Multiplex PCR method for MinION sequencing of Bagaza virus isolated from wild caught mosquitoes in South Africa.

Bagaza virus (BAGV) is a mosquito-borne orthoflavivirus known to occur in regions of southern Europe, Africa, India and the Middle East. The virus has been associated with neurological disease and fatalities in various wild bird species. Association with human disease is not confirmed although limited serological evidence has suggested human infection. Surveillance programs for screening mosquitoes for evidence of arbovirus infection play an important role in providing information regarding the circulation and spread of viruses in specific regions. BAGV was detected in a mosquito pool during surveillance of mosquitoes collected in central South Africa between November 2019 and March 2023. Homogenized mosquito pools were screened for flaviviral RNA using conventional RT-PCR and virus isolation was attempted on positive samples. BAGV was detected and subsequently isolated using cell culture. A multiplex tiling PCR method for targeted enrichment using a PCR based or amplicon sequencing approach of the complete genome of BAGV was developed and optimized. Primers were designed using alignment of complete genome sequence data retrieved from GenBank to identify suitable primer sites that would generate overlapping fragments spanning the complete genome. Six forward primers and eight reverse primers were identified that target the complete genome and amplified nine overlapping fragments, that ranged in length from 1954 to 2039 with an overlap ranging from 71 to 711 base pairs. The design strategy included multiple forward and reverse primer pairs for the 5' and 3' ends. Phylogenetic analysis with other isolates was performed and BAGV isolate VBD 74/23/3 was shown to share high similarity with previous BAGV isolates from all regions, with genetic distance ranging from 0.026 to 0.083. VBD 74/23/3 was most closely related to previous isolates from southern Africa, ZRU96/16/2 isolated from a post-mortem sample from a pheasant in 2016 and MP-314-NA-2018 isolated from mosquitoes in northwestern Namibia with genetic distance 0.0085 and 0.016 respectively. Currently there is limited complete genome sequence data available for many of the arboviruses circulating in Africa. The multiplex tiling method provided a simple and cost-effective method for obtaining complete genome sequence. This method can be readily applied to other viruses using sequence data from publicly available databases and would have important application facilitating genomic surveillance of arboviruses in low resource countries.

Determination of the complete genome and functional analysis of HPV6 isolate VBD19/10 from a patient with aggressive recurrent respiratory papillomatosis.

Human papillomavirus (HPV) types 6 and 11 are the aetiological agent of recurrent respiratory papillomatosis (RRP). The complete genome of an HPV6 isolate with a 170 base pair (bp) duplication identified within the long control region (LCR) from a patient with aggressive recurrent respiratory papillomatosis was determined. The promoter sequence from the HPV LCR including the 170 bp duplication was placed upstream of a heterologous reporter gene and the activity of the reporter gene product determined using transfected cells. In total, mutations were observed at 157 nucleotide positions of the complete genome and included nucleotide substitutions, deletions and insertions, resulting in amino acid changes at 43 residue positions. Reporter gene activity using an HPV-derived LCR region with a 170 bp duplication was significantly higher than that using an HPV-derived LCR region with no duplication within this region. The results suggest that novel HPV variants warrant further investigation for potential biomarkers of aggressive disease.

Identification of human linear B-cell epitope sites on the envelope glycoproteins of Crimean-Congo haemorrhagic fever virus.

A peptide library was used to screen for regions containing potential linear B-cell epitope sites in the glycoproteins and nucleoprotein of Crimean-Congo haemorrhagic fever virus (CCHFV) in an enzyme-linked immunosorbent assay (ELISA). The library consisted of 156 peptides, spanning the nucleoprotein and mature GN and GC proteins in a 19-mer with 9-mer overlap format. Using pooled serum samples from convalescent patients to screen the library, six peptides were identified as potential epitope sites. Further testing of these six peptides with individual patient sera identified two of these peptides as probable epitope sites, with peptide G1451-1469 reacting to 13/15 and peptide G1613-1631 to 14/15 human sera. These peptides are situated on the GC protein at amino acid positions 1451-1469 (relative to CCHFV isolate SPU103/97) (TCTGCYACSSGISCKVRIH) and 1613-1631 (FMFGWRILFCFKCCRRTRG). Identified peptides may have application in ELISA for diagnostic or serosurveillance purposes.

