Research Articles (Medical Virology)

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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.
The performance of single and combination test strategies using visual inspection, cytology, high-risk HPV DNA and HPV16/18 to screen South African women with and without HIV-infection
(BMC, 2024-05) Dreyer, Greta; Visser, Cathy; Dreyer, Gerrit Jan; Botha, Matthys H.; Van der Merwe, Frederick H.; Richter, Karin Louise; Snyman, Leon Cornelius
BACKGROUND : Cervical cancer screening strategies should ideally be informed by population-specific data. Strategies recommended for secondary prevention, are often inadequately studied in populations with high cervical disease burdens. This report describes the test performance measured against CIN2 + /CIN3 + histology in HIV-positive women (HPW) and HIV-negative women (HNW) with the aim to determine the most effective strategies to identify South African women at risk. METHODS : Primary screening using visual inspection, cytology and HPV DNA (cobas®) was performed in two South African provinces on 456 HPW and 639 HNW participating in the multicentric DiaVACCS trial. Histology was obtained for 91.7% screen-positive and 42.7% screen-negative participants, and unavailable histology was determined by multiple imputation to adjust for verification bias. Cross-sectional test performance was calculated for single and combination test strategies with and without intermediate risk categories using different cut-offs. Minimum acceptability for sensitivity and specificity, treatment and follow-up numbers were considered to evaluate strategies. RESULTS : The only single test to reach acceptability in HPW was cytology (LSIL) [sensitivity 71.2%; specificity 90.5%; treatment 33.4%]; in HNW only HPV (hr) qualified [sensitivity 68.2%; specificity 85.2%; treatment 23.5%]. The universally best performing strategy which also resulted in smaller treatment numbers without intermediate risk group was primary HPV(hr), with treatment of both HPV(16/18) and cytology (ASCUS +) [HPW: sensitivity 73.6%; specificity 89.7%; treatment 34.7%. HNW: sensitivity 59.1%; specificity 93.6%; treatment 13.9%]. DNA testing for hrHPV (any) and hrHPV (16/18) was the best universally acceptable strategy with an intermediate risk category (early follow-up) in HPW [sensitivity 82.1%; specificity 96.4%; treatment 17.1%; follow-up 31.4%] and HNW [sensitivity 68.2%; specificity 96.7%; treatment 7.6%; follow-up 15.9%]. In comparison, using both HPV (16/18) and cytology (ASCUS +) as secondary tests in hrHPV positive women, decreased follow-up [HPW 13.8%, HNW 9.6%], but increased treatment [HPW 34.7%, HNW 13.9%]. CONCLUSION : Using hrHPV (any) as primary and both HPV16/18 and cytology as secondary tests, was universally acceptable without an intermediate risk group. Strategies with follow-up groups improved screening performance with smaller treatment numbers, but with effective management of the intermediate risk group as prerequisite.
WSV2023-The second meeting of the world society for virology : One health - One world - One virology
(Elsevier, 2024-06) Abdel-Moneim, Ahmed S.; Murovska, Modra; Soderlund-Venermo, Maria; Vakharia, Vikram N.; Wilson, William C.; Gladue, Douglas P.; Moore, Matthew D.; Alonso, Covadonga; Abdelwahab, Sayed F.; Venter, Marietjie; Malik, Yashpal S.; Zhengli, Shi; Saxena, Shailendra K.; Varma, Anupam; Kuhn, Richard J.; marietjie.venter@up.ac.za
The Second International Conference of the World Society for Virology (WSV), hosted by Riga Stradiņš University, was held in Riga, Latvia, on June 15–17th, 2023. It prominently highlighted the recent advancements in different disciplines of virology. The conference had fourteen keynote speakers covering diverse topics, including emerging virus pseudotypes, Zika virus vaccine development, herpesvirus capsid mobility, parvovirus invasion strategies, influenza in animals and birds, West Nile virus and Marburg virus ecology, as well as the latest update in animal vaccines. Discussions further explored SARS-CoV-2 RNA replicons as vaccine candidates, SARS-CoV-2 in humans and animals, and the significance of plant viruses in the ‘One Health' paradigm. The presence of the presidents from three virology societies, namely the American, Indian, and Korean Societies for Virology, highlighted the event's significance. Additionally, past president of the American Society for Virology (ASV), formally declared the partnership between ASV and WSV during the conference.
