Research Articles (Medical Virology)

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Detection of Dengue virus 1 and mammalian orthoreovirus 3, with novel reassortments, in a South African family returning from Thailand, 2017
(MDPI, 2024-08-09) Jansen van Vuren, Petrus; Parry, Rhys H.; Paweska, Janusz Tadeusz
In July 2017, a family of three members, a 46-year-old male, a 45-year-old female and their 8-year-old daughter, returned to South Africa from Thailand. They presented symptoms consistent with mosquito-borne diseases, including fever, headache, severe body aches and nausea. Mosquito bites in all family members suggested recent exposure to arthropod-borne viruses. Dengue virus 1 (Genus Orthoflavivirus) was isolated (isolate no. SA397) from the serum of the 45-year-old female via intracerebral injection in neonatal mice and subsequent passage in VeroE6 cells. Phylogenetic analysis of this strain indicated close genetic identity with cosmopolitan genotype 1 DENV1 strains from Southeast Asia, assigned to major lineage K, minor lineage 1 (DENV1I_K.1), such as GZ8H (99.92%) collected in November 2018 from China, and DV1I-TM19-74 isolate (99.72%) identified in Bangkok, Thailand, in 2019. Serum samples from the 46-year-old male yielded a virus isolate that could not be confirmed as DENV1, prompting unbiased metagenomic sequencing for virus identification and characterization. Illumina sequencing identified multiple segments of a mammalian orthoreovirus (MRV), designated as Human/SA395/SA/2017. Genomic and phylogenetic analyses classified Human/SA395/SA/2017 as MRV-3 and assigned a tentative genotype, MRV-3d, based on the S1 segment. Genomic analyses suggested that Human/SA395/SA/2017 may have originated from reassortments of segments among swine, bat, and human MRVs. The closest identity of the viral attachment protein σ1 (S1) was related to a human isolate identified from Tahiti, French Polynesia, in 1960. This indicates ongoing circulation and co-circulation of Southeast Asian and Polynesian strains, but detailed knowledge is hampered by the limited availability of genomic surveillance. This case represents the rare concurrent detection of two distinct viruses with different transmission routes in the same family with similar clinical presentations. It highlights the complexity of diagnosing diseases with similar sequelae in travelers returning from tropical areas.
Attempted transmission of Marburg virus by bat-associated fleas Thaumapsylla breviceps breviceps (Ischnopsyllidae: Thaumapsyllinae) to the Egyptian Rousette bat (Rousettus aegyptiacus)
(MDPI, 2024-07-25) Paweska, Janusz Tadeusz; Storm, Nadia; Jansen van Vuren, Petrus; Markotter, Wanda; Kemp, Alan; wanda.markotter@up.ac.za
Egyptian rousette bats (ERBs) are implicated as reservoir hosts for Marburg virus (MARV), but natural mechanisms involved in maintenance of MARV in ERB populations remain undefined. A number of hematophagous ectoparasites, including fleas, parasitize bats. Subcutaneous (SC) inoculation of ERBs with MARV consistently results in viremia, suggesting that infectious MARV could be ingested by blood-sucking ectoparasites during feeding. In our study, MARV RNA was detected in fleas that took a blood meal during feeding on viremic bats on days 3, 7, and 11 after SC inoculation. Virus concentration in individual ectoparasites was consistent with detectable levels of viremia in the blood of infected host bats. There was neither seroconversion nor viremia in control bats kept in close contact with MARV-infected bats infested with fleas for up to 40 days post-exposure. In fleas inoculated intracoelomically, MARV was detected up to 14 days after intracoelomic (IC) inoculation, but the virus concentration was lower than that delivered in the inoculum. All bats that had been infested with inoculated, viremic fleas remained virologically and serologically negative up to 38 days after infestation. Of 493 fleas collected from a wild ERB colony in Matlapitsi Cave, South Africa, where the enzootic transmission of MARV occurs, all tested negative for MARV RNA. While our findings seem to demonstrate that bat fleas lack vectorial capacity to transmit MARV biologically, their role in mechanical transmission should not be discounted. Regular blood-feeds, intra- and interhost mobility, direct feeding on blood vessels resulting in venous damage, and roosting behaviour of ERBs provide a potential physical bridge for MARV dissemination in densely populated cave-dwelling bats by fleas. The virus transfer might take place through inoculation of skin, mucosal membranes, and wounds when contaminated fleas are squashed during auto- and allogrooming, eating, biting, or fighting.
