Publications by authors named "Waasila Jassat"

30 Publications

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A global systematic analysis of the occurrence, severity, and recovery pattern of long COVID in 2020 and 2021.

medRxiv 2022 May 27. Epub 2022 May 27.

Importance: While much of the attention on the COVID-19 pandemic was directed at the daily counts of cases and those with serious disease overwhelming health services, increasingly, reports have appeared of people who experience debilitating symptoms after the initial infection. This is popularly known as long COVID.

Objective: To estimate by country and territory of the number of patients affected by long COVID in 2020 and 2021, the severity of their symptoms and expected pattern of recovery.

Design: We jointly analyzed ten ongoing cohort studies in ten countries for the occurrence of three major symptom clusters of long COVID among representative COVID cases. The defining symptoms of the three clusters (fatigue, cognitive problems, and shortness of breath) are explicitly mentioned in the WHO clinical case definition. For incidence of long COVID, we adopted the minimum duration after infection of three months from the WHO case definition. We pooled data from the contributing studies, two large medical record databases in the United States, and findings from 44 published studies using a Bayesian meta-regression tool. We separately estimated occurrence and pattern of recovery in patients with milder acute infections and those hospitalized. We estimated the incidence and prevalence of long COVID globally and by country in 2020 and 2021 as well as the severity-weighted prevalence using disability weights from the Global Burden of Disease study.

Results: Analyses are based on detailed information for 1906 community infections and 10526 hospitalized patients from the ten collaborating cohorts, three of which included children. We added published data on 37262 community infections and 9540 hospitalized patients as well as ICD-coded medical record data concerning 1.3 million infections. Globally, in 2020 and 2021, 144.7 million (95% uncertainty interval [UI] 54.8-312.9) people suffered from any of the three symptom clusters of long COVID. This corresponds to 3.69% (1.38-7.96) of all infections. The fatigue, respiratory, and cognitive clusters occurred in 51.0% (16.9-92.4), 60.4% (18.9-89.1), and 35.4% (9.4-75.1) of long COVID cases, respectively. Those with milder acute COVID-19 cases had a quicker estimated recovery (median duration 3.99 months [IQR 3.84-4.20]) than those admitted for the acute infection (median duration 8.84 months [IQR 8.10-9.78]). At twelve months, 15.1% (10.3-21.1) continued to experience long COVID symptoms.

Conclusions And Relevance: The occurrence of debilitating ongoing symptoms of COVID-19 is common. Knowing how many people are affected, and for how long, is important to plan for rehabilitative services and support to return to social activities, places of learning, and the workplace when symptoms start to wane.

Key Points: What are the extent and nature of the most common long COVID symptoms by country in 2020 and 2021? Globally, 144.7 million people experienced one or more of three symptom clusters (fatigue; cognitive problems; and ongoing respiratory problems) of long COVID three months after infection, in 2020 and 2021. Most cases arose from milder infections. At 12 months after infection, 15.1% of these cases had not yet recovered. The substantial number of people with long COVID are in need of rehabilitative care and support to transition back into the workplace or education when symptoms start to wane.
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http://dx.doi.org/10.1101/2022.05.26.22275532DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9164454PMC
May 2022

SARS-CoV-2 cases reported from long-term residential facilities (care homes) in South Africa: a retrospective cohort study.

BMC Public Health 2022 May 24;22(1):1035. Epub 2022 May 24.

Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Johannesburg, South Africa.

Background: Globally, long-term care facilities (LTCFs) experienced a large burden of deaths during the COVID-19 pandemic. The study aimed to describe the temporal trends as well as the characteristics and risk factors for mortality among residents and staff who tested positive for SARS-CoV-2 in selected LTCFs across South Africa.

Method: We analysed data reported to the DATCOV sentinel surveillance system by 45 LTCFs. Outbreaks in LTCFs were defined as large if more than one-third of residents and staff had been infected or there were more than 20 epidemiologically linked cases. Multivariable logistic regression was used to assess risk factors for mortality amongst LTCF residents.

Results: A total of 2324 SARS-CoV-2 cases were reported from 5 March 2020 through 31 July 2021; 1504 (65%) were residents and 820 (35%) staff. Among LTCFs, 6 reported sporadic cases and 39 experienced outbreaks. Of those reporting outbreaks, 10 (26%) reported one and 29 (74%) reported more than one outbreak. There were 48 (66.7%) small outbreaks and 24 (33.3%) large outbreaks reported. There were 30 outbreaks reported in the first wave, 21 in the second wave and 15 in the third wave, with 6 outbreaks reporting between waves. There were 1259 cases during the first COVID-19 wave, 362 during the second wave, and 299 during the current third wave. The case fatality ratio was 9% (138/1504) among residents and 0.5% (4/820) among staff. On multivariable analysis, factors associated with SARS-CoV-2 mortality among LTCF residents were age 40-59 years, 60-79 years and ≥ 80 years compared to < 40 years and being a resident in a LTCF in Free State or Northern Cape compared to Western Cape. Compared to pre-wave 1, there was a decreased risk of mortality in wave 1, post-wave 1, wave 2, post-wave 2 and wave 3.

Conclusion: The analysis of SARS-CoV-2 cases in sentinel LTCFs in South Africa points to an encouraging trend of decreasing numbers of outbreaks, cases and risk for mortality since the first wave. LTCFs are likely to have learnt from international experience and adopted national protocols, which include improved measures to limit transmission and administer early and appropriate clinical care.
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http://dx.doi.org/10.1186/s12889-022-13403-6DOI Listing
May 2022

Clinical severity of COVID-19 in patients admitted to hospital during the omicron wave in South Africa: a retrospective observational study.

Lancet Glob Health 2022 Jul 18;10(7):e961-e969. Epub 2022 May 18.

National Institute for Communicable Diseases, National Health Laboratory Service, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa.

Background: Up to the end of January, 2022, South Africa has had four recognisable COVID-19 pandemic waves, each predominantly dominated by one variant of concern: the ancestral strain with an Asp614Gly mutation during the first wave, the beta variant (B.1.351) during the second wave, the delta variant (B.1.617.2) during the third wave, and lastly, the omicron variant (B.1.1.529) during the fourth wave. We aimed to assess the clinical disease severity of patients admitted to hospital with SARS-CoV-2 infection during the omicron wave and compare the findings with those of the preceding three pandemic waves in South Africa.

Methods: We defined the start and end of each pandemic wave as the crossing of the threshold of weekly incidence of 30 laboratory-confirmed SARS-CoV-2 cases per 100 000 population. Hospital admission data were collected through an active national COVID-19-specific surveillance programme. We compared disease severity across waves by post-imputation random effect multivariable logistic regression models. Severe disease was defined as one or more of the following: acute respiratory distress, receipt of supplemental oxygen or mechanical ventilation, admission to intensive care, or death.

Findings: We analysed 335 219 laboratory-confirmed SARS-CoV-2 hospital admissions with a known outcome, constituting 10·4% of 3 216 179 cases recorded during the four waves. During the omicron wave, 52 038 (8·3%) of 629 617 cases were admitted to hospital, compared with 71 411 (12·9%) of 553 530 in the Asp614Gly wave, 91 843 (12·6%) of 726 772 in the beta wave, and 131 083 (10·0%) of 1 306 260 in the delta wave (p<0·0001). During the omicron wave, 15 421 (33·6%) of 45 927 patients admitted to hospital had severe disease, compared with 36 837 (52·3%) of 70 424 in the Asp614Gly wave, 57 247 (63·4%) of 90 310 in the beta wave, and 81 040 (63·0%) of 128 558 in the delta wave (p<0·0001). The in-hospital case-fatality ratio during the omicron wave was 10·7%, compared with 21·5% during the Asp614Gly wave, 28·8% during the beta wave, and 26·4% during the delta wave (p<0·0001). Compared with those admitted to hospital during the omicron wave, patients admitted during the other three waves had more severe clinical presentations (adjusted odds ratio 2·07 [95% CI 2·01-2·13] in the Asp614Gly wave, 3·59 [3·49-3·70] in the beta wave, and 3·47 [3·38-3·57] in the delta wave).

