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Worldwide, neonatal diarrhea is one of the most important health issues affecting dairy calves, and rotavirus A (RVA) is one of its primary causes. Among the measures to mitigate the risk of diarrhea outbreaks, cow vaccination stands out as one of the most important. However, the immune pressure resulting from routine vaccination may be able to select specific G and P genotypes in RVA field strains. This study aimed to determine the frequency and intensity of neonatal diarrhea and the incidence of RVA and attempted to monitor the G and P genotypes present in the RVA strains circulating in a high milk yield cattle herd vaccinated with RVA G6P[5] strain. Fecal samples (n = 1220) from 122 Holstein heifer calves between 0-30 days old that were born from RVA-vaccinated cows were collected at 10 different time points, regardless of the presence or absence of diarrhea. The presence of RVA in fecal samples was determined by the polyacrylamide gel electrophoresis (PAGE) technique and confirmed by reverse transcription polymerase chain reaction (RT-PCR). G and P amplicons from 10 RVA-positive fecal samples from calves of different ages and collections were subjected to nucleotide sequencing. The proportion of the calves and fecal samples that were positive for RVA were 62.3% (76/122) and 8.1% (99/1220), respectively. Using sequence analysis, all 10 RVA field strains presented genotype G10P[11]. The protection of G6P[5] vaccination is clear, as this genotype was not detected in this study, and it is known that vaccination against RVA reduces the incidence of diarrhea independent of genotype involved. This result demonstrates the importance of epidemiological monitoring of RVA genotypes circulating in vaccinated dairy cattle herds to the early detection of new potential pathogenic RVA strains., (Copyright © 2019 Elsevier B.V. All rights reserved.)

Papillomaviruses (PVs) are oncogenic and infect the skin and mucosa of various host species. Considering the recent advances in research on PVs using rolling circle amplification (RCA) followed by high-throughput sequencing (HTS), in this study, we aimed to investigate the bovine papillomavirus (BPV) types associated with proliferative lesions in the upper alimentary tract of an affected bull and characterize the viral strains through complete genome sequencing using this strategy. We analyzed the PV strains associated with two hyperplastic esophageal lesions through PCR using degenerate primer pairs and RCA, followed by HTS. HTS of the libraries generated using RCA products provided the whole genome sequence of BPV4 present in squamous papilloma, whereas the complete genome sequence of BPV2 and subgenomic fragments of BPV4 were identified in carcinoma in situ (CIS). For the first time, we have sequenced BPV2 identified from the CIS of the bovine upper alimentary canal. Additionally, RCA followed by HTS allowed characterization of the mixed infection by BPV2 and BPV4 in this lesion. These data reveal that BPV4 is not the only BPV type present in CIS of the esophageal mucous membrane; moreover, a mixed infection caused by BPV2 and BPV4 at the tested anatomical site was demonstrated. [ABSTRACT FROM AUTHOR]

Aichivirus B has been reported worldwide in calves and adult cattle with and without diarrhea. The aim of this study was to describe the molecular characteristics of the RdRP and VP1 genes of aichivirus B strains identified as the most frequent etiologic agent in a neonatal diarrhea outbreak in a high-production Brazilian dairy cattle herd. Preliminary laboratory analysis ruled out important enteropathogens ( Cryptosporidium spp; Eimeria spp., E. coli F5, and bovine coronavirus). Fecal samples from diarrheic ( n = 24) and asymptomatic ( n = 5) calves up to 30 days old were collected for virological analysis. RT-PCR assays were performed for the detection of aichivirus B RdRP and VP1 genes and for rotavirus A VP7 and VP4 genes in fecal samples. Asymptomatic calves (control group) were negative for both viruses. Aichivirus B and rotavirus A G10P[11] genotypes were found in 54.2% (13/24) and 25% (6/24) of the diarrheic fecal samples, respectively. Aichivirus B was only identified (83.3%, 10/12) in calves up to two weeks old. Phylogenetic analysis based on the RdRP gene grouped the Brazilian strains in a new branch within the aichivirus B group. Comparative analysis of the nucleotide sequence of the VP1 gene of Brazilian and Chinese aichivirus B strains allowed the strains identified in this study to be classified in the putative lineage 1. This is the first description of a high rate of aichivirus B detection in a diarrhea outbreak in dairy calves, and the first phylogenetic study of the VP1 gene of aichivirus B wild-type strains performed in South America. [ABSTRACT FROM AUTHOR]