Mpox : a case study for a one health approach to infectious disease prevention
(Elsevier, 2025-06) Hayman, David T.S.; Koopmans, Marion P.G.; Cunningham, Andrew A.; Bukachi, Salome A.; Masirika, Leandre Murhula; Markotter, Wanda; Mettenleiter, Thomas C.; wanda.markotter@up.ac.za
Mpox has been declared a global health emergency twice by the World Health Organization due to its impacts within and beyond Africa. Enzootic in Central and West African wildlife, mpox outbreaks have resulted from zoonotic spillover, with recent events revealing increased human-to-human transmission. Factors like population growth and environmental disruption, alongside reduced smallpox immunity, increase emergence risk. In addition, the emergence in South Kivu of a distinct subclade of mpox virus points at a currently understudied aspect of mpox virus lineages and their dynamics in reservoir hosts. A One Health approach—integrating human, animal, and environmental science—is essential for reducing the risk of mpox emergence. This approach should encompass ecological studies to understand putative reservoir population dynamics and the potential for interventions, reducing activities that increase human-animal contacts, respectful community engagement to reduce spillover risk from cultural practices (such as hunting multiple species of wildlife for consumption), and socially acceptable and equitable access to medical and non-medical countermeasures to prevent or control ongoing human-to-human transmission. Politically supported collaborative efforts across disciplines with involvement of stakeholders are critical to promote and strengthen socially and environmentally sustainable practices to mitigate future outbreaks. HIGHLIGHTS • Human-human spread and zoonotic spillover of mpox outbreaks is worsened by population growth, habitat change and low immunity • A distinct mpox virus subclade in South Kivu, DRC, highlights the need for further research on virus lineages and reservoir host dynamics. • A One Health approach is key to prevention, using ecology, engagement, and equitable access to interventions.
Temporal and spatial analysis of rabies virus lineages in South Africa
(MDPI, 2025-02) Viljoen, Natalie; Sabeta, Claude Taurai; Markotter, Wanda; Weyer, Jacqueline
Rabies virus (RABV; species Lyssavirus rabies) causes rabies, a disease of the central nervous system that invariably results in the death of the host. In South Africa, studies have indicated that RABV is maintained by animal species that include four wildlife carnivore species—the black-backed jackal (Canis mesomelas), bat-eared fox (Otocyon megalotis), yellow mongoose (Cynictis penicillata), and aardwolf (Proteles cristatus)—and domestic dogs (Canis lupus familiaris). The complex natural ecology holds significant implications for the control and elimination of rabies. In this study, confirmed animal rabies case data, including geospatial features, were analyzed for 12,879 laboratory-confirmed animal cases reported on a database managed by the Department of Agriculture, Land Reform and Rural Development (DALRRD). Sequence data generated from animal rabies cases in South Africa were also analyzed, which included 1374 cytoplasmic domain of the glycoprotein and the G-L intergenic sequences using maximum likelihood (ML) and Bayesian inference. The analysis provides insights into the transmission dynamics involving several wildlife species and domestic dogs in South Africa. This information is crucial for the strategic planning for rabies control and elimination programs, and particularly in understanding the interlinked nature of some lineages and the importance of the cross-border spread of rabies. This analysis provided an improved understanding of the distribution of the RABV lineages in South Africa and identified areas that can be targeted for rabies control strategies to limit future spread of RABV, which is important due to the limited available resources that must be carefully managed to allow optimal control.
Paramyxo- and coronavirus diversity and host associations in non-volant small mammals : evidence of viral sharing
(Oxford University Press, 2025-05) Mortlock, Marinda; Geldenhuys, Marike; Keith, Mark; Rademan, Rochelle; Swanepoel, Lourens H.; Von Maltitz, Emil F.; Kearney, Teresa; Markotter, Wanda; wanda.markotter@up.ac.za
Rodents and other non-volant small mammals (like shrews) maintain major ecological and epidemiological roles as reservoirs of zoonotic pathogens. Their presence within human-modified landscapes and interfaces with people, wildlife, and livestock create frequent opportunities for viral spillover. Despite this, the pathogen diversity and true risk of viral transmission are poorly understood by these hosts in Africa. Here, we explored the diversity and host association of paramyxoviruses and coronaviruses in non-volant small mammals from South Africa through longitudinal and opportunistic sample collection and molecular detection of viral RNA and host genetic barcoding. A high diversity of viruses was identified, with prevalences of 11.9% and 1.79% for paramyxoviruses and coronaviruses, respectively. Five instances of coinfections involving multiple paramyxoviruses and a coronavirus were detected, as well as nine Bayesian-supported paramyxovirus host genus, subfamily, and family switching, signifying frequent unrestrained viral sharing. Though the zoonotic potential of these identified viruses is unknown, the frequency of host switching suggests that these viruses may be more prone to adaptation to new host species or utilize highly conserved entry mechanisms. This highlights the risks for potential cross-species transmission events to livestock, domestic animals, and people, warranting continued surveillance.
