Epidemiological investigation of Shuni virus infections in hospitals in two provinces of South Africa (2019–2021) using molecular and serological surveillance

Shuni Virus (SHUV) is a reemerging zoonotic orthobunyavirus in the Peribunyaviridae family associated with neurological infections and birth defects in humans and animals in Africa and has emerged in the Middle East in the past 10 years. Limited epidemiological data exist in humans, partially due to a lack of clinical awareness and availability of diagnostic assays to determine the incidence of clinical cases and seroprevalence in the population. The goal of this study was to establish serologic and molecular diagnostic assays for SHUV for hospital-based surveillance and to investigate the clinical epidemiology in humans in South Africa. The incidence of SHUV infections was investigated in patients with acute fever of unknown cause with or without neurological signs (AFDUC/N) during the arbovirus season (January-June, 2019–2021). IgM and IgG ELISAs for SHUV were established using baculovirus-expressed glycoproteins and validated against virus-neutralization tests (VNT) positive sera. Orthobunyavirus quantitative RT-PCR (RT-qPCR) and IgM ELISA were used to identify acute infections, and IgG ELISA to define the seroprevalence in patients and healthy control groups in hospitals in Gauteng and Mpumalanga provinces in South Africa. In total, 3/349 (0.84%) AFDUC/N cases tested positive by RT-qPCR and confirmed as SHUV by sequencing. In total, 22/225 (9.7%) AFDUC/N patients had SHUV neutralising antibodies (VNT), of which 11/22 (50.00%) were IgM positive, with an IgM seropositivity of 4.89% (11/225 (4.89%)). Of the RT-PCR and double IgM + VNT+ patients, 60% presented with seizures and 40% with meningitis, of which 36.36% were children and 63.63% were adults, respectively. In total, 9/112 (8%) of the healthy control group tested positive on the IgG ELISA assay. These findings suggest that SHUV is a missed cause of acute neurological infections in hospitalized children and adults in South Africa and should be investigated in humans in Africa and other regions.