Genome Sequencing of Historical Encephalomyocarditis Viruses from South Africa Links the Historical 1993/4 Savanna Elephant () Outbreak to Cryptic Rodents.

From 1993 to 1994, 64 free-ranging elephants () succumbed to encephalomyocarditis in the Kruger National Park, South Africa, of which 83% were adult bulls. rodents were implicated as the reservoir host of the (EMCV) based on serology and RT-PCR. However, in the absence of sequence-confirmation of both the virus and the rodent host, definitive links between the elephant outbreak strains and rodent reservoir could not be established.

Phylogenomic Comparison of Seven African Swine Fever Genotype II Outbreak Viruses (1998-2019) Reveals the Likely African Origin of Georgia 2007/1.

Since the initial report of African swine fever (ASF) in Kenya in 1921, the disease has predominantly been confined to Africa. However, in 2007, an ASF genotype II virus of unknown provenance was introduced to Georgia. This was followed by its rampant spread to 73 countries, and the disease is now a global threat to pig production, with limited effective treatment and vaccine options.

Epidemiology of African swine fever in Africa today: Sylvatic cycle versus socio-economic imperatives.

African swine fever (ASF) is believed to have evolved in eastern and southern Africa in a sylvatic cycle between common warthogs (Phacochoerus africanus) and argasid ticks of the Ornithodoros moubata complex that live in their burrows. The involvement of warthogs and possibly other wild suids in the maintenance of ASF virus means that the infection cannot be eradicated from Africa, but only prevented and controlled in domestic pig populations. Historically, outbreaks of ASF in domestic pigs in Africa were almost invariably linked to the presence of warthogs, but subsequent investigations of the disease in pigs revealed the presence of another cycle involving domestic pigs and ticks, with a third cycle becoming apparent when the disease expanded into West Africa where the sylvatic cycle is not present.

Molecular detection of novel Anaplasmataceae closely related to Anaplasma platys and Ehrlichia canis in the dromedary camel (Camelus dromedarius).

Serological surveys have confirmed Anaplasma marginale and Anaplasma phagocytophilum infections in dromedary camels, but molecular surveys and genetic characterisation of camel-associated Anaplasma species are lacking. In this study, we detected tick-borne Anaplasmataceae in 30 of 100 (30%) healthy dromedary camels screened using a combined 16S rRNA-groEL PCR-sequencing approach. Nucleotide sequencing confirmed Anaplasmataceae genome presence in 28 of the 33 16S rRNA PCR-positive samples, with two additional positive samples, for which 16S rRNA sequence data were ambiguous, being identified by groEL gene characterisation.

Virus genome dynamics under different propagation pressures: reconstruction of whole genome haplotypes of West Nile viruses from NGS data.

Background: Extensive focus is placed on the comparative analyses of consensus genotypes in the study of West Nile virus (WNV) emergence. Few studies account for genetic change in the underlying WNV quasispecies population variants. These variants are not discernable in the consensus genome at the time of emergence, and the maintenance of mutation-selection equilibria of population variants is greatly underestimated.

Population genetics of two key mosquito vectors of Rift Valley Fever virus reveals new insights into the changing disease outbreak patterns in Kenya.

Rift Valley fever (RVF) outbreaks in Kenya have increased in frequency and range to include northeastern Kenya where viruses are increasingly being isolated from known (Aedes mcintoshi) and newly-associated (Ae. ochraceus) vectors. The factors contributing to these changing outbreak patterns are unclear and the population genetic structure of key vectors and/or specific virus-vector associations, in particular, are under-studied.

Positive selection of deleterious alleles through interaction with a sex-ratio suppressor gene in African Buffalo: a plausible new mechanism for a high frequency anomaly.

Although generally rare, deleterious alleles can become common through genetic drift, hitchhiking or reductions in selective constraints. Here we present a possible new mechanism that explains the attainment of high frequencies of deleterious alleles in the African buffalo (Syncerus caffer) population of Kruger National Park, through positive selection of these alleles that is ultimately driven by a sex-ratio suppressor. We have previously shown that one in four Kruger buffalo has a Y-chromosome profile that, despite being associated with low body condition, appears to impart a relative reproductive advantage, and which is stably maintained through a sex-ratio suppressor.

First molecular assessment of the African swine fever virus status of Ornithodoros ticks from Swaziland.

African swine fever (ASF) is an economically significant haemorrhagic disease of domestic pigs. It is caused by the African swine fever virus (ASFV), a deoxyribonucleic acid (DNA)arbovirus. Argasid ticks of the genus Ornithodoros, which are widely distributed throughout southern Africa, play a primary role in virus maintenance and spread within the endemic sylvatic cycle.

Eastern rock sengis as reservoir hosts of Anaplasma bovis in South Africa.

