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1.
Topics in Antiviral Medicine ; 30(1 SUPPL):300-301, 2022.
Article in English | EMBASE | ID: covidwho-1880872

ABSTRACT

Background: South Africa is one of the African countries most affected by the COVID-19 pandemic. SARS-CoV-2 seroprevalence surveys provide valuable epidemiological information given the existence of asymptomatic cases. We report the findings of the first nationwide household-based population estimates of SARS-CoV-2 seroprevalence among people aged 12 years and older in South Africa. Methods: The survey used a cross-sectional multi-stage stratified cluster design undertaken over two separate time periods (November 2020-February 2021 and April-June 2021) which coincided with the second and third waves of the pandemic in South Africa. The Abbott® and Euroimmun® ani-SARS CoV-2 antibody assays were used to test for SARS-CoV-2 antibodies, the latter being the final result. The survey data was weighted with final individual weights benchmarked against 2020 mid-year population estimates by age, race, sex, and province. Frequencies were used to describe characteristics of the study population and SARS-CoV-2 seroprevalence. Bivariate and multivariate logistics regression analysis were used to identify factors associated with SARS-CoV-2 seropositivity. Results: 13640 participants gave a blood sample. The SARS-CoV-2 seroprevalence using the Euroimmun assay was 19.6% (95% CI 17.9-21.3) over the study period, translating to an estimated 8 675 265 (95% CI 7 508 393-9 842 137) estimated infections among people aged 12 years and older across South Africa by June 2021. Seroprevalence was higher in the Free State (26.8%), and Eastern Cape (26.0%) provinces (Figure). Increased odds of seropositivity were associated with prior PCR testing [aOR=1.29 (95% CI: 0.99-1.66)], being female [aOR=1.28 (95% CI 1.00-1.64), p=0.048] and hypertension, [aOR=1.28 (95% CI 1.00-1.640, p=0.048]. Conclusion: These findings highlight the burden of infection in South Africa by June 2021, and support testing strategies that focus on individuals with known exposure or symptoms since universal testing is not feasible. Females and younger people were more likely to be infected suggesting need for additional strategies targeting these populations. The estimated number of infections was 6.5 times higher than the number of SARS-CoV-2 cases reported nationally, suggesting that the country's testing strategy and capacity partly explain the dynamics of the pandemic. It is therefore essential to bolster testing capacity and to rapidly scale up vaccinations in order to contain the spread of the virus in the country.

2.
Topics in Antiviral Medicine ; 30(1 SUPPL):18, 2022.
Article in English | EMBASE | ID: covidwho-1880294

ABSTRACT

Background: The Sisonke Phase IIIB open-label implementation study vaccinated health care workers (HCWs) with the single dose Ad26.COV2.S vaccine during two phases of the South African Covid-19 epidemic, dominated first by the Beta followed by the Delta variant of concern. Methods: HCWs were vaccinated over 3 months (17 February-17 May 2021). Safety was monitored by self-reporting, facility reporting and linkage to national databases. Vaccine effectiveness (VE) against Covid-19 related hospitalisation, hospitalisation requiring critical or intensive care and death, ascertained 28 days or more post vaccination was assessed up until 17 July 2021. Nested sub-cohorts (A and B) from two national medical schemes were evaluated to assess VE using a matched retrospective cohort design. Results: Over the 3-month period, 477234 HCWs were vaccinated in 122 vaccination sites across South Africa. VE derived from the sub-cohorts comprising 215 813 HCWs was 83% (95% CI 75-89) to prevent Covid-19 deaths, 75% (95% CI 69-82) to prevent hospital admissions requiring critical or intensive care and 67% (95% CI 62-71) to prevent Covid-19 related hospitalisations. The VE was maintained in older HCWs and those with comorbidities including HIV infection. VE remained consistent throughout the Beta and Delta dominant phases of the study. 10279 adverse events were reported and 139 (1.4%) were serious, including two cases of thrombosis with thrombocytopenia syndrome and four cases of Guillain-Barré syndrome who recovered. Conclusion: The single dose Ad26.COV2.S was safe and effective against severe Covid-19 disease and death post-vaccination, and against both Beta and Delta variants providing real-world evidence for its use globally.