The aim of this study was to perform the molecular characterization of the eleven genes of a G6P[5] bovine group A rotavirus (RVA) strain detected in a diarrhea outbreak from a vaccinated beef cattle herd. The outbreak affected 80 % of calves between 15-30 days old. RVA was identified by RT-PCR in 12 (70.6 %) out of 17 diarrheic fecal samples evaluated. The rotavirus wild-type strain had the genotype constellation G6(IV)-P[5](IX)-I2c-R2-C2-M2-A3-N2-T6-E2e-H3a. This study confirms the importance of homotypic immunity against the bovine RVA P[5] genotype in neonatal diarrhea in cattle herds that are regularly vaccinated against rotaviruses. [ABSTRACT FROM AUTHOR]

Abstract: A multiplex polymerase chain reaction (multiplex-PCR) to detect and differentiate bovine herpesvirus 1 (BoHV-1) and 5 (BoHV-5) was developed using primers for the gene sequence that encodes the glycoprotein C. The technique was assessed against the BoHV-1 and BoHV-5 cell culture adapted strains, and clinical samples collected from animals with clinical signs of BoHV-1 (n =10) or BoHV-5 (n =7) infection and with diagnosis confirmed by virus isolation in cell culture and semi-nested PCR. Fifteen clinical samples from asymptomatic animals were included as control group. For the evaluation of the amplifiability of the extracted nucleic acid from clinical specimens was included a bovine internal control that amplified a 626bp fragment of the ND5 gene present in the bovine mitochondrial DNA. For DNA extraction, a combination of the phenol/chloroform/isoamyl alcohol and silica/guanidine isothiocyanate methods was used. The specificity of the BoHV-1 and BoHV-5 amplicons from standard strains were confirmed by sequence analysis. All the positive clinical samples for BoHV included in this study were characterized as BoHV-1 or BoHV-5 by the difference in length of the amplified product visualized in a agarose gel (354bp size for BoHV-1, and 159bp for BoHV-5). The internal control was amplified in all clinical specimens. Non-specific reactions were not observed when the multiplex-PCR was assessed with other viruses (bovine viral diarrhea virus and rabies virus) and BoHV-negative clinical samples from fetuses and adult cattle obtained from a slaughterhouse. [Copyright &y& Elsevier]

Abstract: Animal kobuviruses have been described in pigs, cattle, sheep and bats in countries in Asia and Europe. The virus can be detected in fecal and serum samples of infected animals with or without diarrhea, but most of the clinical as well as epidemiological features of kobuvirus infection are still unknown. This study reports the first detection of kobuvirus in farm animals from Brazil and the Netherlands and the molecular analysis of the detected strains. In Brazil, 53% (61/115) of the pigs (suckling, weaned and sows) were shedding porcine kobuvirus in feces, while in the Netherlands 16.7% (3/18) of the tested weaned pigs were infected. Kobuviruses detected in fecal samples of pigs in Brazil showed association (p =0.0002) with diarrhea. In pig serum, kobuvirus was detected at different ages (3, 21, 36, 60, 75, and 180days), with an overall rate of 76.7% (23/30). The sequencing of amplicons detected in serum of pigs of different ages suggested reinfection and no persistent infection. Kobuvirus was also detected in sheep and cattle feces from Brazil and the Netherlands, respectively. Phylogenetic analyses of Brazilian and Dutch kobuviruses from pig, cattle and sheep revealed genetic variability, particularly in one strain detected in sheep feces, which was more closely related to human Aichi virus. The molecular and phylogenetic analyses performed with other published kobuvirus strains and the strains presented in this study, showed that, in most of the cases, kobuvirus seems to group according to host species, but not to geographical region of origin. The data presented in this study contribute to the comprehension of kobuvirus epidemiology and also to the molecular identification of kobuvirus strains circulating worldwide. [Copyright &y& Elsevier]

