Covid-19 Weekly Epidemiology Brief South Africa Week 4 2021

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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

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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)

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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 ofthe 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). This is partly explained by testing risk by districts should be interpreted with caution. differences by province (Table 1). The Western Cape Province reported We estimated the time-varying (weekly) doubling time of the highest cumulative incidence risk (3 848.7 cases per 100 000

www.nicd.ac.za TOLL-FREE NUMBER 0800 029 999 PAGE 3 Number of cases collection, South Africa, 3March 2021 (n=1453 2020- 30January 761) collection, SouthAfrica, cumulativeFigure 1.Numberand numberoflaboratory-confirmed casesof COVID-19 by province date and ofspecimen 43, exceeding the peak in the first wave in all the provinces, except provinces, the all in wave first the in peak the exceeding 43, weeks, all provinces reported increases in number of cases week from subsequent in cases of number in decline a byfollowed 30), week in Eastern Cape peaked earlier different in week 27 at and Northern Cape experienced peaked last risk levels and incidence weeks by the different provinces in July (Western weekly Cape and of peak the Since as aresult delays. ofreporting be could risk incidence weekly 4 week in reductions the of Some 4). (FigureProvinceKwaZulu-Natal the in decrease) (56.5% persons 000 100 per cases 79.7 to Province Cape Eastern the in decrease) (55.4% persons 000 100 per cases 23.0 from ranged risk incidence weekly in decrease The week. previous the tocompared risk, incidence weekly in decrease a reported provinces all week, past the In persons. 000 weekly The 100 per persons). cases 50 below wereprovinces other the 000 all in risk incidence 100 per cases (52.3 and Province persons), State 000 Free 100 per persons), cases 000 (56.5 Province 100 Cape Western per the followed cases 2021, (61.4 of Province 4 KwaZulu-Natal week the in persons) by 000 100 per cases (62.7 risk incidence weekly highest the reported Province Cape Northern The the reporting Province Limpopo lowest cumulative incidence risk (990.7 casesper100000persons). with persons, 000 100 per cases 000 below2 riskprovinces cumulative incidence to report continued the Northern Cape and Province persons),(2 476.0 000 cases per 100 100 000 persons). per The other cases 509.1 (2 Province Gauteng the persons), the Free State Province (2 cases 604.4 per 100 000 persons), 000 100 per cases 731.9 (2 KwaZulu-NatalProvince the persons), 000 persons), followed by the Eastern Cape Province (2 851.2 cases per 100 WEEK 42021 24 3000 27 33 COVID-19 WEEKLY EPIDEMIOLOGY BRIEF 18 21 12 15 60 90 30 00 00 00 00 00 00 00 www.nicd.ac.za 00 00 00 0 0 0 0 0 0 0 0 0

02-Mar 10-Mar 16-Mar

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27-May Cu No Li Kw We

02-Jun mp mu rt aZ st

08-Jun h op er ul la We n

14-Jun u o *Date received specimen where date collected missing ti Ca ve Na

20-Jun st p 26-Jun ta e

02-Jul l DATE SPECIMEN COLLECTED* 08-Jul 14-Jul 20-Jul 26-Jul 01-Aug 07-Aug 13-Aug 2020

19-Aug several weeks after casediagnoses. to delayed be may deaths of reporting and occurrence addition, In hospital. of out deaths than reported be to likely more are in hospital deaths as underestimate an be may CFR The numerator. the to compared denominator the in reduction rapid more a of result a as cases, as case numbers decrease rapidly, the crude CFR may increase to relation in delayed are deaths Because limitations. numerous to subject is cases) diagnosed in of deaths/number calculated of CFR (number A way this 769. 3 to compared 290 3 week, previous the in reported number the than lower was week past the in reported 290 deaths were reported since the last report. The number of deaths 3 additional an 761); 453 164/1 (44 3.0% is (CFR) ratio case-fatality The days to 83.1 days, 70.3% increase) (Figure 48.8 5). (from Province Kwazulu-Natal the and increase), 104.0% days, 163.4 to days80.1 Westernincrease),Province (from Cape 93.2% days, 297.3to days 153.9 Province(from CapeEastern increase), 42.1% days, 116.3 to days 81.8 Province(from State Free the increase), 89.8% days, 114.1 to days 60.1 (from Province Gauteng provinces, all in increased cases of number of time doubling estimated the 2021, of 3 week time. In with varied cases of number of time doubling date, to Africa inSouth cases of the majority reporting provinces five the Among provinces. other in allthe declining since week 51 in the Eastern Cape hasbeen Province and week cases 2 2021 new of the number during Weekly 3). reported (Figure peaks wave those first below risk incidence continued weekly which report Provinceto State Free and Province Cape Eastern 25-Aug 31-Aug 06-Sep 12-Sep 18-Sep 24-Sep 30-Sep 06-Oct