Comparison of SARS-CoV-2 molecular results from the first two COVID-19 waves in Gauteng
(AOSIS, 2024-11-24) Govender, Kreshalen; Mafuyeka, Rendani T.; Lukhwareni, Azwidowi; Meyer, Pieter Willem Adriaan; k.govender@up.ac.za
BACKGROUND : Laboratory-based molecular assays return cycle threshold (Ct) values for each gene target. There is limited hyperlocal information describing the Ct, age and sex trends during the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) waves in South Africa. OBJECTIVES : To analyse the demographic and Ct value trends of SARS-CoV-2 molecular assays from two South African hospitals. METHOD : The Seegene Allplex 2019-nCoV™ results from the first two waves (June–July 2020 and November 2020–January 2021) from two major hospitals in Gauteng, South Africa, were extracted from the laboratory information system. Demographic variables and Ct values were analysed. RESULTS : Overall, 2391 samples were analysed over two waves. In both waves, more women were tested than men; 68.4% versus 31.2% in the first wave and 59.8% versus 39.7% in the second wave. Differences in Ct values among the age groups were non-significant overall; however, most median Ct values in all age groups were < 30. Men had lower median Ct values in the first wave, but this trend reversed in the second wave (p < 0.001). The first wave had significantly lower mean and median Ct values per gene target (p < 0.001). CONCLUSION : Patients tested in the first wave had lower Ct values. All age groups in both waves demonstrated infectivity potential; the demographic analysis agreed with South Africa’s coronavirus disease 2019 (COVID-19) epidemiological trends in both waves. CONTRIBUTION : Granular insight into the basic demographic variables and Ct trends of SARS-CoV-2 real-time polymerase chain reaction (RT-PCR) results within and between SARS-CoV-2 waves in South Africa.
High prevalence and non-suppression of HIV/AIDS in the East and Central African region heightens risk of severe outcomes for Clade I monkeypox virus infection, and may be a driver for subsequent adaptation
(Elsevier, 2025-03) Bosa, Henry Kyobe; Muttamba, Winters; Bakamutumaho, Barnabas; Rwagasore, Edson; Runumu, John; Bbuye, Mudarshiru; Sabiiti, Wilber; Nyanzi, Abdul; Weyer, Jacqueline; Francis, Joel; Kapologwe, Ntuli A.; Katoto, Patrick; Kirenga, Bruce; Wayengera, Misaki
In September 2023, a re-emergence of mpox was noted in the province of South Kivu, in DR Congo. So far, active transmission has been reported in 23 of the 26 provinces. Despite localisation within DRC, there are emerging concerns about possibility of cross-border transmission. In this perspective, we highlight the threat posed to HIV positive patients, particularly those with unsuppressed viral loads. We make several prepositions as part of the preparedness and response plans in the countries in the East and Central Africa region. The six prepositions include: 1) operationalize the Joint Africa Task Force for mpox consistent with Kinshasa declaration on mpox, 2) increased surveillance, 3) deployment of point of care diagnostics, 4) targeted reactive vaccination and enhanced antiretroviral therapy of HIV positive patients in areas of active transmission, 5) community engagement, 6) foster capacity building of national rapid response teams in East and Central Africa in mpox care and management through collaboration with DRC counterparts. HIGHLIGHTS • The ongoing mpox outbreak in regions with a high HIV prevalence is a concern. • In the region, only 90 % of the people with HIV have viral suppression. • Commercial sexual activity is one of the biggest drivers of HIV in this region. • In DRC, up to 29 % of the mpox cases are female sex workers. • There is an imminent danger of double-edged health challenges of mpox and HIV.
