Browsing by Author "Maimuna Carrim"

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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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    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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    SARS-CoV-2 incidence, transmission and reinfection in a rural and an urban setting: results of the PHIRST-C cohort study, South Africa, 2020-2021
    (2021-12-04) Cheryl Cohen; Jackie Kleynhans; Anne von Gottberg; Meredith L McMorrow; Nicole Wolter; Jinal N Bhiman; Jocelyn Moyes; Jacques du Toit; Mignon du Plessis; Francesc Xavier Gómez-Olivé; Fatimah S Dawood; Thulisa Mkhencele; Kaiyun Sun; Cécile Viboud; Maimuna Carrim; Amelia Buys; Neil A Martinson; Kathleen Kahn; Stephen Tollman; Limakatso Lebina; Floi Wafawanaka
    Background: By August 2021, South Africa experienced three SARS-CoV-2 waves; the second and third associated with emergence of Beta and Delta variants respectively. Methods: We conducted a prospective cohort study during July 2020-August 2021 in one rural and one urban community. Mid-turbinate nasal swabs were collected twice-weekly from household members irrespective of symptoms and tested for SARS-CoV-2 using real-time reverse transcription polymerase chain reaction (rRT-PCR). Serum was collected every two months and tested for anti-SARS-CoV-2 antibodies. Results: Among 115,759 nasal specimens from 1,200 members (follow-up rate 93%), 1976 (2%) were SARS-CoV-2-positive. By rRT-PCR and serology combined, 62% (749/1200) of individuals experienced ≥1 SARS-CoV-2 infection episode, and 12% (87/749) experienced reinfection. Of 662 PCR-confirmed episodes with available data, 15% (n=97) were associated with ≥1 symptom. Among 222 households, 200 (90%) had ≥1 SARS-CoV-2-positive individual. Household cumulative infection risk (HCIR) was 25% (213/856). On multivariable analysis, accounting for age and sex, index case lower cycle threshold value (OR 3.9, 95%CI 1.7-8.8), urban community (OR 2.0,95%CI 1.1-3.9), Beta (OR 4.2, 95%CI 1.7-10.1) and Delta (OR 14.6, 95%CI 5.7-37.5) variant infection were associated with increased HCIR. HCIR was similar for symptomatic (21/110, 19%) and asymptomatic (195/775, 25%) index cases (p=0.165). Attack rates were highest in individuals aged 13-18 years and individuals in this age group were more likely to experience repeat infections and to acquire SARS-CoV-2 infection. People living with HIV who were not virally supressed were more likely to develop symptomatic illness, and shed SARS-CoV-2 for longer compared to HIV-uninfected individuals. Conclusions: In this study, 85% of SARS-CoV-2 infections were asymptomatic and index case symptom status did not affect HCIR, suggesting a limited role for control measures targeting symptomatic individuals. Increased household transmission of Beta and Delta variants, likely contributed to successive waves, with >60% of individuals infected by the end of follow-up.
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    Unmasking Pneumococcal Carriage in a High Human Immunodeficiency Virus (HIV) Prevalence Population in two Community Cohorts in South Africa, 2016–2018: The PHIRST Study
    (2022-07-19) Maimuna Carrim; Stefano Tempia; Deus Thindwa; Neil A Martinson; Kathleen Kahn; Stefan Flasche; Orienka Hellferscee; Florette K Treurnicht; Meredith L McMorrow; Jocelyn Moyes; Thulisa Mkhencele; Azwifarwi Mathunjwa; Jackie Kleynhans; Limakatso Lebina; Katlego Mothlaoleng; Floidy Wafawanaka; Francesc Xavier Gómez-Olivé; Cheryl Cohen; Anne von Gottberg; Nicole Wolter
    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.