Interpretation: The trend of increasing cases and admissions across South Africa's first three waves shifted in the omicron wave, with a higher and quicker peak but fewer patients admitted to hospital, less clinically severe illness, and a lower case-fatality ratio compared with the preceding three waves. Omicron marked a change in the SARS-CoV-2 epidemic curve, clinical profile, and deaths in South Africa. Extrapolations to other populations should factor in differing vaccination and previous infection levels.

Funding: National Institute for Communicable Diseases.
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http://dx.doi.org/10.1016/S2214-109X(22)00114-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9116895PMC
July 2022

Disease Severity and Comorbidities among Healthcare Worker COVID-19 Admissions in South Africa: A Retrospective Analysis.

Int J Environ Res Public Health 2022 05 2;19(9). Epub 2022 May 2.

National Health Laboratory Service, National Institute for Occupational Health, Johannesburg 2000, South Africa.

Healthcare workers (HCWs) are among the most vulnerable in regard to contracting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection. Comorbidities are reported to increase the risk for more severe COVID-19 outcomes, often requiring hospitalization. However, the evidence on disease severity and comorbidities among South African HCWs is lacking. This retrospective study analyzed the prevalence of comorbidities among HCW hospitalized with COVID-19 and its association with the severity of outcomes. Data from public and private hospitals in nine provinces of South Africa were extracted from the national hospital surveillance database for COVID-19 admissions. A total of 10,149 COVID-19 HCWs admissions were reported from 5 March 2020 to 31 December 2021. The risk of disease severity among HCWs increased with age, with those older (≥60 years) having seven times the odds of disease severity (aOR 7.0; 95% CI 4.2-11.8) compared to HCWs in the younger age (20-29 years) group. The most commonly reported comorbidity was hypertension (36.3%), followed by diabetes (23.3%) and obesity (16.7%). Hypertension (aOR 1.3; 95% CI 1.0-1.6), diabetes (aOR 1.6; 95% CI 1.3-2.0), and HIV (aOR 1.6; 95% CI 1.2-2.1) were significantly associated with disease severity. In conclusion, age, gender, and existing comorbidities were strong predictors of the prognosis of severe COVID-19 among HCWs in South Africa. The information is important in the development of occupational health policies and vulnerability risk assessments for HCWs in light of future COVID-19 waves or similar outbreaks.
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http://dx.doi.org/10.3390/ijerph19095519DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9104097PMC
May 2022

Clinical features of, and risk factors for, severe or fatal COVID-19 among people living with HIV admitted to hospital: analysis of data from the WHO Global Clinical Platform of COVID-19.

Lancet HIV 2022 Jul 10;9(7):e486-e495. Epub 2022 May 10.

Department of Country Readiness Strengthening, Health Emergencies Programme, WHO, Geneva, Switzerland.

Background: WHO has established a Global Clinical Platform for the clinical characterisation of COVID-19 among hospitalised individuals. We assessed whether people living with HIV hospitalised with COVID-19 had increased odds of severe presentation and of in-hospital mortality compared with individuals who were HIV-negative and associated risk factors.

Methods: Between Jan 1, 2020, and July 1, 2021, anonymised individual-level data from 338 566 patients in 38 countries were reported to WHO. Using the Platform pooled dataset, we performed descriptive statistics and regression analyses to compare outcomes in the two populations and identify risk factors.

Findings: Of 197 479 patients reporting HIV status, 16 955 (8·6%) were people living with HIV. 16 283 (96.0%) of the 16 955 people living with HIV were from Africa; 10 603 (62·9%) were female and 6271 (37·1%) were male; the mean age was 45·5 years (SD 13·7); 6339 (38·3%) were admitted to hospital with severe illness; and 3913 (24·3%) died in hospital. Of the 10 166 people living with HIV with known antiretroviral therapy (ART) status, 9302 (91·5%) were on ART. Compared with individuals without HIV, people living with HIV had 15% increased odds of severe presentation with COVID-19 (aOR 1·15, 95% CI 1·10-1·20) and were 38% more likely to die in hospital (aHR 1·38, 1·34-1·41). Among people living with HIV, male sex, age 45-75 years, and having chronic cardiac disease or hypertension increased the odds of severe COVID-19; male sex, age older than 18 years, having diabetes, hypertension, malignancy, tuberculosis, or chronic kidney disease increased the risk of in-hospital mortality. The use of ART or viral load suppression were associated with a reduced risk of poor outcomes; however, HIV infection remained a risk factor for severity and mortality regardless of ART and viral load suppression status.

Interpretation: In this sample of hospitalised people contributing data to the WHO Global Clinical Platform for COVID-19, HIV was an independent risk factor for both severe COVID-19 at admission and in-hospital mortality. These findings have informed WHO immunisation policy that prioritises vaccination for people living with HIV. As the results mostly reflect the data contribution from Africa, this analysis will be updated as more data from other regions become available.

Funding: None.

Translation: For the French translation of the abstract see Supplementary Materials section.
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http://dx.doi.org/10.1016/S2352-3018(22)00097-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9090268PMC
July 2022

Estimating disease severity of Omicron and Delta SARS-CoV-2 infections.

Nat Rev Immunol 2022 05;22(5):267-269

Division of Public Health Surveillance and Response, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa.

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http://dx.doi.org/10.1038/s41577-022-00720-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9002222PMC
May 2022

Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous waves in the Western Cape Province, South Africa.

Trop Med Int Health 2022 Jun 10;27(6):564-573. Epub 2022 May 10.

Groote Schuur Hospital, Western Cape Government: Health, Cape Town, South Africa.

Objectives: The objective was to compare COVID-19 outcomes in the Omicron-driven fourth wave with prior waves in the Western Cape, assess the contribution of undiagnosed prior infection to differences in outcomes in a context of high seroprevalence due to prior infection and determine whether protection against severe disease conferred by prior infection and/or vaccination was maintained.

Methods: In this cohort study, we included public sector patients aged ≥20 years with a laboratory-confirmed COVID-19 diagnosis between 14 November and 11 December 2021 (wave four) and equivalent prior wave periods. We compared the risk between waves of the following outcomes using Cox regression: death, severe hospitalisation or death and any hospitalisation or death (all ≤14 days after diagnosis) adjusted for age, sex, comorbidities, geography, vaccination and prior infection.

Results: We included 5144 patients from wave four and 11,609 from prior waves. The risk of all outcomes was lower in wave four compared to the Delta-driven wave three (adjusted hazard ratio (aHR) [95% confidence interval (CI)] for death 0.27 [0.19; 0.38]. Risk reduction was lower when adjusting for vaccination and prior diagnosed infection (aHR: 0.41, 95% CI: 0.29; 0.59) and reduced further when accounting for unascertained prior infections (aHR: 0.72). Vaccine protection was maintained in wave four (aHR for outcome of death: 0.24; 95% CI: 0.10; 0.58).