Gastrointestinal shedding of rubulaviruses from Egyptian rousette bats : temporal dynamics and spillover implications
(MDPI, 2024-12-04) Muvengi, Tauya Stansilous; Mortlock, Marinda; Kain, Morgan P.; Markotter, Wanda; marinda.mortlock@up.ac.za
Bats are recognized as reservoirs for diverse paramyxoviruses, some of which are closely related to known human pathogens or directly implicated in zoonotic transmission. The emergence of the zoonotic Sosuga virus (SOSV) from Egyptian rousette bats (ERBs), which caused an acute febrile illness in a reported human case in Africa, has increased the focus on the zoonotic potential of the Rubulavirinae subfamily. Previous studies identified human parainfluenza virus 2 (HPIV2)- and mumps (MuV)-related viruses in ERBs from South Africa, with HPIV2-related viruses restricted to gastrointestinal samples, an underexplored target for rubulavirus biosurveillance, suggesting that sample-type bias may have led to their oversight. To address this, we performed a longitudinal analysis of population-level fecal samples from an ERB maternity roost for rubulavirus RNA, employing a broadly reactive hemi-nested RT-PCR assay targeting the polymerase gene. We detected HPIV2- and MuV-related viruses in addition to numerous pararubulaviruses, highlighting significant viral diversity. Temporal analysis of three major clades revealed peaks in rubulavirus shedding that correlated with seasonal environmental changes and host reproductive cycles, although shedding patterns varied between clades. These findings identify specific periods of increased risk for the spillover of bat-associated rubulaviruses to humans, providing critical information for developing targeted mitigation strategies to minimize zoonotic transmission risk within the local community.
Severe mpox in an immunocompromised patient, South Africa 2024
(South African Medical Association, 2024-10) Vardas, E.; Naidoo, M.; Chopdat, N.A.I.; Weyer, Jacqueline; Ranchod, A.I.; Moosa, L.; Glass, A.J.; Blumberg, L.H.; Elsie, J.; Garyson, W.; Pitjadi, T.M.; Kalla, Z.; Ranchod, A.
A previously healthy 35-year-old male belonging to the men who have sex with men (MSM) community, practising both penetrative and receptive anal sex for the past 10 years, and with no travel history outside South Africa, presented initially with a prodrome of fever, sore throat, night sweats, myalgia and fatigue. A week after the onset of these nonspecific symptoms, the patient noted painless, non-pruritic skin lesions measuring 2 - 15 mm in diameter on the dorsum of his hands. Three days later he developed rigors, watery diarrhoea and similar lesions on his genital and perianal areas. A week later, the patient presented to the emergency department with extensive lesions encompassing almost his entire body. He was admitted with suspected mpox infection. Imaging showed extensive lymphadenopathy, and the diagnosis was confirmed by mpox polymerase chain reaction testing. During the admission, he was also newly diagnosed with HIV infection. Treatment with tecovirimat was initiated, and the patient recovered, albeit with significant depigmentation and scarring.
Standardized phylogenetic classification of human respiratory syncytial virus below the subgroup level
(Centers for Disease Control and Prevention (CDC), 2024-08) Goya, Stephanie; Ruis, Christopher; Neher, Richard A.; Meijer, Adam; Aziz, Ammar; Hinrichs, Angie S.; von Gottberg, Anne; Roemer, Cornelius; Amoako, Daniel G.; Acuna, Dolores; McBroome, Jakob; Otieno, James R.; Bhiman, Jinal N.; Everatt, Josie; Munoz-Escalante, Juan C.; Ramaekers, Kaat; Duggan, Kate; Presser, Lance D.; Urbanska, Laura; Venter, Marietjie; Wolter, Nicole; Peret, Teresa C.T.; Potdar, Varsha; Borges, Vitor; Viegas, Mariana
A globally implemented unified phylogenetic classification for human respiratory syncytial virus (HRSV) below the subgroup level remains elusive. We formulated global consensus of HRSV classification on the basis of the challenges and limitations of our previous proposals and the future of genomic surveillance. From a high-quality curated dataset of 1,480 HRSV-A and 1,385 HRSV-B genomes submitted to GenBank and GISAID (https://www.gisaid.org) public sequence databases through March 2023, we categorized HRSV-A/B sequences into lineages based on phylogenetic clades and amino acid markers. We defined 24 lineages within HRSV-A and 16 within HRSV-B and provided guidelines for defining prospective lineages. Our classification demonstrated robustness in its applicability to both complete and partial genomes. We envision that this unified HRSV classification proposal will strengthen HRSV molecular epidemiology on a global scale.
