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Viljoen N, Burt F, Weyer J. Coding-complete genome of human alphaherpesvirus 1 isolated from a case of fulminant hepatitis. Microbiol Resour Announc 2023; 12:e0035523. [PMID: 37747240 PMCID: PMC10586135 DOI: 10.1128/mra.00355-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 08/03/2023] [Indexed: 09/26/2023] Open
Abstract
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.
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Affiliation(s)
- Natalie Viljoen
- Center for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Disease of the National Health Laboratory Service, Sandringham, South Africa
- Division of Virology, University of the Free State, Bloemfontein, South Africa
- Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
| | - Felicity Burt
- Division of Virology, University of the Free State, Bloemfontein, South Africa
- Division of Virology, National Health Laboratory Service, Universitas, Bloemfontein, South Africa
| | - Jacqueline Weyer
- Center for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Disease of the National Health Laboratory Service, Sandringham, South Africa
- Centre for Viral Zoonoses, Department of Medical Virology, University of Pretoria, Pretoria, South Africa
- Department of Microbiology and Infectious Diseases, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa
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Carrim M, Tempia S, Thindwa D, Martinson NA, Kahn K, Flasche S, Hellferscee O, Treurnicht FK, McMorrow ML, Moyes J, Mkhencele T, Mathunjwa A, Kleynhans J, Lebina L, Mothlaoleng K, Wafawanaka F, Gómez-Olivé FX, Cohen C, von Gottberg A, Wolter N. Unmasking Pneumococcal Carriage in a High Human Immunodeficiency Virus (HIV) Prevalence Population in two Community Cohorts in South Africa, 2016-2018: The PHIRST Study. Clin Infect Dis 2023; 76:e710-e717. [PMID: 35717655 PMCID: PMC10169447 DOI: 10.1093/cid/ciac499] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Revised: 06/09/2022] [Accepted: 06/14/2022] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Longitudinal pneumococcus colonization data in high human immunodeficiency virus (HIV) prevalence settings following pneumococcal conjugate vaccine introduction are limited. METHODS In 327 randomly selected households, 1684 individuals were enrolled and followed-up for 6 to 10 months during 2016 through 2018 from 2 communities. Nasopharyngeal swabs were collected twice weekly and tested for pneumococcus using quantitative lytA real-time polymerase chain reaction. A Markov model was fitted to the data to define the start and end of an episode of colonization. We assessed factors associated with colonization using logistic regression. RESULTS During the study period, 98% (1655/1684) of participants were colonized with pneumococcus at least once. Younger age (<5 years: adjusted odds ratio [aOR], 14.1; 95% confidence [CI], 1.8-111.3, and 5-24 years: aOR, 4.8, 95% CI, 1.9-11.9, compared with 25-44 years) and HIV infection (aOR, 10.1; 95% CI, 1.3-77.1) were associated with increased odds of colonization. Children aged <5 years had fewer colonization episodes (median, 9) than individuals ≥5 years (median, 18; P < .001) but had a longer episode duration (<5 years: 35.5 days; interquartile range, 17-88) vs. ≥5 years: 5.5 days (4-12). High pneumococcal loads were associated with age (<1 year: aOR 25.4; 95% CI, 7.4-87.6; 1-4 years: aOR 13.5, 95% CI 8.3-22.9; 5-14 years: aOR 3.1, 95% CI, 2.1-4.4 vs. 45-65 year old patients) and HIV infection (aOR 1.7; 95% CI 1.2-2.4). CONCLUSIONS We observed high levels of pneumococcus colonization across all age groups. Children and people with HIV were more likely to be colonized and had higher pneumococcal loads. Carriage duration decreased with age highlighting that children remain important in pneumococcal transmission.
