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1.
Lancet HIV ; 9(7): e486-e495, 2022 07.
Article in English | MEDLINE | ID: covidwho-1931220

ABSTRACT

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.


Subject(s)
COVID-19 , HIV Infections , Hypertension , Adolescent , Aged , COVID-19/epidemiology , Female , HIV Infections/complications , HIV Infections/drug therapy , HIV Infections/epidemiology , Hospitals , Humans , Hypertension/complications , Hypertension/epidemiology , Male , Middle Aged , Risk Factors , World Health Organization
2.
Lancet Child Adolesc Health ; 6(5): 294-302, 2022 05.
Article in English | MEDLINE | ID: covidwho-1927003

ABSTRACT

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.


Subject(s)
COVID-19 , Adolescent , Adult , COVID-19/epidemiology , COVID-19 Testing , Child , Hospitalization , Humans , SARS-CoV-2 , South Africa/epidemiology
4.
South African Journal of Science ; 118(5/6):1-14, 2022.
Article in English | ProQuest Central | ID: covidwho-1912361

ABSTRACT

Older age, male sex, and non-white race have been reported to be risk factors for COVID-19 mortality. Few studies have explored how these intersecting factors contribute to COVID-19 outcomes. This study aimed to compare demographic characteristics and trends in SARS-CoV-2 admissions and the health care they received. Hospital admission data were collected through DATCOV an active national COVID-19 surveillance programme. Descriptive analysis was used to compare admissions and deaths by age, sex, race, and health sector as a proxy for socio-economic status. COVID-19 mortality and healthcare utilisation were compared by race using random effect multivariable logistic regression models. On multivariable analysis, black African patients (adjusted OR [aOR] 1.3, 95% confidence interval [CI] 1.2, 1.3), coloured patients (aOR 1.2, 95% CI 1.1, 1.3), and patients of Indian descent (aOR 1.2, 95% CI 1.2, 1.3) had increased risk of in-hospital COVID-19 mortality compared to white patients;and admission in the public health sector (aOR 1.5, 95% CI 1.5, 1.6) was associated with increased risk of mortality compared to those in the private sector. There were higher percentages of COVID-19 hospitalised individuals treated in ICU, ventilated, and treated with supplemental oxygen in the private compared to the public sector. There were increased odds of non-white patients being treated in ICU or ventilated in the private sector, but decreased odds of black African patients being treated in ICU (aOR 0.5;95% CI 0.4, 0.5) or ventilated (aOR 0.5;95% CI 0.4, 0.6) compared to white patients in the public sector. These findings demonstrate the importance of collecting and analysing data on race and socio-economic status to ensure that disease control measures address the most vulnerable populations affected by COVID-19.

5.
BMC Public Health ; 22(1): 1035, 2022 05 24.
Article in English | MEDLINE | ID: covidwho-1862121

ABSTRACT

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.


