Estimation of sensitivity and specificity of two diagnostics tests for bovine immunodeficiency virus using Bayesian techniques

Molecular detection of bovine immunodeficiency virus in water buffaloes (Bubalus bubalis) from the Amazon region, Brazil

Bovine immunodeficiency is a chronic progressive disease caused by a lentivirus that affects cattle and buffaloes. Although the infection has been described in cattle in some countries, including in Brazil, there are only two reports of infection in buffaloes: one in Pakistan and one in Cambodia. The aim of the present study was to survey the occurrence of bovine immunodeficiency virus (BIV) in water buffaloes from the Amazon region, Pará state, Brazil. BIV proviral DNA was surveyed in 607 whole blood samples of water buffaloes from 10 farms located in the state of Pará using semi-nested polymerase chain reaction (PCR) (PCR-SN) to amplify the pol region of the viral genome. Of the 607 samples tested, 27 (4.4 %) were positive for BIV proviral DNA. The amplified fragments were confirmed by sequence analysis after cloning and nucleotide sequencing. The sequence obtained had 99 % similarity to the reference strain (R-29). The present study provides important epidemiological data because BIV was detected for the first time in water buffaloes in Brazil. Further, the results suggest the possibility of the virus being a risk factor for herd health because it may be a potential causal agent of chronic disease and, also may be associated to other infectious diseases.

Estimation of diagnostic test accuracy without full verification: a review of latent class methods

The performance of a diagnostic test is best evaluated against a reference test that is without error. For many diseases, this is not possible, and an imperfect reference test must be used. However, diagnostic accuracy estimates may be biased if inaccurately verified status is used as the truth. Statistical models have been developed to handle this situation by treating disease as a latent variable. In this paper, we conduct a systematized review of statistical methods using latent class models for estimating test accuracy and disease prevalence in the absence of complete verification.

Comparison of immunoassay and real-time PCR methods for the detection of Jembrana disease virus infection in Bali cattle

A sensitive diagnostic assay for the detection of infections with the bovine lentivirus Jembrana disease virus (JDV) is required in Indonesia to control the spread of Jembrana disease. Immunoassays are used routinely but are compromised by cross-reactive epitopes in the capsid (CA) protein of JDV and the genetically related bovine immunodeficiency virus (BIV). JDV gag-specific primers were tested in a real-time PCR assay to detect proviral DNA in peripheral blood mononuclear cells from 165 cattle from the Tabanan district of Bali. JDV-specific amplicons were detected in 9% of the cattle and only 33% of the real-time PCR positive cattle were seropositive. The delayed seroconversion that occurs after infection with JDV could explain the low concordance between these assays but other factors may be responsible. BIV proviral DNA was not detected in any of the PBMC DNA samples. A high concordance value of 98.6% was found between the JDV plasma-derived antigen Western blot and the JDV p26-his recombinant protein ELISA. Only 21% of the seropositive cattle had detectable levels of proviral DNA suggesting that the proviral load in recovered cattle is low. A combination of real-time PCR and JDV p26-his ELISA is recommended for the detection of infection with JDV in Indonesia.

Test characteristics from latent-class models of the California Mastitis Test

We evaluated (using latent-class models) the ability of the California Mastitis Test (CMT) to identify cows with intramammary infections on the day of dry-off. The positive and negative predictive values of this test to identify cows requiring dry-cow antibiotics (i.e. infected) was also assessed. We used 752 Holstein-Friesian cows from 11 herds for this investigation. Milk samples were collected for bacteriology, and the CMT was performed cow-side, prior to milking on the day of dry-off. At the cow-level, the sensitivity and specificity of the CMT (using the four quarter results interpreted in parallel) for identifying all pathogens were estimated at 70 and 48%, respectively. If only major pathogens were considered the sensitivity of the CMT increased to 86%. The negative predictive value of the CMT was >95% for herds with major-pathogen intramammary-infection prevalence <15%, so that selective dry-cow therapy might be reasonable for such herds if cows were screened with the CMT.

Estimating the true prevalence of Fasciola hepatica in cattle slaughtered in Switzerland in the absence of an absolute diagnostic test

A survey of 1,331 cattle presented for slaughter at two abattoirs in Switzerland was used to estimate the true prevalence of Fasciola hepatica infection and the diagnostic parameters of visual meat inspection, coproscopy after sedimentation technique, a commercial ELISA test for specific antibody detection in serum and the post mortem microscopic detection of eggs in bile. Faeces, blood and the gall bladder were taken from most cattle presented for slaughter. In addition, livers that were rejected by the meat inspectors were also dissected to examine for the presence of liver fluke. Bayesian techniques (Markov Chain-Monte Carlo) were used to estimate the diagnostic parameters of each of these procedures and the true prevalence of bovine fasciolosis. The true prevalence of F. hepatica infection was estimated at 18.0% (95% credible intervals 15.9-20.3%). The diagnostic sensitivity of coproscopy, bile examination, antibody ELISA and meat inspection were estimated at 69.0% (57.3-79.7%), 93.4% (88.0-97.5%), 91.7% (87.2-95.2%) and 63.2% (55.6-70.6%), respectively. The diagnostic specificity of the ELISA test was estimated at 93.7% (91.7-95.2%). These results demonstrate that the prevalence of bovine fasciolosis is higher than previously thought due to the low sensitivity of meat inspection. They also demonstrate that traditional coproscopy can be very efficient if there is repeated sampling, resulting in sensitivity of approximately 92%.

