COVID-19 SURVEILLANCE REPORTS
NATIONAL COVID-19 DAILY REPORT DASHBOARD
Please note that due to a technical problem, the reported number of new tests in the public sector for today includes tests from 25 May 2020 that were not reflected in yesterday’s report.
The purpose of this report is to project estimated COVID-19 cases at national and provincial.
The National COVID-19 Epi Model (NCEM) for the National and Provincial long-term projections released on the 6th May 2020 and the short-term projections released on the 12th of June 2020.
This report includes an analysis of data on laboratory-confirmed COVID-19 deaths to estimate the effective reproductive number (R) of SARS-CoV-2 over time in South Africa nationally and in selected provinces where sufficient data are available. The effective reproduction number (R) is the average number of secondary cases per infectious case in a population composed of both susceptible and nonsusceptible hosts (once the infectious agent is circulating).
-During the stage 3 lockdown, the daily R varied slightly, with an average of 1.05 (95%CI: 1.01 – 1.09), between 1 June and 1 August, dropping below 1 during the last weeks of July. This indicates ongoing transmission at a steadily slowing rate over this period, with numbers of new cases per infectious case dropping below 1 towards the end of the period.
-In provinces where estimation was possible for stages 5, 4 and 3 (Western Cape, Gauteng, Eastern Cape and KwaZulu-Natal provinces), the R during the stage 5 and 4 lockdown ranged between 1.5 and 1.0. Generally, R showed reductions during the stage 3 lockdown indicating slowing of transmission in all three provinces by the end of July
-This report includes new estimates of R during the stage 3 lockdown for Mpumalanga and Free State provinces, indicating steady declines in R over this period.
The report is based on data collected from 5 March to 04 October 2020 (week 40 of 2020).
- In provinces with sufficient levels of reporting (Eastern Cape, Free State, Gauteng, KwaZulu-Natal, Limpopo, North-West, and Western Cape), respiratory hospital admissions in all ages combined increased throughout the lockdown period reducing in recent weeks. Since the initiation of lockdown measures in late March, respiratory hospitalizations in young children (<5 years) have been substantially below those expected in the absence of COVID-19, likely due to diminished transmission of the respiratory syncytial virus (RSV), influenza, and other seasonal viruses. Respiratory admissions for adult age groups (20-49 years, ≥50 years) increased during the lockdown period and reached numbers several times higher than those observed in past influenza seasons during Alert Level 3.
- Outpatient general practitioner respiratory consultations spiked in early March, consistent with “worried well” health-seeking behaviour, then declined sharply across South African provinces and age groups, reflecting the impact of the lockdown.
- Outpatient emergency department consultations at private hospitals experienced a “worried well” spike in early March, though to a lesser degree than observed for general practitioner providers. Since the initiation of lockdown measures in late March, respiratory visits in children (<5 years, 5-19 years) are substantially below baseline numbers expected in the absence of COVID-19.
This report summarises data from national laboratory-based surveillance that is used to monitor the COVID-19 pandemic in South Africa. This report is based on data collected up to 10 October 2020 (week 41 of 2020).
-As of 10 October 2020, a total of 692 471 laboratory-confirmed COVID-19 cases, including 17 780 deaths (case fatality ratio 2.6%), had been detected in South Africa. Of these, 9 634 were cases detected in week 41, representing a 7.2% decrease in number of new cases detected in week 41 compared to the number of new cases detected in week 40 (10 377).
-Similar to the past two weeks, in the past week, Free State Province reported the highest number of new cases (2 139/9 634, 22.2%), followed by Gauteng Province (1 895/9 634, 19.7%), and Western Cape Province (1 402/9 634, 14.6%).
-In the past week seven provinces reported a decline in weekly incidence risk, compared to week 40; reduction ranged from 33 cases per 100 000 persons (32% reduction) in Northern Cape Province to 1 case per 100 000 persons (14% reduction in Limpopo Province, 11% reduction in Mpumalanga Province, and 10% reduction in Eastern Cape Province). There was an increase in weekly incidence risk of 5 cases per 100 000 persons in Western Cape Province (33% increase).
The report is based on data collected from 5 March to 11 October 2020 (week 41 of 2020).
-Numbers of respiratory hospitalisations show a slight increase.
-The proportion of respiratory or COVID-19 hospitalisations in all ages is decreasing but remains at the very high level among individuals aged 20-49 years.
-Percentage of general practitioner and emergency department visits coded as respiratory is also declining.