Conclusions: In the Omicron-driven wave, severe COVID-19 outcomes were reduced mostly due to protection conferred by prior infection and/or vaccination, but intrinsically reduced virulence may account for a modest reduction in risk of severe hospitalisation or death compared to the Delta-driven wave.
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http://dx.doi.org/10.1111/tmi.13752DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9115442PMC
June 2022

The intersecting pandemics of tuberculosis and COVID-19: population-level and patient-level impact, clinical presentation, and corrective interventions.

Lancet Respir Med 2022 06 23;10(6):603-622. Epub 2022 Mar 23.

McGill International TB Centre, McGill University, Montreal, QC, Canada.

The global tuberculosis burden remains substantial, with more than 10 million people newly ill per year. Nevertheless, tuberculosis incidence has slowly declined over the past decade, and mortality has decreased by almost a third in tandem. This positive trend was abruptly reversed by the COVID-19 pandemic, which in many parts of the world has resulted in a substantial reduction in tuberculosis testing and case notifications, with an associated increase in mortality, taking global tuberculosis control back by roughly 10 years. Here, we consider points of intersection between the tuberculosis and COVID-19 pandemics, identifying wide-ranging approaches that could be taken to reverse the devastating effects of COVID-19 on tuberculosis control. We review the impact of COVID-19 at the population level on tuberculosis case detection, morbidity and mortality, and the patient-level impact, including susceptibility to disease, clinical presentation, diagnosis, management, and prognosis. We propose strategies to reverse or mitigate the deleterious effects of COVID-19 and restore tuberculosis services. Finally, we highlight research priorities and major challenges and controversies that need to be addressed to restore and advance the global response to tuberculosis.
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http://dx.doi.org/10.1016/S2213-2600(22)00092-3DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8942481PMC
June 2022

SARS-CoV-2 Seroprevalence after Third Wave of Infections, South Africa.

Emerg Infect Dis 2022 05 23;28(5):1055-1058. Epub 2022 Mar 23.

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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http://dx.doi.org/10.3201/eid2805.220278DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9045427PMC
May 2022

Effectiveness of the Ad26.COV2.S vaccine in health-care workers in South Africa (the Sisonke study): results from a single-arm, open-label, phase 3B, implementation study.

Lancet 2022 03;399(10330):1141-1153

National Department of Health, Pretoria, South Africa.

Background: We aimed to assess the effectiveness of a single dose of the Ad26.COV2.S vaccine (Johnson & Johnson) in health-care workers in South Africa during two waves of the South African COVID-19 epidemic.

Methods: In the single-arm, open-label, phase 3B implementation Sisonke study, health-care workers aged 18 years and older were invited for vaccination at one of 122 vaccination sites nationally. Participants received a single dose of 5 × 10 viral particles of the Ad26.COV2.S vaccine. Vaccinated participants were linked with their person-level data from one of two national medical insurance schemes (scheme A and scheme B) and matched for COVID-19 risk with an unvaccinated member of the general population. The primary outcome was vaccine effectiveness against severe COVID-19, defined as COVID-19-related admission to hospital, hospitalisation requiring critical or intensive care, or death, in health-care workers compared with the general population, ascertained 28 days or more after vaccination or matching, up to data cutoff. This study is registered with the South African National Clinical Trial Registry, DOH-27-022021-6844, ClinicalTrials.gov, NCT04838795, and the Pan African Clinical Trials Registry, PACTR202102855526180, and is closed to accrual.

Findings: Between Feb 17 and May 17, 2021, 477 102 health-care workers were enrolled and vaccinated, of whom 357 401 (74·9%) were female and 119 701 (25·1%) were male, with a median age of 42·0 years (33·0-51·0). 215 813 vaccinated individuals were matched with 215 813 unvaccinated individuals. As of data cutoff (July 17, 2021), vaccine effectiveness derived from the total matched cohort was 83% (95% CI 75-89) to prevent COVID-19-related deaths, 75% (69-82) to prevent COVID-19-related hospital admissions requiring critical or intensive care, and 67% (62-71) to prevent COVID-19-related hospitalisations. The vaccine effectiveness for all three outcomes were consistent across scheme A and scheme B. The vaccine effectiveness was maintained in older health-care workers and those with comorbidities including HIV infection. During the course of the study, the beta (B.1.351) and then the delta (B.1.617.2) SARS-CoV-2 variants of concerns were dominant, and vaccine effectiveness remained consistent (for scheme A plus B vaccine effectiveness against COVID-19-related hospital admission during beta wave was 62% [95% CI 42-76] and during delta wave was 67% [62-71], and vaccine effectiveness against COVID-19-related death during beta wave was 86% [57-100] and during delta wave was 82% [74-89]).

Interpretation: The single-dose Ad26.COV2.S vaccine shows effectiveness against severe COVID-19 disease and COVID-19-related death after vaccination, and against both beta and delta variants, providing real-world evidence for its use globally.

Funding: National Treasury of South Africa, the National Department of Health, Solidarity Response Fund NPC, The Michael & Susan Dell Foundation, The Elma Vaccines and Immunization Foundation, and the Bill & Melinda Gates Foundation.
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http://dx.doi.org/10.1016/S0140-6736(22)00007-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8930006PMC
March 2022

Seroprevalence of SARS-CoV-2 after the second wave in South Africa in HIV-infected and uninfected persons: a cross-sectional household survey.

Clin Infect Dis 2022 Mar 10. Epub 2022 Mar 10.

Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases (NICD) of the National Health Laboratory Service, Johannesburg, South Africa.

Background: Seroprevalence studies are important for quantifying the burden of SARS-CoV-2 infections in resource-constrained countries.

Methods: We conducted a cross-sectional household survey spanning the second pandemic wave (November 2020 - April 2021) in three communities. Blood was collected for SARS-CoV-2 antibody (two ELISA assays targeting spike and nucleocapsid) and HIV testing. An individual was considered seropositive if testing positive on ≥1 assay. Factors associated with infection, and the age-standardised infection to case detection rate (ICR), infection hospitalisation rate (IHR) and infection fatality rate (IFR) were calculated.

Results: Overall 7959 participants were enrolled, with a median age of 34 years and HIV prevalence of 22.7%. SARS-CoV-2 seroprevalence was 45.2% (95% confidence interval 43.7% - 46.7%), and increased from 26.9% among individuals enrolled in December 2020 to 47.1% among individuals in April 2021. On multivariable analysis, seropositivity was associated with age, sex, race, being overweight/obese, having respiratory symptoms, and low socioeconomic status. Persons living with HIV (PLWHIV) with high viral load were less likely to be seropositive compared to HIV-uninfected individuals. The site-specific ICR, IHR and IFR ranged across sites from 4.4% to 8.2%, 1.2% to 2.5% and 0.3% to 0.6%, respectively.

Conclusions: South Africa has experienced a large burden of SARS-CoV-2 infections, with <10% of infections diagnosed. Lower seroprevalence among non-virally suppressed PLWHIV, likely as a result of inadequate antibody production, highlights the need to prioritise this group for intervention.
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http://dx.doi.org/10.1093/cid/ciac198DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC9047164PMC
March 2022

Assessing the clinical severity of the Omicron variant in the Western Cape Province, South Africa, using the diagnostic PCR proxy marker of RdRp target delay to distinguish between Omicron and Delta infections - a survival analysis.

Int J Infect Dis 2022 May 27;118:150-154. Epub 2022 Feb 27.

Division of Medical Virology, University of Cape Town, Cape Town, Western Cape, South Africa; National Health Laboratory Service, South Africa; Wellcome Centre for Infectious Diseases Research in Africa, Institute of Infectious Disease and Molecular Medicine, University of Cape Town, South Africa.

Background: At present, it is unclear whether the extent of reduced risk of severe disease seen with SARS-Cov-2 Omicron variant infection is caused by a decrease in variant virulence or by higher levels of population immunity.