3.
Topics in Antiviral Medicine ; 30(1 SUPPL):331-332, 2022.
Article in English | EMBASE | ID: covidwho-1880280

ABSTRACT

Background: SARS-CoV2 antibody testing is an important auxillary test especially for retrospective diagnosis or in patients with long COVID-19 or multisystem inflammatory syndrome of childhood. Epidemiological serology studies may also assist public health planning. Access to formal laboratory testing is not universal in many low-and middle-income (LMIC) countries and rapid lateral flow antibody tests are an attractive alternative. Performance of these tests has been inconsistent. A large-scale study was undertaken in South Africa, during the beta and delta waves, to assess the field-based performance of rapid point of care (POC) COVID-19 antibody tests. Methods: Symptomatic, ambulatory persons under investigation (PUIs) aged 18 years and older, presenting for SARS-CoV-2 diagnosis at public health facilities in three provinces, South Africa were enrolled at baseline. All patients completed a questionnaire regarding symptoms. Nasopharyngeal swabs were taken and processed for SARS-CoV-2 PCR testing using a GeneXpert (Cepheid, USA), or manual assay (ThermoFisher TaqPath assay or Seegene Allplex assay) on a real-time platform at routine accredited National Health Laboratory Service laboratories as per routine national protocols. Concomitantly, trained study staff performed three facility-based POC lateral flow antibody tests on a on a fingerstick sample and blood was collected for formal serology. POC tests were selected following a rapid in-laboratory evaluation. Asymptomatic contacts of people with confirmed COVID-19 were recruited into the asymptomatic study arm and rapid tests and PCR were performed. PCR and rapid positive patients and 500 negative controls were followed up at 5-14 days. Antibody tests were compared with formal serology performed on 2 platforms-Euroimmun (Euroimmun, Lubeck) IgA and IgG anti-S antibodies and Abbott Architect IgG test. Results: The sensitivity (S), specificity (Sp), positive (PPV) and negative predictive (NPV) values of tests for PUIs and contacts were calculated (Table 1)∗. Analyses using serology as a reference are forthcoming. Conclusion: Compared with PCR, performance of rapid POC COVID-19 antibody tests was poor with low sensitivity. This may reflect the patient cohort tested as humoral responses typically develop from day 7-14. The tests are unlikely to be useful for acute diagnosis but sensitivity may improve at later timepoints and further follow up data will be analysed by duration of symptom onset, severity of symptoms and wave (beta versus delta).

4.
Topics in Antiviral Medicine ; 30(1 SUPPL):331, 2022.
Article in English | EMBASE | ID: covidwho-1880279

ABSTRACT

Background: Access to SARS-CoV-2 polymerase chain reaction (PCR) testing is a bottleneck globally, especially in low-and middle-income countries (LMICs). Reliable point-of-care (POC) diagnostics for coronavirus disease 2019 (COVID-19) are cheaper and easier to scale-up than PCR especially in LMICs, and will facilitate interruption of transmission. We report the field-based effectiveness of rapid point-of-care (POC) antigen COVID-19 tests during the beta and delta waves, in South Africa. Methods: We enrolled symptomatic, ambulatory persons under investigation (PUIs) aged 18 years and older, presenting for SARS-CoV-2 diagnosis at public health facilities in three provinces, South Africa. All patients completed a questionnaire regarding symptoms. Nasopharyngeal swabs were taken and processed for SARS-CoV-2 PCR testing using either GeneXpert (Cepheid, USA), or with a manual assay (ThermoFisher TaqPath assay or Seegene Allplex assay) on a real-time PCR platform at routine, accredited National Health Laboratory Service laboratories, as per routine national protocols. Concomitantly, trained study staff performed three facility-based POC antigen tests on a nasal/nasopharyngeal swab, as recommended by the manufacturer. Asymptomatic contacts of people with confirmed COVID-19 were recruited into the asymptomatic study arm and rapid tests and PCR were performed. The sensitivity (S), specificity (Sp), positive (PPV) and negative predictive (NPV) values of tests for PUIs and contacts were calculated using PCR as the reference standard. Results: Between Oct 2020-2021 1816 participants were enrolled;472 (26%) tested PCR or rapid test positive;235 positives (49.8%) and 532 negatives were followed up at 5-14 days;574 asymptomatic contacts were enrolled, of which 21 (3.7%) were PCR positive. Performance of the three antigen tests are shown in Table 1∗. Conclusion: In a real world setting, during the beta and delta waves, compared with PCR the sensitivity of rapid antigen tests ranged from 35-68%. This may reflect low viral loads at diagnosis. Further work will compare antigen test performance in patients with high versus lower cycle threshold (Ct) values. Meanwhile, PCR testing capacity needs urgent scale-up in LMICs and improved POC diagnostics are needed to facilitate COVID-19 diagnosis in LMICs.