12-Oct 18-Oct 24-Ovt 30-Oct 05-Oct

11-Nov 17-Nov 23-Nov 29-Nov 05-Dec 11-Dec

2021 17-Dec 23-Dec 29-Dec 04-Jan 06-Jan 13-Jan PAGE 4 20-Jan 27-Jan 11 9 1 12 13 14 15 8 0 1 2 30000 40000 50000 6 7 00000 0000 0000 0000 0000 00000 0000 0 0000 0000 0000 0000 000

0 0 0 0 0 0 0 0 0 0 0 0 0 Cumulative number of cases of number Cumulative Number of cases persons by province, South Africa, 3Marchpersons 2020-30 by 2021 (n=1453 province, January 761) SouthAfrica, cumulative/weeklyTable 1.Numberand incidence risk oflaboratory-confirmed casesof COVID-19 and per100000 testing of the same reporting week reporting same of the received incurrent week); reporting 1 specimen collection, South Africa, 3March 2020-30 2021 (n=1453 January 761) collection,specimen SouthAfrica, cumulativeFigure 2.Numberand numberoflaboratory-confirmed cases of COVID-19, by laboratorytesting sector date and of New casesrefer to sampleswere caseswhose collected orreceived current inthe week; reporting Total Unknown Western Cape Northern Cape Northern WestNorth Mpumalanga Limpopo KwaZulu-Natal Gauteng Free State Eastern Cape Province 24 3000 27 33 18 21 12 15 90 60 WEEK 42021 30 COVID-19 WEEKLY EPIDEMIOLOGY BRIEF 00 00 00 00 00 00 00 00 00 00 www.nicd.ac.za 0 0 0 0 0 0 0 0 0

02-Mar 10-Mar 16-Mar 22-Mar 28-Mar 03-Apr Cu Cu Cu Pr Pu

09-Apr iv mu mu mu bl at

15-Apr ic e- la la la -s se ti ti ti 21-Apr ec TOLL-FREE NUMBER0800 029 999 (percentage, n/ ve ve ve ct South Africa) total casesin to 388 620 (26.7) 3 269 633 (18.5)

2020 Mid-year population Statistics South Africa 2020 Mid-year populationStatisticsSouthAfrica 27-Apr 315 033 (21.7) n n n 191 997 (13.2) Cumulative or 65 054(4.5) 76 279 (5.2) r 57 981(4.0) 32 010 (2.2) 57 154(3.9) um um um cases (n) 1 453 761 03-May

09-May be be be 0 15-May r r r of publ pr t

21-May iv ot at ic

27-May al e- -s c se 02-Jun ec as ct to

08-Jun es or n (percentage2, r week 4(24-30 January 2021), January c 14-Jun ca detected in as New cases se 6486 (23.7)6486 7078 (25.8) 3957 (14.4) *Date received specimen where date collected missing 2470 (9.0)

1634 (6.0) 20-Jun 1245 (4.5) 2191 (8.0) es 1531 (5.6) 810 (3.0) s n/total) 27 402 26-Jun

0 02-Jul

DATE SPECIMEN COLLECTED* 08-Jul 14-Jul

1 20-Jul 26-Jul

Population in 01-Aug mid-2020

59 622350 07-Aug 15 488 13715 488 4 679 786 2 928 903 6 734 001 5 852 553 852 5 11 531 628 7 005741 4 108816 1 292 786 4

Data on number of tests conducted sourced from COVID-19Data onnumberoftests conducted sourced weekly from testing report 13-Aug

2020 19-Aug 0 25-Aug

3 31-Aug , n 06-Sep 2 Percentage=n/total numberofnew collected cases(specimen or 12-Sep 18-Sep incidence risk incidence Cumulative

(cases per 24-Sep persons) 100000 2 438.3 2 604.4 3 848.7 2 509.0 2 467.0

2 851.2 30-Sep 2 731.9 1 391.0 1 390.1 990.7 06-Oct

12-Oct 18-Oct 24-Ovt 30-Oct

(cases/100 000 (cases/100 05-Oct Incidence risk Incidence of new cases 11-Nov in week 4 detected persons) 17-Nov 46.0 39.8 52.8 62.7 56.5 37.4 52.3 61.4 41.9 18.5 23-Nov 29-Nov 05-Dec 11-Dec 2021 17-Dec 23-Dec 24-30 January Tests 000 persons, 29-Dec 04-Jan 386.3 346.8 206.9 378.6 144.6 451.6 467.1 476.1 230.1 512.6 2021