Methods: RdRp target delay (RTD) in the Seegene Allplex 2019-nCoV PCR assay is a proxy marker for the Delta variant. The absence of this proxy marker in the transition period was used to identify suspected Omicron infections. Cox regression was performed for the outcome of hospital admission in those who tested positive for SARS-CoV-2 on the Seegene Allplex assay from November 1 to December 14, 2021 in the Western Cape Province, South Africa, in the public sector. Adjustments were made for vaccination status and prior diagnosis of infection.

Results: A total of 150 cases with RTD and 1486 cases without RTD were included. Cases without RTD had a lower hazard of admission (adjusted hazard ratio [aHR], 0.56; 95% confidence interval [CI], 0.34-0.91). Complete vaccination was protective against admission, with an aHR of 0.45 (95% CI, 0.26-0.77).

Conclusion: Omicron has resulted in a lower risk of hospital admission compared with contemporaneous Delta infection, when using the proxy marker of RTD. Under-ascertainment of reinfections with an immune escape variant remains a challenge to accurately assessing variant virulence.
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http://dx.doi.org/10.1016/j.ijid.2022.02.051DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8882068PMC
May 2022

Population Immunity and Covid-19 Severity with Omicron Variant in South Africa.

N Engl J Med 2022 04 23;386(14):1314-1326. Epub 2022 Feb 23.

From the South African Medical Research Council Vaccine and Infectious Diseases Analytics Research Unit (S.A.M., G.K., N.D., C.K.M., A.J.N., P.C.M.) and African Leadership in Vaccinology Expertise (S.A.M., G.K.), University of the Witwatersrand, the National Institute for Communicable Diseases, National Health Laboratory Service (W.J., L.B., R.W.), and ResearchLinkMe (N.N.-M.), Johannesburg, the Centre for Environmental and Occupational Health Research, School of Public Health and Family Medicine, University of Cape Town, Cape Town (J.E.M.), and Right to Care, Centurion (L.B.) - all in South Africa.

Background: The B.1.1.529 (omicron) variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) was first identified on November 25, 2021, in Gauteng province, South Africa. Data regarding the seroprevalence of SARS-CoV-2 IgG in Gauteng before the fourth wave of coronavirus disease 2019 (Covid-19), in which the omicron variant was dominant, are needed.

Methods: We conducted a seroepidemiologic survey from October 22 to December 9, 2021, in Gauteng to determine the seroprevalence of SARS-CoV-2 IgG. Households included in a previous seroepidemiologic survey (conducted from November 2020 to January 2021) were contacted; to account for changes in the survey population, there was a 10% increase in the households contacted, with the use of the same sampling framework. Dried-blood-spot samples were tested for IgG against SARS-CoV-2 spike protein and nucleocapsid protein with the use of quantitative assays. We also evaluated Covid-19 epidemiologic trends in Gauteng, including cases, hospitalizations, recorded deaths, and excess deaths from the start of the pandemic through January 12, 2022.

Results: Samples were obtained from 7010 participants, of whom 1319 (18.8%) had received a Covid-19 vaccine. The seroprevalence of SARS-CoV-2 IgG ranged from 56.2% (95% confidence interval [CI], 52.6 to 59.7) among children younger than 12 years of age to 79.7% (95% CI, 77.6 to 81.5) among adults older than 50 years of age. Vaccinated participants were more likely to be seropositive for SARS-CoV-2 than unvaccinated participants (93.1% vs. 68.4%). Epidemiologic data showed that the incidence of SARS-CoV-2 infection increased and subsequently declined more rapidly during the fourth wave than it had during the three previous waves. The incidence of infection was decoupled from the incidences of hospitalization, recorded death, and excess death during the fourth wave, as compared with the proportions seen during previous waves.

Conclusions: Widespread underlying SARS-CoV-2 seropositivity was observed in Gauteng before the omicron-dominant wave of Covid-19. Epidemiologic data showed a decoupling of hospitalizations and deaths from infections while omicron was circulating. (Funded by the Bill and Melinda Gates Foundation.).
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http://dx.doi.org/10.1056/NEJMoa2119658DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8908853PMC
April 2022

Paediatric hospitalisations due to COVID-19 during the first SARS-CoV-2 omicron (B.1.1.529) variant wave in South Africa: a multicentre observational study.

Lancet Child Adolesc Health 2022 05 18;6(5):294-302. Epub 2022 Feb 18.

Department of Paediatrics and Child Health, University of Pretoria, Pretoria, South Africa; Centre for Maternal, Fetal, Newborn and Child Health Care Strategies, University of Pretoria, Pretoria, South Africa; Maternal and Infant Health Care Strategies Research Unit, South African Medical Research Council, Pretoria, South Africa; Tshwane District Health Services, Gauteng Department of Health, Pretoria, South Africa.

Background: South Africa reported a notable increase in COVID-19 cases from mid-November, 2021, onwards, starting in Tshwane District, which coincided with the rapid community spread of the SARS-CoV-2 omicron (B.1.1.529) variant. This increased infection rate coincided with a rapid increase in paediatric COVID-19-associated admissions to hospital (hereafter referred to as hospitalisations).

Methods: The Tshwane Maternal-Child COVID-19 study is a multicentre observational study in which we investigated the clinical manifestations and outcomes of paediatric patients (aged ≤19 years) who had tested positive for SARS-CoV-2 and were admitted to hospital for any reason in Tshwane District during a 6-week period at the beginning of the fourth wave of the COVID-19 epidemic in South Africa. We used five data sources, which were: (1) COVID-19 line lists; (2) collated SARS-CoV-2 testing data; (3) SARS-CoV-2 genomic sequencing data; (4) COVID-19 hospitalisation surveillance; and (5) clinical data of public sector COVID-19-associated hospitalisations among children aged 13 years and younger.

Findings: Between Oct 31 and Dec 11, 2021, 6287 children and adolescents in Tshwane District were recorded as having COVID-19. During this period, 2550 people with COVID-19 were hospitalised, of whom 462 (18%) were aged 19 years or younger. The number of paediatric cases was higher than in the three previous SARS-CoV-2 waves, uncharacteristically increasing ahead of adult hospitalisations. 75 viral samples from adults and children in the district were sequenced, of which 74 (99%) were of the omicron variant. Detailed clinical notes were available for 138 (75%) of 183 children aged ≤13 years with COVID-19 who were hospitalised. 87 (63%) of 138 children were aged 0-4 years. In 61 (44%) of 138 cases COVID-19 was the primary diagnosis, among whom symptoms included fever (37 [61%] of 61), cough (35 [57%]), shortness of breath (19 [31%]), seizures (19 [31%]), vomiting (16 [26%]), and diarrhoea (15 [25%]). Median length of hospital stay was 2 days [IQR 1-3]). 122 (88%) of 138 children with available data needed standard ward care and 27 (20%) needed oxygen therapy. Seven (5%) of 138 children were ventilated and four (3%) died during the study period, all related to complex underlying copathologies. All children and 77 (92%) of 84 parents or guardians with available data were unvaccinated to COVID-19.

Interpretation: Rapid increases in paediatric COVID-19 cases and hospitalisations mirror high community transmission of the SARS-CoV-2 omicron variant in Tshwane District, South Africa. Continued monitoring is needed to understand the long-term effect of the omicron variant on children and adolescents.

Funding: South African Medical Research Council, South African Department of Science & Innovation, G7 Global Health Fund.
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http://dx.doi.org/10.1016/S2352-4642(22)00027-XDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8856663PMC
May 2022

Early assessment of the clinical severity of the SARS-CoV-2 omicron variant in South Africa: a data linkage study.

