Browsing by Author "Stefano Tempia"

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Characteristics of infections with ancestral Beta and Delta variants of SARSCoV2 in the PHIRSTC community cohort study South Africa 20202021
(BIOMED CENTRAL LTD) Cheryl Cohen; Jacoba Kleynhans; Anne Von Gottberg; M McMorrow; Nicole Wolter; Jinal Bhiman; Jocelyn Moyes; Maimuna Carrim; A Buys; Neil Martinson; Stephen Tollman; Limakatso Lebina; Floidy Wafawanaka; Jaques Du Toit; Francesc Gomez-Olive Casas; F Dawood; T Mkhencele; Stefano Tempia
Characteristics of infections with ancestral Beta and Delta variants of SARSCoV2 in the PHIRSTC community cohort study South Africa20202021
(BIOMED CENTRAL LTD) Cheryl Cohen; Jacoba Kleynhans; Anne Von Gottberg; M McMorrow; Nicole Wolter; Jinal Bhiman; Jocelyn Moyes; Mignonette Du Plessis; Maimuna Carrim; A Buys; Neil Martinson; Kathleen Kahn; Stephen Tollman; Limakatso Lebina; Floidy Wafawanaka; F Dawood; T Mkhencele; Stefano Tempia
Comparing adults with severe SARSCoV2 or influenza infection South Africa 20162021
F Els; Jacoba Kleynhans; Nicole Wolter; Mignonette Du Plessis; Fahima Moosa; Stefano Tempia; M Makhasi; Jeremy Nel; H Dawood; S Meiring; Anne Von Gottberg; Cheryl Cohen; Sibongile Walaza
Coronavirus Host Genomics Study: South Africa (COVIGen-SA)
(2022-10-06) Andrew K. May; Heather Seymour; Harriet Etheredge; Heather Maher; Marta C. Nunes; ShabirA.Madhi; SimisoM. Sokhela; W. D. FrancoisVenter; Neil Martinson; Firdaus Nabeemeeah; Cheryl Cohen; Jocelyn Moyes; Sibongile Walaza; Stefano Tempia; Jackie Kleynhans; Anne von Gottberg; Jeremy Nel; Halima Dawood; Ebrahim Variava; Stephen Tollman; Kathleen Kahn; KobusHerbst; EmilyB.Wong; CarolineT.Tiemessen; Alex van Blydenstein; Lyle Murray; Michelle Venter; June Fabian; Miche´le Ramsay
However, continental Africans are yet to be adequately represented in such studies despite the importance of genetic factors in understanding Africa’s response to the pandemic. We describe the development of a research resource for coronavirus host genomics studies in South Africa known as COVIGen-SA—a multicollaborator strategic partnership designed to provide harmonised demographic, clinical, and genetic information specific to Black South Africans with COVID-19. Over 2,000 participants have been recruited to date. Preliminary results on 1,354 SARS-CoV-2 positive participants from four participating studies showed that 64.7% were female, 333 had severe disease, and 329 were people living with HIV. *rough this resource, we aim to provide insights into host genetic factors relevant to African-ancestry populations, using both genome-wide association testing and targeted sequencing of important genomic loci. *is project will promote and enhance partnerships, build skills, and develop resources needed to address the COVID-19 burden and associated risk factors in South African communities.
