Effect of pooling and multiplexing on the detection of bluetongue virus RNA by real-time RT-PCR

Quadruplex Real-Time TaqMan® RT-qPCR Assay for Differentiation of Equine Group A and B Rotaviruses and Identification of Group A G3 and G14 Genotypes

Equine rotavirus A (ERVA) is the leading cause of diarrhea in foals, with G3P[12] and G14P[12] genotypes being the most prevalent. Recently, equine G3-like RVA was recognized as an emerging infection in children, and a group B equine rotavirus (ERVB) was identified as an emergent cause of foal diarrhea in the US. Thus, there is a need to adapt molecular diagnostic tools for improved detection and surveillance to identify emerging strains, understand their molecular epidemiology, and inform future vaccine development. We developed a quadruplex TaqMan® RT-qPCR assay for differentiation of ERVA and ERVB and simultaneous G-typing of ERVA strains, evaluated its analytical and clinical performance, and compared it to (1) a previously established ERVA triplex RT-qPCR assay and (2) standard RT-PCR assay and Sanger sequencing of PCR products. This quadruplex RT-qPCR assay demonstrated high sensitivity (>90%)/specificity (100%) for every target and high overall agreement (>96%). Comparison between the triplex and quadruplex assays revealed only a slightly higher sensitivity for the ERVA NSP3 target using the triplex format (p-value 0.008) while no significant differences were detected for other targets. This quadruplex RT-qPCR assay will significantly enhance rapid surveillance of both ERVA and ERVB circulating and emerging strains with potential for interspecies transmission.

Study of molecular diagnosis and viremia of bluetongue virus in sheep and cattle

Bluetongue virus (BTV) is an RNA virus that infects cattle and sheep. The objective of this study was to compare two real-time PCRs for the detection of BTV and to monitor Orbivirus viremia in sheep and cattle for 6 months. The PCR results showed the occurrence of infected animals throughout the experiment without records of clinical signs. The number of positive animals reduced during the experiment, but some animals were positive for BTV RNA during the entire experiment. The performance of the two RT-qPCRs for BTV detection techniques used in this work revealed a kappa index of 0.71 for cattle and 0.75 for sheep.

Evaluating the most appropriate pooling ratio for EDTA blood samples to detect Bluetongue virus using real-time RT-PCR

The control of Bluetongue virus (BTV) presents a significant challenge to European Union (EU) member states as trade restrictions are placed on animals imported from BTV-affected countries. BTV surveillance programs are costly to maintain, thus, pooling of EDTA blood samples is used to reduce costs and increase throughput. We investigated different pooling ratios (1:2, 1:5, 1:10 and 1:20) for EDTA blood samples to detect a single BTV positive animal. A published real-time RT-PCR assay (Hofmann et al., 2008) and a commercial assay (ThermoFisher VetMax™ BTV NS3 kit) were used to analyse BTV RNA extracted from pooled EDTA blood samples. The detection rate was low for the onset of infection sample (0-2 days post infection (dpi); C_T 36) irrespective of the pooling ratio. Both assays could reliably detect a single BTV-positive animal at early viraemia (3-6 dpi; C_T 33) when pooled, however, detection rate diminished with increasing pooling ratio. A statistical model indicated that pooling samples up to 1:20, is suitable to detect a single BTV positive animal at peak viraemia (7-12 dpi) or late infection (13-30 dpi) with a probability of detection of >80% and >94% using the Hofmann et al. (2008) and VetMAX assays, respectively. Using the assays highlighted in our study, pooling at ratios of 1:20 would be technically suitable in BTV-endemic countries for surveillance purposes. As peak viraemia occurs between 7-12 days post infection, a 1:10 pooling ratio is appropriate for post-import testing when animals are sampled within a similar time frame post-import.

