Arbovirus surveillance detects mosquito-borne viruses in central South Africa

Surveillance plays an important role in early detection of circulating arboviruses with potential to cause outbreaks of disease. In South Africa (SA) there are several endemic mosquito-borne viruses of medical and veterinary importance associated with outbreaks of disease in humans and domestic animals (livestock and horses) usually occurring after heavy rainfall. In addition, there are historical reports of viruses that were isolated from mosquitoes during vector surveillance studies with demonstration of antibodies in human populations during serosurveys. However, for many of these viruses detected historically there is no recent evidence of their circulation in the country. This study was initiated to screen mosquitoes in central South Africa for evidence of known and less common mosquito-borne viruses. Mosquitoes were collected from selected sites including two urban sites, a rural and a conservation area in central South Africa and were screened for arboviruses from the families Togaviridae, Orthoflaviviridae and Peribunyaviridae. A total of 10 332 mosquitoes were collected between November 2019 and March 2023. Most of the collection was obtained from the two urban sites in Bloemfontein, 8 236/10 332 (79.7 %), 1 075/10 332 (10.4 %) from the conservation site and 1 021/10 332 (9.9 %) from the rural site. Mosquito pool homogenates were screened using nested in-house RT-PCR. The nucleotide sequence of each amplicon of predicted size was determined using Sanger sequencing or Oxford Nanopore sequencing, and the virus identification confirmed using BLASTn analysis. Partial genes for Sindbis virus (SINV) genotype 1 were detected in three mosquito pools, for Middelburg virus (MIDV) in two pools, for Germiston virus (GERV) in one pool, for bunyamwera virus (BUNV) in four pools, for West Nile virus (WNV) lineage 2 in four pools, for Bagaza virus (BAGV) in one pool, and an insect specific virus was detected in one pool. Due to the short length of sequence data obtained, cluster maps were used to determine relationships with previous isolates using sequence data retrieved from GenBank. Cluster maps confirmed that none of the isolates were newly introduced but closely related to isolates previously detected in the country. Sindbis virus genotype 1 and WNV lineage 2 are known to cause outbreaks of human disease after heavy rainfall, favoring an increase in mosquito populations. Middelburg virus has been associated with neurological disease in horses and some recent evidence in humans. Bunyamwera virus has previously been associated with mild febrile disease and GERV with laboratory acquired infections, but the public health significance is not well known and similarly with BAGV. This study confirmed the current circulation of mosquito-borne viruses other than the common viruses and suggest further investigation to determine the medical significance would be important.