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Affiliation(s)
- Maimuna Carrim
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Stefano Tempia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa
- MassGenics, Duluth, Georgia, USA
| | - Deus Thindwa
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
- Malawi Liverpool Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Neil A Martinson
- Perinatal HIV Research Unit, MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, University of the Witwatersrand, Johannesburg, South Africa
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, University of the Witwatersrand, Johannesburg, South Africa
- Johns Hopkins University Center for TB Research, Baltimore, Maryland, USA
| | - Kathleen Kahn
- MRC/Wits Rural Public Health and Health Transitions Research Unit (Agincourt), Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Stefan Flasche
- Centre for the Mathematical Modelling of Infectious Diseases, Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Orienka Hellferscee
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Florette K Treurnicht
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Department of Virology, National Health Laboratory Service, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
| | - Meredith L McMorrow
- Influenza Division, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Jocelyn Moyes
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Thulisa Mkhencele
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Azwifarwi Mathunjwa
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Jackie Kleynhans
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Limakatso Lebina
- Perinatal HIV Research Unit, MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, University of the Witwatersrand, Johannesburg, South Africa
- Africa Health Research Institute, KwaZulu-Natal, South Africa
| | - Katlego Mothlaoleng
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- Perinatal HIV Research Unit, MRC Soweto Matlosana Collaborating Centre for HIV/AIDS and TB, University of the Witwatersrand, Johannesburg, South Africa
| | - Floidy Wafawanaka
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, University of the Witwatersrand, Johannesburg, South Africa
| | - Francesc Xavier Gómez-Olivé
- DST/NRF Centre of Excellence for Biomedical Tuberculosis Research, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Nicole Wolter
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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Burke A, Dahan-Moss Y, Duncan F, Qwabe B, Coetzee M, Koekemoer L, Brooke B. Anopheles parensis contributes to residual malaria transmission in South Africa. Malar J 2019; 18:257. [PMID: 31358015 PMCID: PMC6664530 DOI: 10.1186/s12936-019-2889-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Accepted: 07/22/2019] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Understanding the contribution of outdoor-resting Anopheles mosquitoes to residual malaria transmission is important in terms of scaling up vector control towards malaria elimination in South Africa. The aim of this project was to assess the potential role of Anopheles parensis and other Anopheles species in residual malaria transmission, using sentinel surveillance sites in the uMkhanyakude District of northern KwaZulu-Natal Province. METHODS Monthly vector surveillance was conducted at the sentinel sites from January 2017 to May 2018. Outdoor-placed clay pot resting traps were used to collect male and female adult Anopheles mosquitoes. All Anopheles gambiae complex and Anopheles funestus group specimens collected were identified to species and all females were screened for Plasmodium falciparum circumsporozoite protein (CSP) by enzyme-linked immunosorbent assay (ELISA). Samples showing infectivity for P. falciparum were further verified by a nested PCR and subsequent DNA sequence analysis. RESULTS From a sample of 491 anophelines, Anopheles arabiensis (n = 228) and An. parensis (n = 194) were the most abundant. Other species collected included Anopheles merus (n =11), Anopheles quadriannulatus (n = 10), Anopheles leesoni (n = 29), Anopheles rivulorum (n =18), and Anopheles vaneedeni (n =1). Of the 317 female specimens screened for P. falciparum CSP, one Anopheles arabiensis and one An. parensis showed positive by ELISA and Plasmodium nested PCR. For the An. parensis specimen, confirmation of its species identity was based on sequence analysis of the ITS2 region, and the presence of P. falciparum DNA was further confirmed by sequence analysis. CONCLUSIONS Anopheles parensis is a potential vector of malaria in South Africa although its contribution to transmission is likely to be minimal at best owing to its strong zoophilic tendency. By contrast, An. arabiensis is a major vector that is primarily responsible for the bulk of residual malaria transmission in South Africa. As all recently collected sporozoite-positive Anopheles mosquitoes were found in outdoor-placed resting traps, it is necessary to introduce interventions that can be used to control outdoor-resting vector populations while maintaining the efficacy of South Africa's indoor house spraying operations.
