The 2 Covid-19 Wave in South Africa: Transmissibility & A 501.V2 Variant

The 2nd Covid-19 wave in South Africa:

Transmissibility & a 501.V2 variant

Ministerial Briefing, 18 December 2020

Salim S. Abdool Karim, FRS

Director: CAPRISA
CAPRISA Professor of Global Health, Columbia University
Co-Chair: Ministerial Advisory Committee on COVID-19
Member: African Task Force for Coronavirus
Pro Vice-Chancellor (Research): University of KwaZulu-Natal
Adjunct Professor in Immunology and Infectious Diseases, Harvard University
Adjunct Professor of Medicine: Cornell University
CAPRISA hosts a MRC HIV-TB Pathogenesis
CAPRISA hosts a and Treatment Research Unit
DST-NRF Centre of
Excellence in CAPRISA hosts a DoH-MRC Special Initiative
HIV Prevention CAPRISA is the UNAIDS Collaborating for HIV Prevention Technology
Centre for HIV Research and Policy
Covid-19 in South Africa
7-day moving average of new cases, sentinel hospital admissions and
Covid-19 deaths – to 17 Dec
Before lockdown Level 5 doubling: Level 4 doubling: Level 3 doubling – L2 doubling – L1 doubling – L1 doubling (start of 2nd wave) –
Doubling: 2 days 15 days 12 days Jun- 16 Aug: 25 days 17 Aug – 20 Sept: 21 Sept – 28 Nov: 29 Nov – 16 Dec: 102 days
206 days 276 days
14000 3500
7-day moving average of daily cases

13000 Hospital admissions (116,335)

admissions to DATCOV sentinel

7-day moving average of daily
12000 Cases (892,813) 3000
11000
Deaths (24,011)

hospitals and deaths

10000 2500
9000
8000 2000
New cases
7000
Hospital
6000 Admissions 1500
5000
4000 1000
3000
2000 500
1000 Deaths
0 0
02-Jul
09-Jul
16-Jul
23-Jul
30-Jul
07-May
14-May
21-May
28-May
04-Jun
11-Jun
18-Jun
25-Jun

05-Nov
12-Nov
19-Nov
26-Nov
03-Dec
10-Dec
17-Dec
05-Mar
12-Mar
19-Mar
26-Mar

06-Aug
13-Aug
20-Aug
27-Aug
03-Sep
10-Sep
17-Sep
24-Sep
01-Oct
08-Oct
15-Oct
22-Oct
29-Oct
02-Apr
09-Apr
16-Apr
23-Apr
30-Apr

Source of hospital admissions data: Lucille Blumberg and Waasila Jassat – DATCOV, NICD
7-day moving average of national daily cases
per 100,000 population

0
5
10
15
20
25
30
35
40
45
05-Mar
12-Mar
19-Mar
26-Mar
02-Apr
09-Apr

National
Gauteng
Limpopo
16-Apr

Free State
North West
23-Apr
Mpumalanga

Eastern Cape
30-Apr

Western Cape

Northern Cape
KwaZulu-Natal

07-May
14-May
21-May
28-May
04-Jun
11-Jun
18-Jun
25-Jun
02-Jul
09-Jul
16-Jul
23-Jul
30-Jul
06-Aug
13-Aug
20-Aug
27-Aug
03-Sep
10-Sep
17-Sep
24-Sep
01-Oct
08-Oct
15-Oct
22-Oct
29-Oct
05-Nov
12-Nov
19-Nov
26-Nov
03-Dec
10-Dec
17-Dec
Confirmed SARS-Cov-2 cases by province

Gauteng
National
KwaZulu-Natal
Eastern Cape
Western Cape
(7-day moving average cases per 100,000 population – up to 17 December)

0
1
2
3
4
5
01-Nov
02-Nov
03-Nov
04-Nov
05-Nov
06-Nov
07-Nov
08-Nov
09-Nov
10-Nov
11-Nov
12-Nov
13-Nov
14-Nov
15-Nov
16-Nov
17-Nov
18-Nov
19-Nov
20-Nov
21-Nov
22-Nov
23-Nov
24-Nov
25-Nov
26-Nov
27-Nov
Limpopo