Theoretical and Experimental Approaches to Estimate the Usefulness of Pooled Serum Samples for the Diagnosis of Postweaning Multisystemic Wasting Syndrome

Classical postweaning multisystemic wasting syndrome (PMWS) diagnosis is based on postmortem findings (histopathology plus viral detection in lymphoid tissues). Because one of the major differences between PMWS-affected and nonaffected pigs is Porcine circovirus-2 (PCV-2) load in serum and tissues, real-time quantitative polymerase chain reaction (qPCR) has been suggested as a potential diagnostic technique for the disease. The objective of the present study was to assess the applicability of qPCR to quantify PCV-2 loads in pooled serum samples as an easy-to-use PMWS diagnostic tool at the herd level. The experimental design included two simulation studies with several serum pool sizes from pigs already screened for PMWS (by histopathology and detection of PCV-2 by qPCR). Several qPCR thresholds were defined and validated with experimental pools created in the laboratory. Quantitative PCR on pooled serum samples did not result in a sufficiently reliable alternate method to the classical PMWS diagnosis method based on individual clinical, histopathological, and PCV-2 detection criteria. However, serum pools seemed to be an alternative at a low economic cost for the quantification of PCV-2 loads in suspicious herds. A targeted (including only clinically diseased animals) sampling approach did not give better estimates compared with a random sampling approach.

Salmonid alphavirus (SAV) and pancreas disease (PD) in Atlantic salmon, Salmo salar L., in freshwater and seawater sites in Norway from 2006 to 2008

A cohort study was initiated in the spring of 2006 to investigate epidemiological aspects and pathogenesis of salmonid alphavirus (SAV) subtype 3 infections and pancreas disease (PD). The aims were to assess involvement of the freshwater production phase, the extent and frequency of subclinical infections and to follow PD-affected populations throughout the entire seawater production cycle, as well as investigate possible risk factors for PD outbreaks. Fish groups from 46 different Atlantic salmon freshwater sites in six counties were sampled once prior to seawater transfer and followed onto their seawater sites. A total of 51 Atlantic salmon seawater sites were included, and fish groups were sampled three times during the seawater production phase. SAV subtype 3 was not identified by real-time RT-PCR from samples collected in the freshwater phase, nor were any SAV-neutralizing antibodies or histopathological changes consistent with PD. In the seawater phase, SAV was detected in samples from 23 of 36 (63.9%) studied sites located within the endemic region. No SAV subtype 3 was detected in samples from seawater sites located outside the endemic region. The cumulative incidence of PD during the production cycle amongst sites with SAV detected was 87% (20 of 23 sites). Average fish weight at time of PD diagnosis ranged from 461 to 5978 g, because of a wide variation in the timing of disease occurrence throughout the production cycle. Mortality levels following a PD diagnosis varied greatly between populations. The mean percentage mortality was 6.9% (+/-7.06) (range 0.7-26.9), while the mean duration of increased mortality following PD diagnosis was 2.8 months (+/-1.11) (range 1-6).

Simultaneous detection of bluetongue virus RNA, internal control GAPDH mRNA, and external control synthetic RNA by multiplex real-time PCR

Bluetongue is an insect-borne disease of domestic and wild ruminants that requires strict monitoring by sensitive, reproducible and robust methods. Real-time reverse transcription polymerase chain reaction (RT-qPCR) analysis has become the method of choice for routine viral diagnosis. As false-negative test results can have serious implications; an internal/external control system should be incorporated in each analysis to detect RT-qPCR failure due to poor sample quality, improper nucleic acid extraction and/or PCR inhibition. To increase the diagnostic capacity and reduce costs, it is recommended to use a multiplex strategy which enables the amplification of multiple targets in a single reaction. This chapter describes the application of a triplex RT-qPCR for the simultaneous detection of bluetongue viral RNA, an internal control and an external control. The primer and probe sequences of the BTV RT-qPCR were taken from Toussaint et al. (J Virol Methods 140:115-123, 2007), whereas the internal and external RT-qPCRs were specifically designed to detect endogenous glyceraldehyde-3-phosphate dehydrogenase mRNA and a synthetic RNA, respectively. To maximize the sensitivity of the assay, the primer concentrations of the internal/external control reactions were limited and the amount of Taq DNA polymerase was increased. A comparison of the singleplex versus triplex RT-qPCR indicated that the triplex RT-qPCR exhibits a higher analytical sensitivity. Due to the incorporation of the internal/external control system, the triplex RT-qPCR allows an even more reliable and rapid diagnosis of bluetongue than the previously described singleplex RT-qPCR (J Virol Methods 140:115-123, 2007).