Emergence of novel norovirus GII.4 variant
(Centers for Disease Control and Prevention, 2024-01) Chhabra, Preeti; Tully, Damien C.; Mans, Janet; Niendorf, Sandra; Barclay, Leslie; Cannon, Jennifer L.; Montmayeur, Anna M.; Pan, Chao-Yang; Page, Nicola Anne; Williams, Rachel; Tutill, Helena; Roy, Sunando; Celma, Cristina; Beard, Stuart; Mallory, Michael L.; Manouana, Gedeon Prince; Velavan, Thirumalaisamy P.; Adegnika, Ayola Akim; Kremsner, Peter G.; Lindesmith, Lisa C.; Hue, Stephane; Baric, Ralph S.; Breuer, Judith; Vinje, Jan
We detected a novel GII.4 variant with an amino acid insertion at the start of epitope A in viral protein 1 of noroviruses from the United States, Gabon, South Africa, and the United Kingdom collected during 2017–2022. Early identification of GII.4 variants is crucial for assessing pandemic potential and informing vaccine development.
Review and meta-analysis of correlates of home range size in bats
(Oxford University Press, 2024-10) Wood, Matthew Roger; De Vries, J. Low; Monadjem, Ara; Markotter, Wanda; wanda.markotter@up.ac.za
Home range is an ecological concept that affects many aspects of the life of vertebrates and hence understanding how it varies between species is crucial. Mammalian home range size has been linked to body size and diet, but these studies were based predominantly on terrestrial species and most specifically excluded bats. As the only group of flying mammals, bats experience distinctly different constraints on movement, and hence home range. However, despite their diversity, relatively little is known about the home ranges of bats, and this is the first global review assessing correlates of their home range size. Our hypothesis is that home range will be impacted by different ecological conditions experienced by the bats and by the biological traits of the bats themselves. We performed a meta-analysis based on published data for 81 bat species to identify variables that contribute most to home range size. Sex, wing loading, functional group, colony size, dietary class, distance from the equator (latitudinal region), habitat type, and the interaction between habitat type and latitudinal region were all important explanatory variables. Wing loading was positively correlated with home range size—while females, open-air foragers, large colony sizes, and bats in temperate regions consistently had large home ranges. Understanding the correlates of home range has important implications, for example, for bat conservation and for assessing the risk of spillover of zoonotic pathogens from bats to humans and livestock.
Genome sequencing of historical encephalomyocarditis viruses from South Africa links the historical 1993/4 savanna elephant (Loxodonta africana) outbreak to cryptic mastomys rodents
(MDPI, 2024-03) Van Meer, Vanessa; Paweska, Janusz Tadeusz; Swanepoel, Robert; Grobbelaar, Antoinette; Bastos, Armanda D.S.; armanda.bastos@up.ac.za
From 1993 to 1994, 64 free-ranging elephants (Loxodonta africana) succumbed to encephalomyocarditis in the Kruger National Park, South Africa, of which 83% were adult bulls. Mastomys rodents were implicated as the reservoir host of the Encephalomyocarditis virus (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. In this study, we generate the first reference genome sequences for three historical EMCVs isolated from two Mastomys rodents and one Mastomys-associated mite, Laelaps muricola, in Gauteng Province, South Africa, in 1961. In addition, near-complete genome sequences were generated for two elephant outbreak virus strains, for which data were previously limited to the P1 and 3D genome regions. The consensus sequence of each virus was determined using a PCRSanger sequencing approach. Phylogenetic analysis confirmed the three near-identical (99.95–99.97%) Mastomys-associated viruses to be sister to the two near-identical (99.85%) elephant outbreak strains, differing from each other at 6.4% of sites across the ~7400-nucleotide region characterised. This study demonstrates a link between Mastomys-associated viruses and the historical elephant outbreak strains and implicates Mastomys as reservoirs of EMCV in South Africa.
An integrated inventory of One Health tools : mapping and analysis of globally available tools to advance One Health
(CAB International, 2024-06-22) Behravesh, Casey Barton; Charron, Dominique F.; Liew, Amanda; Becerra, Natalia Cediel; Machalaba, Catherine; Hayman, David T.S.; Zanella, Janice R. Ciacci; Farag, Elmoubasher; Chaudhary, Abhishek; Belles, Hayley; Adisasmito, Wiku B.; Almuhairi, Salama; Bilivogui, Pepe; Bukachi, Salome A.; Casas, Natalia; Cunningham, Andrew A.; Debnath, Nitish; Dar, Osman; Dungu, Baptiste; Gao, George F.; Khaitsa, Margaret; Koopmans, Marion P.G.; Mackenzie, John S.; Morand, Serge; Smolenskiy, Vyacheslav; Zhou, Lei; Markotter, Wanda; Mettenleiter, Thomas C.
