Assessing the zoonotic potential of arboviruses of African origin

Several African arboviruses have emerged over the past decade in new regions where they caused major outbreaks in humans and/or animals including West Nile virus, Chikungunya virus and Zika virus. This raise questions regarding the importance of less known zoonotic arboviruses in local epidemics in Africa and their potential to emerge internationally. Syndromic surveillance in animals may serve as an early warning system to detect zoonotic arbovirus outbreaks. Rift Valley fever and Wesselsbronvirus are for example associated with abortion storms in livestock while West Nile-virus, Shuni virus and Middelburg virus causes neurological disease outbreaks in horses and other animals. Death in birds may signal Bagaza virus and Usutu virus outbreaks. This short review summarise data on less known arboviruses with zoonotic potential in Africa.The arbovirus surveillance and research programme was funded by several grants over the years including the Poliomyelitis Research Foundation of South Africa, the National Research Foundation, the Medical Research council and the Global Disease Detection Programme of the US-CDC (1 U19GH00057102: Investigation of vector-borne viruses as the cause of neurological disease of humans and animals.) Collaboration agreement with the National Institute for Communicable Diseases).https://www.journals.elsevier.com/current-opinion-in-virology2019-02-01hj2018Medical Virolog

West nile virus lineage 2 as a cause of zoonotic neurological disease in humans and horses in Southern Africa

West Nile virus (WNV) is widely distributed in South Africa, but since a few cases of neurological disease have been reported from this region, endemic lineage 2 strains were postulated to be of low virulence. Several cases of nonfatal encephalitis in humans as well as fatal cases in a foal, dog, and ostrich chicks have, however, been associated with lineage 2 WNV in South Africa. The pathogenesis of lineage 2 WNV strains was investigated using mouse neuroinvasive experiments, gene expression experiments, and genome sequence comparisons which indicated that lineage 2 strains that are highly pathogenic exist. To determine whether cases of WNV were being missed in South Africa, horses with fever and neurological disease were investigated. Several cases of WNV were identified, all associated with severe neurological disease, 85% of which had to be euthanized or died. All cases positive by RT-PCR were shown to belong to lineage 2 WNV by DNA sequencing and phylogenetic analysis. Two cases of occupational infection were investigated, including a case of zoonotic transmission to a veterinarian who performed an autopsy on one of the horses as well as a laboratory infection after a needle stick injury with a neuroinvasive lineage 2 strain. Both resulted in neurological disease. Cytokine expression was investigated in the second case to assess the immunopathogenesis of WNV. Collectively, these studies suggest that lineage 2 WNV may be significantly under estimated as a cause of neurological disease in South Africa.The authors thank the National Research Foundation, The Poliomyelitis Research foundation, and the National Health Laboratory Services for funding

An investigation of culicoides (Diptera: Ceratopogonidae) as potential vectors of medically and veterinary important arboviruses in South Africa

Culicoides-borne viruses such as bluetongue, African horse sickness, and Schmallenberg virus cause major economic burdens due to animal outbreaks in Africa and their emergence in Europe and Asia. However, little is known about the role of Culicoides as vectors for zoonotic arboviruses. In this study, we identify both veterinary and zoonotic arboviruses in pools of Culicoides biting midges in South Africa, during 2012–2017. Midges were collected at six surveillance sites in three provinces and screened for Alphavirs, Flavivirus, Orthobunyavirus, and Phlebovirus genera; equine encephalosis virus (EEV); and Rhaboviridae, by reverse transcription polymerase chain reaction. In total, 66/331 (minimum infection rate (MIR) = 0.4) pools tested positive for one or more arbovirus. Orthobunyaviruses, including Shuni virus (MIR = 0.1) and EEV (MIR = 0.2) were more readily detected, while only 2/66 (MIR = 0.1) Middelburg virus and 4/66 unknown Rhabdoviridae viruses (MIR = 0.0) were detected. This study suggests Culicoides as potential vectors of both veterinary and zoonotic arboviruses detected in disease outbreaks in Africa, which may contribute to the emergence of these viruses to new regionsA US CDC Global Disease Detection grant for Zoonotic arboviruses, the NRF, the Meat Industry Trust and the Poliomyelitis Research foundation.https://medicalpapers.cn1699.com/journal/viruses-baselpm2022Medical Virolog