Subject(s)
COVID-19 , SARS-CoV-2 , Adult , COVID-19/epidemiology , Disease Outbreaks , Humans , Long-Term Care , Middle Aged , Pandemics , Residential Facilities , Retrospective Studies , South Africa/epidemiology
6.
Wulf Hanson, Sarah, Abbafati, Cristiana, Aerts, Joachim, Al-Aly, Ziyad, Ashbaugh, Charlie, Ballouz, Tala, Blyuss, Oleg, Bobkova, Polina, Bonsel, Gouke, Borzakova, Svetlana, Buonsenso, Danilo, Butnaru, Denis, Carter, Austin, Chu, Helen, De Rose, Cristina, Diab, Mohamed Mustafa, Ekbom, Emil, El Tantawi, Maha, Fomin, Victor, Frithiof, Robert, Gamirova, Aysylu, Glybochko, Petr, Haagsma, Juanita, Javanmard, Shaghayegh Haghjooy, Hamilton, Erin, Harris, Gabrielle, Heijenbrok-Kal, Majanka, Helbok, Raimund, Hellemons, Merel, Hillus, David, Huijts, Susanne, Hultström, Michael, Jassat, Waasila, Kurth, Florian, Larsson, Ing-Marie, Lipcsey, Miklós, Liu, Chelsea, Loflin, Callan, Malinovschi, Andrei, Mao, Wenhui, Mazankova, Lyudmila, McCulloch, Denise, Menges, Dominik, Mohammadifard, Noushin, Munblit, Daniel, Nekliudov, Nikita, Ogbuoji, Osondu, Osmanov, Ismail, Peñalvo, José, Petersen, Maria Skaalum, Puhan, Milo, Rahman, Mujibur, Rass, Verena, Reinig, Nickolas, Ribbers, Gerard, Ricchiuto, Antonia, Rubertsson, Sten, Samitova, Elmira, Sarrafzadegan, Nizal, Shikhaleva, Anastasia, Simpson, Kyle, Sinatti, Dario, Soriano, Joan, Spiridonova, Ekaterina, Steinbeis, Fridolin, Svistunov, Andrey, Valentini, Piero, van de Water, Brittney, van den Berg-Emons, Rita, Wallin, Ewa, Witzenrath, Martin, Wu, Yifan, Xu, Hanzhang, Zoller, Thomas, Adolph, Christopher, Albright, James, Amlag, Joanne, Aravkin, Aleksandr, Bang-Jensen, Bree, Bisignano, Catherine, Castellano, Rachel, Castro, Emma, Chakrabarti, Suman, Collins, James, Dai, Xiaochen, Daoud, Farah, Dapper, Carolyn, Deen, Amanda, Duncan, Bruce, Erickson, Megan, Ewald, Samuel, Ferrari, Alize, Flaxman, Abraham, Fullman, Nancy, Gamkrelidze, Amiran, Giles, John, Guo, Gaorui, Hay, Simon, He, Jiawei, Helak, Monika, Hulland, Erin, Kereselidze, Maia, Krohn, Kris, Lazzar-Atwood, Alice, Lindstrom, Akiaja, Lozano, Rafael, Magistro, Beatrice, Malta, Deborah Carvalho, Månsson, Johan, Mantilla Herrera, Ana, Mokdad, Ali, Monasta, Lorenzo, Nomura, Shuhei, Pasovic, Maja, Pigott, David, Reiner, Robert, Reinke, Grace, Ribeiro, Antonio Luiz, Santomauro, Damian Francesco, Sholokhov, Aleksei, Spurlock, Emma Elizabeth, Walcott, Rebecca, Walker, Ally, Wiysonge, Charles Shey, Zheng, Peng, Bettger, Janet Prvu, Murray, Christopher J. L.; Vos, Theo.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-337680

ABSTRACT

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 Question What are the extent and nature of the most common long COVID symptoms by country in 2020 and 2021? Findings 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. Meaning 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.

7.
Lancet Glob Health ; 10(7): e961-e969, 2022 07.
Article in English | MEDLINE | ID: covidwho-1852287

ABSTRACT

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.


Subject(s)
COVID-19 , Influenza, Human , COVID-19/epidemiology , Hospitals , Humans , Influenza, Human/epidemiology , Pandemics , SARS-CoV-2 , South Africa/epidemiology
8.
Int J Infect Dis ; 118: 150-154, 2022 May.
Article in English | MEDLINE | ID: covidwho-1838855

ABSTRACT

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 AllplexTM 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 AllplexTM 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.


Subject(s)
COVID-19 , Hepatitis D , COVID-19/diagnosis , Humans , Polymerase Chain Reaction , RNA-Dependent RNA Polymerase , SARS-CoV-2/genetics , South Africa/epidemiology , Survival Analysis
9.
Int J Environ Res Public Health ; 19(9)2022 05 02.
Article in English | MEDLINE | ID: covidwho-1820267

ABSTRACT

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.


Subject(s)
COVID-19 , Hypertension , Adult , COVID-19/epidemiology , Comorbidity , Health Personnel , Hospitalization , Humans , Hypertension/epidemiology , Middle Aged , Retrospective Studies , SARS-CoV-2 , Severity of Illness Index , South Africa/epidemiology , Young Adult
10.
Nat Rev Immunol ; 22(5): 267-269, 2022 05.
Article in English | MEDLINE | ID: covidwho-1799587
11.
Trop Med Int Health ; 27(6): 564-573, 2022 06.
Article in English | MEDLINE | ID: covidwho-1784751

ABSTRACT

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.


Subject(s)
COVID-19 , Clinical Laboratory Techniques , SARS-CoV-2 , Adult , COVID-19/diagnosis , COVID-19/epidemiology , COVID-19/prevention & control , COVID-19/virology , COVID-19 Testing , COVID-19 Vaccines/administration & dosage , Cohort Studies , Female , Humans , Male , SARS-CoV-2/genetics , SARS-CoV-2/isolation & purification , Seroepidemiologic Studies , South Africa/epidemiology , Young Adult
12.
Emerg Infect Dis ; 28(5): 1055-1058, 2022 05.
Article in English | MEDLINE | ID: covidwho-1760190

ABSTRACT

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.