The global demand from multi-sectoral partners for operational tools for One Health implementation and capacity building is increasing, yet a validated global inventory of One Health tools did not exist. Here, we map and analyze available One Health tools and assess their suitability to support One Health implementation, including the One Health Joint Plan of Action 2022–2026 (OH JPA). Our objectives were to identify (i) publicly available One Health tools to support capacity building and OH JPA implementation; (ii) optimal outcomes for countries/regions using available One Health tools; (iii) linkages to OH JPA Action Tracks and pathways in the One Health Theory of Change (TOC); and (iv) gaps and priorities for the development of additional One Health tools. One Health High Level Expert Panel (OHHLEP) members compiled information on One Health tools that were publicly available and released up to June 30, 2023, via online sources and partner networks including the Quadripartite organizations. Inclusion criteria addressed One Health relevance, use at the national, subnational, or regional level in ≥5 locations, and publicly available information. Tools were assessed for applicability by OH JPA action track, TOC pathway, scope, and intended outcomes, as well as the extent to which tools addressed gender equality, social inclusion, and environmental dimensions of One Health. Of 132 candidate tools, 50 (38%) met the inclusion criteria. These tools addressed all six OH JPA Action Tracks, but relatively fewer tools addressed Action Tracks 4 (Food Safety), 5 (Antimicrobial Resistance), and 6 (Environmental Integration). Tools were available to support all three TOC outcome pathways, and many addressed more than one Action Track and TOC outcome pathway. Most available One Health tools addressed assessment and to a lesser extent implementation, with fewer tools available for action planning, prioritization, and monitoring. Gaps and opportunities for improving One Health tools were identified, including the integration of the environment dimension, gender equality, and social inclusion. Ultimately, our findings will contribute to further the advancement of One Health globally, including via OH JPA implementation, while spurring adjustments to existing One Health tools and the development of new ones to address key gaps. OONE HEALTH IMPACT STATEMENT The One Health approach is gaining momentum globally, and this study represents the first integrated mapping and analysis of globally available One Health tools. Our findings aim to improve the quality, applicability, and availability of tools to support One Health implementation at the subnational, national, regional, and global levels, including through the Quadripartite’s One Health Joint Plan of Action. By using the OHHLEP definition of One Health to assess available One Health tools and map them onto the One Health Joint Plan of Action, we identify the need for a systematic approach and enhanced integration across dimensions of One Health to lead to sustainable One Health systems.
Performance of an in-house multiplex PCR assay for HIV-1 drug resistance testing – a cheaper alternative
(Elsevier, 2024-12) Fortuin, Tumelo L.; Nkone, Paballo; Glass, Allison J.; Viana, Raquel; Moeng, Keitumetse; Loubser, Shayne; Tiemessen, Caroline T.; Mayaphi, Simnikiwe Horatious; sim.mayaphi@up.ac.za
BACKGROUND : Currently, most HIV drug resistance PCR assays amplify the protease-reverse transcriptase (PR-RT) fragment separately from the integrase (IN) fragment. The aim of this study was to develop a multiplex PCR assay that simultaneously amplifies PR-RT and IN fragments for HIV-1 drug-resistance testing. METHODS : The in-house multiplex PCR assay was evaluated on extracted total nucleic acids obtained from the National Health Laboratory Service (NHLS) and Lancet laboratories. Sanger sequencing was performed on amplicons, and HIV-1 drug-resistance mutations (DRMs) were assessed using HIV Stanford drug resistance database. RESULTS : This study tested 59 patient samples with known HIV-1 viral load and DRM results; 41 from Lancet and 18 from NHLS. In-house multiplex PCR assay detected one or both fragments in most samples but had higher sensitivity for detection of IN fragment (93.2 %) compared to PR-RT fragment (83.1 %). There was 100 % concordance between Lancet assay versus in-house assay sequence data for IN DRMs, but lower concordance with PR-RT (87.0 %). The in-house multiplex PCR assay’s precision and reproducibility analysis showed ≥99.9 % sequence similarity and yielded similar DRM results for both PR-RT and IN fragments. CONCLUSIONS : The in-house multiplex PCR assay demonstrated satisfactory performance and higher sensitivity for IN fragment amplification. This could be a cost-effective method for HIV-1 drug resistance testing as both PR-RT and IN fragments are successfully amplified in one reaction in most samples.