Abstract: The amplification by degenerate primers FAP59/FAP64 and sequencing allowed the detection of 15 putative new BPV types in cutaneous warts as well as in healthy skin. Four of these isolates were recently recognized as new BPV types (BPV-7, -8, -9, and -10) after determination of their complete genome sequences. In Brazil, investigations involving the definition of BPV types present in skin warts are still rare. The aim of the current study was to identify the BPV types associated with cutaneous papillomatosis observed in Brazilian cattle herds. Twenty-two cutaneous papilloma specimens were submitted to PCR assay employing the FAP primer pair. All PCR products with approximately 480bp were submitted to direct sequencing. Cloning was performed for the amplicons which prior analysis revealed as putative new BPV types. From 16 cutaneous lesions, BPV-1, -2, and -6 were identified in two, six, and eight papilloma specimens, respectively. In addition, four putative new BPV types were identified in other six skin warts, and then designated as BPV/BR-UEL2 to -5. The detection of the BPV-1, -2, and -6 types in skin wart specimens supports the existence of these BPV types throughout the Brazilian cattle herd. In addition, the identification of four putative new BPV types is the first report of the presence of different BPV types in the American continent. [Copyright &y& Elsevier]

Abstract: Bovine coronavirus (BCoV), a positive sense single-stranded RNA virus, is an important causative agent of neonatal diarrhoea in calves from beef and dairy cattle worldwide. The routine detection and diagnosis of BCoV have been mainly dependent on assays with low sensitivity. The aim of the present study was to develop and evaluate a semi-nested PCR (SN-PCR) to amplify a 251bp fragment of BCoV N gene from fresh (n =25) and frozen (n =25) diarrhoeic faecal samples of naturally infected calves. To improve detection of BCoV in faecal samples by the SN-PCR an internal control was developed, and the results were compared with a conventional RT-PCR assay. The rates of positive samples by SN-PCR and RT-PCR were 24% (12/50) and 8% (4/50), respectively (K =0.43). Only fresh samples were positive in RT-PCR while the SN-PCR detected BCoV in both fresh and frozen faecal samples. The sensitivity of SN-PCR was determined by 10-fold serial dilutions of the BCoV Kakegawa strain (HA titre: 256) that was detected until 10−7 dilution. The specificity of the amplicons was assessed by restriction fragment length polymorphism and sequence analysis. The inclusion of an internal control provides a way to detect assay inhibition in faecal samples and failure of nucleic acid extraction that allow reduction of the number of false-negative results. [Copyright &y& Elsevier]

Abstract: Bovine Papillomavirus type 2 (BPV-2) and chronic intoxication by bracken fern ingestion were associated with urinary bladder lesions and the clinical signs of enzootic haematuria in adult cattle. Clinically enzootic haematuria is characterized by intermittent haematuria followed by animal death. Enzootic haematuria causes considerable economical impact on extensive cattle breeding worldwide. The demonstration of BPV-2 participation in the etiology of bovine urinary bladder carcinoma by conventional virological methods is not easy and the integrity of epidemiological studies relies on methods that are sensitive and specific for BPV-2 detection and typing. A multiplex-PCR was evaluated for BPV-2 L1 gene and bovine mitochondrial genome ND5 gene (internal control) detection followed by a second round of BPV-2 amplification by a semi-nested PCR (SN-PCR). Six skin papilloma samples were used for PCR technique development. Twenty-two urinary bladder samples from symptomatic (n =12) and asymptomatic (n =10, control group) cows and 25 blood samples from cows grazed on enzootic haematuria-endemic (n =14) and enzootic haematuria-free (n =11, control group) geographical regions of Parana State, Brazil were analyzed. The SN-PCR detected BPV-2 in seven urinary bladder and 10 whole blood samples collected from cows with enzootic haematuria and in one urinary bladder and one whole blood samples of asymptomatic cows. The specificity of the amplicon was performed by restriction fragment length polymorphism and sequence analysis. The SN-PCR technique developed in this study will make possible the realization of diagnosis and comparative epidemiological studies to evaluate BPV-2 infection rates in cattle, and the association of this infection with bracken fern chronic intoxication in the etiology of enzootic haematuria and opens the possibility of ante mortem studies by lymphocytes analysis. [Copyright &y& Elsevier]