PAGE 5 06-Jan 4 per100 13-Jan 20-Jan 27-Jan- 0 1 2 30000 40000 50000 6 7 8 9 1 11 12 13 14 15 0000 00000 0000 0000 0000 0000 0000 0 0000 0000 0000 0000 000 0 0 0 0 0 0 0 0 0 0 0 0 0 0 0 COVID-19 WEEKLY EPIDEMIOLOGY BRIEF WEEK 4 2021

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Epidemiologic week

Figure 3. Cumulative incidence risk of laboratory-confirmed cases of COVID-19 by province and epidemiologic week, South Africa, 3 March 2020-30 January 2021 (n= 1 453 761)

350 Eastern Cape Free State Gauteng KwaZulu-Natal

Limpopo Mpumalanga North West Northern Cape

300 Western Cape South Africa

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(cases per 100 000 persons) 100

0 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 2020 2021

Epidemiologic week

Figure 4. Weekly incidence risk of laboratory-confirmed cases of COVID-19 by province and epidemiologic week, South Africa, 3 March 2020- 30 January 2021 (n=1 453 761)

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Eastern Cape Free State Gauteng 1100 KwaZulu-Natal Western Cape 1000

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2020 2021 Epidemiologic week

Figure 5. Doubling time of number of laboratory-confirmed cases of COVID-19 by province (for 5 provinces with the majority of cases) and epidemiologic week, South Africa, 23 March-2020- 23 January 2021 (n= 1 426 272)

Characteristics of COVID-19 cases in South Africa by age and sex

Cases of COVID-19 were reported across all age groups. The was in the 0-4-year age group (6.8 cases per 100 000 persons) median age of COVID-19 cases in South Africa to date was (Figure 8 and table 2). 40 years with an interquartile range (IQR) of 29-53 years. The To date, the majority of COVID-19 cases reported were female distribution of cases varied by age, with highest number of 57.8% (831 905/1 438 239). This trend continued in the past all cases to date in the 35-39-year (172 086/1 440 842, 11.9%) week where 57.3% (15 493/27 060) of cases were female. The and 30-34-year (167 304/1 440 842, 11.6%) age groups (Figure cumulative incidence risk has remained consistently higher 6). Similarly, among the cases reported in the past week, the among females (2 705.5 cases per 100 000 persons) than highest number of cases was in the 35-39-year-age group among males (2 065.2 cases per 100 000 persons) (Figure 9). (2 788/27 036, 10.3%) followed by the 30-34-year age group The peak cumulative incidence risk was in the 50-54-year-age (2 704/27 036, 10.0%). The median age for cases reported in group (5 205.2 cases per 100 000 persons) for females, and in week 4 was similar (43 years, IQR 31-57), to that of total cases the ≥80-year-age group (4 903.6 cases per 100 000 persons) (40 years). The highest cumulative incidence risk remained and 55-59-year-age group (4 737.6 cases per 100 000 persons) among cases aged 50-54 years (4 967.9 cases per 100 000 for males (Figure 10). In week 4, the highest weekly incidence persons), followed by cases aged 55-59 years (4 892.0 cases risk for both females and males was in the ≥80-year-age group per 100 000 persons) and 80+ years (4 721.3 cases per 100 000 (132.2 cases per 100 000 persons), and (123.0 cases per 100 000 persons). The lowest cumulative incidence risk was reported persons), respectively, this is similar to the previous week. in the younger age-groups, 294.6 cases per 100 000 persons The higher prevalence and incidence risk among females and 367.0 cases per 100 000 persons in the 0-4-and 5-9-year compared to males could be explained by the fact that females age groups, respectively (Figure 7 and Table 2). The highest are likely to be more represented in occupations, which put weekly incidence risk among cases detected in week 4 of 2021 them in close proximity to others and thus exposing them to was reported in cases aged 80+ years (131.3 cases per 100 000 a higher risk of infection (e.g. teaching and health). This may persons), followed by cases in the 60-64-year-age group (101.7 also be partly explained by varying testing practices by age cases per 100 000 persons), 55-59-year-age group (101.4 cases and sex (data not shown) and by different health seeking per 100 000 persons), and the lowest weekly incidence risk behaviour.

