Investigation of Shuni virus strains identified in neurological cases in humans, horses, and mosquito vectors in South Africa

Abstract

Emerging and re-emerging infectious diseases are an important global problem as they can lead to major disease outbreaks. These may result in disease manifestation with increased morbidity and mortality rates in different geographic areas. Arboviruses (arthropod-borne viral diseases) contribute significantly to such diseases worldwide. Shuni virus (SHUV) is a suspected re-emerging arbovirus of the Orthobunyavirus genus in the Peribunyaviridae family. It has previously been implicated in causing neurological diseases in horses, livestock, wildlife and potentially humans. This study aimed to use a One Health approach to investigate the epidemiology of SHUV in horses, humans, and mosquito vectors in South Africa. SHUV specific molecular tests were performed and evaluated for diagnostic and screening purposes. This was achieved by comparing the specificity and sensitivity of three PCRs i.e. SHUV specific HybProbe nested real-time RT-PCR, a TaqMan one-step SHUV real-time RT-PCR and a TaqMan Orthubunyavirus one-step genus specific real-time RT-PCR all targeting the nucleocapsid (S-segment) gene. A total of 24/1820 (1.3%) SHUV positive horse cases presenting with febrile and nervous disease were identified as SHUV between 2009-2019 using RT-PCR assays. Annually most cases were reported between January and April, with most horses displaying neurological signs (21/24, 87.5%), followed by death (12/24, 50%) and fever (7/24, 29.2%). The geographic distribution showed that SHUV cases could be identified in all nine provinces of SA with most cases detected in Gauteng (9/24 (37.5%)), followed by the Western Cape (4/24 (16.7%)). Phylogenetically, the SHUV strains clustered together with the SHUV index strain. The TaqMan Orthubunyavirus one-step RT-PCR additionally detected 7/129 (5.4%) Shuni-like human cases in 2017 and 3/215 (1,4%) Shuni-like mosquito vector pools in 2015 and 2016. This study suggested that SHUV is circulating in South Africa although less frequent relative to other arboviruses such as West Nile Virus (WNV) and Middleburg virus. Further investigations into the reservoir hosts, vectors and transmission cycle are needed to understand the epidemiology of SHUV in Africa especially in South Africa. Its importance as a human pathogen still needs to be defined. Therefore, this project also allowed us to determine the health issues related to the virus and potentially identifying improved options for control strategies.