Lancet 2022 01 19;399(10323):437-446. Epub 2022 Jan 19.

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. Electronic address:

Background: The SARS-CoV-2 omicron variant of concern was identified in South Africa in November, 2021, and was associated with an increase in COVID-19 cases. We aimed to assess the clinical severity of infections with the omicron variant using S gene target failure (SGTF) on the Thermo Fisher Scientific TaqPath COVID-19 PCR test as a proxy.

Methods: We did data linkages for national, South African COVID-19 case data, SARS-CoV-2 laboratory test data, SARS-CoV-2 genome data, and COVID-19 hospital admissions data. For individuals diagnosed with COVID-19 via TaqPath PCR tests, infections were designated as either SGTF or non-SGTF. The delta variant was identified by genome sequencing. Using multivariable logistic regression models, we assessed disease severity and hospitalisations by comparing individuals with SGTF versus non-SGTF infections diagnosed between Oct 1 and Nov 30, 2021, and we further assessed disease severity by comparing SGTF-infected individuals diagnosed between Oct 1 and Nov 30, 2021, with delta variant-infected individuals diagnosed between April 1 and Nov 9, 2021.

Findings: From Oct 1 (week 39), 2021, to Dec 6 (week 49), 2021, 161 328 cases of COVID-19 were reported in South Africa. 38 282 people were diagnosed via TaqPath PCR tests and 29 721 SGTF infections and 1412 non-SGTF infections were identified. The proportion of SGTF infections increased from two (3·2%) of 63 in week 39 to 21 978 (97·9%) of 22 455 in week 48. After controlling for factors associated with hospitalisation, individuals with SGTF infections had significantly lower odds of admission than did those with non-SGTF infections (256 [2·4%] of 10 547 vs 121 [12·8%] of 948; adjusted odds ratio [aOR] 0·2, 95% CI 0·1-0·3). After controlling for factors associated with disease severity, the odds of severe disease were similar between hospitalised individuals with SGTF versus non-SGTF infections (42 [21%] of 204 vs 45 [40%] of 113; aOR 0·7, 95% CI 0·3-1·4). Compared with individuals with earlier delta variant infections, SGTF-infected individuals had a significantly lower odds of severe disease (496 [62·5%] of 793 vs 57 [23·4%] of 244; aOR 0·3, 95% CI 0·2-0·5), after controlling for factors associated with disease severity.

Interpretation: Our early analyses suggest a significantly reduced odds of hospitalisation among individuals with SGTF versus non-SGTF infections diagnosed during the same time period. SGTF-infected individuals had a significantly reduced odds of severe disease compared with individuals infected earlier with the delta variant. Some of this reduced severity is probably a result of previous immunity.

Funding: The South African Medical Research Council, the South African National Department of Health, US Centers for Disease Control and Prevention, the African Society of Laboratory Medicine, Africa Centers for Disease Control and Prevention, the Bill & Melinda Gates Foundation, the Wellcome Trust, and the Fleming Fund.
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http://dx.doi.org/10.1016/S0140-6736(22)00017-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8769664PMC
January 2022

Outcomes of laboratory-confirmed SARS-CoV-2 infection in the Omicron-driven fourth wave compared with previous waves in the Western Cape Province, South Africa.

medRxiv 2022 Jan 12. Epub 2022 Jan 12.

Groote Schuur Hospital, Western Cape Government: Health.

Objectives: We aimed to compare COVID-19 outcomes in the Omicron-driven fourth wave with prior waves in the Western Cape, the contribution of undiagnosed prior infection to differences in outcomes in a context of high seroprevalence due to prior infection, and whether protection against severe disease conferred by prior infection and/or vaccination was maintained.

Methods: In this cohort study, we included public sector patients aged ≥20 years with a laboratory confirmed COVID-19 diagnosis between 14 November-11 December 2021 (wave four) and equivalent prior wave periods. We compared the risk between waves of the following outcomes using Cox regression: death, severe hospitalization or death and any hospitalization or death (all ≤14 days after diagnosis) adjusted for age, sex, comorbidities, geography, vaccination and prior infection.

Results: We included 5,144 patients from wave four and 11,609 from prior waves. Risk of all outcomes was lower in wave four compared to the Delta-driven wave three (adjusted Hazard Ratio (aHR) [95% confidence interval (CI)] for death 0.27 [0.19; 0.38]. Risk reduction was lower when adjusting for vaccination and prior diagnosed infection (aHR:0.41, 95% CI: 0.29; 0.59) and reduced further when accounting for unascertained prior infections (aHR: 0.72). Vaccine protection was maintained in wave four (aHR for outcome of death: 0.24; 95% CI: 0.10; 0.58).

Conclusions: In the Omicron-driven wave, severe COVID-19 outcomes were reduced mostly due to protection conferred by prior infection and/or vaccination, but intrinsically reduced virulence may account for an approximately 25% reduced risk of severe hospitalization or death compared to Delta.
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http://dx.doi.org/10.1101/2022.01.12.22269148DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8764730PMC
January 2022

Epidemiology of SARS-CoV-2 infection and SARS-CoV-2 positive hospital admissions among children in South Africa.

Influenza Other Respir Viruses 2022 01 18;16(1):34-47. Epub 2021 Nov 18.

National Institute for Communicable Diseases, National Health Laboratory Services, Johannesburg, South Africa.

Introduction: We describe epidemiology and outcomes of confirmed SARS-CoV-2 infection and positive admissions among children <18 years in South Africa, an upper-middle income setting with high inequality.

Methods: Laboratory and hospital COVID-19 surveillance data, 28 January - 19 September 2020 was used. Testing rates were calculated as number of tested for SARS-CoV-2 divided by population at risk; test positivity rates were calculated as positive tests divided by total number of tests. In-hospital case fatality ratio (CFR) was calculated based on hospitalized positive admissions with outcome data who died in-hospital and whose death was judged SARS-CoV-2 related by attending physician.

Findings: 315 570 children aged <18 years were tested for SARS-CoV-2; representing 8.9% of all 3 548 738 tests and 1.6% of all children in the country. Of children tested, 46 137 (14.6%) were positive. Children made up 2.9% (n = 2007) of all SARS-CoV-2 positive admissions to sentinel hospitals. Among children, 47 died (2.6% case-fatality). In-hospital deaths were associated with male sex [adjusted odds ratio (aOR) 2.18 (95% confidence intervals [CI] 1.08-4.40)] vs female; age <1 year [aOR 4.11 (95% CI 1.08-15.54)], age 10-14 years [aOR 4.20 (95% CI1.07-16.44)], age 15-17 years [aOR 4.86 (95% 1.28-18.51)] vs age 1-4 years; admission to a public hospital [aOR 5.07(95% 2.01-12.76)] vs private hospital and ≥1 underlying conditions [aOR 12.09 (95% CI 4.19-34.89)] vs none.

Conclusions: Children with underlying conditions were at greater risk of severe SARS-CoV-2 outcomes. Children > 10 years, those in certain provinces and those with underlying conditions should be considered for increased testing and vaccination.
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http://dx.doi.org/10.1111/irv.12916DOI Listing
January 2022

SARS-CoV-2 Seroprevalence in a Rural and Urban Household Cohort during First and Second Waves of Infections, South Africa, July 2020-March 2021.