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80000 Female Male

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0 9 + 9 4 9 9 9 9 9 4 4 9 4 4 4 4 4 -1 -1 5- -6 -2 -3 -5 -7 -2 -3 -4 -5 -7 0- -6 -4 80 15 10 25 35 55 65 75 20 30 45 50 70 60 40

Age group (years)

Figure 6. Number of laboratory-confirmed cases of COVID-19 by age group and sex, South Africa, 3 March 2020-30 January 2021 (n = 1 426 580, sex/age missing for 27 181)

5000 0-4 5-9 10-14 15-19 4500 20-39 40-59 60 All ages

4000 )

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0 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 2020 2021

Epidemiologic week

Figure 7. Cumulative incidence risk of laboratory-confirmed cases of COVID-19 by age group in years and epidemiologic week, South Africa, 3 March 2020-30 January 2021 (n= 1 440 842, 12 919 missing age)

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500

450 0-4 5-9 10-14 15-19 20-39 40-59 60 All ages

400 )

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(Cases per 100 000 persons 100

0 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 2020 2021

Epidemiologic week

Figure 8. Weekly incidence risk of laboratory-confirmed cases of COVID-19 by age group in years and epidemiologic week, South Africa, 3 March 2020-30 January 2021 (n= 1 440 842, 12 919 missing age)

3000 Female Male All 2750

2500

) 2250

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1000 Cumulatve incidence risk (cases per 100 000 persons

750

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0 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 2020 2021

Epidemiologic week

Figure 9. Cumulative incidence risk by sex and epidemiologic week, South Africa, 3 March 2020-30 January 2021 (n= 1 438 239, sex missing for 15 522)

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Table 2. Number of laboratory-confirmed cases of COVID-19 and cumulative/weekly incidence risk by age group, South Africa, 3 March 2020- 30 January 2021 (n= 1 440 842, 12 919 missing age)

Age group Cumulative cases New cases1 detected in Population in Cumulative Incidence risk of (years) (n) (percentage, n/ week 4 (24-30 January mid-20203, n incidence risk (cases new cases detected total cases in South 2021), n (percentage2, n/ per 100 000 persons) in week 4 (cases/100 Africa) total) 000 persons) 0-4 16 920 (1.2) 390 (1.4) 5743 450 294.6 6.8 5-9 20 980 (1.5) 480 (1.8) 5715 952 367.0 8.4 10-14 35 444 (2.5) 795 (2.9) 5591 553 633.9 14.2 15-19 58 375 (4.1) 988 (3.7) 4774 579 1 222.6 20.7 20-24 87 215 (6.1) 1 346 (5.0) 4823 367 1 808.2 27.9 25-29 141 356 (9.8) 2 120 (7.8) 5420 754 2 607.7 39.1 30-34 167 304(11.6) 2 704 (10.0) 5641 750 2 965.5 47.9 35-39 172 086 (11.9) 2 788 (10.3) 4798 293 3 586.4 58.1 40-44 148 989 (10.3) 2 620 (9.7) 3733 942 3 990.1 70.2 45-49 141 346 (9.8) 2 584 (9.6) 3169 648 4 459.4 81.5 50-54 127 739 (8.9) 2 498 (9.2) 2571 263 4 967.9 97.2 55-59 108 177 (7.5) 2 242 (8.3) 2211 309 4 892.0 101.4 60-64 77 252(5.4) 1 827 (6.8) 1796 316 4 300.6 101.7 65-69 51 389 (3.6) 1 351 (5.0) 1408 665 3 648.1 95.9 70-74 36 292 (2.5) 970 (3.6) 1007 174 3 603.3 96.3 75-79 22 723 (1.6) 575 (2.1) 637 062 3 566.8 90.3 ≥80 27 255 (1.9) 758 (2.8) 577 273 4 721.3 131.3 Unknown 12 919 366 Total 1 453 761 27 402 59 622 350 2 438.3 46.0

1New cases refer to cases whose samples were collected or received in the current reporting week; 2Percentage=n/total number of new cases (specimen collected or received in current reporting week); 32020 Mid-year population Statistics South Africa

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4500 Female incidence Male incidence

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0 9 9 9 9 9 4 4 4 + 4 4 9 9 9 4 4 4 -1 -1 5- -2 -3 -5 -2 -3 -5 -6 0- -7 -4 -6 -7 -4 80 15 10 25 35 55 20 30 50 65 75 45 60 70 40

Age group (years)

Figure 10. Cumulative incidence risk by age group and sex, South Africa, 3 March 2020- 30 January 2021 (n= 1 426 580, sex/age missing for 27 181)