Next-generation sequencing of southern African Crimean-Congo haemorrhagic fever virus isolates reveals a high frequency of M segment reassortment.

Crimean Congo haemorrhagic fever virus (CCHFV) is a bunyavirus with a single-stranded RNA genome consisting of three segments (S, M, L), coding for the nucleocapsid protein, envelope glycoproteins and RNA polymerase, respectively. To date only five complete genome sequences are available from southern African isolates. Complete genome sequences were generated for 10 southern African CCHFV isolates using next-generation sequencing techniques. The maximum-likelihood method was used to generate tree topologies for 15 southern African plus 26 geographically distinct complete sequences from GenBank. M segment reassortment was identified in 10/15 southern African isolates by incongruencies in grouping compared to the S and L segments. These reassortant M segments cluster with isolates from Asia/Middle East, while the S and L segments cluster with strains from South/West Africa. The CCHFV M segment shows a high level of genetic diversity, while the S and L segments appear to co-evolve. The reason for the high frequency of M segment reassortment is not known. It has previously been suggested that M segment reassortment results in a virus with high fitness but a clear role in increased pathogenicity has yet to be shown.

Detection of IgG antibody against Crimean-Congo haemorrhagic fever virus using ELISA with recombinant nucleoprotein antigens from genetically diverse strains.

Crimean-Congo haemorrhagic fever virus (CCHFV) has the propensity to cause nosocomial infections with a high fatality rate. Handling the virus requires biosafety level-4 facilities, limiting accessibility for many laboratories. Advances in molecular techniques have allowed preparation of safe recombinant antigens that have application in diagnosis and serosurveillance of CCHFV. The aim of this study was to determine genetic diversity in CCHFV based on all available complete sequence data for the S gene encoding CCHFV nucleoprotein (NP) and antibody cross-reactivity between the NP of a South African isolate and the NP of a Greek isolate (AP92), the most genetically diverse CCHFV strain. The nucleotide sequence diversity and amino-acid diversity between genotypes, within genotypes and the pairwise distances were calculated for a dataset of 45 CCHFV isolates retrieved from GenBank. The most diverse virus, AP92, isolated from a tick in Greece, displayed the highest amino-acid difference (8·7%) with SPU415/85, isolated from a human infection in South Africa. Recombinant NP encoded for by codon-optimized S genes of SPU415/85 and AP92 were expressed in a bacterial host system and used to develop an in-house ELISA to detect IgG antibody against CCHFV in South African patients who survived infection. A total of 14/14 sera reacted with the South African recombinant NP and 13/14 reacted with the Greek recombinant NP. The serological cross-reactivity of the two NP antigens suggests that recombinant antigens prepared from geographically distinct CCHFV will have diagnostic and epidemiological applications worldwide.

Human defined antigenic region on the nucleoprotein of Crimean-Congo hemorrhagic fever virus identified using truncated proteins and a bioinformatics approach.

Crimean-Congo hemorrhagic fever virus (CCHFV) is a tick-borne viral zoonosis widely distributed in Africa, Asia and eastern Europe. In this study, amino acid sequence data for the CCHFV nucleoprotein (NP) was used to identify potential linear epitopic regions which were subsequently included in the design of large and small truncated recombinant NP antigens and peptide libraries. Two truncated recombinant CCHFV NP antigens were prepared based on results of prediction studies to include epitopic regions and exclude hydrophobic regions that could influence protein expression and solubility. Serum samples were collected from acute and convalescent patients. An IgG antibody response was detected in 16/16 samples tested using the large recombinant NP-based ELISA and in 2/16 using the small recombinant NP-based ELISA. A total of 60 peptides covering predicted epitopic regions of the NP were synthesized and peptide NRGGDENPRGPVSR at amino acid position 182-195, reacted with 13/16 human serum samples. In summary, functional assays are required to determine the biological activity of predicted epitopes for development of peptide based assays for antibody detection. Bacterially expressed complete NP antigens have previously been shown to be useful tools for antibody detection. Truncation of the antigen to remove the hydrophobic C terminus had no impact on the ability of the antigen to detect IgG antibody in human sera. The results indicate that the region from amino acids 123 to 396 includes a highly antigenic region of the NP with application in development of antibody detection assays.