Emerg Infect Dis 2021 12 3;27(12):3020-3029. Epub 2021 Sep 3.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections may be underestimated because of limited access to testing. We measured SARS-CoV-2 seroprevalence in South Africa every 2 months during July 2020-March 2021 in randomly selected household cohorts in 2 communities. We compared seroprevalence to reported laboratory-confirmed infections, hospitalizations, and deaths to calculate infection-case, infection-hospitalization, and infection-fatality ratios in 2 waves of infection. Post-second wave seroprevalence ranged from 18% in the rural community children <5 years of age, to 59% in urban community adults 35-59 years of age. The second wave saw a shift in age distribution of case-patients in the urban community (from persons 35-59 years of age to persons at the extremes of age), higher attack rates in the rural community, and a higher infection-fatality ratio in the urban community. Approximately 95% of SARS-CoV-2 infections were not reported to national surveillance.
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http://dx.doi.org/10.3201/eid2712.211465DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8632160PMC
December 2021

The importation and establishment of community transmission of SARS-CoV-2 during the first eight weeks of the South African COVID-19 epidemic.

EClinicalMedicine 2021 Sep 12;39:101072. Epub 2021 Aug 12.

Background: We describe the epidemiology of COVID-19 in South Africa following importation and during implementation of stringent lockdown measures.

Methods: Using national surveillance data including demographics, laboratory test data, clinical presentation, risk exposures (travel history, contacts and occupation) and outcomes of persons undergoing COVID-19 testing or hospitalised with COVID-19 at sentinel surveillance sites, we generated and interpreted descriptive statistics, epidemic curves, and initial reproductive numbers (Rt).

Findings: From 4 March to 30 April 2020, 271,670 SARS-CoV-2 PCR tests were performed (462 tests/100,000 persons). Of these, 7,892 (2.9%) persons tested positive (median age 37 years (interquartile range 28-49 years), 4,568 (58%) male, cumulative incidence of 13.4 cases/100,000 persons). Hospitalization records were found for 1,271 patients (692 females (54%)) of whom 186 (14.6%) died. Amongst 2,819 cases with data, 489/2819 (17.3%) travelled internationally within 14 days prior to diagnosis, mostly during March 2020 (466 (95%)). Cases diagnosed in April compared with March were younger (median age, 37 vs. 40 years), less likely female (38% vs. 53%) and resident in a more populous province (98% vs. 91%). The national initial was 2.08 (95% confidence interval (CI): 1.71-2.51).

Interpretation: The first eight weeks following COVID-19 importation were characterised by early predominance of imported cases and relatively low mortality and transmission rates. Despite stringent lockdown measures, the second month following importation was characterised by community transmission and increasing disease burden in more populous provinces.
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http://dx.doi.org/10.1016/j.eclinm.2021.101072DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8360332PMC
September 2021

Risk factors for COVID-19-related in-hospital mortality in a high HIV and tuberculosis prevalence setting in South Africa: a cohort study.

Lancet HIV 2021 09 4;8(9):e554-e567. Epub 2021 Aug 4.

Department of Medicine, Charlotte Maxeke Johannesburg Academic Hospital, University of the Witwatersrand, Johannesburg, South Africa.

Background: The interaction between COVID-19, non-communicable diseases, and chronic infectious diseases such as HIV and tuberculosis is unclear, particularly in low-income and middle-income countries in Africa. South Africa has a national HIV prevalence of 19% among people aged 15-49 years and a tuberculosis prevalence of 0·7% in people of all ages. Using a nationally representative hospital surveillance system in South Africa, we aimed to investigate the factors associated with in-hospital mortality among patients with COVID-19.

Methods: In this cohort study, we used data submitted to DATCOV, a national active hospital surveillance system for COVID-19 hospital admissions, for patients admitted to hospital with laboratory-confirmed SARS-CoV-2 infection between March 5, 2020, and March 27, 2021. Age, sex, race or ethnicity, and comorbidities (hypertension, diabetes, chronic cardiac disease, chronic pulmonary disease and asthma, chronic renal disease, malignancy in the past 5 years, HIV, and past and current tuberculosis) were considered as risk factors for COVID-19-related in-hospital mortality. COVID-19 in-hospital mortality, the main outcome, was defined as a death related to COVID-19 that occurred during the hospital stay and excluded deaths that occurred because of other causes or after discharge from hospital; therefore, only patients with a known in-hospital outcome (died or discharged alive) were included. Chained equation multiple imputation was used to account for missing data and random-effects multivariable logistic regression models were used to assess the role of HIV status and underlying comorbidities on COVID-19 in-hospital mortality.

Findings: Among the 219 265 individuals admitted to hospital with laboratory-confirmed SARS-CoV-2 infection and known in-hospital outcome data, 51 037 (23·3%) died. Most commonly observed comorbidities among individuals with available data were hypertension in 61 098 (37·4%) of 163 350, diabetes in 43 885 (27·4%) of 159 932, and HIV in 13 793 (9·1%) of 151 779. Tuberculosis was reported in 5282 (3·6%) of 146 381 individuals. Increasing age was the strongest predictor of COVID-19 in-hospital mortality. Other factors associated were HIV infection (adjusted odds ratio 1·34, 95% CI 1·27-1·43), past tuberculosis (1·26, 1·15-1·38), current tuberculosis (1·42, 1·22-1·64), and both past and current tuberculosis (1·48, 1·32-1·67) compared with never tuberculosis, as well as other described risk factors for COVID-19, such as male sex; non-White race; underlying hypertension, diabetes, chronic cardiac disease, chronic renal disease, and malignancy in the past 5 years; and treatment in the public health sector. After adjusting for other factors, people with HIV not on antiretroviral therapy (ART; adjusted odds ratio 1·45, 95% CI 1·22-1·72) were more likely to die in hospital than were people with HIV on ART. Among people with HIV, the prevalence of other comorbidities was 29·2% compared with 30·8% among HIV-uninfected individuals. Increasing number of comorbidities was associated with increased COVID-19 in-hospital mortality risk in both people with HIV and HIV-uninfected individuals.

Interpretation: Individuals identified as being at high risk of COVID-19 in-hospital mortality (older individuals and those with chronic comorbidities and people with HIV, particularly those not on ART) would benefit from COVID-19 prevention programmes such as vaccine prioritisation as well as early referral and treatment.

Funding: South African National Government.
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http://dx.doi.org/10.1016/S2352-3018(21)00151-XDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8336996PMC
September 2021

Difference in mortality among individuals admitted to hospital with COVID-19 during the first and second waves in South Africa: a cohort study.

Lancet Glob Health 2021 09 9;9(9):e1216-e1225. Epub 2021 Jul 9.

National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa; School of Public Health, Faculty of Health Sciences, University of Witwatersrand, Johannesburg, South Africa.

Background: The first wave of COVID-19 in South Africa peaked in July, 2020, and a larger second wave peaked in January, 2021, in which the SARS-CoV-2 501Y.V2 (Beta) lineage predominated. We aimed to compare in-hospital mortality and other patient characteristics between the first and second waves.

Methods: In this prospective cohort study, we analysed data from the DATCOV national active surveillance system for COVID-19 admissions to hospital from March 5, 2020, to March 27, 2021. The system contained data from all hospitals in South Africa that have admitted a patient with COVID-19. We used incidence risk for admission to hospital and determined cutoff dates to define five wave periods: pre-wave 1, wave 1, post-wave 1, wave 2, and post-wave 2. We compared the characteristics of patients with COVID-19 who were admitted to hospital in wave 1 and wave 2, and risk factors for in-hospital mortality accounting for wave period using random-effect multivariable logistic regression.