Bacteria classified in Mycoplasma ( M. bovis and M. bovigenitalium ) and Ureaplasma ( U. diversum ) genera are associated with granular vulvovaginitis that affect heifers and cows at reproductive age. The traditional means for detection and speciation of mollicutes from clinical samples have been culture and serology. However, challenges experienced with these laboratory methods have hampered assessment of their impact in pathogenesis and epidemiology in cattle worldwide. The aim of this study was to develop a PCR strategy to detect and primarily discriminate between the main species of mollicutes associated with reproductive disorders of cattle in uncultured clinical samples. In order to amplify the 16S-23S rRNA internal transcribed spacer region of the genome, a consensual and species-specific nested-PCR assay was developed to identify and discriminate between main species of mollicutes. In addition, 31 vaginal swab samples from dairy and beef affected cows were investigated. This nested-PCR strategy was successfully employed in the diagnosis of single and mixed mollicute infections of diseased cows from cattle herds from Brazil. The developed system enabled the rapid and unambiguous identification of the main mollicute species known to be associated with this cattle reproductive disorder through differential amplification of partial fragments of the ITS region of mollicute genomes. The development of rapid and sensitive tools for mollicute detection and discrimination without the need for previous cultures or sequencing of PCR products is a high priority for accurate diagnosis in animal health. Therefore, the PCR strategy described herein may be helpful for diagnosis of this class of bacteria in genital swabs submitted to veterinary diagnostic laboratories, not demanding expertise in mycoplasma culture and identification. [ABSTRACT FROM AUTHOR]

Bovine gammaherpesvirus 6 (BoGHV6), formerly known as bovine lymphotropic virus, is a member of the Macavirus genus, subfamily Gammaherpesvirinae , family Herpesviridae , that was initially associated with proliferative diseases in cattle. While the Macavirus genus contains agents, including alcelaphine gammaherpesvirus 1 (AlGHV1), ovine gammaherpesvirus 2 (OvGHV2), and caprine gammaherpesvirus-2 (CpGHV2), known to cause malignant catarrhal fever (MCF), and are collectively referred to as MCF virus (MCFV) group of organisms, diseases and/or clinical syndromes have not been associated with BoGHV6 and porcine lymphotropic herpesvirus (PLHV). This report investigated the occurrence of BoGHV6 in tissues of aborted dairy fetuses known to be infected by Histophilus somni to identify possible disease patterns associated with infection by this Macavirus. A nested-PCR (nPCR) assay was used to amplify the BoGHV6 polymerase gene from multiple tissues of 13 fetuses and the cow of one of these which were derived from seven dairy herds located in three geographical regions of Brazil. Direct sequencing confirmed the results of the nPCR assays. Additionally, all fetal tissues were previously investigated for the presence of H. somni, Listeria monocytogenes, Neospora caninum, Brucella abortus, Leptospira spp., bovine alphaherpesvirus 1, and bovine viral diarrhea virus (BVDV) by PCR and/or RT-PCR assays. The nPCR assay amplified BoGHV6 DNA from fetuses of most dairy herds (85.7%; 6/7) investigated, resulting in the amplification of BoGHV6 from 76.9% (10/13) of all fetuses evaluated from two geographical and important cattle-producing regions of Brazil. Furthermore, only BoGHV6 was identified in the spleen (n = 3), myocardium, and kidney (n = 2) of five fetuses, and BoGHV6 was the only agent associated with myocarditis in one of these. Nevertheless, dual, triple, and quadruple infections (including BVDV, B. abortus , and N. caninum) were identified in fetuses that were concomitantly infected by H. somni. Phylogenetic analysis revealed that the strain herein identified has 100% nucleotide (nt) sequence identity with wild type strains of BoGHV6 circulating in ruminants from Brazil and 99.8% nt identity with the reference strain of BoGHV6 but was 72.2–73.3% and 67.4–68.2% different from members of the MCFV group and PLHV, respectively. These results demonstrated that 76.9% of the fetuses evaluated were infected by BoGHV6, most likely via vertical infection resulting in transplacental transmission. Considering that most fetuses were concomitantly infected by BoGHV6 and H. somni the real impact of this viral infection cannot be efficiently determined. However, since BoGHV6 was the only pathogen identified in the myocardium of one fetus with myocarditis by histopathology, the possible participation of this Macavirus in the etiopathogenesis of the myocardial disease observed in this fetus cannot be ignored or discarded. However, the mere amplification of BoGHV6 DNA from the myocardium is not enough to establish a definite association between cause and effect, since in situ evaluations and experimental studies would be needed to confirm this agent in the etiopathogenesis of fetal diseases and/or abortions in cattle. Consequently, additional studies are needed to determine the exact role, if any, of BoGHV6 in the development of fetal disease, and possibly fetal mortality. • BoGHV6 was identified in multiple tissues of aborted fetuses concomitantly infected by Histophilus somni. • Only BoGHV6 was identified in several organs of aborted fetuses. • Myocarditis was identified in a fetus that was infected only by BoGHV6. • BoGHV6 can be transmitted vertically via transplacental infection. • BoGHV6 should be considered a putative agent of fetal infection in cattle. [ABSTRACT FROM AUTHOR]