Subject(s)
COVID-19 , SARS-CoV-2 , COVID-19/epidemiology , Humans , Seroepidemiologic Studies , South Africa/epidemiology
13.
Lancet Respir Med ; 10(6): 603-622, 2022 06.
Article in English | MEDLINE | ID: covidwho-1758001

ABSTRACT

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.


Subject(s)
COVID-19 , Tuberculosis , COVID-19/epidemiology , Humans , Incidence , Pandemics , Tuberculosis/diagnosis , Tuberculosis/epidemiology , Tuberculosis/therapy
14.
Lancet ; 399(10330): 1141-1153, 2022 03 19.
Article in English | MEDLINE | ID: covidwho-1747473

ABSTRACT

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 × 1010 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.


Subject(s)
COVID-19 , HIV Infections , Vaccines , Adolescent , Adult , Aged , COVID-19/epidemiology , COVID-19/prevention & control , Female , Humans , Male , SARS-CoV-2 , South Africa/epidemiology
15.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-329751

ABSTRACT

Background Post COVID-19 Condition (PCC) as defined by WHO refers to a wide range of new, returning, or ongoing health problems experienced by COVID-19 survivors, and represents a rapidly emerging public health priority. We aimed to establish how this developing condition has impacted patients in South Africa and which population groups are at risk. Methods In this prospective cohort study, participants ≥18 years who had been hospitalised with laboratory-confirmed SARS-CoV-2 infection during the second and third wave between December 2020 and August 2021 underwent telephonic follow-up assessment up at one-month and three-months after hospital discharge. Participants were assessed using a standardised questionnaire for the evaluation of symptoms, functional status, health-related quality of life and occupational status. Multivariable logistic regression models were used to determine factors associated with PCC. Findings In total, 1,873 of 2,413 (78%) enrolled hospitalised COVID-19 participants were followed up at three-months after hospital discharge. Participants had a median age of 52 years (IQR 41-62) and 960 (51.3%) were women. At three-months follow-up, 1,249 (66.7%) participants reported one or more persistent COVID-related symptom(s), compared to 1,978/2,413 (82.1%) at one-month post-hospital discharge. The most common symptoms reported were fatigue (50.3%), shortness of breath (23.4%), confusion or lack of concentration (17.5%), headaches (13.8%) and problems seeing/blurred vision (10.1%). On multivariable analysis, factors associated with new or persistent symptoms following acute COVID-19 were age ≥65 years [adjusted odds ratio (aOR) 1.62;95%confidence interval (CI) 1.00-2.61];female sex (aOR 2.00;95% CI 1.51-2.65);mixed ethnicity (aOR 2.15;95% CI 1.26-3.66) compared to black ethnicity;requiring supplemental oxygen during admission (aOR 1.44;95% CI 1.06-1.97);ICU admission (aOR 1.87;95% CI 1.36-2.57);pre-existing obesity (aOR 1.44;95% CI 1.09-1.91);and the presence of ≥4 acute symptoms (aOR 1.94;95% CI 1.19-3.15) compared to no symptoms at onset. Interpretation The majority of COVID-19 survivors in this cohort of previously hospitalised participants reported persistent symptoms at three-months from hospital discharge, as well as a significant impact of PCC on their functional and occupational status. The large burden of PCC symptoms identified in this study emphasises the need for a national health strategy. This should include the development of clinical guidelines and training of health care workers, in identifying, assessing and caring for patients affected by PCC, establishment of multidisciplinary national health services, and provision of information and support to people who suffer from PCC.

16.
Clin Infect Dis ; 2022 Mar 10.
Article in English | MEDLINE | ID: covidwho-1735548

ABSTRACT

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.

