Detection and genetic characterization of bovine kobuvirus from calves in Egypt

Abstract

Kobuviruses are small non-enveloped RNA viruses that probably cause diarrhea in cattle and swine. Since its discovery in 2003, few studies have addressed bovine kobuvirus (BKoV; a species of Aichivirus B) infections. BKoV has been reported in Europe, Asia, and South America, suggesting a worldwide distribution. To investigate the presence of BKoV in Egypt, 36 fecal specimens from diarrheic calves in two different Egyptian provinces (Cairo and Sharkia) were screened by RT-PCR and 24 (66.7%) were found positive for BKoV. RNA from one of the positive samples (BKoV/Egy-1/KY407744) was subjected to next-generation sequencing to determine the complete BKoV genome sequence. When compared to the only recorded BKoV genome sequence (BKoV/U-1/AB084788), the studied strain showed 94 amino acid (aa) substitutions through its entire polyprotein (2463 aa), one nucleotide (nt) insertion and one nt deletion in the 2B gene and 4-nt deletions in the UTRs (2 each). Additionally, five VP1 and seven 3D sequences were obtained from other samples by using RT-PCR and Sanger sequencing. A discrepancy in the phylogenetic topography of VP1 and 3D was observed, where the Egyptian VP1 sequences were classified as a distinct cluster within the proposed lineage 1 (genotype A), which also contained strains from the UK, Brazil, and Japan. While, the 3D sequences from Cairo were related to those of Chinese strains unlike Sharkia ones that were more closer to Korean strains. To the best of our knowledge, this is the first detection and genomic characterization of BKoV in Egypt or indeed Africa.

Bovine Kobuvirus in Calves with Diarrhea, United States

“…Leyi (1). Since then, BKV has been reported in Thailand, Hungary, the Netherlands, Korea, Italy, Brazil, China, and Egypt (2)(3)(4)(5)(6)(7)(8)(9). However, circulation of BKV in North America remains unclear.…”

TaqMan probe qRT-PCR detects bovine parvovirus and applies clinically

“…Currently, the majority of the data available for these viruses are epidemiological. Few effective measures are offered for the treatment or prevention of Bocaparvovirus infections [6,21]. The normalization is crucial to control the variation introduced by various steps of qRT-PCR assay.…”

Synchronous Detection of BPV and BVDV with Duplex Taqman qPCR Method

“…However, this differs in the efficiency of RNA extraction, reverse transcription or PCR reactions, leading to unstable the sensitivity and specificity of this technique [18,25]. In order to overcome these faults, we designed one pair specificprimers (BPV-qF/qR and BVDV-qF/qR) and a specific Taqman probe (BPVprobe and BVDV-probe) targeting the highly conserved 5′ -untranslated region (5′ UTR) [20,21].…”

“…The specificity of Taqman qPCR was confirmed by the negative control and other viruses, including JEV, RABV, CSFV, BRV, BPIV, BAV and FMDV. The results showed that Taqman qPCR could only detect BPV and BVDV [21,27]. An internally controlled Taqman probe qPCR was developed and evaluated for detection and quantification of BPV and BVDV 5′ UTR genes.…”