Evaluation of the serum virome in calves persistently infected with Pestivirus A, presenting or not presenting mucosal disease

Abstract

Bovine viral diarrhea virus 1, reclassified as Pestivirus A, causes an economically important cattle disease that is distributed worldwide. Pestivirus A may cause persistent infection in that calves excrete the virus throughout their lives, spreading the infection in the herd. Many persistently infected (PI) calves die in the first 2 years of life from mucosal disease (MD) or secondary infections, probably as a consequence of virus-induced immune depression. Here, high-throughput sequencing (HTS) was applied for evaluation of the total virome in sera of (i) PI calves displaying clinically apparent MD (n = 8); (ii) PI calves with no signs of MD (n = 8); and (iii) control, Pestivirus A-free calves (n = 8). All the groups were collected at the same time and from the same herd. Serum samples from calves in each of the groups were pooled, submitted to viral RNA/DNA enrichment, and sequenced by HTS. Viral genomes of Pestivirus A, Ungulate erythroparvovirus 1, bosavirus (BosV), and hypothetical circular Rep-encoding single-stranded DNA (CRESS-DNA) viruses were identified. Specific real-time PCR assays were developed to determine the frequency of occurrence of such viruses in each of the groups. The absolute number of distinct viral genomes detected in both PI calf groups was higher than in the control group, as revealed by higher number of reads, contigs, and genomes, representing a wider range of taxons. Genomes representing members of the family Parvoviridae, such as U. erythroparvovirus 1 and BosV, were most frequently detected in all the three groups of calves. Only in MD-affected PI calves, we found two previously unreported Hypothetical single-stranded DNA genomes clustered along with CRESS-DNA viruses. These findings reveal that parvoviruses were the most frequently detected viral genomes in cattle serum; its frequency of detection bears no statistical correlation with the status of calves in relation to Pestivirus A infection, since clinically normal or MD-affected/non-affected PI calves were infected with similar U. erythroparvovirus 1 genome loads. Moreover, MD-affected PI calves were shown to support viremia of CRESS-DNA viral genomes; however, the meaning of such correlation remains to be established.

Virome of crab-eating (Cerdocyon thous) and pampas foxes (Lycalopex gymnocercus) from southern Brazil and Uruguay

“…Our study, which employed nonspecific amplification, revealed the presence of commonly reported dog viruses and previously unknown viral agents (Table 1). The outstanding presence of Parvoviridae and Anelloviridae members is consistent with the findings reported in domestic dogs (Weber et al, 2018a(Weber et al, , 2018b. We also observed the presence of highly prevalent viral agents in domestic dogs from Brazil, such as CPV-2 and CDV (Alves et al, 2018b), that are genetically closely related to those reported in dogs of the same Brazilian region where the wild canids were sampled.…”

“…The anellovirus-related sequences were the most abundant viral sequences detected by HTS in the present study (Table 1). The predominance of anelloviruses in the mesenteric lymph nodes and spleen of both wild canid species is similar to what was reported in the serum of domestic dogs (Weber et al, 2018a(Weber et al, , 2018b. Moreover, we described two complete genomes (Fig.…”

“…1). Previous works described the virome in samples obtained in domestic dogs (Canis lupus familiaris) (Li et al, 2011;Moreno et al, 2017;Weber et al, 2018aWeber et al, , 2018b, but only a limited number of works analyzed wild canids as wolves (Canis lupus signatus) (Conceição-Neto et al, 2017) and red foxes (Vulpes vulpes) (Lojkić et al, 2016). Our study, which employed nonspecific amplification, revealed the presence of commonly reported dog viruses and previously unknown viral agents (Table 1).…”

“…Thus, the knowledge of the virus genetic diversity present in different host species can be improved. HTS sequencing has been applied in the knowledge of the virome of domestic dogs (Moreno et al, 2017;Weber et al, 2018aWeber et al, , 2018b, but reports of its application in wild canids remain scarce. Therefore, the present study aimed to evaluate and characterize the spleen and mesenteric lymph node virome of crab-eating and Pampas foxes from southern Brazil and Uruguay using HTS.…”

Identification of a novel bovine copiparvovirus in pooled fetal bovine serum

“…Further, related, but unclassified viruses have since been reported including two viruses identified in pigs-porcine parvovirus 5 [8] and porcine parvovirus 6 [9] and a virus termed Sesavirus found in the feces of a Californian sea lion pup [10]. During an investigation of the bovine virome of US calf serum, bosavirus was identified [3] and has been found in cattle persistently infected with pestiviruses [11]. A virus identified in sera from European roe deer has been designated Ungulate copiparvovirus 3 and this virus was first detected in Ioxodes ricinus ticks found on the deer [12].…”