Validation of molecular-diagnostic techniques in the parasitological laboratory

Diagnostic laboratories today often operate according to standard quality management procedures such as ISO/IEC 17025. This requires that only validated methods are used. Validation procedures help to document that a particular protocol used by the accredited laboratory has a guaranteed performance in that particular laboratory. Several study designs exist for validation procedures. Computer programmes are available to help with the statistical analysis of validation results. The agreement beyond chance of results obtained in the protocol that is to be validated can be compared to those achieved in an already established test (agreement). For a method that is used under routine conditions or for epidemiological studies, it is necessary to assess the diagnostic sensitivity and diagnostic specificity of the technique. These parameters can be estimated by comparing the method that needs to be validated with an existing reliable method ('gold standard'). This is done by testing a standard set of well-documented samples using both techniques in parallel. Approaches using Bayes' theorem are used to perform gold standard-free validations. Many PCR-based methods are characterised by an excellent analytical sensitivity and are thus good candidates for diagnostic tools of the required diagnostic sensitivity. However, the high level of analytical sensitivity can also make molecular techniques susceptible to cross-contamination and carry-over problems leading to false-positive results. Moreover, the presence of inhibitors can cause false-negative results. After an initial validation, test performance needs to be continuously monitored, e.g. by using combined Shewhart-CUSUM control routines, and test results compared to those obtained by other laboratories (proficiency testing).

Detection of extracellular factor-positive Streptococcus suis serotype 2 strains in tonsillar swabs of live sows by PCR

In this study, the sensitivity (Se) and specificity (Sp) of a PCR for the detection of EF-positive Streptococcus suis serotype 2 strains in tonsillar swabs of live sows were assessed. We sampled 471 sows originating from four farrow-to-finish farms by tonsillar swabbing and collected their tonsils after slaughter. On these specimens, a PCR, a bacterial examination (BE) or both were performed for the detection of EF-positive S. suis serotype 2 strains. Swab-PCR, Tonsil-PCR and Tonsil-BE were regarded as three integral tests. A Bayesian approach was used to calculate the Se and Sp of the tests. Se and Sp for Swab-PCR were 0.63 (95% credibility interval <0.52, 0.74>) and 0.96 (<0.92, 0.99>), respectively. Values for Se and Sp of Tonsil-PCR amounted to 0.88 (<0.75, 0.96>) and 0.94 (<0.87, 0.99>), respectively. For Tonsil-BE, Se was 0.65 (<0.51, 0.76>) and Sp was 0.97 (<0.91, 0.99>). Repetition of the swabbing procedure after 10 min resulted in a higher Se 0.85 (<0.67, 0.96>) than the Se of the first-Swab-PCR. Repetition of the PCR on the same sample did not result in any significant changes in the outcome of the analysis.

Transmissible spongiform encephalopathy risk assessment: the UK experience

Transmissible spongiform encephalopathy (TSE) risk assessments undertaken in the United Kingdom have mainly had the objective of determining the risks posed to humans from exposure to the causal agents associated with bovine spongiform encephalopathy (BSE) and variant Creutzfeld-Jakob disease (vCJD). In this article, I examine 19 of these risk assessments published to date and consider how their results might be influenced by underlying model assumptions and methodology. Three separate aspects common to all the assessments are infective load estimation, exposure pathway identification, and risk estimation. These are each discussed in detail.

An evaluation of United Kingdom environmental bovine spongiform encephalopathy risk assessment

As a member of the group of diseases known as transmissible spongiform encephalopathies (TSEs), bovine spongiform encephalopathy (BSE) has been causally associated with a new variant of Creutzfeldt-Jakob disease (vCJD) in humans. Given the many uncertainties on the transmission and persistence of TSE pathogens in the environment, quantitative assessment of risks to humans and animals continues to remain a public health issue. This paper reviews quantitative BSE risk assessments undertaken in the United Kingdom since 1997 to address the potential for human exposure and theoretical health risks through environmental pathways. The review focuses on how model assumptions and methodology may influence the results.

Sensitive and specific detection of bovine immunodeficiency virus and bovine syncytial virus by 5' Taq nuclease assays with fluorescent 3' minor groove binder-DNA probes

Sensitive assays are required to detect bovine retroviruses in donor cattle used for the in vivo preparation of Australian tick fever vaccines. 5' Taq nuclease assays using 3' minor groove binder DNA probes (TaqMan)MGB) were developed and compared to conventional PCR assays for the sensitive detection of bovine syncytial virus (BSV) and bovine immunodeficiency virus (BIV). Seven beef and dairy herds were screened to evaluate these tests. Comparative sensitivities of PCR tests were determined by testing log(10) dilutions of plasmids with inserts containing corresponding provirus sequences. Published PCR assays targeting BIV env sequences did not adequately amplify Australian BIV sequences. Pol sequences from Australian strains of BIV and BSV were used to design TaqMan MGB assays, which improved sensitivity 10-fold (BIV) and 100-fold (BSV), respectively, over conventional PCR tests. This is the first report of Australian sequences of BIV and BSV and the first 5' Taq nuclease assays described to detect these viruses. These methods could be applied to future studies requiring sensitive detection of these two bovine retroviruses.