Abstract: This report describes the complete genomic sequence and taxonomic position of BPV type 13. The BPV13 genome was amplified using the multiply primed rolling-circle amplification technique and long-template PCR employing two specific primers. The two long PCR fragments obtained were cloned and sequenced via primer walking. The complete genomic sequence of the BPV13 contains 7961bp encoding eight proteins, E1, E2, E4, E5, E6, E7, L1, and L2. Similarly to the E5 gene in BPVs 1 and 2, the putative BPV13 E5 ORF encodes a small transforming protein that contains a hydrophobic transmembrane domain. Meanwhile, the retinoblastoma tumor suppressor-binding domain is absent in the putative BPV13 E7 protein. The presence of these two specific molecular features has been recognized as a distinct marker for the development of fibropapilloma in artiodactyl PV-induced lesions. The phylogenetic analysis demonstrated that BPV13 is a new member of the Deltapapillomavirus genus, to be classified as the third representative of the Delta 4 species. The characterization of the genomic sequence of this novel PV will aid in the interpretation of the pathologies described to be related to this virus and provide support for the development of diagnostic tools for epidemiological surveillance of BPV13 in its potential natural hosts. [Copyright &y& Elsevier]

• BALF is a good biological sample for the molecular diagnosis of BRD in dairy calves. • Mixed infections of viruses and bacteria were frequent in dairy calves with respiratory disease. • BVDV 1d in BALF samples of dairy heifer calves in a BRD outbreak was characterized. • The calf rearing unit without prophylactic measures for respiratory infections represent a risk factor for BRD. The etiological agents involved in a bovine respiratory disease (BRD) outbreak were investigated in a dairy heifer calf rearing unit from southern Brazil. A battery of PCR assays was performed to detect the most common viruses and bacteria associated with BRD, such as bovine viral diarrhea virus (BVDV), bovine respiratory syncytial virus (BRSV), bovine alphaherpesvirus 1 (BoHV-1), bovine coronavirus (BCoV), bovine parainfluenza virus 3 (BPIV-3), Mannheimia haemolytica , Pasteurella multocida , Histophilus somni , and Mycoplasma bovis. Bronchoalveolar lavage fluid (BALF) samples were taken from 21 heifer calves (symptomatic n = 15; asymptomatic n = 6) that, during the occurrence of the BDR outbreak, were aged between 6 and 90 days. At least one microorganism was detected in 85.7 % (18/21) of the BALF samples. Mixed infections were more frequent (72.2 %) than single infections (27.7 %). The interactions between viruses and bacteria were the most common in coinfections (55.5 %). The frequencies of BRD agents were 38.1 % for BRSV, 28.6 % for BVDV, 33.3 % for BCoV, 42.85 % for P. multocida, 33.3 % for M. bovis , and 19 % for H. somni. BoHV-1, BPIV-3, and M. haemolytica were not identified in any of the 21 BALF samples. Considering that BALF and not nasal swabs were analyzed, these results demonstrate the etiological multiplicity that may be involved in BRD outbreaks in dairy calves. [ABSTRACT FROM AUTHOR]