total absence of Bordetella avium. The upper respiratory tract in turkeys was dominated by two major phyla Firmicutes and Proteobacteria. At the genus level, the genera Ornithobacterium, Mycoplasma, Gallibacterium, Avibacterium, and Escherichia-Shigella were found which may include pathogenic bacteria that can cause clinical symptoms. The results of the analysis of multiple infection carried out in flocks with respiratory signs are probably associated with outbreaks of ornithobacteriosis in turkey flocks in Poland.

Introduction: Traditionally, evolutionary analysis of equine influenza virus (EIV) is based on the HA gene. However, the specificity of the influenza virus enables the classification of viral strains into different phylogenetic groups, depending on the gene being analysed. The aim of the study was to analyse phylogenetic paths of EIV based on M gene with reference to the HA gene. Material and Methods: M gene of Polish isolates has been sequenced and analysed along with all M sequences of EIV available in GenBank database. Phylogenetic analysis was performed using BioEdit, ClustalW, and MEGA7 softwares. Results: The clustering of the strains isolated not only from Asia but also from Europe into one common Asian-like group of EIV was observed. Twelve nucleotide substitutions in the M gene of strains from the Asian-like group were crucial for the evolutionary analysis. We also observed homology in the M gene of the Asian-like and H7N7 strains. Conclusions: M gene specific for the Asian-like group is present in strains recently isolated in Europe and Asia, which were classified previously in the Florida 2 clade based on HA. Therefore, Asian-like group does not seem to be assigned to a specific geographical region. Traces of H7N7 strains in more conservative genes like M of some contemporary EIV strains may indicate the link between the old phylogenetic group and recent H3N8 strains. Analysis of conservative genes may be more useful in tracking the direction of virus evolution than in the genes where the high variability rate may blur the original relationships.

Introduction: The genomes of nine H5 subtypes of low pathogenic avian influenza virus (LPAIV) strains identified in wild birds in Poland between 2010 and 2015 were sequenced, and their phylogenetic relationship was determined. Material and Methods: AIV genome segments were amplified by RT-PCR and the PCR products were sequenced using Sanger method. Phylogenetic trees were generated in MEGA6 software and digital genotyping approach was used to visualise the relationship between analysed strains and other AIVs. Results: High genetic diversity was found in the analysed strains as multiple subgroups were identified in phylogenetic trees. In the HA tree, Polish strains clustered in two distinct subclades. High diversity was found for PB2, PB1, PA and NP, since 5-8 sublineages could be distinguished. Each strain had a different gene constellation, although relationship of as much as six out of eight gene segments was observed between two isolates. A relationship with poultry isolates was found for at least one segment of each Polish strain. Conclusion: The genome configuration of tested strains indicates extensive reassortment, although the preference for specific gene constellation could be noticed. A significant relationship with isolates of poultry origin underlines the need for constant monitoring of the AIV gene pool circulating in the natural reservoir.