Novel HPV-6 variants of human papillomavirus causing recurrent respiratory papillomatosis in southern Africa.

There is currently no information regarding the genetic diversity of HPV-6 variants circulating in South Africa. The aim of this study was to determine the HPV-6 variants affecting patients with recurrent respiratory papillomatosis, to determine whether mutations correlate with disease severity and identify molecular determinants of virulence with prognostic relevance. HPV-6 variants were identified based on genome changes within the 712-991 bp region encompassing the non-coding region (URR) of the genome, with variations in length resulting from insertions and duplications, and the 453-bp gene encoding the E6 protein. Based on manual comparison of sequence data from the URR, the isolates were identified as HPV-6a and HPV-6vc variants. Three novel HPV-6 variants were identified: one based on a mutation in the E6 region; two based on changes in the URR including a unique substitution detected in three isolates and an insertion and 170-bp duplication in the URR genome in one patient, who had clinical features of severe disease.

Encephalomyocarditis virus mortality in semi-wild bonobos (Pan panicus).

BACKGROUND: Fatal myocarditis from encephalomyocarditis virus (EMCV) infection has previously been identified in sporadic and epidemic forms in many species of captive non-human primates probably including one bonobo (Pan paniscus). METHODS: We investigated the deaths of two bonobos that were suspicious of EMCV using a combination of histopathology, immunohistochemistry and, for one of the two bonobos, reverse transcription PCR. RESULTS: Histopathological examination of heart tissue from the two bonobos showed changes characteristic of EMCV. Immunohistochemical studies confirmed the presence of EMCV antigen in heart tissue of both and in kidney and intestine of one of the bonobos. EMCV RNA was also isolated from the serum of the bonobo tested. CONCLUSION: Together, these findings confirm that EMCV was responsible for deaths of the two bonobos. Strict separation of bonobos in particular and captive primates in general from potential sources of EMCV contamination should be maintained to prevent mortality caused by EMCV.

HPV types causing juvenile recurrent laryngeal papillomatosis in South Africa.

OBJECTIVES: To identify human papillomavirus (HPV) types associated with juvenile onset recurrent laryngeal papillomatosis (RLP) in southern Africa, to determine if there is a correlation between HPV type and disease aggressiveness and to determine the diagnostic and prognostic value of rapid molecular techniques for detection and typing of HPV using laryngeal biopsies. METHODS: Laryngeal biopsies from patients undergoing surgery for RLP were screened for HPV using conventional and real-time PCR techniques. Amplicons were sequenced to determine the HPV type involved. Clinical features were correlated with HPV type. RESULTS: HPV was identified in papillomata from 18 out of 19 patients. Only HPV-6 and HPV-11 were identified, with no co-infections. There was 100% concordance between conventional and real-time PCR techniques. Patients with HPV-11 disease required more procedures and tended to have higher Derkay scores than those with HPV-6 disease. The HPV types identified in our patients were genetically similar to HPV types from geographically distinct regions. CONCLUSIONS: RLP in our patient population appears to be exclusively due to HPV-6 or HPV-11. HPV-11 disease appears to be more aggressive than HPV-6 disease. Identification of the HPV types provides motivation for inclusion of vaccines against these types in vaccination programs to protect women against infection and subsequently reduce the incidence of RLP.

An alphavirus replicon-derived candidate vaccine against Rift Valley fever virus.

