Assessment of Rapid MinION Nanopore DNA Virus Meta-Genomics Using Calves Experimentally Infected with Bovine Herpes Virus-1.

Bovine respiratory disease (BRD), which is the leading cause of morbidity and mortality in cattle, is caused by numerous known and unknown viruses and is responsible for the widespread use of broad-spectrum antibiotics despite the use of polymicrobial BRD vaccines. Viral metagenomics sequencing on the portable, inexpensive Oxford Nanopore Technologies MinION sequencer and sequence analysis with its associated user-friendly point-and-click Epi2ME cloud-based pathogen identification software has the potential for point-of-care/same-day/sample-to-result metagenomic sequence diagnostics of known and unknown BRD pathogens to inform a rapid response and vaccine design. We assessed this potential using in vitro viral cell cultures and nasal swabs taken from calves that were experimentally challenged with a single known BRD-associated DNA virus, namely, bovine herpes virus 1. Extensive optimisation of the standard Oxford Nanopore library preparation protocols, particularly a reduction in the PCR bias of library amplification, was required before BoHV-1 could be identified as the main virus in the in vitro cell cultures and nasal swab samples within approximately 7 h from sample to result. In addition, we observed incorrect assignment of the bovine sequence to bacterial and viral taxa due to the presence of poor-quality bacterial and viral genome assemblies in the RefSeq database used by the EpiME Fastq WIMP pathogen identification software.

Assessment of the long-term effect of vaccination on transmission of infectious bovine rhinotracheitis virus in cattle herds hyperimmunized with glycoprotein E-deleted marker vaccine.

OBJECTIVE: To assess long-term effects and risk factors for the efficacy of hyperimmunization protocols against infectious bovine rhinotracheitis (IBR) during a longitudinal field study of dairy and dairy-beef mixed farms. ANIMALS: Approximately 7,700 cows from 72 farms. PROCEDURES: Farms were assigned to 3 treatment groups (hyperimmunization groups [HIGs] 1 and 2, which were hyperimmunized with glycoprotein E [gE]-deleted marker vaccines, and a nonintervention group [NIG]). Cattle in HIG 1 were initially vaccinated with an attenuated vaccine, whereas cattle in HIG 2 were initially vaccinated with an inactivated-virus vaccine. Cattle in both HIGs received booster inoculations with inactivated-virus vaccines at 6-month intervals. The risk for gE seroconversion was compared among experimental groups via a shared frailty model with a piecewise constant baseline risk to correct for seasonal and secular effects. RESULTS: Risk for gE seroconversion significantly decreased over time for the HIGs, compared with the NIG. Seasonal changes in the risk of gE seroconversion were detected, with a higher risk during winter periods, compared with grazing periods. No significant difference was detected between HIGs 1 and 2. The only significant risk factor was the number of buildings for cattle on a farm; the higher the number of buildings, the lower the risk for gE seroconversion. Prevalence of IBR decreased over time in both HIGs but remained constant or increased in the NIG. CONCLUSIONS AND CLINICAL RELEVANCE: Hyperimmunization via repeated administration of attenuated and inactivated-virus gE-deleted marker vaccines as well as inactivated-virus vaccines may provide a method for control of IBR.

[Infectious bovine rhinotracheitis outbreak on a mostly BHV-1 free farm can result in great damage]. / Infectieuze boviene rhinotracheïtisuitbraak op een nagenoeg BHV1-vrij bedrijfkan tot grote problemen leiden.

In a suckler herd with 110 cows (without young stock born in 2003) 5 cows died within 10 days, 6 calves were born dead prematurely and 5 calves were born alive but prematurely. The diagnosis BHV1-infection was based on clinical symptoms and confirmed with PCR. The clinical signs, diagnostic methods, therapy, risk-analysis and prevention are discussed.