Provincial trends of COVID-19 cases weekly incidence risk (Figure 11). All districts reported a declining trend in numbers since week 2. In the final weeks of 2020, the majority of provinces The majority of cases from the Eastern Cape Province (excluding Eastern Cape where numbers had been were in the 40-59-year old age group (69 140/190 002, dropping since week 51) reported an increase in the 36.4%), followed by the 20-39-year age group (65 314/190 number of new cases and weekly incidence risks. 002, 34.4%) and by the ≥60 -year age group (33 804/190 However, from week 1 of 2021 in the majority of provinces, 002, 17.8%). In the past week, the ≥60-year age group the magnitude of increase in numbers had slowed or (55.0 cases per 100 000 persons), followed by 40-59-year numbers were going down, with all provinces reporting age group (32.1 cases per 100 000 persons) reported the a decline in numbers in week 2 to date. Trends by district highest weekly incidence risk. The weekly incidence and age group for each province are presented below. risk in all other age groups was below 15 cases per 100 000 persons. In the past three weeks, all age groups reported a decrease in weekly incidence risk (Figure 12). Eastern Cape Province From week 47 to week 2, ≥60-year-age group reported a higher weekly incidence risk compared to the peak in Of the 191 997 cases reported from the Eastern Cape the first wave in week 28, whereas the other age groups Province, 170 381 (88.7%) cases had allocation by district. continued reporting weekly incidence risks below those The Nelson Mandela Bay Metro (46 941/170 381, 27.6%) reported in the first wave. followed by the Buffalo City Metro (30 897/170 381, 18.1%) contributed the majority of cases from the Eastern Cape. In week 4, the Joe Gqabi (40.9 cases per 100 000 persons), followed by the Chris Hani (22.8 cases per 100 000 persons) districts reported the highest

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Alfred Nzo Amathole Buffalo City Metro

450 Chris Hani Joe Gqabi Nelson Mandela Bay Metro O R Tambo Sarah Baartman Eastern Cape Province

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2020 2021 Epidemiologic week

Figure 11. Weekly incidence risk of laboratory-confirmed cases of COVID-19 by district and epidemiologic week, Eastern Cape Province, 3 March 2020- 30 January 2021 (n= 170 381, 21 616 missing district)

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Epidemiologic week

Figure 12. Weekly incidence risk of laboratory-confirmed cases of COVID-19 by age group in years and epidemiologic week, Eastern Cape Province, 3 March 2020 – 30 January 2021 (n= 190 002, 1 995 missing age)

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Western Cape Province week 2. The majority of cases from the Western Cape Province were in the 20-39-year old age group (106 878/268 Of the 269 633 cases reported from the Western Cape 702, 39.8%), followed by the 40-59-year age group (100 Province, 251 976 (93.5%) cases had allocation by district. 670/268 702, 37.5%). In the past week, the ≥60-year age The City of Cape Town District (166 715/251 976, 66.2%) group (213.5 cases per 100 000 persons), followed by 40- followed by the Cape Winelands District (30 863/251 59-year age group (170.7 cases per 100 000 persons), and 976, 12.3%), and the Garden Route District (28 524/251 20-39-year age group (98.8 cases per 100 000 persons) 976, 11.3%) contributed the majority of cases, all other reported the highest weekly incidence risk. The weekly districts contributed <10% each. In the past week, the incidence risk in all other age groups remained below West Coast (90.7 cases per 100 000 persons) followed by 15 cases per 100 000 persons. In the past three weeks, the Overberg (70.7 cases per 100 000 persons) districts all age groups reported a decrease in weekly incidence reported the highest weekly incidence risk (Figure 13). risk (Figure 14). From week 51 to week 3, all age groups The increasing trend in weekly incidence risk reported reported the highest weekly incidence risks compared from the different districts during the second wave to the peaks in the first wave in different weeks. varied by district, with all the districts reporting the highest weekly incidence risks from week 50 to week 2, higher than the peaks in the first wave. Number of cases have been decreasing since week 51 in some districts, with all districts reporting a decrease in numbers since

Cape Winelands Central Karoo City of Cape Town Metro Garden Route Overberg West Coast 600 Western Cape Province

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Figure 13. Weekly incidence risk of laboratory-confirmed cases of COVID-19 by district and epidemiologic week, Western Cape Province, 3 March 2020 - 30 January 2021 (n= 251 976, 17 657 missing district)

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Figure 14. Weekly incidence risk of laboratory-confirmed cases of COVID-19 by age group in years and epidemiologic week, Western Cape Province, 3 March 2020- 30 January 2021 (n= 268 702, 931 missing age)

Gauteng Province reported a higher weekly incidence in week 1 compared to the first wave peak in week 29 (Figure 15). From week Of the 388 620 cases reported from the Gauteng 1 2021, numbers reported have been decreasing. Province, 339 732 (87.4%) had allocation by district. The City of Johannesburg Metro (129 956/339 732, 38.3 %), The majority of cases from Gauteng Province were in the followed by the City of Tshwane Metro (92 061/339 732, 20-39-year-age group (164 328/384 408, 42.7%), followed 27.1%), and the Ekurhululeni Metro (71 122/339 732, 20.9%) by 40-59-year-age group (141 048/384 408, 36.7%). In the contributed the majority of cases, all other districts past week, all age groups reported a decrease in weekly contributed below 15% each. In week 4, the City of incidence risk, compared to the previous week (Figure Tshwane (44.5 cases per 100 000 persons) and the West 16). Rand District (44.2 cases per 100 000 persons) reported the highest weekly incidence risk. All the districts reported an increase in number of new cases and weekly incidence risk from week 48 to week 1 which remained below that reported during the first peak, except the City of Tshwane Metro and Ekurhululeni District which

