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Covid-19 Weekly Epidemiology Brief South Africa Week 4 2021

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Covid-19 Weekly Epidemiology Brief South Africa Week 4 2021 COVID-19 WEEKLY EPIDEMIOLOGY BRIEF SOUTH AFRICA WEEK 4 2021 CUMULATIVE DATA FROM 03 30 MARCH JANUARY CASES PERSONS 1 453 761 2 438,3 IN TOTAL INCIDENCE RISK* 27 402 40 THIS WEEK MEDIAN AGE LIMPOPO PROVINCES AT 57 981 990,7 IN TOTAL /100,000* A GLANCE CASES NORTH WEST GAUTENG 57 154 1 391,0 388 620 2 509,1 IN TOTAL /100,000* IN TOTAL /100,000* CASES CASES NORTHERN CAPE MPUMALANGA 32 010 2 476,0 65 054 1 390,1 IN TOTAL /100,000* IN TOTAL /100,000* CASES CASES WESTERN CAPE KWAZULU-NATAL 269 633 3 848,7 315 033 2 731,9 IN TOTAL /100,000* IN TOTAL /100,000* CASES CASES EASTERN CAPE FREE STATE 191 997 2 851,2 76 279 2 604,4 IN TOTAL /100,000* * Incidence risk - cases per 100 000 persons IN TOTAL /100,000* CASES ** based on samples collected/received in current reporting CASES week www.nicd.ac.za TOLL-FREE NUMBER 0800 029 999 PAGE 1 COVID-19 WEEKLY EPIDEMIOLOGY BRIEF WEEK 4 2021 SUMMARY Overview of report Disease surveillance is a core function of the National Institute for Communicable Diseases (NICD), a division of the National Health Laboratory Service (NHLS). This report summarises data from a national laboratory-based surveillance system that is used to monitor the coronavirus disease 2019 (COVID-19) pandemic in South Africa. This report is based on data collected up to 30 January 2021 (week 4 of 2021). Note: COVID-19 is the name of the disease and SARS-CoV-2 is the name of the virus. Trends in numbers of new cases by province and age group may be affected by changes in testing practice and delays in testing of specimens. The numbers reported may change as more data become available. Highlights • As of 30 January 2021, a total of 1 453 761 laboratory-confirmed COVID-19 cases had been detected in South Africa. Of these, 40 775 were cases reported since INCIDENCE the last report (week 3 of 2021). There was a 53.0% decrease in number of new RISK FOR cases detected in week 4 (27 402) compared to the number of new cases CURRENT WEEK detected in week 3 (58 263), possibly related in part to delays in reporting. • An additional 3 290 deaths were reported since the last report. The overall case- fatality ratio is 3.0% (44 164/1 453 761). 46,0 • In the past week, the KwaZulu-Natal Province reported the highest proportion of the new cases detected (7 078/27 402, 25.8%), followed by the Gauteng Province CASES PER (6 486/27 402, 23.7%), and the Western Cape Province (3 957/27 402, 14.4%). 100 000 • In keeping with past two weeks, in the past week, all provinces reported a PERSONS decrease in weekly incidence risk, compared to the previous week. The decrease in weekly incidence risk ranged from 23.0 cases per 100 000 persons (55.4% decrease) in the Eastern Cape Province to 79.7 cases per 100 000 persons (56.5% decrease) in the KwaZulu-Natal Province. • In week 4 Northern Cape Province reported the highest weekly incidence risk (62.7 cases per 100 000 persons), followed by the KwaZulu-Natal Province (61.4 25,8% cases per 100 000 persons), the Western Cape Province (56.5 cases per 100 000 OF CASES persons), and the Free State Province (52.3 cases per 100 000 persons). REPORTED IN • From week 3 of 2021 to date all districts in South Africa reported a decrease in KWAZULU-NATAL IN weekly incidence risks. CURRENT WEEK IN CURRENT WEEK, THE HIGHEST WEEKLY INCIDENCE RISK WAS IN CASES AGED 80+ YEARS (131,3 CASES PER 100 000 PERSONS) www.nicd.ac.za TOLL-FREE NUMBER 0800 029 999 PAGE 2 COVID-19 WEEKLY EPIDEMIOLOGY BRIEF WEEK 4 2021 Methods the COVID-19 epidemic for the provinces with sufficient data and from weeks with sufficient number of cases and Testing for SARS-CoV-2 began on 28 January 2020 at the complete data (week 12 to the week before the current NICD and after the first case was confirmed in early March reporting period). The unit of analysis (epidemiological 2020, testing was expanded to a larger network of private and week) was defined from Sunday to the following Saturday. NHLS laboratories. Respiratory specimens were submitted We first estimated the weekly growth rate of the epidemic from persons under investigation (PUI). Initially, tested by fitting a linear regression model to the logarithm of the individuals were those who had travelled to countries with daily cumulative number of laboratory-confirmed COVID-19 COVID-19 transmission but the PUI definition was changed cases. We then estimated the doubling time for each over time. Community symptom