-The 2020 influenza season has not yet started. Only one detection of influenza A(H1N1)pdm09 has been made in week 24 (week starting 8 June 2020), since the localised outbreak of influenza A(H1N1)pdm09 and to a lesser extent influenza B(Victoria) in the Western Cape Province, in the first three months of the year.
-Although the 2020 respiratory syncytial virus (RSV) season has not started, with only sporadic detections since mid-April, there has been a moderate increase in detection since week 29 (week ending 19 July) in the pneumonia surveillance severe acute respiratory illness (SARI) programme and to a lesser extent in the influenza-like illness (ILI) programme.
-Since the last report 14 additional patients tested positive for SARS-CoV-2 of which 7 were detected in the current reporting week (week 41), 4 in SARI and 3 in ILI surveillance. To date, 614 cases have been detected from all surveillance programmes. Of the 432 hospitalised COVID-19 cases with available data on outcome, 56 (13%) died.
– As of 19 September, children and adolescents ≤18 years made up 8.0% of laboratory-confirmed COVID-19 cases and 3.2% of all COVID-19-associated admissions at sentinel hospitals.
-The cumulative incidence of laboratory-confirmed COVID-19 cases aged ≤18 years was 256 per 100 000 populations, six times lower than that in adults (1544 per 100 000). The cumulative incidence was lowest in Limpopo province and highest in Free State province was higher in females compared to males and increased with age among individuals aged ≥1 year.
-The weekly incidence of laboratory-confirmed COVID-19 cases aged ≤18 years and cases admitted to sentinel hospitals peaked during weeks 26-30 for all provinces except Northern Cape and has been declining since then. This mirrored trends among adults >18 years.
-There were 2229 reported COVID-19-associated admissions among individuals aged ≤18 years; of these, 1605 (72.0%) had data on underlying conditions and of these 240 (14.9%) had ≥1 underlying conditions. Asthma and other chronic pulmonary conditions and HIV were the commonest underlying conditions.
-As of 10 October, 87 565 COVID-19 admissions were reported from 584 facilities (340 public-sector and 244 private-sector) in all nine provinces of South Africa. DATCOV coverage is now 96% of public and 100% of private hospitals that have had COVID-19 admissions. There was an increase of 71 additional public hospitals reporting and 16 973 additional admissions reported since the last report, although these mainly reflect historic admissions and not new admissions. There were 40 003 (46%) and 47 562 (54%) admissions reported in public and private sector respectively. The majority of COVID-19 admissions were reported from four provinces, Gauteng (27 903, 32%), followed by Western Cape (18 880, 22%), KwaZulu-Natal (13 413, 15%) and Eastern Cape (11 481, 13%). Hospital admissions peaked in South Africa in week 29 and 30.
-Of the 87 565 admissions, 6370 (7%) patients were in hospital at the time of this report, 66 417 (76%) patients were discharged alive or transferred out and 14 778 (17%) patients had died. There were 2 163 additional deaths since the last report.
-Of the 79 820 COVID-19 patients who had recorded in-hospital outcome (died and discharged), the case fatality ratio (CFR) was 19%. On multivariable analysis, factors associated with in-hospital mortality were older age groups; male sex; Black African, Coloured and Indian race; admission in the public sector; and having comorbid hypertension, diabetes, chronic cardiac disease, chronic renal disease, malignancy, HIV, current tuberculosis alone or both current and past tuberculosis, and obesity. Compared to the Western Cape Province, individuals hospitalised in Eastern Cape, Free State, Gauteng, KwaZulu-Natal, Limpopo, North West and Northern Cape provinces were more likely to die in hospital.
This report summarises national laboratory testing for SARS-CoV-2, the virus causing COVID-19, in South Africa. This report is based on data collected up to 10 October 2020 (week 41 of 2020)
-In the period 1 March 2020 through 10 October 2020, 3,810,698 laboratory tests for SARS-CoV-2 have been conducted nationally. Weekly testing volumes have decreased since a peak in week 28, however the number of tests performed in week 41 were slightly higher than in recent weeks.
-Free State (335 per 100,000 persons) and Northern Cape (316 per 100,000 persons) provinces had the highest testing rates in week 41.
-Percentage testing positive has been decreasing weekly since the peak of 31.3% in week 29. In week 41 the percentage testing positive continued to decrease to 9.9%. Percentages testing positive were ≥20% in Northern Cape and Free State, between 10-19% in North West, Mpumalanga and Limpopo, and <10% in Gauteng, KwaZulu-Natal, Western Cape and Eastern Cape.