Browsing by Author "Stefano Tempia"

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    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
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    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.
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    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
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    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
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    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
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    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
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    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"
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    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.
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    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
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    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
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    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
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    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.
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    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.
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    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
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    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.
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    Rapidly shifting immunologic landscape and severity of SARS-CoV-2 in the Omicron era in South Africa
    (2022-08-19) Kaiyuan Sun; Stefano Tempia; Jackie Kleynhans; Anne von Gottberg; Meredith L McMorrow; Nicole Wolter; Jinal N. Bhiman; Jocelyn Moyes; Maimuna Carrim; Neil A Martinson; Kathleen Kahn; Limakatso Lebina; Jacques D. du Toit; Thulisa Mkhencele; Cécile Viboud; Cheryl Cohen; PHIRST group
    South Africa was among the first countries to detect the SARS-CoV-2 Omicron variant. Propelled by increased transmissibility and immune escape properties, Omicron displaced other globally circulating variants within 3 months of its emergence. Due to limited testing, Omicron’s attenuated clinical severity, and an increased risk of reinfection, the size of the Omicron BA.1 and BA.2 subvariants (BA.1/2) wave remains poorly understood in South Africa and in many other countries. Using South African data from urban and rural cohorts closely monitored since the beginning of the pandemic, we analyzed sequential serum samples collected before, during, and after the Omicron BA.1/2 wave to infer infection rates and monitor changes in the immune histories of participants over time. Omicron BA.1/2 infection attack rates reached 65% (95% CI, 60% – 69%) in the rural cohort and 58% (95% CI, 61% – 74%) in the urban cohort, with repeat infections and vaccine breakthroughs accounting for >60% of all infections at both sites. Combined with previously collected data on pre-Omicron variant infections within the same cohorts, we identified 14 distinct categories of SARS-CoV-2 antigen exposure histories in the aftermath of the Omicron BA.1/2 wave, indicating a particularly fragmented immunologic landscape. Few individuals (<6%) remained naïve to SARS-CoV-2 and no exposure history category represented over 25% of the population at either cohort site. Further, cohort participants were more than twice as likely to get infected during the Omicron BA.1/2 wave, compared to the Delta wave. Prior infection with the ancestral strain (with D614G mutation), Beta, and Delta variants provided 13% (95% CI, -21% – 37%) , 34% (95% CI, 17% – 48%), and 51% (95% CI, 39% – 60%) protection against Omicron BA.1/2 infection, respectively. Hybrid immunity (prior infection and vaccination) and repeated prior infections (without vaccination) reduced the risks of Omicron BA.1/2 infection by 60% (95% CI, 42% – 72%) and 85% (95% CI, 76% – 92%) respectively. Reinfections and vaccine breakthroughs had 41% (95% CI, 26% – 53%) lower risk of onward transmission than primary infections. Our study sheds light on a rapidly shifting landscape of population immunity, along with the changing characteristics of SARS-CoV-2, and how these factors interact to shape the success of emerging variants. Our findings are especially relevant to populations similar to South Africa with low SARS-CoV-2 vaccine coverage and a dominant contribution of immunity from prior infection. Looking forward, the study provides context for anticipating the long-term circulation of SARS-CoV-2 in populations no longer naïve to the virus.
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    Risk Factors for Severe COVID19 Among Children and Adolescents Enrolled in Acute Respiratory Infection Sentinel Surveillance in South Africa 20202022
    (WILEY-BLACKWELL) K Bishop; S Meiring; Stefano Tempia; Anne Von Gottberg; Nicole Wolter; Jacoba Kleynhans; F Moosa; M du Plessis; Gary Reubenson; Cheryl Cohen; E "et al"
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    SARS-CoV-2 Seroprevalence after Third Wave of Infections, South Africa
    (2022-05) Jackie Kleynhans; Stefano Tempia; Nicole Wolter; Anne von Gottberg; Jinal N. Bhiman; Amelia Buys; Jocelyn Moyes; Meredith L. McMorrow; Kathleen Kahn; F. Xavier Gómez-Olivé; Stephen Tollman; Neil A. Martinson; Floidy Wafawanaka; Limakatso Lebina; Jacques D. du Toit; Waasila Jassat; Mzimasi Neti; Marieke Brauer; Cheryl Cohen
    By November 2021, after the third wave of severe acute respiratory syndrome coronavirus 2 infections in South Africa, seroprevalence was 60% in a rural community and 70% in an urban community. High seroprevalence before the Omicron variant emerged may have contributed to reduced illness severity observed in the fourth wave.
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    The attributable fraction of respiratory syncytial virus among patients of different age with influenza-like illness and severe acute respiratory illness in a high HIV prevalence setting, South Africa, 2012-2016 Running title: The attributable fraction of RSV in South Africa (all ages), South Africa 2012- 2016
    (2022-11-22) Jocelyn Moyes; Stefano Tempia; Sibongile Walaza; Meredith L. McMorrow; Adam L. Cohen; Florette Treurnicht; Orienka Hellferscee; Nicole Wolter; Anne Von Gottberg; Halima Dawood; Ebrahim Variava; Kathleen Kahn; Shabir A. Madhi; Cheryl Cohen
    Introduction The detection of respiratory syncytial virus (RSV) in upper airway samples does not necessarily infer causality of illness. Calculating the attributable fraction (AF) of RSV in clinical syndromes could refine disease burden estimates. Methods Using unconditional logistic regression models, we estimated the AF of RSV-associated influenza-like illness (ILI) and severe-acute respiratory illness (SARI) cases by comparing RSVdetection prevalence among ILI and SARI cases to those of healthy controls in South Africa, 2012-2016. The analysis, stratified by HIV serostatus, was conducted in the age categories <1, 1-4, 5-24, 25-44, 45-64, ≥65 years. Results We included 12,048 individuals: 2,687 controls, 5,449 ILI cases and 5,449 SARI cases. RSVAFs for ILI were significant in <1, 1-4, 5-24, 25-44-year age groups: 84.9%(95% confidence interval (CI) 69.3%-92.6%), 74.6%(95%CI 53.6%-86.0%), 60.8%(95%CI 21.4%-80.5%) and 64.1%(95%CI 14.9%-84.9%), respectively. Similarly, significant RSV-AFs for SARI were 95.3%(95%CI 91.1%-97.5) and 83.4%(95%CI 70.9-90.5) in the <1 and 1-4-year age groups respectively. In HIV-infected persons, RSV was significantly associated with ILI cases versus controls in individuals aged 5-44 years. Conclusion High RSV-AFs in young children confirm RSV detection is associated severe respiratory illness in South African children, specifically infants. These estimates will assist with refining burden estimates and cost effectiveness models