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City of Johannesburg Metro City of Tshwane Metro Ekurhuleni Metro Sedibeng West Rand Gauteng Province

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Epidemiologic week

Figure 15. Weekly incidence risk of laboratory-confirmed cases of COVID-19 by district and epidemiologic week, Gauteng Province, 3 March 2020- 30 January 2021 (n= 339 732 159, 48 888 missing district)

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Figure 16. Weekly incidence risk of laboratory-confirmed cases of COVID-19 by age group in years and epidemiologic week, Gauteng Province, 3 March 2020-30 January 2021 (n= 384 408, 4 212 missing age).

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KwaZulu-Natal Province per 100 000 persons), Ugu (182.0 vs 107.0 cases per 100 000 persons), uThukela (217.9 vs 94.5 cases per 100 000 Of the 315 033 cases reported from KwaZulu-Natal persons), uMkhanyakude (116.0 vs 61.7 cases per 100 Province, 237 329 (75.3%) had allocation by district. 000 persons), uMzinyathi (146.4 vs 94.3 cases per 100 The eThekwini Metro (119 833/237 329, 50.5%) followed 000 persons), uMgungundlovu (258.6 vs 183.7 cases by uMgungundlovu Metro (25 186/237 329, 10.6%) per 100 000 persons), and Zululand (140.4 vs 99.9 cases contributed the majority of cases. In week 4, King per 100 000 persons), except Amajuba District which Cetshwayo (53.1 cases per 100 000 persons), followed continued to report weekly incidence risk below the first by eThekwini Metro (51.7 cases per 100 000 persons) wave peaks (Figure 17). In the past 3 weeks, all districts and uMgungundlovu (50.5 cases per 100 000 persons) reported a decrease in weekly incidence risk. districts reported the highest weekly incidence risk. In The majority of cases from KwaZulu-Natal Province the past three weeks, all districts reported a decrease in were in the 20-39-year-age group (119 736/311 854, 38.4%), weekly incidence risk. The decrease in week 4 incidence followed by 40-59-year-age group (107 993/311 854, is possibly due to reporting delays. 34.6%). In week 52 to week 53, all age groups reported Following the decline in number of cases after the weekly incidence risks higher than those reported in the first wave, an increasing trend in weekly incidence first wave peaks. From week 2 to date, all age groups risk which varied by districts, had been reported since reported a decrease in weekly incidence risk (Figure 18). week 48. During this period, all the districts reported weekly incidence risks higher than those reported in the first peaks; eThekwini Metro (380.8 vs 165.8 cases per 100 000 persons), iLembe (169.2 cases vs 96.2 per 100 000 persons), Harry Gwala (156.2 vs. 85.2 cases per 100 000 persons), King Cetshwayo (267.9 vs 121.9 cases

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Epidemiologic week

Figure 17. Weekly incidence risk of laboratory-confirmed cases of COVID-19 by district and epidemiologic week, KwaZulu-Natal Province, 3 March 2020-30 January 2021 (n= 237 329, 77 704 missing district)

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2020 2021 Epidemiologic week

Figure 18. Weekly incidence risk of laboratory-confirmed cases of COVID-19 by age group in years and epidemiologic week, KwaZulu-Natal Province, 3 March 2020-30 January 2021 (n= 311 854, 3 179 missing age)

Free State Province except for Mangaung, which reported an increase until week 1. The increase in numbers and incidence risk Of the 76 279 cases reported from the Free State reported during the second wave in all the districts Province, 69 411 (91.0%) had allocation by district. The remained below that reported during the first peak Mangaung Metro (26 230/69 411, 37.8%), followed by the (Figure 19). In the past two weeks all districts reported a Lejweleputswa (16 503/69 411, 23.8%), and the Thabo decreasing trend in number of new cases. Mofutsanyane (13 673/69 411, 19.7%) districts contributed the majority of cases, all other districts contributed The majority of cases from the Free State Province below 15% each. In week 4, the Thabo Mofutsanyane were in the 20-39-year-age group (28 905/75 956, 38.1%), District (63.7 cases per 100 000 persons), followed by followed by 40-59-year-age group (27 249/75 956, 35.9%). the Fezile Dabi District (52.1 cases per 100 000 persons) In the past week, all age groups reported a decrease in reported the highest weekly incidence risk. All the weekly incidence risk, compared to the previous week districts reported an increase in number of new cases (Figure 20). and weekly incidence risk from week 50 to week 2,