Findings: Peak rates of COVID-19 cases, admissions, and in-hospital deaths in the second wave exceeded rates in the first wave: COVID-19 cases, 240·4 cases per 100 000 people vs 136·0 cases per 100 000 people; admissions, 27·9 admissions per 100 000 people vs 16·1 admissions per 100 000 people; deaths, 8·3 deaths per 100 000 people vs 3·6 deaths per 100 000 people. The weekly average growth rate in hospital admissions was 20% in wave 1 and 43% in wave 2 (ratio of growth rate in wave 2 compared with wave 1 was 1·19, 95% CI 1·18-1·20). Compared with the first wave, individuals admitted to hospital in the second wave were more likely to be age 40-64 years (adjusted odds ratio [aOR] 1·22, 95% CI 1·14-1·31), and older than 65 years (aOR 1·38, 1·25-1·52), compared with younger than 40 years; of Mixed race (aOR 1·21, 1·06-1·38) compared with White race; and admitted in the public sector (aOR 1·65, 1·41-1·92); and less likely to be Black (aOR 0·53, 0·47-0·60) and Indian (aOR 0·77, 0·66-0·91), compared with White; and have a comorbid condition (aOR 0·60, 0·55-0·67). For multivariable analysis, after adjusting for weekly COVID-19 hospital admissions, there was a 31% increased risk of in-hospital mortality in the second wave (aOR 1·31, 95% CI 1·28-1·35). In-hospital case-fatality risk increased from 17·7% in weeks of low admission (<3500 admissions) to 26·9% in weeks of very high admission (>8000 admissions; aOR 1·24, 1·17-1·32).

Interpretation: In South Africa, the second wave was associated with higher incidence of COVID-19, more rapid increase in admissions to hospital, and increased in-hospital mortality. Although some of the increased mortality can be explained by admissions in the second wave being more likely in older individuals, in the public sector, and by the increased health system pressure, a residual increase in mortality of patients admitted to hospital could be related to the new Beta lineage.

Funding: DATCOV as a national surveillance system is funded by the National Institute for Communicable Diseases and the South African National Government.
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http://dx.doi.org/10.1016/S2214-109X(21)00289-8DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8270522PMC
September 2021

'We had to manage what we had on hand, in whatever way we could': adaptive responses in policy for decentralized drug-resistant tuberculosis care in South Africa.

Health Policy Plan 2021 Apr;36(3):249-259

Department of Infectious Diseases, Livingstone Hospital, Lindsay Rd, Industrial, Port Elizabeth, 6020, South Africa.

In 2011, the South African National TB Programme launched a policy of decentralized management of drug-resistant tuberculosis (DR-TB) in order to expand the capacity of facilities to treat patients with DR-TB, minimize delays to access care and improve patient outcomes. This policy directive was implemented to varying degrees within a rapidly evolving diagnostic and treatment landscape for DR-TB, placing new demands on already-stressed health systems. The variable readiness of district-level systems to implement the policy prompted questions not only about differences in health systems resources but also front-line actors' capacity to implement change in resource-constrained facilities. Using a grounded theory approach, we analysed data from in-depth interviews and small group discussions conducted between 2016 and 2018 with managers (n = 9), co-ordinators (n = 15), doctors (n = 7) and nurses (n = 18) providing DR-TB care. Data were collected over two phases in district-level decentralized sites of three South African provinces. While health systems readiness assessments conventionally map the availability of 'hardware', i.e. resources and skills to deliver an intervention, a notable absence of systems 'hardware' meant that systems 'software', i.e. health care workers (HCWs) agency, behaviours and interactions provided the basis of locally relevant strategies for decentralized DR-TB care. 'Software readiness' was manifest in four areas of DR-TB care: re-organization of service delivery, redressal of resource shortages, creation of treatment adherence support systems and extension of care parameters for vulnerable patients. These strategies demonstrate adaptive capacity and everyday resilience among HCW to withstand the demands of policy change and innovation in stressed systems. Our work suggests that a useful extension of health systems 'readiness' assessments would include definition and evaluation of HCW 'software' and adaptive capacities in the face of systems hardware gaps.
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http://dx.doi.org/10.1093/heapol/czaa147DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8059133PMC
April 2021

Pregnancy outcomes and birth defects from an antiretroviral drug safety study of women in South Africa and Zambia.

AIDS 2014 Sep;28(15):2259-68

aCentre for Infectious Disease Research in Zambia, Lusaka, Zambia bUniversity of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina cHarvard University School of Public Health, Boston, Massachusetts, USA dUniversity of Limpopo Medical University of Southern Africa, Pretoria eHealth Systems Trust, Durban fUniversity of Pretoria, Pretoria, South Africa gElizabeth Glaser Pediatric AIDS Foundation hGeorge Washington University School of Public Health and Health Services, Washington, District of Columbia, USA.

Objective: To evaluate the safety of combination antiretroviral therapy (ART) in conception and pregnancy in different health systems.

Design: A pilot ART registry to measure the prevalence of birth defects and adverse pregnancy outcomes in South Africa and Zambia.

Methods: HIV-infected pregnant women on ART prior to conception were enrolled until delivery, and their infants were followed until 1 year old.

Results: Between October 2010 and April 2011, 600 women were enrolled. The median CD4 cell count at study enrollment was lower in South Africa than Zambia (320 vs. 430 cells/μl; P < 0.01). The most common antiretroviral drugs at the time of conception included stavudine, lamivudine, and nevirapine. There were 16 abortions (2.7%), one ectopic pregnancy (0.2%), 12 (2.0%) stillbirths, and 571 (95.2%) live infants. Deliveries were more often preterm (29.7 vs. 18.4%; P = 0.01) and the infants had lower birth weights (2900 vs. 2995 g; P = 0.11) in Zambia compared to South Africa. Thirty-six infants had birth defects: 13 major and 23 minor. There were more major anomalies detected in South Africa and more minor ones in Zambia. No neonatal deaths were attributed to congenital birth defects.

Conclusions: An Africa-specific, multi-site antiretroviral drug safety registry for pregnant women is feasible. Different prevalence for preterm delivery, delivery mode, and birth defect types between women on preconception ART in South Africa and Zambia highlight the potential impact of health systems on pregnancy outcomes. As countries establish ART drug safety registries, documenting health facility limitations may be as essential as the specific ART details.
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http://dx.doi.org/10.1097/QAD.0000000000000394DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5454497PMC
September 2014

Comparing a paper based monitoring and evaluation system to a mHealth system to support the national community health worker programme, South Africa: an evaluation.

BMC Med Inform Decis Mak 2014 Aug 9;14:69. Epub 2014 Aug 9.

School of Public Health, University of the Western Cape, Cape Town, South Africa.

Background: In an attempt to address a complex disease burden, including improving progress towards MDGs 4 and 5, South Africa recently introduced a re-engineered Primary Health Care (PHC) strategy, which has led to the development of a national community health worker (CHW) programme. The present study explored the development of a cell phone-based and paper-based monitoring and evaluation (M&E) system to support the work of the CHWs.

Methods: One sub-district in the North West province was identified for the evaluation. One outreach team comprising ten CHWs maintained both the paper forms and mHealth system to record household data on community-based services. A comparative analysis was done to calculate the correspondence between the paper and phone records. A focus group discussion was conducted with the CHWs. Clinical referrals, data accuracy and supervised visits were compared and analysed for the paper and phone systems.

Results: Compared to the mHealth system where data accuracy was assured, 40% of the CHWs showed a consistently high level (>90% correspondence) of data transfer accuracy on paper. Overall, there was an improvement over time, and by the fifth month, all CHWs achieved a correspondence of 90% or above between phone and paper data. The most common error that occurred was summing the total number of visits and/or activities across the five household activity indicators. Few supervised home visits were recorded in either system and there was no evidence of the team leader following up on the automatic notifications received on their cell phones.