Recent work has identified the presence of Anaplasma bovis, a tick-borne pathogen of cattle, in a previously undescribed species of tick collected from eastern rock sengis, Elephantulus myurus, in Limpopo Province, South Africa. These small insectivores are endemic to Africa and are important hosts of immature ticks, however, their role as reservoirs of tick-borne pathogens has not been investigated. In order to elucidate the role of sengis in the epidemiology of A.

Phytochemical analysis and in-vitro anti-African swine fever virus activity of extracts and fractions of Ancistrocladus uncinatus, Hutch and Dalziel (Ancistrocladaceae).

Background: African swine fever (ASF), a highly contagious fatal acute haemorrhagic viral disease of pigs currently has no treatment or vaccination protocol and it threatens the pig industry worldwide. Recent outbreaks were managed by farmers with ethnoveterinary preparations with various claims of effectiveness.

Results: We identified 35 compounds using GC-MS protocol and ASF virus (NIG 99) was significantly reduced by some extracts and fractions of the plant.

Common host-derived chemicals increase catches of disease-transmitting mosquitoes and can improve early warning systems for Rift Valley fever virus.

Rift Valley fever (RVF), a mosquito-borne zoonosis, is a major public health and veterinary problem in sub-Saharan Africa. Surveillance to monitor mosquito populations during the inter-epidemic period (IEP) and viral activity in these vectors is critical to informing public health decisions for early warning and control of the disease. Using a combination of field bioassays, electrophysiological and chemical analyses we demonstrated that skin-derived aldehydes (heptanal, octanal, nonanal, decanal) common to RVF virus (RVFV) hosts including sheep, cow, donkey, goat and human serve as potent attractants for RVFV mosquito vectors.

African swine fever virus eradication in Africa.

African swine fever was reported in domestic pigs in 26 African countries during the period 2009-2011. The virus exists in an ancient sylvatic cycle between warthogs (Phacochoerus africanus) and argasid ticks of the Ornithodoros moubata complex in many of the countries reporting outbreaks and in two further countries in the region. Eradication of the virus from the countries in eastern and southern Africa where the classic sylvatic cycle occurs is clearly not an option.

Sheep skin odor improves trap captures of mosquito vectors of Rift Valley fever.

In recent years, the East African region has seen an increase in arboviral diseases transmitted by blood-feeding arthropods. Effective surveillance to monitor and reduce incidence of these infections requires the use of appropriate vector sampling tools. Here, trapped skin volatiles on fur from sheep, a known preferred host of mosquito vectors of Rift Valley fever virus (RVFV), were used with a standard CDC light trap to improve catches of mosquito vectors.

Retrospective genetic characterisation of Encephalomyocarditis viruses from African elephant and swine recovers two distinct lineages in South Africa.

Encephalomyocarditis virus (EMCV) outbreaks are rare in southern Africa. Only two have been reported to date from South Africa, both coinciding with rodent irruptions. The first outbreak manifested as acute myocarditis in pigs in 1979, whilst the second, occurring from 1993 to 1994, was linked to the deaths of 64 free-ranging adult African elephants (Loxodonta africana).

Trapping of Rift Valley Fever (RVF) vectors using light emitting diode (LED) CDC traps in two arboviral disease hot spots in Kenya.

Background: Mosquitoes' response to artificial lights including color has been exploited in trap designs for improved sampling of mosquito vectors. Earlier studies suggest that mosquitoes are attracted to specific wavelengths of light and thus the need to refine techniques to increase mosquito captures following the development of super-bright light-emitting diodes (LEDs) which emit narrow wavelengths of light or very specific colors. Therefore, we investigated if LEDs can be effective substitutes for incandescent lamps used in CDC light traps for mosquito surveillance, and if so, determine the best color for attraction of important Rift Valley Fever (RFV) vectors.

Genetic monitoring detects an overlooked cryptic species and reveals the diversity and distribution of three invasive Rattus congeners in South Africa.

Background: South Africa's long and extensive trade activity has ensured ample opportunities for exotic species introduction. Whereas the rich biodiversity of endemic southern African fauna has been the focus of many studies, invasive vertebrates are generally overlooked despite potential impacts on biodiversity, health and agriculture. Genetic monitoring of commensal rodents in South Africa which uncovered the presence of Rattus tanezumi, a South-East Asian endemic not previously known to occur in Africa, provided the impetus for expanded studies on all invasive Rattus species present.

Rainfall-driven sex-ratio genes in African buffalo suggested by correlations between Y-chromosomal haplotype frequencies and foetal sex ratio.

Background: The Y-chromosomal diversity in the African buffalo (Syncerus caffer) population of Kruger National Park (KNP) is characterized by rainfall-driven haplotype frequency shifts between year cohorts. Stable Y-chromosomal polymorphism is difficult to reconcile with haplotype frequency variations without assuming frequency-dependent selection or specific interactions in the population dynamics of X- and Y-chromosomal genes, since otherwise the fittest haplotype would inevitably sweep to fixation. Stable Y-chromosomal polymorphism due one of these factors only seems possible when there are Y-chromosomal distorters of an equal sex ratio, which act by negatively affecting X-gametes, or Y-chromosomal suppressors of a female-biased sex ratio.

