A genetic profile of bovine pestiviruses circulating in Brazil (1998-2018)

Outbreak of persistently infected heifer calves with bovine viral diarrhea virus subgenotypes 1b and 1d in a BVDV-vaccinated open dairy herd

Bovine viral diarrhea virus (BVDV) infection has a significant economic impact on beef and dairy industries worldwide. Fetal infection with a non-cytopathic strain may lead to the birth of persistently infected (PI) offspring, which is the main event in the epidemiological chain of BVDV infection. This report describes the birth of 99 BVDV-PI heifer calves within 52 days of birth in a regular BVDV-vaccinated Brazilian dairy cattle herd and the subgenotypes of the infecting field strains. This study was conducted in a high-yielding open dairy cattle herd that frequently acquired heifers from neighboring areas for replacement. The farm monitors the birth of PI calves by screening all calves born using an ELISA (IDEXX) for BVDV antigen detection. All calves aged 1-7 days were evaluated. For positive and suspected results, the ELISA was repeated when the calves were close to one month old. A total of 294 heifer calves were evaluated between February and March 2021. Of these, 99 (33.7 %) had positive ELISA results and were considered PI calves. To evaluate the predominant BVDV species and subgenotypes in this outbreak, whole blood samples were collected from 31 calves born during the study period. All samples were submitted to the RT-PCR assay for the partial amplification of the BVDV 5'-UTR region, and these amplicons were subjected to nucleotide sequencing. Phylogenetic analysis identified BVDV-1b and BVDV-1d in 16 and 13 heifer calves, respectively. In two calves, it was not possible to determine the BVDV-1 subgenotype. Detection of PI animals and monitoring of circulating BVDV subgenotype strains are central to disease control. This study shows that regular BVDV vaccination alone may be insufficient to prevent BVDV infection in high-yielding open dairy cattle herds. Other biosecurity measures must be adopted to avoid the purchase of cattle with acute infections by BVDV or BVDV-PI, which can cause a break in the health profile of the herd and economic losses.

Novel genomic targets for proper subtyping of bovine viral diarrhea virus 1 (BVDV-1) and BVDV-2

Whole-genome phylogenetic analysis, the most suitable strategy for subtyping bovine viral diarrhea virus 1 (BVDV-1) and BVDV-2, is not feasible for many laboratories. Consequently, BVDV isolates/strains have been frequently subtyped based on analysis of single genomic regions, mainly the 5' untranslated region (UTR). This approach, however, may lead to inaccurate and/or poorly statistically supported viral classification. Herein, we describe novel primer sets whose amplicons may be easily sequenced and used for BVDV subtyping. Initially, genomic regions previously described as the most suitable targets for BVDV subtyping were analyzed for design of high-coverage primers. The putative amplicons were analyzed in silico for their suitability to reproduce the phylogenetic classification of 118 BVDV-1 and 88 BVDV-2 complete/near-complete genomes (CNCGs) (GenBank). This analysis was also performed considering the region amplifiable by primers HCV90-368, 324-326 and BP189-389 (5'UTR), which have been used for BVDV diagnosis and/or classification. After confirming the agreement between the analyses of our primers' amplicon versus the CNCGs, we optimized the RT-PCRs and evaluated their performance for amplification of BVDV isolates/strains (n = 35 for BVDV-1; n = 33 for BVDV-2). Among the potential targets for BVDV subtyping, we designed high-coverage primers for NS3-NS4A (BVDV-1) (526 bp amplicon) and NS5B (BVDV-2) (728 bp). The classification based on these regions fully reproduced the subtyping of all CNCGs. On the other hand, subtyping based on the putative amplicons from primers HCV90-368, 324-326 and BP189-389 showed disagreements in relation the CNCG analysis. The NS3-NS4A and NS5B primers also allowed the amplification of all BVDV isolates/strains tested. Finally, we suggest the use of these primers in future phylogenetic and epidemiological studies of BVDVs.

Causes of fetal death in the Flemish cattle herd in Brazil

Background and Aim

Flemish cattle in Brazil are on the brink of extinction and are found only in one herd in Lages, Santa Catarina State. This study aimed to uncover the reasons for the recurring abortions in the Flemish cattle herd.