Conclusions: The evaluation emphasizes the need for regular supervision for both systems and rigorous and ongoing assessments of data quality for the paper system. Formalization of a mHealth M&E system for PHC outreach teams delivering community based services could offer greater accuracy of M&E and enhance supervision systems for CHWs.
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http://dx.doi.org/10.1186/1472-6947-14-69DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4150556PMC
August 2014

Impact of supplemental immunisation activity (SIA) campaigns on health systems: findings from South Africa.

J Epidemiol Community Health 2013 Nov 23;67(11):947-52. Epub 2013 Aug 23.

Department of Global Health, University of Washington, , Seattle, Washington, USA.

Background: Supplemental immunisation activity (SIA) campaigns provide children with an additional dose of measles vaccine and deliver other child health interventions including vitamin A supplements, deworming medications and oral polio vaccines. They also require the mobilisation of a large health workforce. We assess the impact of the implementation of SIA campaigns on selected routine child and maternal health services in South Africa (SA).

Methods: We use district-level monthly headcount data for 52 South African districts for the period 2001-2010, sourced from the District Health Information System, SA. The data include 12 child and maternal health headcount indicators including routine immunisation, and maternal and reproductive health indicators. We analyse the association between the implementation of the 2010 SIA campaign and the change (decrease/increase) in headcounts, using a linear regression model.

Results: We find a significant decrease for eight indicators. The total number of fully immunised children before age 1 decreased by 29% (95% CI 23% to 35%, p<0.001) during the month of SIA implementation; contraceptive use and antenatal visits decreased by 7-17% (p ≤ 0.02) and about 10% (p<0.001), respectively.

Conclusions: SIA campaigns may negatively impact health systems during the period of implementation by disrupting regular functioning and diverting resources from other activities, including routine child and maternal health services. SIA campaigns present multidimensional costs that need to be explicitly considered in benefit-cost assessments.
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http://dx.doi.org/10.1136/jech-2012-202216DOI Listing
November 2013

Supplementary immunization activities (SIAs) in South Africa: comprehensive economic evaluation of an integrated child health delivery platform.

Glob Health Action 2013 Mar 1;6:1-9. Epub 2013 Mar 1.

Department of Global Health, University of Washington, Seattle, WA 98104, USA.

Background: Supplementary immunization activity (SIA) campaigns provide children with an additional dose of measles vaccine and deliver other interventions, including vitamin A supplements, deworming medications, and oral polio vaccines.

Objective: To assess the cost-effectiveness of the full SIA delivery platform in South Africa (SA).

Design: We used an epidemiologic cost model to estimate the cost-effectiveness of the 2010 SIA campaign. We used province-level campaign data sourced from the District Health Information System, SA, and from planning records of provincial coordinators of the Expanded Programme on Immunization. The data included the number of children immunized with measles and polio vaccines, the number of children given vitamin A supplements and Albendazole tablets, and costs.

Results: The campaign cost $37 million and averted a total of 1,150 deaths (95% uncertainty range: 990-1,360). This ranged from 380 deaths averted in KwaZulu-Natal to 20 deaths averted in the Northern Cape. Vitamin A supplementation alone averted 820 deaths (95% UR: 670-1,040); measles vaccination alone averted 330 deaths (95% UR: 280-370). Incremental cost-effectiveness was $27,100 (95% UR: $18,500-34,400) per death averted nationally, ranging from $11,300 per death averted in the Free State to $91,300 per death averted in the Eastern Cape.

Conclusions: Cost-effectiveness of the SIA child health delivery platform varies substantially across SA provinces, and it is substantially more cost-effective when vitamin A supplementation is included in the interventions administered. Cost-effectiveness assessments should consider health system delivery platforms that integrate multiple interventions, and they should be conducted at the sub-national level.
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http://dx.doi.org/10.3402/gha.v6i0.20056DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3587392PMC
March 2013

Rodent control in urban communities in Johannesburg, South Africa: from research to action.

Int J Environ Health Res 2013 Dec 21;23(6):474-83. Epub 2013 Jan 21.

a Medical Research Council of South Africa, Environment and Health Research Unit , Johannesburg , South Africa .

Introduction: Rodents are troublesome urban pests, with potentially serious health implications. Preventive efforts require greater understanding of social contexts in which they are prevalent. This study aimed to determine rodent prevalence and identify factors associated with rodent infestations in urban residential settings.

Methods: The Health, Environment and Development study is a longitudinal panel study conducted in five settlements across Johannesburg. Data on socio-economic status, domestic behaviour and housing quality are collected annually. Logistic regression revealed risk factors for rodent prevalence at household level.

Results: Rodents are a major household problem in all study areas (prevalence 54%). Factors associated with increased prevalence of rats included lower income, living in informal areas, overcrowding, cracks in dwelling walls and internal damp.

Conclusion: Socio-economic status, housing quality, domestic behaviour and environmental health services are associated with exposure to rodents in urban Johannesburg communities. This information served as a platform to launch rodent awareness campaigns at study sites.
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http://dx.doi.org/10.1080/09603123.2012.755156DOI Listing
December 2013

Measles control in Sub-Saharan Africa: South Africa as a case study.

Vaccine 2012 Feb 9;30(9):1594-600. Epub 2012 Jan 9.

Department of Global Health, University of Washington, Seattle, WA 98104, USA.

Background: Due to intensified measles immunization efforts, measles mortality has decreased substantially worldwide, particularly in Sub-Saharan Africa (SSA). The World Health Organization (WHO) estimated a 92% decrease in measles-related deaths in the WHO AFRO region for the period 2000-2008. Recently, the AFRO region established a measles pre-elimination goal and experts have suggested engaging in a measles eradication campaign at the global level. However, recent large-scale outbreaks in many Sub-Saharan African countries present a challenge to measles control efforts. This paper examines measles immunization and the impact of measles supplemental immunization activities (SIAs) on routine immunization coverage in South Africa (SA).

Methods: We reported on immunization coverage trends in SA for the period 2001-2010 at the province and district levels. The data included routine immunization for 1st and 2nd doses of measles vaccine (MCV1, MCV2), SIAs, 1st dose of Bacille Calmette-Guérin vaccine, 1st and 3rd doses of oral polio vaccine (OPV1, OPV3), 3rd dose of Diphtheria-Tetanus-Pertussis-Haemophilus-influenzae-B vaccine (DTP-Hib3), and the number of under-one-year-olds having completed a primary course of immunization (Imm1). A regression model looked at the SIA impact on routine coverage.

Results: Over the past decade, MCV1 and MCV2 coverage have increased nationally from 68% and 57% in 2001 to 95% and 83% in 2010, respectively. SIA coverage has remained at high levels, around 90%, over the same period. Substantial heterogeneity in MCV1 and MCV2 coverage is present across SA districts, with differences in coverage of 56% (MCV1) and 51% (MCV2) in 2010. In any given year, occurrence of SIAs was associated with a decrease in routine immunization coverage of MCV1, MCV2, OPV1, OPV3, DTP-Hib3, and Imm1, at the district level.

Conclusions: The heterogeneity in measles vaccination coverage across SA districts challenges the goal of measles elimination in SA and SSA. The reduction in routine immunization coverage associated with the occurrence of SIAs raises the legitimate concern that SIAs may negatively impact health systems' functioning.
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http://dx.doi.org/10.1016/j.vaccine.2011.12.123DOI Listing
February 2012

How to stop public health conferences becoming trade fairs.

Public Health Nutr 2009 Sep;12(9):1581-3

Centre for International Health University of Bologna Italy.

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http://dx.doi.org/10.1017/S1368980009990863DOI Listing
September 2009
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