Genetic characterization of upper respiratory tract virome from nonvaccinated Egyptian cow-calf operations

Abstract

Bovine respiratory disease (BRD) is the costliest complex disease affecting the cattle industry worldwide, with significant economic losses. BRD pathogenesis involves several interactions between microorganisms, such as bacteria and viruses, and management factors. The present study aimed to characterize the nasal virome from 43 pooled nasal swab samples collected from Egyptian nonvaccinated cow-calf operations with acute BRD from January to February 2020 using metagenomic sequencing. Bovine herpesvirus-1 (BHV-1), first detection of bovine herpesvirus-5 (BHV-5), and first detection of bovine parvovirus-3 (BPV-3) were the most commonly identified in Egyptian cattle. Moreover, phylogenetic analysis of glycoprotein B revealed that the BHV-1 isolate is closely related to the Cooper reference strain (genotype 1.1), whereas the BHV-5 isolate is closely related to the reference virus GenBank NP_954920.1. In addition, the whole-genome sequence of BPV-3 showed 93.02% nucleotide identity with the reference virus GenBank AF406967.1. In this study, several DNA viruses, such as BHV-1 and first detection BHV-5, and BPV-3, were detected and may have an association with the BRD in Egyptian cattle. Therefore, further research, including investigating more samples from different locations to determine the prevalence of detected viruses and their contributions to BRD in cattle in Egypt, is needed.

Fig 1. A map of herd locations in Egypt from which animal’s samples were collected.

Fig 2. Phylogenetic analysis of BHV-1 gB.

The evolutionary history was inferred using the neighbor-joining method [20]. The percentages of the replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches [21]. The evolutionary distances were computed using the maximum composite likelihood method [22] and are shown as the number of base substitutions per site. The codon positions included were 1^st + 2^nd + 3^rd + Noncoding. Evolutionary analyses were conducted in MEGA X [19]. Different identical sequences were included to increase the robustness of the constructed tree.

Fig 3. Phylogenetic analysis of BHV-5 gB.

The evolutionary history was inferred using the neighbor-joining method [20]. The percentages of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches [21]. The evolutionary distances were computed using the maximum composite likelihood method [22] and are shown as the number of base substitutions per site. The codon positions included were 1^st + 2^nd + 3^rd + Noncoding. Evolutionary analyses were conducted in MEGA X [19]. Different identical sequences were included to increase the robustness of the constructed tree.

Fig 4. Phylogenetic analysis of the partial NS protein gene of BPV-3.

The evolutionary history was inferred using the neighbor-joining method [20]. The percentages of replicate trees in which the associated taxa clustered together in the bootstrap test (1000 replicates) are shown next to the branches [21]. The evolutionary distances were computed using the maximum composite likelihood method [22] and are shown as the number of base substitutions per site. The codon positions included were 1^st + 2^nd + 3^rd + Noncoding. Evolutionary analyses were conducted in MEGA X [19].