Shuni virus in cases of neurologic disease in humans, South Africa

We describe Shuni virus (SHUV) detection in human neurologic disease cases in South Africa. SHUV RNA was identified in 5% of cerebrospinal fluid specimens collected during the arbovirus season from public sector hospitals. This finding suggests that SHUV may be a previously unrecognized cause of human neurologic infections in Africa.The National Research Foundation, Poliomyelitis Research Foundation and the German Federal Ministry of Education and Research.www.cdc.gov/eidam2022Medical Virolog

Replacement of previously circulating respiratory syncytial virus subtype B strains with the BA genotype in South Africa

Respiratory Syncytial Virus (RSV) is a major cause of bronchiolitis and pneumonia in infants, immunocompromised and the elderly in both developed and developing countries. Re-infections are common and G protein variability is one mechanism to overcome herd immunity. This is illustrated by the appearance of the BA genotype with a 60 nucleotide duplication dominating the subtype B genotypes in epidemics worldwide. To investigate the evolution of subtype B in South Africa (SA) since 2002 the genetic variability of the G protein was analyzed in all recent strains isolated over four years (2006-2009) in SA hospitals. Bayesian analysis revealed a replacement of all subtype B genotypes previously identified in SA with the BA genotype since 2006, while subtype A genotypes identified in previous years are still circulating. Compared to BA strains from other countries, the evolutionary rate of the SA BA genotype was shown to be 2.305 x 10-3 nucleotide substitutions/site/year and drift was evident. The most recent common ancestor (MRCA) of the SA BA viruses was determined to date back to 1996. All SA BA isolates clustered with the BA-IV sub genotype and the appearance of new sub-genotypes within this branch may occur if drift continues. Sequencing of the complete G protein of selected SA strains revealed an additional 6 nucleotide deletion. Acquisition of the 60 nucleotide duplication appeared to have improved the fitness of this virus and more recent subtype B strains may need to be included in experimental vaccines to evaluate their efficacy in the current setting of evolved circulating strains.Poliomyelites Research Foundationhttp://jvi.asm.or

Epidemiology of Shuni virus in horses in South Africa

The Orthobunyavirus genus, family Peribunyaviridae, contains several important emerging and re-emerging arboviruses of veterinary and medical importance. These viruses may cause mild febrile illness, to severe encephalitis, fetal deformity, abortion, hemorrhagic fever and death in humans and/or animals. Shuni virus (SHUV) is a zoonotic arbovirus thought to be transmitted by hematophagous arthropods. It was previously reported in a child in Nigeria in 1966 and horses in Southern Africa in the 1970s and again in 2009, and in humans with neurological signs in 2017. Here we investigated the epidemiology and phylogenetic relationship of SHUV strains detected in horses presenting with febrile and neurological signs in South Africa. In total, 24/1820 (1.3%) horses submitted to the zoonotic arbovirus surveillance program tested positive by real-time reverse transcription (RT-PCR) between 2009 and 2019. Cases were detected in all provinces with most occurring in Gauteng (9/24, 37.5%). Neurological signs occurred in 21/24 (87.5%) with a fatality rate of 45.8%. Partial sequencing of the nucleocapsid gene clustered the identified strains with SHUV strains previously identified in South Africa (SA). Full genome sequencing of a neurological case detected in 2016 showed 97.8% similarity to the SHUV SA strain (SAE18/09) and 97.5% with the Nigerian strain and 97.1% to the 2014 Israeli strain. Our findings suggest that SHUV is circulating annually in SA and despite it being relatively rare, it causes severe neurological disease and death in horses.The National Research Foundation, Poliomyelitis Research Foundation, the German Federal Ministry of Education and Research; the G7 Global Health program, the US-CDC Global Disease Detection grant for Zoonotic arboviruses, Non-Research CoAg with the NHLS project 23, the University of Pretoria Zoonotic Arbo- and Respiratory Virus Program development funds and the Leap Agri, LEARN EU/NRF grant.https://www.mdpi.com/journal/virusesdm2022Medical VirologyParaclinical Science

