A Bayesian latent class estimation of the diagnostic accuracy of clinical examination and laboratory assays to identify bovine ephemeral fever virus infection in South African cattle

Abstract

Bovine ephemeral fever (BEF) is an economically important vector-borne viral disease of cattle and water buffalo in Africa, Australia and parts of Asia. The control of BEF is centred around vaccination, and therefore accurate, early identification of disease outbreaks are key to minimize its economic and welfare impact. In Africa, control programs are hampered by limited diagnostic capabilities and poor infrastructure for rapid transportation of diagnostic specimens. The primary objective of this study was to estimate the sensitivity (Se) and specificity (Sp) of four tests, namely clinical examination by a veterinarian, virus isolation and two different conventional PCR assays, to identify an acute bovine ephemeral fever virus (BEFV) infection in diseased, naturally infected South African cattle, without the assumption of a reference standard. Samples and data were collected from cattle with clinical signs suggestive of BEF rather than a random sample of cattle. A case was categorised as clinical examination positive if the examining veterinarian considered acute BEFV-infection as the most likely aetiology. Virus isolation was performed using the buffy coat of heparin blood samples on baby hamster kidney cell cultures, evaluating cytopathic effect and confirming virus morphology by transmission electron microscopy. PCR was performed using two previously published protocols: The Ephemerovirus L-gene PCR (targeting the RNA-dependent RNA polymerase gene) and a BEFV G-gene PCR (targeting the neutralising G1 epitope of the glycoprotein). A single population, four test Bayesian latent class model with conditional dependence between the two PCR assays was implemented. The prevalence of BEFV-infection was high in this study population of clinical suspects at 67 %, (95 % Probability Interval (PI) 52 %; 81 %). Clinical examination provided a reasonable indication of acute BEFV infection (Se of 86 % (PI 77 %; 93 %) and Sp of 67 % (PI 52 %; 82 %)). Virus isolation was the most specific (99 % (PI 97 %; 100 %)), but least sensitive assay (30 % (PI 20 %; 44 %)). Of the two conventional PCRs, the L-gene PCR outperformed the G-gene PCR: The L-gene Se was 64 % (PI 51 %; 76 %) and Sp 96 % (PI 84 %; 100 %) compared to Se of 50 % (PI 38 %; 61 %) and Sp of 89 % (PI 75 %; 98 %) for the G-gene. While the laboratory assays presented excellent positive predictive values within this high disease prevalence population, the poor negative predictive values limit their usefulness to field veterinarians attempting to exclude BEF as diagnosis. Novel pen-side diagnostics should be developed due to the limitations of currently available assays and infrastructure constraints prevalent in Africa.