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.

Characterisation of the Upper Respiratory Tract Virome of Feedlot Cattle and Its Association with Bovine Respiratory Disease

“…However, the pooling of samples has proven to be a robust method to efficiently increase the number of samples that can be evaluated for identifying pathogens [ 73 , 74 ]. Nagy et al [ 75 ] were able to expand the repertoire of viruses associated with BRD in affected Egyptian cattle using a pool of 43 nasal swabs. In comparison, the pool of six samples utilised in the current study is considered to be a balanced and conservative approach.…”

Unmapped short reads from whole-genome sequencing indicate potential infectious pathogens in German Black Pied cattle

“…Infection with the Bovine parvovirus 3 , which was found in the unmapped sequence information of four DSN animals, has been linked so far only to bovine respiratory disease [ 23 , 24 ]. However, cases of diarrhea in neonatal calves and respiratory and reproductive diseases in adult cattle have been associated with other bovine parvoviruses [ 25 ].…”