Materials and Methods

Seventeen Flemish fetuses underwent postmortem examinations, with samples collected for histopathology and microbiology culture tests, polymerase chain reaction (PCR) test for Neospora caninum, and reverse transcription-PCR (RT-PCR) test for bovine viral diarrhea virus (BVDV) from 2015 to 2020.

Results

Of the 17 fetuses, N. caninum was the most common diagnosis and was found in 88% (15/17). One fetus (5.8%) had a coinfection with N. caninum and Citrobacter amalonaticus, leading to fibrinonecrotic pericarditis. All fetuses tested negative for BVDV by RT-PCR. Of the 107 dams tested by indirect immunofluorescence assay, 26 (25.2%) were anti-N. caninum seropositive, with 17 (65.4%) aborting and 5 (19.2%) having estrus repetition. Reverse transcription-PCR results showed that 9 (8.4%) of the serum samples collected from dams tested positive, which tested follow-up test 3 months later, indicating a BVDV transient infection. The factors that contributed to neosporosis included dogs' access to pastures and improper disposal of fetal remains, which made it easier for dogs to consume them.

Conclusion

This study warns the occurrence of N. caninum as a cause of reproductive disorders that can lead to abortion in the studied Flemish cattle herd.

HoBi-like Pestivirus Is Highly Prevalent in Cattle Herds in the Amazon Region (Northern Brazil)

Pestiviruses are globally distributed and cause substantial economic losses to the cattle industry. In Brazil, the country with the world's largest cattle population, pestivirus infections are well described in some regions, such as in the south, where a high frequency of BVDV-2 is described and contrasts with the high prevalence of HoBi-like pestivirus (HoBiPeV) in the northeast. However, there is a lack of information about pestiviruses in the Amazon Region, in northern Brazil, with a cattle population estimated at 55.7 million head, which has a significant impact on the international livestock market. Therefore, this study investigated the seroprevalence and genetic variability of ruminant pestiviruses in 944 bovine serum samples from four states in northern Brazil: Pará (PA), Amapá (AP), Roraima (RR), and Amazonas (AM). Our results showed that 45.4% of the samples were seropositive (19.8% for BVDV-1, 14.1% for BVDV-2, and 20.9% for HoBiPeV). All samples were tested by RT-qPCR, and three were positive and classified as HoBiPeV in a phylogenetic analysis. These serological and molecular results contrast with those from other regions of the world, suggesting that the northern Brazilian states have a high prevalence of all bovine pestiviruses including HoBiPeV.

Temporal and geographic dynamics of bovine viral diarrhea virus in American countries

Bovine viral diarrhea virus (BVDV) is a worldwide distributed pathogen of livestock classified into three species, BVDV-1 (Pestivirus A), BVDV-2 (Pestivirus B), and HoBi-like pestivirus (HoBiPeV; Pestivirus H). Despite being considered endemic in several regions of the Americas, the spatiotemporal distribution of BVDV is scarcely known. This study aimed to reconstruct the population dynamics of BVDV in American countries. The analyses performed with the partial 5´UTR gene showed that BVDV-1 and -2 would have started their diversification in the 1670s and 1790s in the United States, whereas HoBiPeV probably emerged in the 1980s in Brazil. No evident geographic clustering was observed in the Bayesian trees, which may indicate that multiple introductions events would have occurred following the first introduction. This study provides new insights into BVDV dynamics, although further analyses including sequences from other American countries and continents will help to expand the knowledge of BVDV evolution and transmission.

Temporal analysis of bovine pestivirus diversity in Brazil

In this study, phylogenetic and evolutionary analyses of cattle pestiviruses (BVDV-1, 2 and HoBiPeV) originating in Brazil were used to investigate the temporal diversification of subgenotypes in the country. Inferred dated phylogeny and time of the most recent common ancestor (tMRCA) demonstrated that some BVDV subgenotypes (1a, 1b, 1d, 1e, and 2b) and HoBi-like sequences clustered according to the region in which they were collected and that the diversification of subgenotypes appears to have occurred around the introduction of first Bos taurus and then Bos indicus, followed by expansion to form the adapted Brazilian breeds. The present results help to elucidate the temporal facts that led to diversification of ruminant pestiviruses in cattle in Brazil.