Rift Valley fever virus (RVFV) is a mosquito-transmitted bunyavirus (genus Phlebovirus) associated with severe disease in livestock and fatal encephalitis or haemorrhagic fever in a proportion of infected humans. Although live attenuated and inactivated vaccines have been used in livestock, and on a limited scale in humans, there is a need for improved anti-RVFV vaccines. Towards this goal, Sindbis virus replicon vectors expressing the RVFV Gn and Gc glycoproteins, as well as the non-structural nsM protein, were constructed and evaluated for their ability to induce protective immune responses against RVFV. These replicon vectors were shown to produce the RVFV glycoproteins to high levels in vitro and to induce systemic anti-RVFV antibody responses in immunized mice, as determined by RVFV-specific ELISA, fluorescent antibody tests, and demonstration of a neutralizing antibody response. Replicon vaccination also provided 100% protection against lethal RVFV challenge by either the intraperitoneal or intranasal route. Furthermore, preliminary results indicate that the replicon vectors elicit RVFV-specific neutralizing antibody responses in vaccinated sheep. These results suggest that alphavirus-based replicon vectors can induce protective immunity against RVFV, and that this approach merits further investigation into its potential utility as a RVFV vaccine.

Genetic relationship in southern African Crimean-Congo haemorrhagic fever virus isolates: evidence for occurrence of reassortment.

Crimean-Congo haemorrhagic fever (CCHF) is a tick-borne viral zoonosis widely distributed in Africa, Asia and eastern Europe. Reassortment of CCHF genome segments has been shown to occur in nature. We therefore investigated the genetic relationship of southern African isolates using partial sequence data for each RNA segment, S, M and L, and comparing the tree topologies constructed using a neighbour joining method. A total of 21 southern African isolates were studied. The incongruencies which were identified in S, M and L sequence datasets involved group switching implying reassortment for 15 isolates. A higher fatality rate occurred in patients infected with isolates which had apparently acquired M segments from a group in which predominantly Asian strains are usually found. This suggests that reassortment may affect the pathogenicity of the virus.

Use of a molecular epidemiological database to track human rabies case histories in South Africa.

The KwaZulu Natal and Eastern Cape provinces of South Africa have experienced a serious dog rabies epidemic over the past three decades. Towards a better understanding of this epidemic, we have previously analysed nucleotide sequences of 142 rabies virus specimens that were obtained from these regions during 2003-2004 and provided a molecular description of the geographical distribution of rabies viral variants in the affected provinces. Here, as an extension, we studied five human cases that occurred during 2002-2003 and demonstrated the use of the sequence database in tracking unknown human rabies case histories. We were able to identify the geographical origin of viruses responsible for each human infection and in one case obtained evidence that suggested a non-bite transmission of rabies virus from an infected dog to a child. We argue for the value of this information in surveillance and epidemiological study and in the follow-up and management of potential exposures.

Molecular epidemiology of African and Asian Crimean-Congo haemorrhagic fever isolates.

Phylogenetic relationships were examined for 70 Crimean-Congo haemorrhagic fever (CCHF) isolates from southern, central and West Africa, the Middle East and Greece using sequence data determined for a region of the S segment of the genome. Analysis revealed up to 18% genetic differences. Tree topology supports previous evidence for the existence of three groups of genetically related isolates, A, B and C. Within group A there are two clades: an African clade and a predominantly Asian clade comprising isolates from Pakistan, China, Iran, Russia and Madagascar. Group B includes isolates from southern and West Africa and Iran, and group C includes a single isolate from Greece. Despite the potential which exists for dispersal of the virus between Africa and Eurasia, it appears that circulation of the virus is largely compartmentalized within the two land masses, and the inference is that the geographic distribution of phylogenetic groups is related to the distribution and dispersal of tick vectors of the virus.

The 2000 epidemic of Rift Valley fever in Saudi Arabia: mosquito vector studies.

