COVID-19 WEEKLY EPIDEMIOLOGY BRIEF...2020/05/09 · TOLL-FREE NUMBER 0800 029 999 PAGE 5 WEEK 19...

S O U T H A F R I C A W E E K 1 9 2 0 2 0

COVID-19 WEEKLY EPIDEMIOLOGY BRIEF

PROVINCES AT A GLANCE

EASTERN CAPE

CASE

S 1 218 18.2 IN TOTAL /100,000*

TEST

S 34 032 507IN TOTAL /100,000**

NORTH WEST

CASE

S 45 3.6IN TOTAL /100,000*

TEST

S 5 213 412IN TOTAL /100,000**

MPUMALANGA

CASE

S 61 1.3IN TOTAL /100,000*

TEST

S 9 823 214IN TOTAL /100,000**

GAUTENG

CASE

S 1 952 12.9IN TOTAL /100,000*

TEST

S 111 630 736IN TOTAL /100,000**

LIMPOPO

CASE

S 54 0.9IN TOTAL /100,000*

TEST

S 7 783 130IN TOTAL /100,000**

KWAZULU-NATAL

CASE

S 1 353 12.0IN TOTAL /100,000*

TEST

S 61 801 547IN TOTAL /100,000**

FREE STATE

CASE

S 135 4.7IN TOTAL /100,000*

TEST

S 17 231 597IN TOTAL /100,000**

NORTHERN CAPE

CASE

S 29 0.7IN TOTAL /100,000*

TEST

S 3 092 77IN TOTAL /100,000**

WESTERN CAPE

CASE

S 5 168 75.5IN TOTAL /100,000*

TEST

S 70 038 1 023IN TOTAL /100,000**

* Incidence risk - cases per 100,000 persons** Tests per 100,000 personsNote: 20 693 tests have not been allocated to a province

TESTSCASES PERSONS

CUMULATIVE DATA FROM

JANUARY MAY31 9

10 015 341 336 17.1

2 795 83 795 37

IN TOTAL IN TOTAL INCIDENCE RISK*

THIS WEEK THIS WEEK MEDIAN AGE

TOLL-FREE NUMBER 0800 029 999 PAGE 1www.nicd.ac.za

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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 information from several surveillance systems that are used to monitor the coronavirus disease 2019 (COVID-19) pandemic in South Africa. This report is based on data collected up to 09 May 2020 (week 19 of 2020). Note: COVID-19 is the name of the disease and SARS-CoV-2 is the name of the virus.

Highlights

∙ As of 23:59 on 09 May 2020, a total of 10015 laboratory-confirmed COVID-19 cases had been detected in South Africa. Of these 2795, 28% of total cases to date, were reported in this reporting period. On 1 May, South Africa moved from stage 5 to 4 of lock-down, this may be associated with increased transmission and the number of cases reported.

∙ Public-sector continues to report more cases than private-sector. This may reflect the increased access to testing in the public sector as well as spread of COVID-19 cases.

∙ Laboratory PCR testing for SARS-CoV-2 continues to increase steadily week-on-week with continued intensive contact tracing/testing and targeted community symptom screening/ referral for testing. In the last week, an additional 83 795 tests were performed, this was 11 541 more tests than the number of tests conducted in the previous week.

∙ Western Cape Province continues to report the highest total number of cases, 51.6% (5168/10015) of total cases, an increase of 5% since the last report. The incidence risk (cumulative incidence) was highest in the Western Cape Province (75.5 cases per 100 000 persons; 95% confidence interval [CI] 73.5-77.6) followed by Eastern Cape (18.2 per 100 000 persons 95% CI 17.1-19.2) and Gauteng (12.9. per 100 000 persons; 95%CI 12.3-13.5). In the last week incidence increased by 26.4, 6.1 and 3.8 persons per 100 000 persons in Western Cape, Eastern Cape and Gauteng, respectively.

∙ The median age of laboratory-confirmed cases was 37 years (interquartile range [IQR], 28-49 years). Children aged <10 years accounted for 3.1% (309/9953). The incidence risk was highest among males in the 75-79 age group (31.2 cases per 100 000 person.