Quantification and potential viability of human noroviruses in final effluent from wastewater treatment works in Pretoria, South Africa
(Springer, 2024-06) Mabasa, V.V.; Van Zyl, Walda B.; Taylor, Maureen B.; Mans, Janet; janet.mans@up.ac.za
Growing global concerns over water scarcity, worsened by climate change, drive wastewater reclamation efforts. Inadequately treated wastewater presents significant public health risks. Previous studies in South Africa (SA) have reported high norovirus levels in final effluent and sewage-polluted surface water, indicating pathogen removal inefficiency. However, the viability of these virions was not explored. This study assessed human norovirus viability in final effluent from wastewater treatment works (WWTWs) in Pretoria, SA. Between June 2018 and August 2020, 200 samples were collected from two WWTWs, including raw sewage and final effluent. Norovirus concentrations were determined using in-house RNA standards. Viability of noroviruses in final effluent was assessed using viability RT-qPCR (vPCR) with PMAxx™-Triton X-100. There was no significant difference in GI concentrations between raw sewage (p=0.5663) and final effluent (p=0.4035) samples at WWTW1 and WWTW2. WWTW1 had significantly higher GII concentrations in raw sewage (p<0.001) compared to WWTW2. No clear seasonal pattern was observed in norovirus concentrations. At WWTW1, 50% (7/14) of GI- and 64.9% (24/37) of GII-positive final effluent samples had no quantifiable RNA after vPCR. At WWTW2, the majority (92.6%, 25/27) of GII-positive final effluent samples showed a 100% RNA reduction post vPCR. PMAxx™-Triton X-100 vPCR provides a more accurate refection of discharge of potentially viable noroviruses in the environment than standard RT-qPCR. Despite significant reductions in potentially viable noroviruses after wastewater treatment, the levels of potentially viable viruses in final effluent are still of concern due to the high initial load and low infectious dose of noroviruses.
Water-based epidemiological investigation of hepatitis E Virus in South Africa
(Springer, 2024-09) Salemane, Karabo; Coetzee, Leanne Z.; Pocock, Gina; Genthe, Bettina; Taylor, Maureen B.; Mans, Janet; janet.mans@up.ac.za
Hepatitis E virus (HEV) is an emerging zoonotic pathogen that exhibits great host diversity. The primary means of transmission of the virus in low- and middle-income countries is contaminated water, often due to a lack of access to proper sanitation, which leads to faecal contamination of water sources. Environmental surveillance is an important tool that can be used to monitor virus circulation and as an early warning system for outbreaks. This study was conducted to determine the prevalence and genetic diversity of HEV in wastewater, surface water (rivers and standpipe/ablution water), and effluent from a piggery in South Africa. A total of 536 water samples were screened for HEV using real-time reverse transcription polymerase chain reaction. Overall, 21.8% (117/536) of the wastewater, river, and ablution water samples tested positive for HEV, whereas 74.4% (29/39) of the samples from the piggery tested positive. Genotyping revealed sequences belonging to HEV genotypes 3 (98%, 53/54) and 4 (2%, 1/54), with subtypes 3c, 3f, and 4b being identified.
Bat handlers, bat bites, and rabies : vaccination and serological testing of humans at risk
(Canadian Science Publishing, 2024-11) Fenton, M. Brock; Faure, Paul A.; Bernard, Enrico; Becker, Daniel J.; Jackson, Alan C.; Kingston, Tigga; Lina, Peter H.C.; Markotter, Wanda; Moore, Susan M.; Mubareka, Samira; Racey, Paul A.; Rupprecht, Charles Edward; Worledge, Lisa
Globally, bats provide critical ecosystem services. Rabies, caused by rabies virus and related lyssaviruses, is one of the most significant zoonoses associated with bats. Bat biologists study bats in the laboratory and the field. To minimize the risk of disease, all bat handlers should be vaccinated against rabies and undergo routine serological testing to measure their rabies virus neutralizing antibody levels. They should use best practices to avoid exposures, such as personal protective equipment, especially gloves appropriate to the size of the bat(s) being handled. Attention to such details will prevent unnecessary exposures and avoid some of the accompanying negative perceptions that endanger bats on a global level. The small body sizes of many bats (<50 g, many <20 g) and small teeth makes their defensive bites easy to overlook. Breaks in the skin, however small, may result in exposure to lyssaviruses in the animals’ saliva. Exposure to blood-feeding bats is less common because these species are geographically restricted to the Neotropics and are the only species whose natural feeding behavior could involve transmission of rabies virus. Understanding viral transmission, preventing exposures, and responding appropriately to bites will minimize the consequences of this deadly zoonosis.