5.
17th International Scientific Conference on eLearning and Software for Education, eLSE 2021 ; : 88-94, 2021.
Article in English | Scopus | ID: covidwho-1786289

ABSTRACT

The COVID-19 pandemic has caused beyond example change in the educational system worldwide. Apart from the economic and social impacts, that the pandemic has created, there is a reluctance to accept the new educational system “e-learning” by students from various educational institutions. In particular, universities students, but also professors have to deal with several types of environmental, electronic and mental struggles due to COVID-19. To cope with the new changes, Transilvania University of Brasov has improved its two online platforms “intranet” and “e-lerning” to ensure that all students benefit from education. This study focus attention on the need to guarantee the continuity of the educational process in crisis situation. It highlights the positive and negative effects of the COVID-19 pandemic in higher education institutions especially in the case of law schools. It also deals with the issue of online law teaching and the difficulties encountered by a university professor. © 2021, National Defence University - Carol I Printing House. All rights reserved.

6.
South African Medical Journal ; 112(2 b), 2022.
Article in English | EMBASE | ID: covidwho-1706330

ABSTRACT

Sisonke is a multicentre, open-label, single-arm phase 3B vaccine implementation study of healthcare workers (HCWs) in South Africa, with prospective surveillance for 2 years. The primary endpoint is the rate of severe COVID-19, including hospitalisations and deaths. The Sisonke study enrolled and vaccinated participants nationally at potential vaccination roll-out sites between 17 February and 26 May 2021. After May 2021, additional HCWs were vaccinated as part of a sub-study at selected clinical research sites. We discuss 10 lessons learnt to strengthen national and global vaccination strategies: (i) consistently advocate for vaccination to reduce public hesitancy;(ii) an electronic vaccination data system (EVDS) is critical;(iii) facilitate access to a choice of vaccination sites, such as religious and community centres, schools, shopping malls and drive-through centres;(iv) let digitally literate people help elderly and marginalised people to register for vaccination;(v) develop clear 'how to' guides for vaccine storage, pharmacy staff and vaccinators;(vi) leverage instant messaging platforms, such as WhatsApp, for quick communication among staff at vaccination centres;(vii) safety is paramount - rapid health assessments are needed at vaccination centres to identify people at high risk of serious adverse events, including anaphylaxis or thrombosis with thrombocytopenia syndrome. Be transparent about adverse events and contextualise vaccination benefits, while acknowledging the small risks;(viii) provide real-time, responsive support to vaccinees post vaccination and implement an accessible national vaccine adverse events surveillance system;(ix) develop efficient systems to monitor and investigate COVID-19 breakthrough infections;and (x) flexibility and teamwork are essential in vaccination centres across national, provincial and district levels and between public and private sectors.

7.
Embase;
Preprint in English | EMBASE | ID: ppcovidwho-327037

ABSTRACT

Following the results of the ENSEMBLE 2 study, which demonstrated improved vaccine efficacy of a two-dose regimen of Ad26.COV.2 vaccine given 2 months apart, we expanded the Sisonke study which had provided single dose Ad26.COV.2 vaccine to almost 500 000 health care workers (HCW) in South Africa to include a booster dose of the Ad26.COV.2. Sisonke 2 enrolled 227 310 HCW from the 8 November to the 17 December 2021. Enrolment commenced before the onset of the Omicron driven fourth wave in South Africa affording us an opportunity to evaluate early VE in preventing hospital admissions of a homologous boost of the Ad26.COV.2 vaccine given 6-9 months after the initial vaccination in HCW. We estimated vaccine effectiveness (VE) of the Ad26.COV2.S vaccine booster in 69 092 HCW as compared to unvaccinated individuals enrolled in the same managed care organization using a test negative design. We compared VE against COVID19 admission for omicron during the period 15 November to 20 December 2021. After adjusting for confounders, we observed that VE for hospitalisation increased over time since booster dose, from 63% (95%CI 31-81%);to 84% (95% CI 67-92%) and then 85% (95% CI: 54-95%), 0-13 days, 14-27 days, and 1-2 months post-boost. We provide the first evidence of the effectiveness of a homologous Ad26.COV.2 vaccine boost given 6-9 months after the initial single vaccination series during a period of omicron variant circulation. This data is important given the increased reliance on the Ad26.COV.2 vaccine in Africa.