SUMMARY

58%

83 795

OVERALL CASES WERE FEMALE

TESTS PERFORMED THIS WEEK

17.1 /100 000

OVERALL RISK INCIDENCE

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Methods

Testing for SARS-CoV-2 began on 28 January 2020 at the NICD and after the first case was confirmed in early March 2020, testing was expanded to a larger network of private and NHLS laboratories. Respiratory specimens were submitted from persons under investigation (PUI). Initially, tested individuals were those who had travelled to countries with COVID-19 transmission but the PUI definition was changed over time. Targeted community symptom screening and referral for PCR testing was implemented in April 2020. Contacts of cases were traced and tested if symptomatic. However, in some provinces, asymptomatic contacts were tested. Laboratories used any one of several in-house and commercial PCR assays to test for the presence of SARS-CoV-2 RNA. Test results were automatically fed into a data warehouse. We excluded specimens collected outside South Africa. Date of specimen receipt in the laboratory was used when date of specimen collection was missing. A case of COVID-19 was defined as any person, resident in South Africa, with a first positive SARS-CoV-2 PCR test. We used 2019 mid-year population estimates from Statistics South Africa to calculate the incidence risk or cumulative incidence (expressed as cases per 100 000 persons). Outcomes of cases (i.e. deaths or recoveries) were not collected through this surveillance system.

National and provincial trends

As of 09 May 2020, 341 336 tests were performed (83 795 additional test since last report). In total, 10015 cases were detected in South Africa (2 795 new cases since last report) (Figure 1). The overall proportion positive remains at 3%. Western Cape Province continues to report the highest proportion of cases (4809/10015, 52%), followed by Gauteng 1910/10015, 20%) and KwaZulu-Natal (1308/10015, 14%) (Table 1). Western Cape had the highest incidence risk (75.5 cases per 100 000 persons) followed by Eastern Cape (18.2 per 100 000 persons) and Gauteng (12.9. per 100 000 persons). Northern Cape had the lowest incidence risk (0.7 cases per 100 000 persons). The cumulative incidence risk for the country was 17.1 per 100 000 persons. However the cumulative incidence risk varied by province over time (Figure 4). This is partly explained by testing differences by province (Table 1). The number of tests performed per 100 000 persons ranged from 77 in the Northern Cape Province to 1023 in the Western Cape Province.



LABORATORY-CONFIRMED CASES OF COVID-19 IN SOUTH AFRICA

3%

75.5 OVERALL POSITIVE

PROPORTION

/100 000HIGHEST

INCIDENCE RISK IN THE

WESTERN CAPE


W E E K 1 9 2 0 2 0 L A B O R A T O R Y - C O N F I R M E D C A S E S O F C O V I D - 1 9 I N S O U T H A F R I C A


Figure 2. Number and cumulative number of laboratory-confirmed cases of COVID-19 by date of specimen collection, South Africa, 3 March-09 May 2020 (n=9889(126 missing date of specimen collection/receipt))

Figure 1. Number and cumulative number of specimens tested for SARS-CoV-2, by testing laboratory sector and date of specimen collection, South Africa, 31 January 2020-09 May 2020 (n=341 336)

*Date of specimen receipt where date of specimen collection was missing

0

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3000

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6000

7000

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9000

10000

11000

0

100

200

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03-M

ar05

-Mar

07-M

ar09

-Mar

11-M

ar13

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15-M

ar17

-Mar

19-M

ar21

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ar25

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27-M

ar29

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31-M

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ay04

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06-M

ay08

-May

Cumulative num

ber of casesNu

mbe

r of c

ases

Date of specimen collection*

Gauteng Western Cape KwaZulu-Natal Eastern CapeFree State Limpopo Mpumalanga North WestNorthern Cape Cumulative cases


0

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13-M

ar15

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17-M

ar19

-Mar

21-M

ar23

-Mar

25-M

ar27

-Mar

29-M

ar31

-Mar

02-A

pr04

-Apr

06-A

pr08

-Apr

10-A

pr12

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14-A

pr16

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18-A

pr20

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22-A

pr24

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26-A

pr28

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pr02

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ay06

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08-M

ay

Cumulative num

ber of specimens

Num

ber

of sp

ecim

ens

Date result reported

Private-sector Public-sector Cumulative total





Table 1. Number and incidence risk of laboratory-confirmed cases of COVID-19 and testing per 100 000 persons by province, South Africa, 3 March-09 May 2020 (n=10015)

Figure 3. Number and cumulative number of laboratory-confirmed cases of COVID-19, by testing laboratory sector and date of specimen collection, South Africa, 3 March-09 May 2020 (n=9889 (126 missing date of specimen collection/receipt)0


Province Cases (n) Proportion (n/total) (95% confidence

interval)

Population in mid-2019* (n)

Incidence risk (cases per 100 000 persons)