Detection of Victoria lineage influenza B viruses with K162 and N163 deletions in the hemagglutinin gene South Africa 2018
Orienka Hellferscee; Florette Treurnicht; Lucinda Gaelejwe; aLEXANDRA mOERDYK; Gary Reubenson; Meredith McMorrow; Stefano Tempia; Johanna McAnerney; Sibongile Walaza; Nicole Wolter; Anne Von Gottberg; Cheryl Cohen
Difference in mortality among individuals admitted to hospital with COVID19 during the first and second waves in South Africa a cohort study
Waasila jassat; Caroline Mudara; Lovelyn Ozougwu; Stefano Tempia; Lucille Blumberg; E et al; Anne Von Gottberg; Jinal Bhiman; Cheryl Cohen; Sibongile Walaza
Epidemiology of Pertussis in Individuals of All Ages Hospitalized With Respiratory Illness in South Africa January 2013December 2018
Nicole Wolter; Cheryl Cohen; Stefano Tempia; Sibongile Walaza; Fahima Moosa; Mignonette Du Plessis; Meredith L McMorrow; Florette Treurnicht; Orienka Hellferscee; Halima Dawood; Ebrahim Variava; Anne Von Gottberg
Estimated impact of the pneumococcal conjugate vaccine on pneumonia mortality in South Africa 1999 through 2016 An ecological modelling study
J Kleynhans; Stefano Tempia; Kayoko Shioda; Anne Von Gottberg; Daniel Weinberger; Cheryl Cohen
Estimating household contact matrices structure from easily collectable metadata
(PUBLIC LIBRARY SCIENCE) L Amico; Jacoba Kleynhans; L Gauvin; M Tizzoni; L Ozella; Nicole Wolter; Cheryl Cohen; Stefano Tempia; E "et al"
Estimating the contribution of HIV-infected adults to household pneumococcal transmission in South Africa, 2016–2018: A hidden Markov modelling study
(2021-12-23) Deus Thindwa; Nicole Wolter; Amy Pinsent; Maimuna CarrimI; John Ojal; Stefano Tempia; Jocelyn Moyes; Meredith McMorrow; Jackie Kleynhans; Anne von Gottberg; Neil French; PHIRST group; Cheryl Cohen; Stefan Flasche
Human immunodeficiency virus (HIV) infected adults are at a higher risk of pneumococcal colonisation and disease, even while receiving antiretroviral therapy (ART). To help evaluate potential indirect effects of vaccination of HIV-infected adults, we assessed whether HIV-infected adults disproportionately contribute to household transmission of pneumococci. We constructed a hidden Markov model to capture the dynamics of pneumococcal carriage acquisition and clearance observed during a longitudinal household-based nasopharyngeal swabbing study, while accounting for sample misclassifications. Households were followed-up twice weekly for approximately 10 months each year during a three-year study period for nasopharyngeal carriage detection via real-time PCR. We estimated the effect of participant’s age, HIV status, presence of a HIV-infected adult within the household and other covariates on pneumococcal acquisition and clearance probabilities. Of 1,684 individuals enrolled, 279 (16.6%) were younger children (<5 years-old) of whom 4 (1.5%) were HIV-infected and 726 (43.1%) were adults (�18 years-old) of whom 214 (30.4%) were HIV-infected, most (173, 81.2%) with high CD4+ count. The observed range of pneumococcal carriage prevalence across visits was substantially higher in younger children (56.9– 80.5%) than older children (5–17 years-old) (31.7–50.0%) or adults (11.5–23.5%). We estimate that 14.4% (95% Confidence Interval [CI]: 13.7–15.0) of pneumococcal-negative swabs were false negatives. Daily carriage acquisition probabilities among HIV-uninfected younger children were similar in households with and without HIV-infected adults (hazard ratio: 0.95, 95%CI: 0.91–1.01). Longer average carriage duration (11.4 days, 95%CI: 10.2– 12.8 vs 6.0 days, 95%CI: 5.6–6.3) and higher median carriage density (622 genome equivalents per millilitre, 95%CI: 507–714 vs 389, 95%CI: 311.1–435.5) were estimated in HIVinfected vs HIV-uninfected adults. The use of ART and antibiotics substantially reduced carriage duration in all age groups, and acquisition rates increased with household size. Although South African HIV-infected adults on ART have longer carriage duration and density than their HIV-uninfected counterparts, they show similar patterns of pneumococcal acquisition and onward transmission.