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Fezile Dabi Lejweleputswa Mangaung Metro Thabo Mofutsanyane Xhariep Free State Province

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Epidemiologic week

Figure 19. Weekly incidence risk of laboratory-confirmed cases of COVID-19 by district and epidemiologic week, Free State Province, 3 March 2020-30 January 2021 (n= 69 411, 6 868 missing district)

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Epidemiologic week

Figure 20. Weekly incidence risk of laboratory-confirmed cases of COVID-19 by age group in years and epidemiologic week, Free State Province, 3 March 2020-30 January 2021 (n= 75 956, 323 missing age)

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Limpopo Province 000 persons), Waterberg (192.8 vs 60.2 cases per 100 000 persons), Mopani (182.6 vs 28.7 cases per 100 000 Of the 57 981 cases reported from the Limpopo persons), and Sekhukhune District (74.2 vs 33.0 cases Province, 50 944 (87.9%) had allocation by district. per 100 000 persons) (Figure 21). The number of new The Capricorn (16 197/50 944, 31.8%), followed by the cases and weekly incidence reported from all districts Vhembe (10 507/50 944, 20.6%) districts contributed the risk has been decreasing in the last 3 weeks majority of cases, all other districts contributed below The majority of cases from Limpopo Province were in 20% each. In week 4, the Waterberg (37.1 cases per 100 the 40-59-year-age group (22 917/57 659, 39.7), followed 000 persons), followed by the Capricorn (34.3 cases per by 20-39-year-age group (21 959/57 659, 38.1%). In the 100 000 persons) districts reported the highest weekly past week, all age groups reported a decrease in weekly incidence risk. All the districts reported a gradual incidence risk, compared to the previous week (Figure increase in number of new cases and weekly incidence 21). In week 1, all age groups reported weekly incidence risk from week 49 to week 50, then sharp increase from risks higher than those reported during the first peaks week 51 to week 1. The weekly incidence risk reported in week 30 (Figure 22). in week 1 exceeded those reported in the first peak in the Vhembe District (183.9 vs 15.0 cases per 100 000 persons), Capricorn District (255.5 vs 47.3 cases per 100

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Epidemiologic week

Figure 21. Weekly incidence risk of laboratory-confirmed cases of COVID-19 by district and epidemiologic week, Limpopo Province, 3 March 2020-30 January 2021 (n= 50 944, 7 037 missing district)

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Epidemiologic week

Figure 22. Weekly incidence risk of laboratory-confirmed cases of COVID-19 by age group in years and epidemiologic week, Limpopo Province, 3 March 2020- 30 January 2021 (n= 57 659, 322 missing age)

Mpumalanga Province The majority of cases from Mpumalanga Province were in the 20-39-year-age group (26 982/63 976, 42.2%), Of the 65 054 cases reported from the Mpumalanga followed by 40-59-year-age group (22 981/63 976, 35.9%). Province, 53 342 (82.0%) had allocation by district. All the In the past week, all age groups reported a decrease in districts contributed similar number of cases, Ehlanzeni weekly incidence risk, compared to the previous week (20 941/53 342, 39.3%), Nkangala (17 662/53 342, 33.1%) (Figure 24). In week 1, all age groups reported weekly and the Gert Sibande (14 739/53 342, 27.6%) districts. incidence risks higher than those reported in the first In week 4, the Gert Sibande District (41.5 cases per 100 wave peaks. 000 persons), followed by the Ehlanzeni District (41.3 cases per 100 000 persons) reported the highest weekly incidence risk. All the districts reported an increase in number of new cases and weekly incidence risk from week 50 to week 1. The increase in numbers and incidence risk reported during the second wave from all the districts was higher than that reported during the first peak (Figure 23). The number of new cases reported from all districts has been decreasing since week 2 of 2021.