Results from the second WHO external quality assessment for the molecular detection of respiratory syncytial virus, 2019– 2020
(Wiley, 2023-01) Williams, Thomas; Jackson, Sandra; Barr, Ian; Bi, Shabana; Bhiman, Jinal N.; Ellis, Joanna; Von Gottberg, Anne; Lindstrom, Stephen; Peret, Teresa; Rughooputh, Sanjiv; Viegas, Mariana; Hirve, Siddhivinayak; Zambon, Maria; Zhang, Wenqing; WHO RSV Surveillance Group; MH Al-Nabet, Ajaeb Dakhilalla; Abubakar, Abdinasir; Tivane, Almiro; Barakat, Amal; Naguib, Amel; Aziz, Ammar; Vicari, Andrea; Moen, Ann; Govindakarnavar, Arunkumar; Hall, Aron; Darmaa, Badarch; Bastien, Nathalie; Herring, Belinda; Caetano, Braulia C.; Whittaker, Brett; Baumeister, Elsa; Nakoune, Emmanuel; Guthrie, Erica; Inbanathan, Francis; Nair, Harish; Campbell, Harry; Kadjo, Herve A.; Oumzil, Hicham; Heraud, Jean-Michel; Mott, Joshua A.; Namulondo, Joyce; Leite, Juliana; Nahapetyan, Karen; Al Ariqi, Lubna; Gazo, Mahmoud Hamad Ibraheem; Chadha, Mandeep; Pisareva, Maria; Venter, Marietjie; Siqueira, Marilda M.; Lumandas, Mayan; Niang, Mbayame; Albuaini, Mona; Salman, Muhammad; Dia, Ndongo; Razanazatovo, Norosoa; Oberste, Steve; Srikantiah, Padmini; Tang, Patrick; Couto, Paula; Smith, Peter; Coyle, Peter Valentine; Dussart, Philippe; Nguyen, Phuong Nam; Okada, Pilailuk Akkapaiboon; Wijesinghe, Pushpa Ranjan; Samuel, Reuben; Brown, Richard; Pebody, Richard; Fasce, Rodrigo; Jha, Runa; Lindstrom, Stephen; Gerber, Sue; Potdar, Varsha; Dong, Xiaomin; Deng, Yi Mo
BACKGROUND : External quality assessments (EQAs) for the molecular detection of human respiratory syncytial virus (RSV) are necessary to ensure the standardisation of reliable results. The Phase II, 2019–2020 World Health Organization (WHO) RSV EQA included 28 laboratories in 26 countries. The EQA panel evaluated performance in the molecular detection and subtyping of RSV-A and RSV-B. This manuscript describes the preparation, distribution, and analysis of the 2019–2020 WHO RSV EQA. METHODS : Panel isolates underwent whole genome sequencing and in silico primer matching. The final panel included nine contemporary, one historical virus and two negative controls. The EQA panel was manufactured and distributed by the UK National External Quality Assessment Service (UK NEQAS). National laboratories used WHO reference assays developed by the United States Centers for Disease Control and Prevention, an RSV subtyping assay developed by the Victorian Infectious Diseases Reference Laboratory (Australia), or other in-house or commercial assays already in use at their laboratories. RESULTS : An in silico analysis of isolates showed a good match to assay primer/probes. The panel was distributed to 28 laboratories. Isolates were correctly identified in 98% of samples for detection and 99.6% for subtyping. CONCLUSIONS : The WHO RSV EQA 2019–2020 showed that laboratories performed at high standards. Updating the composition of RSV molecular EQAs with contemporary strains to ensure representation of circulating strains, and ensuring primer matching with EQA panel viruses, is advantageous in assessing diagnostic competencies of laboratories. Ongoing EQAs are recommended because of continued evolution of mismatches between current circulating strains and existing primer sets.
