Development of a TaqMan assay for sensitive detection of all pestiviruses infecting cattle, including the emerging HoBi-like strains

An outbreak of neonatal enteritis in buffalo calves associated with astrovirus

Background

Enteritis of an infectious origin is a major cause of productivity and economic losses to cattle producers worldwide. Several pathogens are believed to cause or contribute to the development of calf diarrhea. Astroviruses (AstVs) are neglected enteric pathogens in ruminants, but they have recently gained attention because of their possible association with encephalitis in humans and various animal species, including cattle.

Objectives

This paper describes a large outbreak of neonatal diarrhea in buffalo calves (Bubalus bubalis), characterized by high mortality, which was associated with an AstV infection.

Methods

Following an enteritis outbreak characterized by high morbidity (100%) and mortality (46.2%) in a herd of Mediterranean buffaloes (B. bubalis) in Italy, 16 samples from buffalo calves were tested with the molecular tools for common and uncommon enteric pathogens, including AstV, kobuvirus, and torovirus.

Results

The samples tested negative for common enteric viral agents, including Rotavirus A, coronavirus, calicivirus, pestivirus, kobuvirus, and torovirus, while they tested positive for AstV. Overall, 62.5% (10/16) of the samples were positive in a single round reverse transcription polymerase chain reaction (PCR) assay for AstV, and 100% (16/16) were positive when nested PCR was performed. The strains identified in the outbreak showed a clonal origin and shared the closest genetic relationship with bovine AstVs (up to 85% amino acid identity in the capsid).

Conclusions

This report indicates that AstVs should be included in a differential diagnosis of infectious diarrhea in buffalo calves.

HoBi-Like Pestivirus and Reproductive Disorders

HoBi-like pestivirus (HoBiPeV) is an emerging group of pestiviruses that has been detected in cattle and other ruminants in South America, Europe, and Asia. Analogous to other bovine pestiviruses, namely bovine viral diarrhea (BVDV) 1 and 2, HoBiPeV is able to cause a variety of clinical forms that range from asymptomatic infections to fatal disease, having a great impact on cattle productions and causing substantial economic losses, mainly as a consequence of the occurrence of reproductive failures. The manuscript aims to provide an updated review of the currently available literature about the impact of HoBiPeV infection on cattle reproduction. The reproductive disorders observed in cattle due to natural and experimental infections caused by this virus are reported along with the few available in-vitro studies involving the reproductive tract. HoBiPeV should be considered among the bovine pathogens that impact on reproduction, but there is a need for more specific and sensitive diagnostic methods, while the cross-protection elicited by commercially available BVDV vaccines should be better investigated.

Identification of astroviruses in bovine and buffalo calves with enteritis

Astroviruses (AstVs) have been identified in the stools of calves with enteritis and in the brain tissues of bovines with encephalitis but their pathogenic role has not been clarified. In this study, we report the detection and characterization of bovine and water buffalo AstV strains identified in young bovine and buffalo calves with enteritis in Italy between 2012 and 2015. By negative staining transmission electron microscopy (TEM) observation, AstV-like particles were identified in the stools of the animals and AstV RNA was confirmed molecularly. The sequence (~3.2-kb) at the 3′ end of the genome was determined for two bovine and two buffalo AstVs. Sequence and phylogenetic analysis on the partial ORF1b and full-length ORF2 revealed a marked genetic diversity although the viruses were distantly related to other AstV identified from ruminants. Gathering sequence information on ruminant AstVs is important to understand the extent of inter-species circulation and for the development of reliable, specific diagnostic tools.

•

Astroviruses in ruminants are neglected enteric viruses.

•

Recently, neurotropic strains have been identified in ruminants.

•

Astrovirus was detected in outbreaks of enteritis in cattle and buffalo in Italy.

•

Genome sequencing of the viruses unveiled marked genetic diversity.

•

Implementing the diagnostics is pivotal to conceive surveillance studies.