Epidemiology of Pestivirus H in Brazil and Its Control Implications

Along with viruses in the Pestivirus A (Bovine Viral Diarrhea Virus 1, BVDV1) and B species (Bovine Viral Diarrhea Virus 2, BVDV2), members of the Pestivirus H are mainly cattle pathogens. Viruses belonging to the Pestivirus H group are known as HoBi-like pestiviruses (HoBiPev). Genetic and antigenic characterization suggest that HoBiPev are the most divergent pestiviruses identified in cattle to date. The phylogenetic analysis of HoBiPev results in at least five subgroups (a–e). Under natural or experimental conditions, calves infected with HoBiPev strains typically display mild upper respiratory signs, including nasal discharge and cough. Although BVDV1 and BVDV2 are widely distributed and reported in many South American countries, reports of HoBiPev in South America are mostly restricted to Brazil. Despite the endemicity and high prevalence of HoBiPev in Brazil, only HoBiPev-a was identified to date in Brazil. Unquestionably, HoBiPev strains in BVDV vaccine formulations are required to help curb HoBiPev spread in endemic regions. The current situation in Brazil, where at this point only HoBiPev-a seems present, provides a more significant opportunity to control these viruses with the use of a vaccine with a single HoBiPev subtype. Despite the lack of differentiation among bovine pestiviruses by current BVDV tests, the reduced genetic variability of HoBiPev in Brazil may allow reliable identification of cases within the region. On the other hand, introducing foreign ruminants, biologicals, and genetic material to South America, especially if it originated from other HoBiPev-endemic countries, should consider the risk of introducing divergent HoBiPev subtypes.

Detection of Pestivirus A (bovine viral diarrhea virus 1) in free-living wild boars in Brazil

Bovine viral diarrhea virus (BVDV) is a major pathogen in cattle herds. Considering the epidemiological importance of pestiviruses and the process of wild boar invasion in Brazil, this study aimed to investigate the presence of BVDV in free-living boars. Forty-nine free-living wild boars were collected by exotic wildlife controller agents in 2017 and 2018. The presence of BVDV antibodies was evaluated in 42 serum samples using the virus neutralization test, and the detection of BVDV RNA was performed from the 5'UTR genomic region by RT-PCR assay in 49 lung tissue samples followed by sequencing of amplicons. BVDV neutralizing antibodies in serum were not identified in any of the evaluated samples. However, 3/49 (6.12%) lung samples were positive for BVDV RNA and classified one as BVDV-1a and two as 1d subgenotype. This report identified BVDV RNA in free-living wild boars and these results should be considered in BVDV control programs, especially in extensive beef cattle rearing systems.

Sequence analysis of the DA domain of glycoprotein E2 of pestiviruses isolated from beef cattle in Southern Brazil

The envelope glycoprotein E2 of pestiviruses is a major target for neutralizing antibodies. In this study, we analyzed the E2 DA domain of 43 pestiviruses from Southern Brazil. The isolates were identified as Bovine viral diarrhea virus (BVDV) subtypes 1a and 1b or BVDV-2b. Compared to reference strains, the BVDV-1 and -2 isolates had four and two mutations in the DA domain, respectively. All BVDV-2 isolates had a deletion of residues 724 and 725. All mutated amino acids in the BVDV isolates had the same aa substitution, and all were in previously identified antibody binding sites. It is possible that an immunity-mediated selection is acting on the pestiviruses circulating in Southern Brazil.

Emerging diseases in international trade in embryos

A significant change in cattle production and germplasm exchange has occurred over the past 50 years. The growth of artificial reproductive technologies and their broad implementation has become commonplace. The production and subsequent import and export of semen and embryos throughout the world has increased significantly. The embryo transfer industry has reached a new record of growth, with approximately 1.5 million transferrable bovine embryos collected and/or produced in 2018. Over 1 million of these embryos were produced invitro . The increased production of invitro -produced embryos leads to greater opportunities involving international trade. However, further research concerning emerging pathogens is imperative to ensure the efficacy and safety of the embryo transfer industry. Appropriate biosecurity protocols, including reliable testing methodology and effective embryo processing procedures, are key in preventing disease due to emerging and re-emerging pathogens that can be transmitted via embryo transfer.