Molecular phylogeny of Duvenhage virus

The Duvenhage virus (DUVV) constitutes one of the 11 species in the Lyssavirus genus and causes fatal rabies encephalitis. The virus is associated with insectivorous bat species and three human cases have been reported, all of which were linked to contact with bats. Few of these isolates have been studied and thus little is known about the phylogeny and epidemiology of this lyssavirus. Until 2007, when an isolate was made from the East African country of Kenya, all isolations of this virus had been from southern Africa. This discovery led to many questions regarding the spread and diversity of this lyssavirus. Phylogenetic analysis indicated that the DUVV isolates constitute two different lineages, in which the southern African isolates group together to form one lineage and the more recent isolate from Kenya constitutes a new, second lineage. We found that the new isolate has a genetic variation that has not yet been seen for DUVV. Not only is our lack of knowledge regarding the geographical distribution of this uniquely African virus emphasised, but we have also demonstrated the potential diversity within this genotype.http://www.sajs.co.z

A sensitive nested real-time RT-PCR for the detection of Shuni virus

Recently Shuni virus (SHUV) has been identified in clinical cases of neurological disease in horses in South Africa. Being that it was one of the less recognized orthobunyaviruses, with limited clinical descriptions of disease dating back to the 1960s and 1970s, SHUV-specific assays were never developed. In this study, the development of a nested real-time PCR assay is described for the detection of SHUV by means of melt-curve analysis using fluorescence resonance energy transfer (FRET) probe technology. The assay was validated against previously positive clinical specimens and a dilution series of controls. This assay was applied in the screening of 386 clinical specimens of horses with neurological signs. SHUV could be amplified from cell culture, blood and tissue specimens from horses with acute disease. This is a rapid and sensitive assay that may be implemented in both diagnostic and research laboratories.National Health Laboratory Service (NHLS) pathology and the Global Disease Detection (GDD) programme of the Centres for Disease Control (CDC).http://www.elsevier.com/locate/jviromethb201

Neurological Alphavirus infections in horses and wildlife in South Africa: a survey (2019 – 2021)

https://drive.google.com/file/d/1FzYXj-Jjwd5ZQ6_RO_2DUaixvJTHZqbG/view?usp=sharinghttps://drive.google.com/drive/folders/1J6-Yn2yBdGbr1mBxNX46yC_lfTisQ4uV?usp=sharinghttps://drive.google.com/drive/folders/1KLf0cI0c1ZXicDTGy67nf03k0N0Eis55?usp=sharin

Confidence versus performance as an indicator of the presence of alternative conceptions and inadequate problem-solving skills in mechanics

This study investigated the use of performance-confidence relationships to signal the presence of alternative conceptions and inadequate problem-solving skills in mechanics. A group of 33 students entering physics at a South African university participated in the project. The test instrument consisted of 20 items derived from existing standardized tests from literature, each of which was followed by a self-reported measure of confidence of students in the correctness of their answers. Data collected for this study included students’ responses to multiple-choice questions and open-ended explanations for their chosen answers. Fixed response physics and confidence data were logarithmically transformed according to the Rasch model to linear measures of performance and confidence. The free response explanations were carefully analysed for accuracy of conceptual understanding. Comparison of these results with raw score data and transformed measures of performance and confidence allowed a re-evaluation of the model developed by Hasan, Bagayoko and Kelley in 1999 for the detection of alternative conceptions in mechanics. Application of this model to raw score data leads to inaccurate conclusions. However, application of the Hasan hypothesis to transformed measures of performance and confidence resulted in the accurate identification of items plagued by alternative conceptions. This approach also holds promise for the differentiation between over-confidence due to alternative conceptions or due to inadequate problem-solving skills. It could become a valuable tool for instructional design in mechanics