screening and referral week using the following formula log(2)/gr (where gr is the for PCR testing was implemented in April 2020 but the estimated weekly growth rate). An increase in the doubling strategy was changed to a more targeted approach in May time may suggest a slowing of transmission but this may also 2020. Community screening was largely discontinued and be affected by changes in testing strategy or care seeking. testing efforts then focussed on areas identified as hot Until the week 29 report, new cases were defined as all cases spots and on investigating clusters. Contacts of cases were reported since the last report, irrespective of when the sample traced and tested if symptomatic. In some provinces and was collected. Subsequent to the week 29 report, new cases in certain circumstances (e.g. closed settings, workplaces), are now defined as cases detected in the past epidemiologic asymptomatic contacts were tested. In recent weeks, testing week based on date of sample collection or sample receipt. It has been prioritised for healthcare workers and hospitalised is therefore possible for numbers reported as new cases for patients. Laboratories used any one of several in-house and the current reporting week not to tally with total additional commercial PCR assays to test for the presence of SARS- cases reported since the last report. This will be the case CoV-2 RNA. Testing for SARS-CoV-2 using rapid antigen-based when there was a delay in reporting of cases. tests was implemented during November 2020. We excluded specimens collected outside South Africa. Date of specimen National and provincial trends of receipt in the laboratory was used when date of specimen collection was missing. A case of COVID-19 was defined as any COVID-19 cases in South Africa person, resident in South Africa, with a single positive SARS- CoV-2 PCR or antigen test. For reports published from week As of 30 January 2021, a total of 1 453 761 laboratory-confirmed 41 onwards we used mid-year population estimates from COVID-19 cases were reported in South Africa (Figures 1 and 2). This is Statistics South Africa for 2020 to calculate the incidence 40 775 more cases than the number reported in the last report (week risk (cumulative or weekly incidence), expressed as cases 3 of 2021 report). The number of new cases detected in week 4 (27 per 100 000 persons. In historical reports published from 402) was lower than the number of new cases detected in week 3 (58 epidemiologic week 10 (during the start of COVID-19 epidemic 263), this represented a 53.0% decrease in the number of new cases in South Africa) to week 40 of 2020, 2019 mid-year population compared to the previous week, possibly in part related to delays in estimates were used. Aggregate data on the number of reporting. In the past week, the KwaZulu-Natal Province reported deaths by province were obtained from the Department of the highest number of new cases (7 078/27 402, 25.8%), followed by Health. Data on number of tests conducted in the past week the Gauteng Province (6 486/27 402, 23.7%), and the Western Cape as reported in the simultaneously-published COVID-19 weekly Province (3 957/27 402, 14.4 %) (Table 1). Five provinces, Gauteng testing report was used to calculate tests conducted per 100 (388 620/1 453 761, 26.7%), KwaZulu-Natal (315 033/ 1 453 761, 21.7%), 000 population. Data on province and district allocation was Western Cape (269 633/1 453 761, 18.5), Eastern Cape (191 997/1 453 761, based on geocoding algorithm using in order of priority (i) 13.2%), and Free State (76 279/1 453 761, 5.2%) continued to report the completeness of patient data, (ii) submitting doctor’s address, majority (1 241 562/1 453 761, 85.4%) of total COVID-19 cases in South (iii) registering doctor’s address and as final option, (iv) the Africa. In keeping with the data reported in the previous weeks, there guarantor’s address data. The geocoding algorithm used was minimal change in percent contribution of cases in the different the most complete data for assigning data on province and provinces from week 3 to week 4 of 2021. district where adequate information was provided on the lab The cumulative incidence risk for the country increased from 2 request form at the time of sample collection. Data on district 392.3 cases per 100 000 persons in week 3 of 2021 to 2 438.3 cases allocation may lag resulting in number of cases in recent per 100 000 persons in week 4. The cumulative incidence risk varied weeks missing district allocation. Prevalence and incidence by province over time (Figure 3).
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