Estimating the costeffectiveness of maternal vaccination and monoclonal antibodies for respiratory syncytial virus in Kenya and South Africa
(BIOMED CENTRAL LTD) Koltai Mihaly; Jocelyn Moyes; Bryan Nyawanda; Joyce Nyiro; Patrick Munywoki; Stefano Tempia; Cheryl Cohen; E et al
Estimating the timevarying reproduction number for COVID19 in South Africa during the first four waves using multiple measures of incidence for public and private sectors across four waves
(PUBLIC LIBRARY SCIENCE) J Bingham; Stefano Tempia; Henry Moultrie; C Viboud; W Jassat; Cheryl Cohen; J Pulliam
Healthcare seeking behaviour for common infectious syndromes among people in three administrative regions of Johannesburg South Africa 2015 a crosssectional study
Relebogile Mapuroma; Cheryl Cohen; Lazarus Kuonza; Alfred Musekiwa; Stefano Tempia; Akhona Tshangela; Claire Von Mollendorf
Household Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 From Adult Index Cases With and Without Human Immunodeficiency Virus in South Africa 20202021 A CaseAscertained Prospective Observational Household Transmission Study
(OXFORD UNIV PRESS INC) Jacoba Kleynhans; Sibongile Walaza; Neil Martinson; M Neti; Anne Von Gottberg; Jinal Bhiman; D Toi; D G Amoako; A Buys; Nicole Wolter; Limakatso Lebina; Lucia Maloma; Stefano Tempia; Cheryl Cohen; E et al
Human respiratory syncytial virus diversity and epidemiology among patients hospitalized with severe respiratory illness in South Africa, 2012–2015
(2015) Ziyaad Valley-Omar; Stefano Tempia; Orienka Hellferscee; Sibongile Walaza; Ebrahim Variava6; Halima Dawood; Kathleen Kahn; Meredith McMorrow; Marthi Pretorius; Senzo Mtshali; Ernest Mamorobela; Nicole Wolter; Marietjie Venter; Anne von Gottberg; Cheryl Cohen; Florette K. Treurnicht
Background: We aimed to describe the prevalence of human respiratory syncytial virus (HRSV) and evaluate associations between HRSV subgroups and/or genotypes and epidemiologic characteristics and clinical outcomes in patients hospitalized with severe respiratory illness (SRI). Methods: Between January 2012 and December 2015, we enrolled patients of all ages admitted to two South African hospitals with SRI in prospective hospital-based syndromic surveillance. We collected respiratory specimens and clinical and epidemiological data. Unconditional random effect multivariable logistic regression was used to assess factors associated with HRSV infection. Results: HRSV was detected in 11.2% (772/6908) of enrolled patients of which 47.0% (363/772) were under the age of 6 months. There were no differences in clinical outcomes of HRSV subgroup A-infected patients compared with HRSV subgroup B-infected patients but among patients aged <5 years, children with HRSV subgroup A were more likely be coinfected with Streptococcus pneumoniae (23/208 11.0% vs. 2/90, 2.0%; adjusted odds ratio 5.7). No significant associations of HRSV A genotypes NA1 and ON1 with specific clinical outcomes were observed. Conclusions: While HRSV subgroup and genotype dominance shifted between seasons, we showed similar genotype diversity as noted worldwide. We found no association between clinical outcomes and HRSV subgroups or genotypes.
Incidence and Transmission Dynamics of Bordetella pertussis Infection in Rural and Urban Communities, South Africa, 2016-2018
(CENTERS DISEASE CONTROL) Fahima Moosa; Stefano Tempia; Jacoba Kleynhans; M McMorrow; Jocelyn Moyes; Mignonette Du Plessis; Maimuna Carrim; Florette Treurnicht; Orienka Hellferscee; T Mkhencele; A Mathunjwa; Neil Martinson; Kathleen Kahn; Limakatso Lebina; Floidy Wafawanaka; Cheryl Cohen; Anne Von Gottberg; Nicole Wolter
Incidence and Transmission Dynamics of Bordetella pertussis Infection in Rural and Urban Communities, South Africa, 2016‒2018
(2023-02-02) Fahima Moosa; Stefano Tempia; Jackie Kleynhans; Meredith McMorrow; Jocelyn Moyes; Mignon du Plessis; Maimuna Carrim; Florette K. Treurnicht; Orienka Helfersee; Thulisa Mkhencele; Azwifarwi Mathunjwa; Neil A. Martinson; Kathleen Kahn; Limakatso Lebina; Floidy Wafawanaka; Cheryl Cohen; Anne von Gottberg; Nicole Wolter
We conducted 3 prospective cohort studies (2016–2018), enrolling persons from 2 communities in South Africa. Nasopharyngeal swab specimens were collected twice a week from participants. Factors associated with Bordetella pertussis incidence, episode duration, and household transmission were determined by using Poisson regression, Weibull accelerated time-failure, and logistic regression hierarchical models, respectively. Among 1,684 participants, 118 episodes of infection were detected in 107 participants (incidence 0.21, 95% CI 0.17–0.25 infections/100 person-weeks). Children <5 years of age who had incomplete vaccination were more likely to have pertussis infection. Episode duration was longer for participants who had higher bacterial loads. Transmission was more likely to occur from male index case-patients and persons who had >7 days infection duration. In both communities, there was high incidence of B. pertussis infection and most cases were colonized.