In mid-September 2000, Rift Valley fever (RVF) virus was diagnosed as the cause of infection in humans and livestock in Jizan Region, Saudi Arabia. This is the first time that this arbovirus has been found outside Africa and Madagascar. Collections of mosquitoes (Diptera: Culicidae) were therefore undertaken (from 25 September to 10 October) at eight sites during the epidemic to obtain mosquitoes for attempted RVF virus isolation. Among 23 699 mosquito females tested, six isolations of RVF virus were made from 15 428 Culex (Culex) tritaeniorhynchus Giles and seven from 8091 Aedes (Aedimorphus) vexans arabiensis Patton [corrected]. Minimum mosquito infection rates per 1000 at sites with infected mosquitoes were 0.3-13.8 Cx. tritaeniorhynchus and 1.94-9.03 Ae. v. arabiensis. Viral activity moved northwards as collecting was in progress and collectors 'caught up' with the virus at the two most northerly sites on the last two trapping evenings. Other species occurred in small numbers and were identified but not tested. Both Cx. tritaeniorhynchus and Ae. v. arabiensis were susceptible to RVF virus and transmitted between hamsters, and an additional quantitative test with Cx. tritaeniorhynchus showed that 71-73% of mosquitoes became infected after ingesting 6.9-7.9 log10 FFU/mL of virus; transmission rates were 10% (post-infection day 14) and 26% (post-infection day 20). It was concluded that both species were vectors on grounds of abundance, distribution, preference for humans and sheep, the virus isolations and vector competence tests.

Clinical virology of Ebola hemorrhagic fever (EHF): virus, virus antigen, and IgG and IgM antibody findings among EHF patients in Kikwit, Democratic Republic of the Congo, 1995.

Ebola hemorrhagic fever (EHF) patients treated at Kikwit General Hospital during the 1995 outbreak were tested for viral antigen, IgG and IgM antibody, and infectious virus. Viral antigen could be detected in virtually all patients during the acute phase of illness, while antibody was not always detectable before death. Virus was also isolated from patients during the course of their febrile illness, but attempts to quantify virus in Vero E6 cells by standard plaque assay were often unsuccessful. IgG and IgM antibody appeared at approximately the same time after disease onset (8-10 days), but IgM persisted for a much shorter period among the surviving convalescent patients. IgG antibody was detectable in surviving patients through about 2 years after onset, the latest time that samples were obtained. Detection of Ebola virus antigens or virus isolation appears to be the most reliable means of diagnosis for patients with suspected acute EHF, since patients with this often-fatal disease (80% mortality) may not develop detectable antibodies before death.

Experimental infection of ostriches with Crimean-Congo haemorrhagic fever virus.

Following the occurrence of an outbreak of Crimean-Congo haemorrhagic fever (CCHF) among workers at an ostrich abattoir in South Africa in 1996, 9 susceptible young ostriches were infected subcutaneously with the virus in order to study the nature of the infection which they undergo. The ostriches developed viraemia which was demonstrable on days 1-4 following infection, with a maximum intensity of 4.0 log10 mouse intracerebral LD50/ml being recorded on day 2 in 1 of the birds. Virus was detectable in visceral organs such as spleen, liver and kidney up to day 5 post-inoculation, 1 day after it could no longer be found in blood. No infective virus was detected in samples of muscle, but viral nucleic acid was detected by reverse transcription-polymerase chain reaction in muscle from a bird sacrificed on day 3 following infection. It was concluded that the occurrence of infection in ostriches at abattoirs could be prevented by keeping the birds free of ticks for 14 days before slaughter.

The use of a reverse transcription-polymerase chain reaction for the detection of viral nucleic acid in the diagnosis of Crimean-Congo haemorrhagic fever.

A reverse transcription-polymerase chain reaction (RT-PCR) was applied retrospectively to 80 stored serum samples from 45 confirmed Crimean-Congo haemorrhagic fever (CCHF) patients in southern Africa, and it was found that viral RNA could be detected in a proportion of samples up to day 16 of illness. Early in the disease there is relatively good correlation between the results obtained by RT-PCR and virus isolation, but after the first week it appears that infective virus is progressively cleared from serum while nucleic acid remains demonstrable in a proportion of patients well into convalescence. A further 47 serum samples from 38 patients with suspected viral haemorrhagic fever, 19 of whom proved to be cases of CCHF, were tested prospectively on being received at the laboratory. The combined use of RT-PCR with ethidium bromide stained gels for the detection of viral RNA, plus indirect immunofluorescence for the detection of IgG and IgM antibodies to CCHF virus, permitted a presumptive diagnosis to be reported within 8 h of receiving the first specimen from 18/19 cases of the disease studied prospectively. The nineteenth case was confirmed within 48 h when antibody response was demonstrated in a second serum sample. Viral nucleic acid was not detected in serum samples from 19 patients in whom alternative diagnoses were established.

