Prevalence and Sequence Analysis of Equine Rhinitis Viruses among Horses in Poland

Abstract

Equine rhinitis A (ERAV) and B (ERBV) viruses are respiratory pathogens with worldwide distribution. The current study aimed to determine the frequency of infection of ERAV and ERBV among horses and foals at Polish national studs, and to determine genetic variability within the viruses obtained. Virus-specific quantitative RT-PCR assays targeting a 5' untranslated region were used to screen nasal swabs collected from 621 horses at 16 national horse studs from throughout Poland, including 553 healthy horses and 68 horses with respiratory disease. A partial DNA polymerase gene was amplified and sequenced from the qRT-PCR-positive samples. The obtained sequences were analysed using phylogeny and genetic network analysis. None of the nasal swabs were positive for ERAV, whereas ERBV was found in 11/621 (1.78%) samples collected from 10 healthy horses and one foal affected by respiratory disease. Partial DNA polymerase gene sequence variability was correlated with individual horses and studs from which samples were collected when only Polish sequences were analysed, but there was no correlation between country of origin and ERBV sequence when Polish and international sequences were included in the network. The report presents the first detection of ERBV in Poland.

Keywords: ERAV; ERBV; equine rhinitis viruses; haplotype network; horses; sequence analysis.

Figure 1

The age structure of horses sampled in the study.

Figure 2

Map of Poland showing the location of the studs (denoted by Arabic numbers). The number of ERBV-positive samples/number of samples collected from each stud are shown in the brackets. Available from: https://d-maps.com/carte.php?num_car=4308&lang=en, accessed on 15 May 2024.

Figure 3

Phylogenetic tree of equine rhinitis B viruses (ERBV) based on 555 bp fragment from 3D polymerase (nt 8152-8707 in ERBV accession number NC_003983.1). The sequences used included Polish ERBV sequences of clones (n = 51), and international sequences (n = 11) sourced from GenBank. The Polish sequences obtained in the current study are labelled PL_ERBV_stud number_horse number_clone number. Accession numbers for sequences from GenBank are listed for each sequence. The evolutionary history was inferred by using the maximum likelihood method with a bootstrap value of 1000 using the Kimura 2-parameter model. The tree with the highest log likelihood (−2419.25) is shown. A discrete Gamma distribution was used to model evolutionary rate differences among sites (5 categories (+G, parameter = 0.2017)). All positions containing gaps and missing data were eliminated (complete deletion option). Evolutionary analyses were conducted in MEGA11 [16]. Coloured rectangles signify geographical origin: Poland (blue), United Arab Emirates (light green), Switzerland (pink), USA (dark green) and Australia (orange). Values greater than 80% are shown.

Figure 4

International haplotype network of ERBV based on partial (555 bp) 3D polymerase region sequences (n = 62) including sequences (n = 51) from Polish horse studs obtained in the current study and sequences from GenBank (n = 11). The number of nucleotide substitutions between haplotypes is represented by ticks on branches. Nodes are scaled based on the number of representative sequences and coloured based on the geographic location of origin. Small closed black circles indicate inferred nodes that are not represented among sequences included in the network.

Figure 5

Median-joining haplotype network based on partial 3D polymerase and 3′ untranslated region of ERBV sequences (concatenated and trimmed to 621 nt) from samples originated in Poland (n = 51). Nodes are scaled based on the number of representative sequences and coloured based on the individual horses from which they were obtained. Horses from the same stud are shown in different shades of the same colour. Small closed black circles indicate inferred nodes that are not represented among sequences included in the network.