Advances in understanding bat infection dynamics across biological scales
(Royal Society Publishing, 2024-03) Sanchez, Cecilia A.; Phelps, Kendra L.; Frank, Hannah K.; Geldenhuys, Marike; Griffiths, Megan E.; Jones, Devin N.; Kettenburg, Gwenddolen; Lunn, Tamika J.; Moreno, Kelsey R.; Mortlock, Marinda; Vicente-Santos, Amanda; Viquez-R, Luis R.; Kading, Rebekah C.; Markotter, Wanda; Reeder, DeeAnn M.; Olival, Kevin J.
Over the past two decades, research on bat-associated microbes such as viruses, bacteria and fungi has dramatically increased. Here, we synthesize themes from a conference symposium focused on advances in the research of bats and their microbes, including physiological, immunological, ecological and epidemiological research that has improved our understanding of bat infection dynamics at multiple biological scales. We first present metrics for measuring individual bat responses to infection and challenges associated with using these metrics. We next discuss infection dynamics within bat populations of the same species, before introducing complexities that arise in multi-species communities of bats, humans and/or livestock. Finally, we outline critical gaps and opportunities for future interdisciplinary work on topics involving bats and their microbes.
Epidemiology and aetiology of moderate to severe diarrhoea in hospitalised patients ≥5 years old living with HIV in South Africa, 2018- 2021 : a case-control analysis
(Public Library of Science, 2023-09-08) Johnstone, Siobhan; Erasmus, Linda; Thomas, Juno; Groome, Michelle J.; Du Plessis, Nicolette Marie; Avenant, Theunis Johannes; De Villiers, Maryke; Page, N.A. (Nicola)
Diarrhoea is a recognised complication of HIV-infection, yet there are limited local aetiological data in this high-risk group. These data are important for informing public health interventions and updating diagnostic and treatment guidelines. This study aimed to determine the pathogenic causes of diarrhoeal admissions in people living with HIV (PLHIV) compared to hospital controls between July 2018 and November 2021. Admitted diarrhoeal cases (n = 243) and non-diarrhoeal hospital controls (n = 101) 5 years of age were enrolled at Kalafong, Mapulaneng and Matikwana hospitals. Stool specimens/rectal swabs were collected and pathogen screening was performed on multiple platforms. Differences in pathogen detections between cases and controls, stratified by HIV status, were investigated. The majority (n = 164, 67.5%) of enrolled diarrhoeal cases with known HIV status were HIVinfected. Pathogens could be detected in 66.3% (n = 228) of specimens, with significantly higher detection in cases compared to controls (72.8% versus 50.5%, p0.001). Amongst PLHIV, prevalence of Cystoisospora spp. was significantly higher in cases than controls (17.7% versus 0.0%, p = 0.028), while Schistosoma was detected more often in controls than cases (17.4% versus 2.4%, p = 0.009). Amongst the HIV-uninfected participants, prevalence of Shigella spp., Salmonella spp. and Helicobacter pylori was significantly higher in cases compared to controls (36.7% versus 12.0%, p = 0.002; 11.4% versus 0.0%, p = 0.012; 10.1% versus 0.0%, p = 0.023). Diarrhoeal aetiology differed by HIV status, with Shigella spp. (36.7%) and Salmonella spp. (11.4%) having the highest prevalence amongst HIV-uninfected cases and Shigella spp. (18.3%), Cystoisospora (17.7%), and Cryptosporidium spp. (15.9%) having the highest prevalence in cases amongst PLHIV. These differences should be considered for the development of diagnostic and treatment guidelines.