Molecular characterisation of African swine fever viruses from Nigeria (2003-2006) recovers multiple virus variants and reaffirms CVR epidemiological utility.

Samples collected from wild and domestic suids in Nigeria, over a 3-year period (2003-2006), were evaluated for African swine fever (ASF) virus genome presence by targeting three discrete genome regions, namely the 478-bp C-terminal p72 gene region advocated for genotype assignment, a 780-bp region spanning the 5'-ends of the pB125R and pB646L (p72) genes and the hypervariable central variable region (CVR) encoded within the 9RL ORF (pB602L). ASF virus (ASFV) presence was confirmed in 23 of the 26 wild and domestic pigs evaluated. No evidence of ASF infection was found in two warthogs from Adamawa State; however, one bushpig from Plateau State was positive.

Role of wild suids in the epidemiology of African swine fever.

There is presently no vaccine to combat African swine fever (ASF), a viral hemorrhagic fever of domestic pigs that causes up to 100% morbidity and mortality in naive, commercial pig populations. In its endemic setting, ASF virus cycles between asymptomatic warthogs and soft ticks, with persistence in exotic locations being ascribed to the almost global distribution of susceptible soft tick and suid hosts. An understanding of the role played by diverse hosts in the epidemiology of this multi-host disease is crucial for effective disease control.

Mass mortality of adult male subantarctic fur seals: are alien mice the culprits?

Background: Mass mortalities of marine mammals due to infectious agents are increasingly reported. However, in contrast to previous die-offs, which were indiscriminate with respect to sex and age, here we report a land-based mass mortality of Subantarctic fur seals with apparent exclusivity to adult males. An infectious agent with a male-predilection is the most plausible explanation for this die-off.

Intraspecific patterns of mitochondrial variation in natural population fragments of a localized desert dung beetle species, Pachysoma gariepinum (Coleoptera: Scarabaeidae).

Phylogenetic, population, and coalescent methods were used to examine the genetic structuring of Pachysoma gariepinum, a flightless dung beetle species endemic to the arid west coast of southern Africa that exhibits interrupted south to north morphological clinal variation along a distributional gradient. Mitochondrial cytochrome oxidase I sequence data of 67 individuals from 5 localities revealed the presence of 3 geographically distinct evolutionary lineages (with an overall nucleotide divergence of 5.7% and a per-locality divergence of 1.

Selection at the Y chromosome of the African buffalo driven by rainfall.

Selection coefficients at the mammalian Y chromosome typically do not deviate strongly from neutrality. Here we show that strong balancing selection, maintaining intermediate frequencies of DNA sequence variants, acts on the Y chromosome in two populations of African buffalo (Syncerus caffer). Significant correlations exist between sequence variant frequencies and annual rainfall in the years before conception, with five- to eightfold frequency changes over short time periods.

Intra-genotypic resolution of African swine fever viruses from an East African domestic pig cycle: a combined p72-CVR approach.

Two of the 22 presently recognised African swine fever (ASF) virus p72 genotypes are genetically homogeneous and are associated with domestic pig cycles. Of these, genotype VIII comprises just two p72 variants, designated 'a' and 'b' in this study, and is confined to four East African countries where it has caused numerous outbreaks between 1961 and 2001. In order to resolve relationships within this homogeneous genotype, the central variable region (CVR) of the 9RL open reading frame of 38 viruses was characterised and the resulting dataset complemented with seven published sequences.

Intra- and inter-genotypic size variation in the central variable region of the 9RL open reading frame of diverse African swine fever viruses.

African swine fever (ASF) viruses are characterised by numerous p72 genotypes, but by low levels of intra-genotypic variation, particularly in domestic pig associated genotypes. As it is precisely these viral lineages that are involved in outbreaks of the disease it is imperative that alternative, more informative gene regions be identified which are suitable for intra-genotypic resolution of relationships. To this end, the central variable region (CVR) of the 9RL open reading frame of diverse ASF viruses was amplified and product sizes scored and compared within and between genotypes.

Molecular epidemiology of SAT3-type foot-and-mouth disease.

VP1 gene nucleotide sequences of 51 SAT3-type foot-and-mouth disease (FMD) viruses from seven southern and eastern African countries were used to infer a gene phylogeny. Results obtained by phylogenetic analysis of the homologous 405 nt region corresponding to the C-terminal 128 amino acids of 1D and adjacent 7 amino acids of 2A indicate that there are six distinct virus lineages evolving independently in different geographical localities in accordance with the FMD topotype concept. Topotypes I-IV occur in southern Africa, whilst topotypes V and VI are unique to East Africa.