Molecular Characterization of Pestiviruses in Fetal Bovine Sera Originating From Argentina: Evidence of Circulation of HoBi-Like Viruses

Serological evidence suggests that HoBi-like viruses, an emerging species within the Pestivirus genus of the Flaviviridae family, are in circulation in Argentina. While HoBi-like viruses were first isolated from Brazilian fetal bovine serum (FBS), no survey of Argentine FBS has been conducted. Therefore, 124 local samples of non-irradiated FBS originating from Argentina were surveyed for the presence of pestiviruses using RT-PCR. Amplicons from pestivirus positive samples were genotyped. Four samples were positive for HoBi virus-specific RT-PCR, while the BVDV-positive samples (n = 45) were classified as BVDV-1b (82.2%), BVDV-1a (13.3%), and BVDV-2 (4.5%). Virus isolation and serological profile assessment were performed for the four HoBi-positive FBS lots. These results confirm the circulation of HoBi-like virus in some regions of the Argentinean territory, highlighting the need to review the diagnostic techniques currently used in the clinical cases suspected of BVDV and in contamination control protocols for adventitious agents in cells and biotechnological products.

Pathogen spread and globalization: The case of Pestivirus heterogeneity in southern Italy

Pestiviruses are responsible for widespread diseases affecting cattle, pigs and other ruminants, presenting a wide range of clinical manifestations, with significant impact on animal production. Given the recent various reports of a relatively high number of new strains and atypical genomic variants, in the present study, ninety-seven genomic sequences from southern Italy have been evaluated applying the palindromic nucleotide substitutions method, based on 5'-UTR secondary structure alignment and computing genetic distance among strains in the internal ribosome entry site. Sequence analysis revealed a highly heterogeneous virus population, indicating the introduction of virus variants of Bovine viral diarrhea virus and Border disease virus species from foreign countries. The application of different analytical procedures was useful to avoid interpretation difficulties. Circulation of heterogeneous virus populations showed the need for more accurate epidemiological investigations and stringent veterinary controls to protect animal health and welfare.

Detection of bovine pestiviruses in sera of beef calves by a RT-PCR based on a newly designed set of pan-bovine pestivirus primers

The pestiviruses bovine viral diarrhea virus 1 and 2 (BVDV-1 and -2, respectively) and HoBi-like pestivirus (HoBiPeV) are important pathogens of cattle, and a number of reverse-transcription PCR (RT-PCR)-based assays have been developed for their detection in clinical specimens. We evaluated a newly designed set of pan-bovine pestivirus primers (BP189-389) in a gel-based RT-PCR screening test for pestiviruses in the sera of beef calves destined for export from southern Brazil. Serum samples positive for BVDV antigens by an antigen ELISA ( n = 135) were submitted to RT-PCR assays using different sets of primers, followed by nucleotide sequencing of the amplicons. RT-PCR with pestivirus primers 324-326 detected 110 positive samples: BVDV-1 ( n = 62), BVDV-2 ( n = 38), and HoBiPeV ( n = 10). A PCR using primers HCV90-368 detected 97 positive samples (64 BVDV-1; 33 BVDV-2). An additional RT-PCR round using BVDV-2-specific primers (2F-2R) detected 45 positive samples (including 38 detected by primers 324-326 and 33 by HCV90-368); whereas a RT-PCR using HoBiPeV-specific primers (N2-R5) detected 26 positive samples (including 10 detected by primers 324-326).The assay using the primers BP189-389 detected all 135 ELISA-positive samples, including the 26 HoBiPeV detected by primers N2-R5. Our results demonstrated that primers BP189-389 compare favorably against other primer sets in the detection of bovine pestiviruses, especially HoBiPeV. This conventional PCR may be useful for efficient detection of pestiviruses in bovine sera and other specimens as well, especially in laboratories without real-time PCR equipment.