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Affiliation(s)
- Ashley Burke
- Wits Research Institute for Malaria and Wits/MRC Collaborating Centre for Multidisciplinary Research On Malaria, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Yael Dahan-Moss
- Wits Research Institute for Malaria and Wits/MRC Collaborating Centre for Multidisciplinary Research On Malaria, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Frances Duncan
- School of Animal, Plant & Environmental Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Bheki Qwabe
- Environmental Health, Malaria and Communicable Disease Control, KwaZulu-Natal Department of Health, Jozini, South Africa
| | - Maureen Coetzee
- Wits Research Institute for Malaria and Wits/MRC Collaborating Centre for Multidisciplinary Research On Malaria, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Lizette Koekemoer
- Wits Research Institute for Malaria and Wits/MRC Collaborating Centre for Multidisciplinary Research On Malaria, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Basil Brooke
- Wits Research Institute for Malaria and Wits/MRC Collaborating Centre for Multidisciplinary Research On Malaria, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
- Centre for Emerging Zoonotic and Parasitic Diseases, National Institute for Communicable Diseases, Johannesburg, South Africa.
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von Mollendorf C, Tempia S, von Gottberg A, Meiring S, Quan V, Feldman C, Cloete J, Madhi SA, O’Brien KL, Klugman KP, Whitney CG, Cohen C. Estimated severe pneumococcal disease cases and deaths before and after pneumococcal conjugate vaccine introduction in children younger than 5 years of age in South Africa. PLoS One 2017; 12:e0179905. [PMID: 28671978 PMCID: PMC5495214 DOI: 10.1371/journal.pone.0179905] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Accepted: 06/06/2017] [Indexed: 01/15/2023] Open
Abstract
Introduction Streptococcus pneumoniae is a leading cause of severe bacterial infections globally. A full understanding of the impact of pneumococcal conjugate vaccine (PCV) on pneumococcal disease burden, following its introduction in 2009 in South Africa, can support national policy on PCV use and assist with policy decisions elsewhere. Methods We developed a model to estimate the national burden of severe pneumococcal disease, i.e. disease requiring hospitalisation, pre- (2005–2008) and post-PCV introduction (2012–2013) in children aged 0–59 months in South Africa. We estimated case numbers for invasive pneumococcal disease using data from the national laboratory-based surveillance, adjusted for specimen-taking practices. We estimated non-bacteraemic pneumococcal pneumonia case numbers using vaccine probe study data. To estimate pneumococcal deaths, we applied observed case fatality ratios to estimated case numbers. Estimates were stratified by HIV status to account for the impact of PCV and HIV-related interventions. We assessed how different assumptions affected estimates using a sensitivity analysis. Bootstrapping created confidence intervals. Results In the pre-vaccine era, a total of approximately 107,600 (95% confidence interval [CI] 83,000–140,000) cases of severe hospitalised pneumococcal disease were estimated to have occurred annually. Following PCV introduction and the improvement in HIV interventions, 41,800 (95% CI 28,000–50,000) severe pneumococcal disease cases were estimated in 2012–2013, a rate reduction of 1,277 cases per 100,000 child-years. Approximately 5000 (95% CI 3000–6000) pneumococcal-related annual deaths were estimated in the pre-vaccine period and 1,900 (95% CI 1000–2500) in 2012–2013, a mortality rate difference of 61 per 100,000 child-years. Conclusions While a large number of hospitalisations and deaths due to pneumococcal disease still occur among children 0–59 months in South Africa, we found a large reduction in this estimate that is temporally associated with PCV introduction. In HIV-infected individuals the scale-up of other interventions, such as improvements in HIV care, may have also contributed to the declines in pneumococcal burden.
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Affiliation(s)
- Claire von Mollendorf
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- * E-mail:
| | - Stefano Tempia
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
- Influenza Program, Centers for Disease Control and Prevention, Pretoria, South Africa
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Susan Meiring
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Vanessa Quan
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Charles Feldman
- Department of Internal Medicine, Charlotte Maxeke Johannesburg Academic Hospital, Johannesburg, South Africa
- Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Jeane Cloete
- Department of Paediatrics and Child Health, University of Pretoria, Steve Biko Academic Hospital, Pretoria, South Africa
| | - Shabir A. Madhi
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Katherine L. O’Brien
- Johns Hopkins Bloomberg School of Public Health, International Vaccine Access Center, Department of International Health, Baltimore, Maryland, United States of America
| | - Keith P. Klugman
- Hubert School of Public Health, Emory University, Atlanta, Georgia, United States of America
| | - Cynthia G. Whitney
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Cheryl Cohen
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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