Incidence and transmission of respiratory syncytial virus in urban and rural South Africa 20172018
(NATURE PUBLISHING GROUP) Cheryl Cohen; J Kleynhans; Jocelyn Moyes; Florette Treurnicht; Orienka Hellferscee; Nicole Wolter; Neil Martinson; Kathleen Kahn; Limakatso Lebina; K Mothlaoleng; Floidy Wafawanaka; Francesc Gomez-Olive Casas; Maimuna Carrim; Anne Von Gottberg; Stefano Tempia; M McMorrow; T Mkhencele; E et al
Mortality in children aged <5 years with severe acute respiratory illness in a high HIVprevalence urban and rural areas of South Africa, 2009–2013
(2021-08-12) Oluwatosin A Ayeni; Sibongile Walaza; Stefano Tempia; Michelle Groome; Kathleen Kahn; Shabir A Madhi; Adam L Cohen; Jocelyn Moyes; Marietjie Venter; Marthi Pretorius; Florette Treurnicht; Orienka Hellferscee; Anne von Gottberg; Nicole Wolter; Cheryl Cohen
Background: Severe acute respiratory illness (SARI) is an important cause of mortality in young children, especially in children living with HIV infection. Disparities in SARI death in children aged <5 years exist in urban and rural areas. Objective: To compare the factors associated with in-hospital death among children aged <5 years hospitalized with SARI in an urban vs. a rural setting in South Africa from 2009-2013. Methods: Data were collected from hospitalized children with SARI in one urban and two rural sentinel surveillance hospitals. Nasopharyngeal aspirates were tested for ten respiratory viruses and blood for pneumococcal DNA using polymerase chain reaction. We used multivariable logistic regression to identify patient and clinical characteristics associated with in-hospital death. Results: From 2009 through 2013, 5,297 children aged <5 years with SARI-associated hospital admission were enrolled; 3,811 (72%) in the urban and 1,486 (28%) in the rural hospitals. In-hospital case-fatality proportion (CFP) was higher in the rural hospitals (6.9%) than the urban hospital (1.3%, p<0.001), and among HIV-infected than the HIV-uninfected children (9.6% vs. 1.6%, p<0.001). In the urban hospital, HIV infection (odds ratio (OR):11.4, 95% confidence interval (CI):5.4-24.1) and presence of any other underlying illness (OR: 3.0, 95% CI: 1.0-9.2) were the only factors independently associated with death. In the rural hospitals, HIV infection (OR: 4.1, 95% CI: 2.3-7.1) and age <1 year (OR: 3.7, 95% CI: 1.9-7.2) were independently associated with death, whereas duration of hospitalization ≥5 days (OR: 0.5, 95% CI: 0.3-0.8) and any respiratory virus detection (OR: 0.4, 95% CI: 0.3-0.8) were negatively associated with death. Conclusion: We found that the case-fatality proportion was substantially higher among children admitted to rural hospitals and HIV infected children with SARI in South Africa. While efforts to prevent and treat HIV infections in children may reduce SARI deaths, further efforts to address health care inequality in rural populations are needed.
Rapid Intrahost Diversification and Evolution of SARSCoV2 in Advanced HIV Infection
(NATURE PUBLISHING GROUP) Sung Hee Ko; Pierce Radecki; Frida Belinky; Jinal Bhiman; D Amoako; Neil Martinson; Limakatso Lebina; Stefano Tempia; Nicole Wolter; Anne Von Gottberg; Cheryl Cohen; E et al