Circulation of multiple subtypes of bovine viral diarrhoea virus type 1 with no evidence for HoBi-like pestivirus in cattle herds of southern Italy

Pestiviruses of cattle include bovine viral diarrhoea 1 (BVDV-1) and 2 (BVDV-2) plus an emerging group, named HoBi-like pestivirus. In the present paper, the results of an epidemiological survey for pestiviruses circulating in cattle in southern Italy are presented. Molecular assays carried out on a total of 924 bovine samples detected 74 BVDV strains, including 73 BVDV-1 and 1 BVDV-2 viruses. Phylogenetic analysis carried out on partial 5'UTR and N^pro sequences revealed the presence of 6 different subtypes of BVDV-1 and a single BVDV-2c strain. BVDV-1 displayed a high level of genetic heterogeneity, which can have both prophylactic and diagnostic implications. In addition, the detection of BVDV-2c highlights the need for a continuous surveillance for the emergence of new pestivirus strains in cattle farms in southern Italy.

Evidence for Circulation of Bovine Viral Diarrhoea Virus Type 2c in Ruminants in Southern Italy

Recently, bovine viral diarrhoea virus type 2c (BVDV-2c) was responsible for a severe outbreak in cattle in northern Europe. Here, we present the results of an epidemiological survey for pestiviruses in ruminants in southern Italy. Pooled serum samples were obtained from 997 bovine, 800 ovine, 431 caprine and eight bubaline farms, and pestiviral RNA was detected by molecular methods in 44 farms consisting of 16 cattle and one buffalo herds and of 21 sheep and six goat flocks. Twenty-nine and 15 farms were infected by BVDV-1 and BVDV-2 strains, respectively. BVDV-1 strains were recovered mainly from cattle and were heterogeneous, belonging to the subtypes 1b, 1u, 1e, 1g and 1h. In contrast, all BVDV-2 viruses but two were detected in sheep or goats and were characterized as BVDV-2c by sequence analysis of 5'UTR. These strains displayed high genetic identity to BVDV-2c circulating in cattle in northern Europe and were more distantly related to a BVDV-2c isolate recovered from a cattle herd in southern Italy more than 10 years before. The circulation of a BVDV-2c in small ruminants suggests the need for a continuous surveillance for the emergence of pestivirus-induced clinical signs in southern Italian farms.

HoBi-Like Pestivirus and Its Impact on Cattle Productivity

The clinical features and economic impact of the infection caused by an emerging group of pestiviruses, namely HoBi-like pestivirus, in a cattle herd of southern Italy are reported. In 2011, the virus was first associated with respiratory disease, causing an abortion storm after 1 year and apparently disappearing for the following 3 years after persistently infected calves were slaughtered. However, in 2014, reproductive failures and acute gastroenteritis were observed in the same herd, leading to a marked decrease of productivity. A HoBi-like strain closely related to that responsible for previous outbreaks was detected in several animals. Application of an intensive eradication programme, based on the detection and slaughtering of HoBi-like pestivirus persistently infected animals, resulted in a marked improvement of the productive performances.

Multiplex real-time RT-PCR assay for bovine viral diarrhea virus type 1, type 2 and HoBi-like pestivirus

HoBi-like pestiviruses are emerging pestiviruses that infect cattle causing clinical forms overlapping to those induced by bovine viral diarrhea virus (BVDV) 1 and 2. As a consequence of their widespread distribution reported in recent years, molecular tools for rapid discrimination among pestiviruses infecting cattle are needed. The aim of the present study was to develop a multiplex real-time RT-PCR assay, based on the TaqMan technology, for the rapid and unambiguous characterisation of all bovine pestiviruses, including the emerging HoBi-like strains. The assay was found to be sensitive, specific and repeatable, ensuring detection of as few as 10(0)-10(1) viral RNA copies. No cross-reactions between different pestiviral species were observed even in samples artificially contaminated with more than one pestivirus. Analysis of field samples tested positive for BVDV-1, BVDV-2 or HoBi-like virus by a nested PCR protocol revealed that the developed TaqMan assay had equal or higher sensitivity and was able to discriminate correctly the viral species in all tested samples, whereas a real-time RT-PCR assay previously developed for HoBi-like pestivirus detection showed cross-reactivity with few high-titre BVDV-2 samples.