Diphtheric aspergillosis tracheitis with gastrointestinal dissemination secondary to viral infections in a dairy calf

Diphtheric aspergillosis tracheitis is an uncommon syndrome described in human pathology, usually associated with immunosuppression in the affected individuals. Interestingly, no comparative/equivalent cases were found in domestic animals. This report describes the pathological and mycological findings associated with diphtheric aspergillosis tracheitis in an immunocompromised calf. The main pathological findings were diphtheric tracheitis and rhinitis, and necrotizing ruminitis associated with intralesional septate, acute branching fungal hyphae consistent with Aspergillus spp. Mycological culture and isolation confirmed the fungal hyphae as A. fumigatus due to characteristic features. Immunohistochemistry (IHC) assays identified intralesional antigens of bovine viral diarrhea virus (BVDV) and malignant catarrhal fever virus (MCFV) at the trachea and small intestine; IHC detected intralesional antigens of bovine alphaherpesvirus 1 (BoHV-1) only at the trachea. These findings confirmed the simultaneous occurrence of A. fumigatus with concomitant infections due to BVDV, MCFV, and BoHV-1 in this calf. Since ovine gammaherpesvirus-2 (OvHV-2) is the cause of MCF in Brail, it is likely that the intralesional MCFV antigens identified were those of OvHV-2. In this case, disseminated aspergillosis was probably associated with the undeveloped immunological status of the calf that was further impaired due to the combined immunodepressive effects of BVDV and BoHV-1 infections. Although BVDV and BoHV-1 are infectious disease pathogens frequently associated with the development of bovine respiratory disease (BRD) in feedlot and dairy cattle, the identification of intralesional OvHV-2-like antigens in several parts of the lungs suggest that this MCFV also played a role in the BRD-associated lesions identified in this calf.

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An unusual presentation of fungal diphtheric tracheitis associated with Aspergillus fumigatus is described in a dairy calf.

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A Malignant Catarrhal Fever Virus, most likely, OvHV-2, was associated with the development of pneumonia in this calf.

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Simultaneous infections in dairy calves may be more frequent than previously reported.

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OvHV-2 should be considered as a possible disease pathogen associated with the development of bovine respiratory disease.

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The immunodepressive effects of BVDV and BoHV-1 were fundamental for the development of the fungal disease observed in this calf.

An Assessment of Secondary Clinical Disease, Milk Production and Quality, and the Impact on Reproduction in Holstein Heifers and Cows from a Single Large Commercial Herd Persistently Infected with Bovine Viral Diarrhea Virus Type 2

The aim of this study was to evaluate secondary clinical disease, milk production efficiency and reproductive performance of heifers and cows persistently infected (PI) with bovine viral diarrhea virus type 2 (BVDV type 2). PI animals (n = 25) were identified using an antigen capture ELISA of ear notch samples. They were distributed into three age groups: ≤ 12 (n = 8), 13 to 24 (n = 6) and 25 to 34 (n = 11) months old. A control group of BVDV antigen ELISA negative female cattle that were age matched to the PI animals was utilized from the same herd. The PI group had a 1.29 higher odds ratio for diarrhea than controls (p = 0.001, IC95% = 1.032–1.623) and 1.615 greater chance of developing bovine respiratory disease (BRD) (p = 0.012, IC95% = 1.155–2.259). The age at first insemination (p = 0.012) and number of insemination attempts required to establish the first pregnancy (p = 0.016) were both higher for PI than controls. Milk production was higher for control cows than PI cows during most of the sampling periods. Somatic cell counts (SCC) were higher in PI cows than the controls at all sampling points across lactation (p ≤ 0.042). PI cattle had a higher incidence of disease, produced less milk, a higher SCC, and poorer reproductive performance than control cattle in this study.

