Abstract:
Viruses in the Orthobunyavirus genus, Peribunyaviridae family, are associated with encephalitis,
birth defects and fatalities in animals, and some are zoonotic. Molecular diagnostic investigations
of animals with neurological signs previously identified Shuni virus (SHUV) as the most significant
orthobunyavirus in South Africa (SA). To determine if other orthobunyaviruses occur in SA, we
screened clinical specimens from animals with neurological signs, abortions, and acute deaths from
across SA in 2021 using a small (S) segment Simbu serogroup specific TaqMan real-time reverse
transcription polymerase chain reaction (RT-PCR). Positive cases were subjected to Sanger sequencing
and phylogenetic analysis to identify specific viruses involved, followed by next-generation sequencing
(NGS) and additional PCR assays targeting the medium (M) segment and the large (L) segment.
In total, 3/172 (1.7%) animals were PCR positive for Simbu serogroup viruses, including two horses
with neurological signs and one aborted goat fetus in 2021. Phylogenetic analyses confirmed that the
two horses were infected with SHUV strains with nucleotide pairwise (p-) distances of 98.1% and
97.6% to previously identified strains, while the aborted goat fetus was infected with a virus closely
related to Shamonda virus (SHAV) with nucleotide p-distances between 94.7% and 91.8%. Virus
isolation was unsuccessful, likely due to low levels of infectious particles. However, phylogenetic
analyses of a larger fragment of the S segment obtained through NGS and partial sequences of the M
and L segments obtained through RT-PCR and Sanger sequencing confirmed that the virus is likely
SHAV with nucleotide p-distances between 96.6% and 97.8%. This is the first detection of SHAV in
an aborted animal in SA and suggests that SHAV should be considered in differential diagnosis for
abortion in animals in Southern Africa.