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Figure 23. Weekly incidence risk of laboratory-confirmed cases of COVID-19 by district and epidemiologic week, Mpumalanga Province, 3 March 2020-30 January 2021 (n= 53 342, 11 712 missing district)

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Figure 24. Weekly incidence risk of laboratory-confirmed cases of COVID-19 by age group and epidemiologic week, Mpumalanga Province, 3 March 2020-30 January 2021 (n= 63 976, 1 078 missing age)

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North West Province than those reported during the first peak, except the Dr Kenneth Kaunda District which continued to report Of the 57 154 cases reported from the North West weekly incidence risk below that reported in the first Province, 47 383 (82.9%) had allocation by district. wave peak (Figure 25). All districts reported a decline in The Bojanala Platinum District (23 936/47 383, 50.5%), number of new cases since week 2 of 2021. followed by the Dr Kenneth Kaunda District (11 595/47 The majority of cases from North West Province were in 383, 24.5%) contributed the majority of cases, all other the 40-59-year-age group (23 393/56 556, 41.4%), followed districts contributed below 20% each. In week 4, Dr by 20-39-year-age group (21 504/56 556, 38.0%). In week Kenneth Kaunda District (39.7 cases per 100 000 1, all age groups reported weekly incidence risk higher persons) reported the highest weekly incidence risk. than those reported in the first wave peaks (Figure 26). All the districts reported a gradual increase in number In the past week, all age groups reported a decrease in of new cases and weekly incidence risk from week 50 weekly incidence risk, compared to the previous week. to week 1, with Bojanala Platinum District showing a sharp increase in week 51 to week 1 2021. The increase in numbers and weekly incidence risk reported during the second wave peak from all the districts was higher

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Epidemiologic week

Figure 25. Weekly incidence risk of laboratory-confirmed cases of COVID-19 by district and epidemiologic week, North West Province, 3 March 2020-30 January 2021 (n= 47 383, 9 771 missing district)

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Figure 26. Weekly incidence risk of laboratory-confirmed cases of COVID-19 by age group in years and epidemiologic week, North West Province, 3 March 2020- 30 January 2021 (n= 56 556, 598 missing age)

Northern Cape Province was higher than those reported during the first peak, except the Frances Baard and John Taolo Gaetsewe Of the 32 010 cases reported from the Northern Cape districts which continued to report weekly incidence Province, 26 786 (83.7%) had allocation by district. The risk below that reported during the first peak (Figure Frances Baard (9 404/26 786, 35.1%), followed by the 27). Since week week 2, all districts reported a decrease Pixley ka Seme (6 861/26 786, 25.6%) districts contributed in number of new cases reported. the majority of cases, all other districts contributed below 20% each. In week 4, the Namakwa (90.8 cases The majority of cases from Northern Cape Province per 100 000 persons), followed by Pixley ka Seme were in the 20-39-year-age group (12 355/31 729, 38.9), (64.5 cases per 100 000 persons) districts reported the followed by 40-59-year-age group (10 860/31 729, 34.2%). highest weekly incidence risk. All the districts reported In week 1, all age groups reported the weekly incidence a gradual increase in number of new cases and weekly risks higher than those reported in the first wave peak incidence risk from week 50 to week 1, with the (Figure 28). In the past week, all age groups reported a Namakwa District showing a sharp increase from week decrease in weekly incidence risk 51 to week 1. The increase in numbers and incidence risk reported during the second wave from all the districts

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2020 2021 Epidemiologic week

Figure 27. Weekly incidence risk of laboratory-confirmed cases of COVID-19 by district and epidemiologic week, Northern Cape Province, 3 March 2020- 30 January 2021 (n= 26 786, 5 224 missing district)

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Figure 28. Weekly incidence risk of laboratory-confirmed cases of COVID-19 by age group in years and epidemiologic week, Northern Cape Province, 3 March 2020- 30 January 2021 (n= 31 729, 281 missing age)

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Limitations Conclusions

This report is based on laboratory-based surveillance of To date, 1 453 761 cases, including 44 164 deaths have laboratory-confirmed cases. The number of reported been reported. The second wave, increase in cases cases is heavily dependent on testing practices. initially reported from the Eastern Cape Province in Although trends over time and comparisons by week 43, seems to have peaked, with all provinces geographic area are presented in this report, changes in reporting a decrease in numbers of new cases and testing practices over time or differences by region may incidence risk reported since week 2. In week 4 all partially explain the results. The crude CFR reported districts reported a decrease in number of new cases. here is subject to numerous limitations: it is likely to Demographic trends have remained unchanged this be an underestimation as reporting of deaths may be reporting period, children aged <10 years had the lowest delayed and deaths which occurred outside health incidence risk and individuals aged 40-59 years had the facilities may be missed. Differences in health-seeking highest incidence. The decreasing trends in numbers of behaviour by age group and sex could also contribute to new cases in recent weeks may be as a result of delay in observed differences in case numbers between groups. reporting or changes in testing practices in the different The reported doubling time estimates are affected provinces. In addition, number of confirmed cases by the number of tests conducted; if fewer tests are diagnosed on antigen tests maybe underestimated performed, this will also increase the doubling time as they are used in a number of different settings and estimate. Delays in reporting may result in incomplete results may not be fully reported yet. data for recent weeks, leading to an apparent reduction in number of cases.