Immunohistochemical and in situ localization of Crimean-Congo hemorrhagic fever (CCHF) virus in human tissues and implications for CCHF pathogenesis.

BACKGROUND: Crimean-Congo hemorrhagic fever (CCHF) is a potentially fatal disease that occurs in parts of Africa, Asia, and eastern Europe, and that is caused by a recently emerged bunyavirus. Rapid laboratory diagnosis of CCHF infection is essential and is currently performed by virus isolation and serology. Histopathologic studies have been limited to a small number of cases, and little is known about the cellular tropism of CCHF virus and the pathogenesis of this disease. DESIGN: We conducted a retrospective case analysis of 12 patients with a diagnosis of CCHF infection, confirmed by virus isolation, who were evaluated at the Special Pathogens Unit, National Institute for Virology, South Africa. The clinicopathologic features of CCHF and the diagnostic role of virus isolation as compared with serology, immunohistochemistry, and in situ hybridization were evaluated. Additionally, the distribution of CCHF virus in human tissues was examined. RESULTS: The clinical and histopathologic features of CCHF resemble those of other viral hemorrhagic fevers. Of the 12 patients with virus isolation-confirmed CCHF infection, 5 were positive by serology, 10 by immunohistochemistry, and 5 by in situ hybridization. Immunohistochemistry and in situ hybridization analyses showed that the mononuclear phagocytes, endothelial cells, and hepatocytes are main targets of infection. Association of parenchymal necrosis in liver with viral infection suggests that cell damage may be mediated by a direct viral cytopathic effect. CONCLUSIONS: The diagnosis of CCHF, suspected by history and clinical features, can be supported histopathologically. However, since the pathologic features resemble those of other viral hemorrhagic fevers, an unequivocal diagnosis can be made only by laboratory tests. The utility of immunohistochemistry as a sensitive and rapid diagnostic modality was established by the high degree of concordance with virus isolation. Infection of mononuclear phagocytes, endothelial cells, and hepatocytes may play a critical role in the pathogenesis of CCHF.

Experimental inoculation of plants and animals with Ebola virus.

Thirty-three varieties of 24 species of plants and 19 species of vertebrates and invertebrates were experimentally inoculated with Ebola Zaire virus. Fruit and insectivorous bats supported replication and circulation of high titers of virus without necessarily becoming ill; deaths occurred only among bats that had not adapted to the diet fed in the laboratory.

Investigation of tick-borne viruses as pathogens of humans in South Africa and evidence of Dugbe virus infection in a patient with prolonged thrombocytopenia.

In the course of investigating suspected cases of viral haemorrhagic fever in South Africa patients were encountered who had been bitten by ticks, but who lacked evidence of infection with Crimean-Congo haemorrhagic fever (CCHF) virus or non-viral tick-borne agents. Cattle sera were tested by enzyme-linked immunoassay to determine whether tick-borne viruses other than CCHF occur in the country. The prevalence of antibody in cattle sera was 905/2116 (42.8%) for CCHF virus, 70/1358 (5.2%) for Dugbe, 21/1358 (1.5%) for louping ill, 6/450 (1.3%) for West Nile, 7/1358 (0.5%) for Nairobi sheep disease, 3/625 (0.5%) for Kadam and 2/450 (0.4%) for Chenuda. No reactions were recorded with Hazara, Bahig, Bhanja, Thogoto and Dhori viruses. The CCHF findings confirmed previous observations that the virus is widely prevalent within the distribution range of ticks of the genus Hyalomma, while antibody activity to Dugbe antigen was detected only within the distribution range of the tick Amblyomma hebraeum. Cross-reactivity for the nairoviruses, Hazara, Nairobi sheep disease and Dugbe, was detected in serum samples from 3/72 human patients with confirmed CCHF infection, and serum from 1/162 other patients reacted monospecifically with Dugbe antigen. The latter patient suffered from febrile illness with prolonged thrombocytopenia.