Identification and molecular characterization of Shamonda virus in an aborted goat fetus in South Africa
(MDPI, 2023-08) Van der Walt, Miné; Rakaki, Matshepo E.; MacIntyre, Caitlin; Mendes, Adriano; Junglen, Sandra; Theron, Cherise; Anthony, Tasneem; O’Dell, Nicolize; Venter, Marietjie; marietjie.venter@up.ac.za
Viruses in the Orthobunyavirus genus, Peribunyaviridae family, are associated with encephalitis, birth defects and fatalities in animals, and some are zoonotic. Molecular diagnostic investigations of animals with neurological signs previously identified Shuni virus (SHUV) as the most significant orthobunyavirus in South Africa (SA). To determine if other orthobunyaviruses occur in SA, we screened clinical specimens from animals with neurological signs, abortions, and acute deaths from across SA in 2021 using a small (S) segment Simbu serogroup specific TaqMan real-time reverse transcription polymerase chain reaction (RT-PCR). Positive cases were subjected to Sanger sequencing and phylogenetic analysis to identify specific viruses involved, followed by next-generation sequencing (NGS) and additional PCR assays targeting the medium (M) segment and the large (L) segment. In total, 3/172 (1.7%) animals were PCR positive for Simbu serogroup viruses, including two horses with neurological signs and one aborted goat fetus in 2021. Phylogenetic analyses confirmed that the two horses were infected with SHUV strains with nucleotide pairwise (p-) distances of 98.1% and 97.6% to previously identified strains, while the aborted goat fetus was infected with a virus closely related to Shamonda virus (SHAV) with nucleotide p-distances between 94.7% and 91.8%. Virus isolation was unsuccessful, likely due to low levels of infectious particles. However, phylogenetic analyses of a larger fragment of the S segment obtained through NGS and partial sequences of the M and L segments obtained through RT-PCR and Sanger sequencing confirmed that the virus is likely SHAV with nucleotide p-distances between 96.6% and 97.8%. This is the first detection of SHAV in an aborted animal in SA and suggests that SHAV should be considered in differential diagnosis for abortion in animals in Southern Africa.
Divergent Hantavirus in Somali shrews (Crocidura somalica) in the semi-arid North Rift, Kenya
(MDPI, 2023-05-07) Omoga, Dorcus Caroline Achieng; Tchouassi, David P.; Venter, Marietjie; Ogola, Edwin; Rotich, Gilbert; Muthoni, Joseph N.; Ondifu, Dickens O.; Torto, Baldwyn; Junglen, Sandra; Sang, Rosemary
Hantaviruses are zoonotic rodent-borne viruses that are known to infect humans and cause various symptoms of disease, including hemorrhagic fever with renal and cardiopulmonary syndromes. They have a segmented single-stranded, enveloped, negative-sense RNA genome and are widely distributed. This study aimed to investigate the circulation of rodent-borne hantaviruses in peridomestic rodents and shrews in two semi-arid ecologies within the Kenyan Rift Valley. The small mammals were trapped using baited folding Sherman traps set within and around houses, then they were sedated and euthanatized through cervical dislocation before collecting blood and tissue samples (liver, kidney, spleen, and lungs). Tissue samples were screened with pan-hantavirus PCR primers, targeting the large genome segment (L) encoding the RNA-dependent RNA polymerase (RdRp). Eleven of the small mammals captured were shrews (11/489, 2.5%) and 478 (97.5%) were rodents. A cytochrome b gene-based genetic assay for shrew identification confirmed the eleven shrews sampled to be Crocidura somalica. Hantavirus RNA was detected in three (3/11, 27%) shrews from Baringo County. The sequences showed 93–97% nucleotide and 96–99% amino acid identities among each other, as well as 74–76% nucleotide and 79–83% amino acid identities to other shrew-borne hantaviruses, such as Tanganya virus (TNGV). The detected viruses formed a monophyletic clade with shrew-borne hantaviruses from other parts of Africa. To our knowledge, this constitutes the first report published on the circulation of hantaviruses in shrews in Kenya.
Developing African arbovirus networks and capacity strengthening in arbovirus surveillance and response : findings from a virtual workshop
(BMC, 2023-04-14) Braack, Leo; Wulandhari, Shobiechah A.; Chanda, Emmanuel; Fouque, Florence; Merle, Corinne S.; Nwangwu, Udoka; Velayudhan, Raman; Venter, Marietjie; Yahouedo, A. Gildas; Lines, Jo; Aung, Poe Poe; Chan, Kallista; Abeku, Tarakegn A.; Tibenderana, James; Clarke, Sian E.
