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We determined complete genome sequences of lineage 2 West Nile virus (WNV) strains isolated from patients in South Africa who had mild or severe WNV infections. These strains had previously been shown to produce either highly or less neuroinvasive infection and induced genes similar to corresponding highly or less neuroinvasive lineage 1 strains in mice. Phylogenetic and amino acid comparison of highly and less neuroinvasive lineage 2 strains demonstrated that the nonstructural genes, especially the nonstructural protein 5 gene, were most variable. All South African lineage 2 strains possessed the envelope-protein glycosylation site previously postulated to be associated with virulence. Major deletions existed in the 3 noncoding region of 2 lineage 2 strains previously shown to be either less or not neuroinvasive relative to the highly neuroinvasive strains sequenced in this study. [ABSTRACT FROM AUTHOR]

The prevalence of neutralizing antibody against West Caucasian bat virus (WCBV) in Miniopterus bats collected in Kenya ranged from 17% to 26%. Seropositive bats were detected in 4 of 5 locations sampled across the country. These findings provide evidence that WCBV, originally isolated in Europe, may emerge in other continents. [ABSTRACT FROM AUTHOR]

We detected Marburg virus RNA in rectal swab samples from Egyptian rousette bats in South Africa in 2017. This finding signifies that fecal contamination of natural bat habitats is a potential source of infection for humans. Identified genetic sequences are closely related to Ravn virus, implying wider distribution of Marburg virus in Africa.

We detected 3 lyssaviruses in insectivorous bats sampled in South Africa during 2003-2018. We used phylogenetic analysis to identify Duvenhage lyssavirus and a potentially new lyssavirus, provisionally named Matlo bat lyssavirus, that is related to West Caucasian bat virus. These new detections highlight that much about lyssaviruses remains unknown.

We detected a high seroprevalence of Marburg virus (MARV) antibodies in fruit bats in South Africa; 19.1% of recaptured bats seroconverted. The MARV RNA isolated closely resembled the 1975 Ozolin strain. These findings indicate endemic MARV circulation in bats in South Africa and should inform policies on MARV disease risk reduction.

As part of a larger survey for detection of pathogens among wildlife in sub-Saharan Africa conducted during 2007-2012, multiple diverse paramyxovirus sequences were detected in renal tissues of bats. Phylogenetic analysis supports the presence of at least 2 major viral lineages and suggests that paramyxoviruses are strongly associated with several bat genera.

We recently identified 2 Mokola viruses from domestic mammals (a dog and a cat) in South Africa. These cases occurred 8 years after the last reported case of infection with this virus. Our findings emphasize the endemicity of rabies-related lyssaviruses in South Africa and the need to better understand the epidemiology of Mokola viruses.

A genotype 2 lyssavirus, Lagos bat virus (LBV), was isolated from a terrestrial wildlife species (water mongoose) in August 2004 in the Durban area of the KwaZulu-Natal Province of South Africa. The virus isolate was confirmed as LBV by antigenic and genetic characterization, and the mongoose was identified as Atilax paludinosus by mitochondrial cytochrome b sequence analysis. Phylogenetic analysis demonstrated sequence homology with previous LBV isolates from South African bats. Studies performed in mice indicated that the peripheral pathogenicity of LBV had been underestimated in previous studies. Surveillance strategies for LBV in Africa must be improved to better understand the epidemiology of this virus and to make informed decisions on future vaccine strategies because evidence is insufficent that current rabies vaccines provide protection against LBV.

Three more isolates of Lagos bat virus were recently recovered from fruit bats in South Africa after an apparent absence of this virus for 13 years. The sporadic occurrence of cases is likely due to inadequate surveillance programs for lyssavirus infections among bat populations in Africa.