8.
Embase;
Preprint in English | EMBASE | ID: ppcovidwho-326920

ABSTRACT

Background: The Sisonke open-label phase 3b implementation study aimed to assess the safety and effectiveness of the Janssen Ad26.CoV2.S vaccine among health care workers (HCWs) in South Africa. Here, we present the safety data. Methods: We monitored adverse events (AEs) at vaccination sites, through self-reporting triggered by text messages after vaccination, health care provider reports and by active case finding. The frequency and incidence rate of non-serious and serious AEs were evaluated from day of first vaccination (17 February 2021) until 28 days after the final vaccination (15 June 2021). COVID-19 breakthrough infections, hospitalisations and deaths were ascertained via linkage of the electronic vaccination register with existing national databases. Findings: Of 477,234 participants, 10,279 (2.2%) reported AEs, of which 139 (1.4%) were serious. Women reported more AEs than men (2.3% vs. 1.6%). AE reports decreased with increasing age (3.2% for 18–30, 2.1% for 31-45, 1.8% for 46-55 and 1.5% in >55-year-olds). Participants with previous COVID-19 infection reported slightly more AEs (2.6% vs. 2.1%). The commonest reactogenicity events were headache and body aches, followed by injection site pain and fever, and most occurred within 48 hours of vaccination. Two cases of Thrombosis with Thrombocytopenia Syndrome and four cases of Guillain-Barre Syndrome were reported post-vaccination. Serious AEs and AEs of special interest including vascular and nervous system events, immune system disorders and deaths occurred at lower than the expected population rates. Interpretation: The single-dose Ad26.CoV2.S vaccine had an acceptable safety profile supporting the continued use of this vaccine in our setting.

9.
S Afr Med J ; 112(2b): 13486, 2021 12 24.
Article in English | MEDLINE | ID: covidwho-1678836

ABSTRACT

Sisonke is a multicentre, open-label, single-arm phase 3B vaccine implementation study of healthcare workers (HCWs) in South Africa, with prospective surveillance for 2 years. The primary endpoint is the rate of severe COVID­19, including hospitalisations and deaths. The  Sisonke study enrolled and vaccinated participants nationally at potential vaccination roll-out sites between 17 February and 26 May 2021. After May 2021, additional HCWs were vaccinated as part of a sub-study at selected clinical research sites. We discuss 10 lessons learnt to strengthen national and global vaccination strategies:(i) consistently advocate for vaccination to reduce public hesitancy; (ii) an electronic vaccination data system (EVDS) is critical; (iii) facilitate access to a choice of vaccination sites, such as religious and community centres, schools, shopping malls and drive-through centres; (iv) let digitally literate people help elderly and marginalised people to register for vaccination; (v) develop clear 'how to' guides for vaccine storage, pharmacy staff and vaccinators; (vi) leverage instant messaging platforms, such as WhatsApp, for quick communication among staff at vaccination centres; (vii) safety is paramount - rapid health assessments are needed at vaccination centres to identify people at high risk of serious adverse events, including anaphylaxis or thrombosis with thrombocytopenia syndrome. Be transparent about adverse events and contextualise vaccination benefits, while acknowledging the small risks; (viii) provide real-time, responsive support to vaccinees post vaccination and implement an accessible national vaccine adverse events surveillance system; (ix) develop efficient systems to monitor and investigate COVID­19 breakthrough infections; and (x) flexibility and teamwork are essential in vaccination centres across national, provincial and district levels and between public and private sectors.


Subject(s)
COVID-19 Vaccines/administration & dosage , COVID-19/prevention & control , Health Personnel , Infectious Disease Transmission, Patient-to-Professional/prevention & control , Mass Vaccination , Humans , Prospective Studies , SARS-CoV-2 , South Africa/epidemiology
10.
21st Conference Information Technologies - Applications and Theory, ITAT 2021 ; 2962:293-300, 2021.
Article in English | Scopus | ID: covidwho-1469210

ABSTRACT

The ongoing SARS-CoV-2 pandemic, which emerged in December 2019, revolutionized genomic surveillance, leading to new means of tracking viral spread and monitoring genetic changes in their genomes over time. One of the key sequencing methods used during the pandemic is based on massively parallel short read sequencing based on Illumina technology. In this work, we present a highly scalable and easily deployable computational pipeline for the analysis of Illumina sequencing data, which is used in Slovak SARS-CoV-2 genomic surveillance efforts. We discuss several issues that arose during the pipeline design, and which could both provide useful insight into the analysis processes and serve as a guideline for optimized future outbreak surveillance projects. Copyright © 2021 for this paper by its authors.