This meeting report presents the key findings and discussion points of a 3-h virtual workshop, held on 21 September 2022, and organized by the “Resilience Against Future Threats through Vector Control (RAFT)” research consortium. The workshop aimed to identify priorities for advancing arbovirus research, network and capacity strengthening in Africa. Due to increasing human population growth, urbanization and global movement (trade, tourism, travel), mosquito-borne arboviral diseases, such as dengue, Chikungunya and Zika, are increasing globally in their distribution and prevalence. This report summarizes the presentations that reviewed the current status of arboviruses in Africa, including: (i) key findings from the recent WHO/Special Programme for Research & Training in Tropical Diseases (WHO/TDR) survey in 47 African countries that revealed deep and widespread shortfalls in the capacity to cope with arbovirus outbreak preparedness, surveillance and control; (ii) the value of networking in this context, with examples of African countries regarding arbovirus surveillance; and (iii) the main priorities identified by the breakout groups on “research gaps”, “networks” and “capacity strengthening”.
Characterization of mosquito host-biting networks of potential Rift Valley fever virus vectors in north-eastern KwaZulu-Natal province, South Africa
(BMC, 2024-08) Makhanthisa, Takalani Irene; Guarido, Milehna M.; Kemp, Alan; Weyer, Jacqueline; Rostal, Melinda K.; Karesh, William B.; Thompson, P.N. (Peter N.); peter.thompson@up.ac.za
BACKGROUND : Rift Valley fever virus (RVFV) is a zoonotic mosquito-borne virus with serious implications for livestock health, human health, and the economy in Africa, and is suspected to be endemic in north-eastern KwaZulu-Natal (KZN), South Africa. The vectors of RVFV in this area are poorly known, although several species, such as Aedes (Neomelaniconion) mcintoshi, Aedes (Neomelaniconion) circumluteolus, Aedes (Aedimorphus) durbanensis, and Culex (Lasioconops) poicilipes may be involved. The aim of the study was to determine the vertebrate blood meal sources of potential RVFV mosquito vectors in north-eastern KZN and to characterize the host-biting network. METHODS : Blood-fed mosquitoes were collected monthly from November 2019 to February 2023 using a backpack aspirator, CO2-baited Centers for Disease Control and Prevention (CDC) miniature light traps and tent traps, in the vicinity of water bodies and livestock farming households. The mosquitoes were morphologically identified. DNA was extracted from individual mosquitoes and used as templates to amplify the vertebrate cytochrome c oxidase I (COI) and cytochrome b (cytb) genes using conventional polymerase chain reaction (PCR). Amplicons were sequenced and queried in GenBank and the Barcode of Life Data systems to identify the vertebrate blood meal sources and confirm mosquito identifications. All mosquitoes were screened for RVFV using real time reverse transcription (RT)-PCR. RESULTS : We identified the mammalian (88.8%) and avian (11.3%) blood meal sources from 409 blood-fed mosquitoes. Aedes circumluteolus (n = 128) made up the largest proportion of collected mosquitoes. Cattle (n = 195) and nyala (n = 61) were the most frequent domestic and wild hosts, respectively. Bipartite network analysis showed that the rural network consisted of more host-biting interactions than the reserve network. All mosquitoes tested negative for RVFV. CONCLUSIONS : Several mosquito species, including Ae. circumluteolus, and vertebrate host species, including cattle and nyala, could play a central role in RVFV transmission. Future research in this region should focus on these species to better understand RVFV amplification.
Coding-complete genome of human alphaherpesvirus 1 isolated from a case of fulminant hepatitis
(American Society for Microbiology, 2023-10) Viljoen, Natalie; Burt, Felicity; Weyer, Jacqueline
We report the coding-complete genome sequence of human alphaherpesvirus 1 (HHV1) isolated from a previously healthy 64-year-old male with fulminant hepatitis, a rare presentation of a common viral agent. The sequence is highly similar to previously described HHV1 sequences. Additional sequence data for fulminant hepatitis cases are required.