Tests per 100 000 persons

Eastern Cape 1218 12.2 (11.5-12.8) 6 712 276 18.2 (17.1-19.2) 507

Free State 135 1.3 (1.1-1.6) 2 887 465 4.7 (3.9-5.5) 597

Gauteng 1952 19.5. (18.7-20.3) 15 176 115 12.9 (12.3-13.5) 736

KwaZulu-Natal 1353 13.5 (12.8-14.2) 11 289 086 12.0 (11.4-12.6) 547

Limpopo 54 0.5 (0.4-0.7) 5 982 584 0.9 (0.7-1.2) 130

Mpumalanga 61 0.6 (0.5-0.8) 4 592 187 1.3 (1.0-1.7) 214

North West 45 0.4 (0.3-0.6) 4 027 160 3.6 (2.6-4.8) 412

Northern Cape 29 0.3 (0.2-0.4) 1 263 875 0.7 (0.5-1.0) 77

Western Cape 5168 51.6 (50.6-52.6) 6 844 272 75.5 (73.5.77.6) 1023

South Africa 10015 100 58 775 020 17.1 (16.7-17.4) 581

*Statistics South Africa 2019 mid-year population estimates

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-Mar

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Cumulative num

ber of casesNu

mbe

r of c

ases

Date of specimen collection*

Private-sector cases Public-sector cases

Cumulative number private-sector cases Cumulative number public-sector cases

Cumulative number total cases





Figure 4. Cumulative incidence risk of PCR-confirmed COVID-19 by province and epidemiologic week, South Africa, 3 March -9 May 2020 (n=10015)


The median age of cases was 37 years (interquartile range [IQR], 28-49 years). The largest proportion of cases was in the 30-34-year age group (1388/9953, 14%) followed by the 35-39-year age group (1346/9953, 13%) (Figure 5). The incidence risk was highest among those in the 40-44-year age group (30.7 cases per 100 000 persons), followed by those in the 50-54-year age group (cases per 100 000 persons), with the lowest incidence risk in the 5-9-year age group (2.5 cases per 100 000 persons). (Figure 6 and Table 2). Fifty-eight per cent (5758/9908) (95% CI, 57-59%) of the cases were female. The overall incidence risk was higher among females than males (19.1 cases per 100 000 persons [95%CI 18.6-19.6] versus 14.5 cases per 100 000 persons [95% CI 14.0-14.69). However, this varied by age group with the peak incidence risk among females aged 35-44 years and males aged 75-79 years (Figure 6). This may also be partially explained by varying testing practices by age and sex (data not shown).

CHARACTERISTICS OF CASES BY AGE AND SEX

14%38

THE HIGHEST PROPORTION OF

CASES IS AGE 35-39

THE MEDIAN AGE OF CASES

0

10

20

30

40

50

60

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80

10 11 12 13 14 15 16 17 18 19

Cum

ulati

ve in

cide

nce

risk

(cas

es p

er 1

00 0

00 p

erso

ns)

Epidemiologic week, 2020

Eastern Cape Free State

Gauteng KwaZulu-Natal

Limpopo Mpumalanga

North West Northern Cape

Western Cape South Africa


W E E K 1 9 2 0 2 0 C H A R A C T E R I S T I C S O F C A S E S B Y A G E A N D S E X


Figure 5. Number of laboratory-confirmed cases of COVID-19 by age group and sex, South Africa, 3 March-9 May 2020 (n=9908, 107 missing data on gender)

0

100

200

300

400

500

600

700

800

900

0-4 5-9

10-1

4

15-1

9

20-2

4

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4

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9

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70-7

4

75-7

9

≥80

Unkn

own

Num

ber o

f cas

es

Age group (years)

Female Male

Age group (years)

Cases (n) Population in mid-2019*, n

Incidence risk (cases per 100 000 persons)

0-4 168 5 733 946 2.9

5-9 144 5 737 439 2.5

10-14 199 5 427 902 3.7

15-19 264 4 660 002 5.7

20-24 794 4 914 186 16.2

25-29 1266 5 528 571 22.9

30-34 1389 5 537 963 25.8

35-39 1350 4 571 175 29.5

40-44 1100 3 585 408 30.7

Table 2. Number of cases and incidence risk by age group, South Africa, 3 March 2020-9 May 2020

45-49 912 3 045 617 29.9

50-54 769 2 535 048 30.3

55-59 584 2 192 512 26.6

60-64 360 1 784 476 20.2

65-69 256 1 370 121 18.7

70-74 181 949 812 19.1

75-79 121 597 874 20.2

≥80 115 602 969 19.1

Unknown 47

Total 10015 58 775 022 17.0

*Statistics South Africa


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Figure 6. Incidence risk by age group and sex, South Africa, 4 March 2020-9 May 2020 (n=9968, age missing for 47cases)

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Inci

denc

e ris

k (c

ases

per

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000

pers

ons)

Age group (years)

Female Male

COVID-19 WEEKLY EPIDEMIOLOGY BRIEF...2020/05/09 · TOLL-FREE NUMBER 0800 029 999 PAGE 5 WEEK 19...

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