11.
S Afr Med J ; 111(2): 100-105, 2021 01 20.
Article in English | MEDLINE | ID: covidwho-1168064

ABSTRACT

The COVID-19 pandemic has resulted in many hospitals severely limiting or denying parents access to their hospitalised children. This article provides guidance for hospital managers, healthcare staff, district-level managers and provincial managers on parental access to hospitalised children during a pandemic such as COVID-19. It: (i) summarises legal and ethical issues around parental visitation rights; (ii) highlights four guiding principles; (iii) provides 10 practical recommendations to facilitate safe parental access to hospitalised children; (iv) highlights additional considerations if the mother is COVID-19-positive; and (v) provides considerations for fathers. In summary, it is a child's right to have access to his or her parents during hospitalisation, and parents should have access to their hospitalised children; during an infectious disease pandemic such as COVID-19, there is a responsibility to ensure that parental visitation is implemented in a reasonable and safe manner. Separation should only occur in exceptional circumstances, e.g. if adequate in-hospital facilities do not exist to jointly accommodate the parent/caregiver and the newborn/infant/child. Both parents should be allowed access to hospitalised children, under strict infection prevention and control (IPC) measures and with implementation of non-pharmaceutical interventions (NPIs), including handwashing/sanitisation, face masks and physical distancing. Newborns/infants and their parents/caregivers have a reasonably high likelihood of having similar COVID-19 status, and should be managed as a dyad rather than as individuals. Every hospital should provide lodger/boarder facilities for mothers who are COVID-19-positive, COVID-19-negative or persons under investigation (PUI), separately, with stringent IPC measures and NPIs. If facilities are limited, breastfeeding mothers should be prioritised, in the following order: (i) COVID-19-negative; (ii) COVID-19 PUI; and (iii) COVID-19-positive. Breastfeeding, or breastmilk feeding, should be promoted, supported and protected, and skin-to-skin care of newborns with the mother/caregiver (with IPC measures) should be discussed and practised as far as possible. Surgical masks should be provided to all parents/caregivers and replaced daily throughout the hospital stay. Parents should be referred to social services and local community resources to ensure that multidisciplinary support is provided. Hospitals should develop individual-level policies and share these with staff and parents. Additionally, hospitals should ideally track the effect of parental visitation rights on hospital-based COVID-19 outbreaks, the mental health of hospitalised children, and their rate of recovery.


Subject(s)
Child Health/standards , Child, Hospitalized/statistics & numerical data , Hospitals/standards , Infection Control/standards , Patient Isolation/standards , Visitors to Patients/statistics & numerical data , COVID-19 , Child , Female , Humans , Infant, Newborn , South Africa
13.
S Afr Med J ; 110(9): 842-845, 2020 07 17.
Article in English | MEDLINE | ID: covidwho-743542

ABSTRACT

Antibody tests for the novel coronavirus, SARS-CoV2, have been developed both as rapid diagnostic assays and for high-throughput formal serology platforms. Although these tests may be a useful adjunct to a diagnostic strategy, they have a number of limitations. Because of the antibody and viral dynamics of the coronavirus, their sensitivity can be variable, especially at early time points after symptom onset. Additional data are required on the performance of the tests in the South African population, especially with regard to development and persistence of antibody responses and whether antibodies are protective against reinfection. These tests may, however, be useful in guiding the public health response, providing data for research (including seroprevalence surveys and vaccine initiatives) and development of therapeutic strategies.


Subject(s)
Betacoronavirus , Clinical Laboratory Techniques , Coronavirus Infections , Immunologic Tests/methods , Pandemics , Pneumonia, Viral , Serologic Tests/methods , Betacoronavirus/genetics , Betacoronavirus/immunology , Betacoronavirus/isolation & purification , COVID-19 , COVID-19 Testing , Clinical Laboratory Techniques/methods , Clinical Laboratory Techniques/standards , Coronavirus Infections/diagnosis , Coronavirus Infections/epidemiology , Coronavirus Infections/immunology , Humans , Pneumonia, Viral/diagnosis , Pneumonia, Viral/epidemiology , Pneumonia, Viral/immunology , Reproducibility of Results , SARS-CoV-2 , Sensitivity and Specificity , Seroepidemiologic Studies , South Africa/epidemiology
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