The values and risks of an intergovernmental Panel for One Health to strengthen pandemic prevention, preparedness, and response
(Elsevier, 2023-08) Hobeika, Alexandre; Stauffer, Maxime Henri Tibault; Dub, Timothee; Van Bortel, Wim; Beniston, Martin; Bukachi, Salome; Burci, Gian Luca; Crump, Lisa; Markotter, Wanda; Sepe, Ludovico Pasquale; Placella, Enrichetta; Roche, Benjamin; Thiongane, Oumy; Wang, Zhanyun; Guerin, Frederique; Van Kleef, Esther
The COVID-19 pandemic has shown the need for better global governance of pandemic prevention, preparedness, and response (PPR) and has emphasised the importance of organised knowledge production and uptake. In this Health Policy, we assess the potential values and risks of establishing an Intergovernmental Panel for One Health (IPOH). Similar to the Intergovernmental Panel on Climate Change, an IPOH would facilitate knowledge uptake in policy making via a multisectoral approach, and hence support the addressing of infectious disease emergence and re-emergence at the human–animal–environment interface. The potential benefits to pandemic PPR include a clear, unified, and authoritative voice from the scientific community, support to help donors and institutions to prioritise their investments, evidence-based policies for implementation, and guidance on defragmenting the global health system. Potential risks include a scope not encompassing all pandemic origins, unclear efficacy in fostering knowledge uptake by policy makers, potentially inadequate speed in facilitating response efforts, and coordination challenges among an already dense set of stakeholders. We recommend weighing these factors when designing institutional reforms for a more effective global health system.
Reported antibiotic use among patients in the multicenter ANDEMIA infectious diseases surveillance study in sub-Saharan Africa
(BMC, 2024-01) Wieters, Imke; Johnstone, Siobhan; Makiala-Mandanda, Sheila; Poda, Armel; Akoua-Koffi, Chantal; Abu Sin, Muna; Eckmanns, Tim; Galeone, Valentina; Kabore, Firmin; Kahwata, François; Leendertz, Fabian H.; Mputu, Benoit; Ouedraogo, Abdoul-Salam; Page, N.A.; Schink, Susanne B.; Toure, Fidele; Traoré, Adjaratou; Venter, Marietjie; Vietor, Ann Christin; Schubert, Grit; Tomczyk, Sara
BACKGROUND: Exposure to antibiotics has been shown to be one of the drivers of antimicrobial resistance (AMR) and is critical to address when planning and implementing strategies for combatting AMR. However, data on antibiotic use in sub-Saharan Africa are still limited. Using hospital-based surveillance data from the African Network for Improved Diagnostics, Epidemiology and Management of Common Infectious Agents (ANDEMIA), we assessed self-reported antibiotic use in multiple sub-Saharan African countries. METHODS: ANDEMIA included 12 urban and rural health facilities in Côte d’Ivoire, Burkina Faso, Democratic Republic of the Congo, and Republic of South Africa. Patients with acute respiratory infection (RTI), acute gastrointestinal infection (GI) and acute febrile disease of unknown cause (AFDUC) were routinely enrolled, and clinical, demographic, socio-economic and behavioral data were collected using standardized questionnaires. An analysis of ANDEMIA data from February 2018 to May 2022 was conducted. Reported antibiotic use in the ten days prior to study enrolment were described by substance and by the WHO AWaRe classification (“Access”, “Watch”, “Reserve”, and “Not recommended” antibiotics). Frequency of antibiotic use was stratified by location, disease syndrome and individual patient factors. RESULTS: Among 19,700 ANDEMIA patients, 7,258 (36.8%) reported antibiotic use. A total of 9,695 antibiotics were reported, including 54.7% (n=5,299) from the WHO Access antibiotic group and 44.7% (n=4,330) from the WHO Watch antibiotic group. The Watch antibiotic ceftriaxone was the most commonly reported antibiotic (n=3,071, 31.7%). Watch antibiotic use ranged from 17.4% (56/322) among RTI patients in Côte d’Ivoire urban facilities to 73.7% (630/855) among AFDUC patients in Burkina Faso urban facilities. Reported antibiotic use included WHO Not recommended antibiotics but no Reserve antibiotics. CONCLUSIONS: Reported antibiotic use data from this multicenter study in sub-Saharan Africa revealed a high proportion of WHO Watch antibiotics. Differences in Watch antibiotic use were found by disease syndrome, country and health facility location, which calls for a more differentiated approach to antibiotic use interventions including further evaluation of accessibility and affordability of patient treatment.

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