The panzootic spread of highly pathogenic avian influenza H5N1 sublineage 2.3.4.4b : a critical appraisal of One Health preparedness and prevention
(Elsevier, 2024-12) Koopmans, Marion P.G.; Barton Behravesh, Casey; Cunningham, Andrew A.; Adisasmito, Wiku B.; Almuhairi, Salama; Bilivogui, Pépé; Bukachi, Salome A.; Casas, Natalia; Cediel Becerra, Natalia; Charron, Dominique F.; Chaudhary, Abhishek; Ciacci Zanella, Janice R.; Dar, Osman; Debnath, Nitish; Dungu, Baptiste; Farag, Elmoubasher; Gao, George F.; Khaitsa, Margaret; Machalaba, Catherine; Mackenzie, John S.; Markotter, Wanda; Mettenleiter, Thomas C.; Morand, Serge; Smolenskiy, Vyacheslav; Zhou, Lei; Hayman, David T.S.; wanda.markotter@up.ac.za
Changes in the epidemiology and ecology of H5N1 highly pathogenic avian influenza are devastating wild bird and poultry populations, farms and communities, and wild mammals worldwide. Having originated in farmed poultry, H5N1 viruses are now spread globally by wild birds, with transmission to many mammal and avian species, resulting in 2024 in transmission among dairy cattle with associated human cases. These ecological changes pose challenges to mitigating the impacts of H5N1 highly pathogenic avian influenza on wildlife, ecosystems, domestic animals, food security, and humans. H5N1 highly pathogenic avian influenza highlights the need for One Health approaches to pandemic prevention and preparedness, emphasising multisectoral collaborations among animal, environmental, and public health sectors. Action is needed to reduce future pandemic risks by preventing transmission of highly pathogenic avian influenza among domestic and wild animals and people, focusing on upstream drivers of outbreaks, and ensuring rapid responses and risk assessments for zoonotic outbreaks. Political commitment and sustainable funding are crucial to implementing and maintaining prevention programmes, surveillance, and outbreak responses.
Characterization of a novel orbivirus from cattle reveals active circulation of a previously unknown and pathogenic orbivirus in ruminants in Kenya
(American Society for Microbiology, 2023-03-16) Omoga, Dorcus C.A.; Tchouassi, David P.; Venter, Marietjie; Ogola, Edwin; Langat, Solomon; Getugi, Caroline; Eibner, Georg; Kopp, Anne; Slothouwer, Inga; Torto, Baldwyn; Junglen, Sandra; Sang, Rosemary
Arboviruses are among emerging pathogens of public and veterinary health significance. However, in most of sub-Saharan Africa, their role in the aetiologies of diseases in farm animals is poorly described due to paucity of active surveillance and appropriate diagnosis. Here, we report the discovery of a previously unknown orbivirus in cattle collected in the Kenyan Rift Valley in 2020 and 2021. We isolated the virus in cell culture from the serum of a clinically sick cow aged 2 to 3 years, presenting signs of lethargy. High-throughput sequencing revealed an orbivirus genome architecture with 10 double-stranded RNA segments and a total size of 18,731 bp. The VP1 (Pol) and VP3 (T2) nucleotide sequences of the detected virus, tentatively named Kaptombes virus (KPTV), shared maximum similarities of 77.5% and 80.7% to the mosquito-borne Sathuvachari virus (SVIV) found in some Asian countries, respectively. Screening of 2,039 sera from cattle, goats, and sheep by specific RT-PCR identified KPTV in three additional samples originating from different herds collected in 2020 and 2021. Neutralizing antibodies against KPTV were found in 6% of sera from ruminants (12/ 200) collected in the region. In vivo experiments with new-born and adult mice induced body tremors, hind limb paralysis, weakness, lethargy, and mortality. Taken together, the data suggest the detection of a potentially disease-causing orbivirus in cattle in Kenya. Its impact on livestock, as well as its potential economic damage, needs to be addressed in future studies using targeted surveillance and diagnostics. IMPORTANCE : The genus Orbivirus contains several viruses that cause large outbreaks in wild and domestic animals. However, there is little knowledge on the contribution of orbiviruses to diseases in livestock in Africa. Here, we report the identification of a novel presumably disease-causing orbivirus in cattle, Kenya. The virus, designated Kaptombes virus (KPTV), was initially isolated from a clinically sick cow aged 2 to 3 years, presenting signs of lethargy. The virus was subsequently detected in three additional cows sampled in neighboring locations in the subsequent year. Neutralizing antibodies against KPTV were found in 10% of cattle sera. Infection of new-born and adult mice with KPTV caused severe symptoms and lead to death. Together, these findings indicate the presence of a previously unknown orbivirus in ruminants in Kenya. These data are of relevance as cattle represents an important livestock species in farming industry and often is the main source of livelihoods in rural areas of Africa.

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