The epidemiology of Sindbis virus in South Africa

Abstract

Sindbis virus (SINV) is a mosquito-borne alphavirus in the family Togaviridae. It is locally amplified in a bird-mosquito enzootic cycle and circulates globally. Five genotypes exist for SINV, however, SINV genotype I (SINV-I) is the only genotype associated with disease outbreaks in humans in South Africa as well as in northern Europe thus far. Although SINV is commonly associated with mild febrile and self-limiting disease, recent studies from South Africa have indicated that it may be associated with more severe symptoms, febrile and neurological disease and fatalities in humans and animals. Little is known about the burden of disease of SINV in humans and animals while data on the molecular epidemiology and genomics of current circulating strains are limited. This study was a retro- and prospective study reporting on the incidence of SINV in humans and animals with acute febrile and neurological disease in South Africa using molecular and serological assays. The study further investigated the genomics of SINV strains in wildlife, equine, domestic animals, and mosquitos. The first chapter gives a comprehensive review of the literature and highlights the importance of zoonotic arboviruses and the role of mosquitoes as disease vectors. It further highlights the importance of alphaviruses and particularly SINV in humans and animals as a cause of febrile and neurological disease. In the second chapter, the molecular epidemiology based on sequencing and phylogenetic analysis of the nsP4 and the E2 glycoprotein genes and characterization of full genomes are being reported. SINV strains identified in mosquitoes and animals through the Zoonotic arbo and Respiratory virus (ZARV) program One Health surveillance system over a period of 13 years were selected and the NSP4 gene reamplified for 33 cases. The E2 protein sequences were obtained following optimization of a nested PCR and sanger sequencing for 6 positive cases. Complete SINV genomes were obtained for four of those cases through virus isolation and next generation sequencing and revealed that SINV genotype I C is currently circulating in South Africa as opposed to previous SINV genotype I B strains seen historically. The evaluation of the partial nsp4 gene revealed that the mosquito SINV strains shared high percentage similarity with strains recently isolated from horses with febrile and neurological signs in this region. The third chapter investigated if SINV contributed to acute febrile disease of unknown cause with or without neurological signs (AFDUC) in hospitalized patients in the highveld (Gauteng province), and the lowveld (Mpumalanga province) of South Africa. Clinical samples of patients from three sentinel hospital surveillance sites (Kalafong, Mapulaneng and Matikwane hospitals) in South Africa were screened for SINV. In total, 38/197 (19.0%) of samples were positive for SINV specific IgM. A total of 25/38 (65.8%) IgM positive samples tested positive for SINV neutralizing antibodies, giving an overall incidence of 12.7%. Furthermore, 2/31 (6.5%) CSF specimens tested positive for IgM but were negative for neutralizing antibodies. A higher incidence of SINV cases was seen in Mpumalanga (26.0%) than Gauteng province (15.0%). SINV contributed to 12.7% of AFDUC cases in hospitalized patients during late summer and autumn months and was significantly associated with arthralgia, meningitis, and headaches. In the fourth chapter, the incidence of SINV infection in horses with neurological and febrile diseases was investigated using SINV IgM serology during a SINV outbreak in South Africa (2017). SINV IgM antibodies were detected in 54/155 (34.8%) cases with febrile and neurological signs in South Africa in late summer (January-May) 2017. Confirmation by serum neutralizing assays suggested SINV was the cause in 29/155 (19%) of the cases. Clinical manifestations included ataxia, recumbency, paresis, seizures, and jaundice in horses. Similar proportions of SINV IgM detection were seen in febrile (36.0%) and neurological cases (34.3%). Results from this study as a whole showed that Sindbis virus is widely distributed in South Africa and the characterization of the circulating strains revealed a subtype of genotype I that had not been previously described. SINV has been identified for many years through the Zoonotic Arbo- and Respiratory Viral Program (ZARV) syndromic arboviral surveillance in South Africa using RT-PCR. In this study, serology was implemented for cases that were missed using molecular methods for detection. A high percentage of SINV specific IgM was detected and most of the cases could be confirmed using SINV neutralization assay. This highlights the importance of surveillance as well as the combination of molecular (RT-PCR) and serological screening of arboviruses in South Africa. The association with neurological signs reported in this study suggest the severity of disease may be underestimated and needs further investigation. Keywords: Alphavirus, arbovirus, genome, Sindbis virus, Neurological, febrile, Sindbis virus, incidence; RT-PCR, IgM, neutralization, South Africa.