Genetic Diversity of Bovine Pestiviruses Detected in Backyard Cattle Farms Between 2014 and 2019 in Henan Province, China

Bovine pestiviruses include Pestivirus A (BVDV-1), Pestivirus B (BVDV-2), and Pestivirus H, which was originally called HoBi-like pestivirus. We conducted an epidemiological investigation for pestiviruses circulating in backyard cattle farms in central China. RT-PCR assays and sequences analysis were conducted on 54 nasal swabs, 26 serum samples, and three lung samples from cattle with respiratory infections and identified 29 pestivirus strains, including 24 Pestivirus A and five Pestivirus H strains. Phylogenetic analysis based on partial 5'-UTR and Npro sequences showed that the genotypes of 24 Pestivirus A strains included Pestivirus A 1b (six isolates), Pestivirus A 1m (six isolates), Pestivirus A 1q (two isolates), Pestivirus A 1u (one isolates), and Pestivirus A 1o (nine isolates, a putative new sub-genotype). In addition, a single Pestivirus H agenotype included all five Pestivirus H strains. This study revealed extensive genetic variations within bovine pestivirus isolates derived from cattle in backyard farms in Central China, and this epidemiological information improves our understanding of the epidemics of bovine Pestiviruses, as well as will be useful in designing and evaluating diagnostic methods and developing more effective vaccines.

Survey for pestiviruses in backyard pigs in southern Brazil

The Pestivirus genus comprises species that affect animal health and productivity worldwide. Members of the Suidae family are hosts for classical swine fever virus (CSFV), an important pathogen tracked by the World Organization for Animal Health (OIE). However, swine are also susceptible to other pestivirus species that can result in disease or compromise CSFV detection. We searched for pestivirus infection in swine sera collected from 320 backyard pig herds in southern Brazil. We used reverse-transcription PCR primers for Bungowannah virus; atypical porcine pestivirus (APPV); and a panpestivirus pair that detects bovine viral diarrhea virus (BVDV)-1, -2, and HoBi-like pestivirus (HoBiPeV), border disease virus (BDV), and CSFV. Two samples were positive using the panpestivirus primer pair and were classified as BVDV-1d and -2a, respectively. Serum samples were tested for virus neutralization against BVDV-1a, -1b, and -2 strains, resulting in 28 (4.4%) positive samples. Of those, 16 samples had the highest titers against BVDV-1a (2), BVDV-1b (5), and BVDV-2 (9). Our results indicate that Bungowannah virus, APPV, CSFV, BDV, and HoBiPeV have not been circulating in these specific backyard swine populations. However, ruminant pestiviruses were detected and must be considered in future pestivirus control programs conducted in Brazil.

HoBi-like pestivirus infection in an outbreak of bovine respiratory disease

HoBi-like is an emerging pestivirus of the family Flaviviridae detected in cattle herds and biological products of bovine origin in many parts of the world, causing disease similar to that observed in bovine viral diarrhea virus (BVDV) infections. In this study we reported the detection of HoBi-like pestivirus in an outbreak of respiratory disease in calves from Brazil, seropositive for viruses of the bovine respiratory disease complex (BRDC). Thus, serum samples and nasal swabs were collected from calves up to one year old, presenting or not clinical signs of respiratory disease. Serum samples were submitted to virus neutralization test (VNT) for BVDV-1, BVDV-2, bovine herpesvirus-1 (BoHV-1), bovine respiratory syncytial virus (BRSV) and bovine parainfluenza-3 (BPIV-3). These samples were also tested for the presence of pestiviruses (BVDV-1, BVDV-2 and HoBi-like) and BoHV-1 by RT-PCR and PCR, respectively. Nasal swabs were analyzed by RT-PCR for pestiviruses, BRSV and BPIV-3. VNT results showed high serological prevalence and a wide range of antibodies titers, for all viruses studied, in calves of different age groups. The RT-PCR amplified the 5'UTR and E2 regions of pestiviruses of four calves, from both nasal swabs and serum samples, which sequencing identified the HoBi-like pestivirus. This is the first detection of HoBi-like in nasal secretions of calves in an outbreak of respiratory disease in Brazil, along with the serological detection of other respiratory viruses. We concluded that HoBi-like pestivirus should be considered as part of the BRDC, as a differential diagnosis, to take correct measures of control and prophylaxis.