17.
EuropePMC; 2022.
Preprint in English | EuropePMC | ID: ppcovidwho-329097

ABSTRACT

Background: Clinical severity of patients hospitalised with SARS-CoV-2 infection during the Omicron (fourth) wave was assessed and compared to trends in the D614G (first), Beta (second), and Delta (third) waves in South Africa. Methods: Weekly incidence of 30 laboratory-confirmed SARS-CoV-2 cases/100,000 population defined the start and end of each wave. Hospital admission data were collected through an active national COVID-19-specific surveillance programme. Disease severity was compared across waves by post-imputation random effect multivariable logistic regression models. Severe disease was defined as one or more of acute respiratory distress, supplemental oxygen, mechanical ventilation, intensive-care admission or death. Results: 335,219 laboratory-confirmed SARS-CoV-2 admissions were analysed, constituting 10.4% of 3,216,179 cases recorded during the 4 waves. In the Omicron wave, 8.3% of cases were admitted to hospital (52,038/629,617) compared to 12.9% (71,411/553,530) in the D614G, 12.6% (91,843/726,772) in the Beta and 10.0% (131,083/1,306,260) in the Delta waves (p<0.001). During the Omicron wave, 33.6% of admissions experienced severe disease compared to 52.3%, 63.4% and 63.0% in the D614G, Beta and Delta waves (p<0.001). The in-hospital case fatality ratio during the Omicron wave was 10.7%, compared to 21.5%, 28.8% and 26.4% in the D614G, Beta and Delta waves (p<0.001). Compared to the Omicron wave, patients had more severe clinical presentations in the D614G (adjusted odds ratio [aOR] 2.07;95% confidence interval [CI] 2.01-2.13), Beta (aOR 3.59;CI: 3.49-3.70) and Delta (aOR 3.47: CI: 3.38-3.57) waves. Conclusion: The trend of increasing cases and admissions across South Africa's first three waves shifted in Omicron fourth wave, with a higher and quicker peak but fewer admitted patients, who experienced less clinically severe illness and had a lower case-fatality ratio. 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 prior infection levels.

18.
N Engl J Med ; 386(14): 1314-1326, 2022 04 07.
Article in English | MEDLINE | ID: covidwho-1703992

ABSTRACT

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.).


Subject(s)
COVID-19 , SARS-CoV-2 , Adolescent , Adult , Antibodies, Viral/blood , Antibodies, Viral/immunology , COVID-19/blood , COVID-19/epidemiology , COVID-19/immunology , COVID-19/virology , COVID-19 Vaccines , Child , Humans , Immunoglobulin G/blood , Immunoglobulin G/immunology , Middle Aged , Public Health Surveillance , SARS-CoV-2/genetics , SARS-CoV-2/immunology , SARS-CoV-2/pathogenicity , Seroepidemiologic Studies , South Africa/epidemiology , Spike Glycoprotein, Coronavirus/immunology , Young Adult
19.
EuropePMC; 2021.
Preprint in English | EuropePMC | ID: ppcovidwho-314594

ABSTRACT

Introduction: We describe epidemiology and outcomes of confirmed SARS-CoV-2 infection and 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 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=2,007) 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 and those with underlying conditions should be considered for increased testing and vaccination.

20.
EuropePMC;
Preprint in English | EuropePMC | ID: ppcovidwho-327744

ABSTRACT

ABSTRACT Early data indicated that infection with Omicron BA.1 sub-lineage was associated with a lower risk of hospitalisation and severe illness, compared to Delta infection. Recently, the BA.2 sub-lineage has increased in many areas globally. We aimed to assess the severity of BA.2 infections compared to BA.1 in South Africa. We performed data linkages for (i) national COVID-19 case data, (ii) SARS-CoV-2 laboratory test data, and (iii) COVID-19 hospitalisations data, nationally. For cases identified using TaqPath COVID-19 PCR, infections were designated as S-gene target failure (SGTF, proxy for BA.1) or S-gene positive (proxy for BA.2). Disease severity was assessed using multivariable logistic regression models comparing individuals with S-gene positive infection to SGTF-infected individuals diagnosed between 1 December 2021 to 20 January 2022. From week 49 (starting 5 December 2021) through week 4 (ending 29 January 2022), the proportion of S-gene positive infections increased from 3% (931/31,271) to 80% (2,425/3,031). The odds of being admitted to hospital did not differ between individuals with S-gene positive (BA.2 proxy) infection compared to SGTF (BA.1 proxy) infection (adjusted odds ratio (aOR) 0.96, 95% confidence interval (CI) 0.85-1.09). Among hospitalised individuals, after controlling for factors associated with severe disease, the odds of severe disease did not differ for individuals with S-gene positive infection compared to SGTF infection (aOR 0.91, 95%CI 0.68-1.22). These data suggest that while BA.2 may have a competitive advantage over BA.1 in some settings, the clinical profile of illness remains similar.

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