Free State

28-Nov
29-Nov
30-Nov
01-Dec
02-Dec
03-Dec
04-Dec
05-Dec
06-Dec
07-Dec
08-Dec
09-Dec
Mpumalanga

10-Dec
Northern Cape

11-Dec
12-Dec
13-Dec
14-Dec
15-Dec
16-Dec
17-Dec
18-Dec
North West

19-Dec
20-Dec
Confirmed SARS-Cov-2 cases by province
Comparison of SARS-Cov-2 cases in first and
second wave in Western Cape
40

Western Cape - second wave Western Cape - first wave

35
Second wave
30

25
Latest results: 59/67
20
(88% are the new variant)
First wave
15

10

0
13
17
21
25
29
33
37
41
45
49
53
57
61
65
69
73
77
81
85
89
93
97
1
5
9

101
105
109
113
117
121
125
129
133
137
141
145
149
153
157
161
165
169
173
177
181
185
189
193
197
201
205
Comparison of SARS-Cov-2 cases in first and second
wave in KwaZulu-Natal
30

KwaZulu-Natal - first wave KwaZulu-Natal - second wave

25

20

15

Second wave
10

First wave

0
13
17
21
25
29
33
37
41
45
49
53
57
61
65
69
73
77
81
85
89
93
97
1
5
9

101
105
109
113
117
121
125
129
133
137
141
145
149
153
157
161
165
169
173
177
181
185
189
193
197
201
205
209
213
217
Expected & actual all-cause deaths during Covid-19
Before lockdown L5 L4 L3 – 1 Jun – 16 Aug L2 - 17 Aug – 20 Sept L1 - 21 Sept
Excess deaths: 210 Excess deaths: -3,714 Excess deaths: -3,894 Excess deaths: 32,809 Excess deaths: 5,132 Excess deaths: 12,116
Covid-19 deaths : 0 Covid-19 deaths: 93 Covid-19 deaths: 667 Covid-19 deaths: 11,483 Covid-19 deaths: 3,854 Covid-19 deaths: 6,314

18000

16000

14000

12000
Recorded deaths
10000

8000
Predicted deaths

Excess deaths COVID-19 deaths Cases

6000

4000
National cases

2000
Source:
0 Bradshaw D, et al
01-Jul
08-Jul
15-Jul
22-Jul
29-Jul

07-Oct
14-Oct
21-Oct
28-Oct
01-Apr
08-Apr
15-Apr
22-Apr
29-Apr
06-May
13-May
20-May
27-May
03-Jun
10-Jun
17-Jun
24-Jun

04-Nov
11-Nov
18-Nov
25-Nov
02-Dec
09-Dec
16-Dec
04-Mar
11-Mar
18-Mar
25-Mar

05-Aug
12-Aug
19-Aug
26-Aug
02-Sep
09-Sep
16-Sep
23-Sep
30-Sep
5 Mar – 31 May: 7,608 less deaths (all-causes) than expected, mostly from fewer non-natural deaths
1 Jun – 16 Aug: 32,809 excess deaths (all-causes) - 11,483 reported Covid-19 deaths
The fine balance between virus and host
• Viruses usually evolve to become more transmissible & less
severe (less pathogenic or less lethal)
• Mostly within humans in response to immune pressure
• Sometimes when they pass through another species

• SARS-CoV-2 relatively stable in 1st wave – SA recorded about

35 lineages (most were the more transmissible D614G variant
from Europe with minor variations)
• 2nd wave now in all provinces with some early signs of it
spreading faster than 1st wave
• Not clear if 2nd wave has more or less deaths (severity unclear)
2nd wave – new 501.V2 variant with 3 RBD
mutations has spread & become predominant

Probably originated in NMB – spread

3 RBD mutations: K417N, E484K, N501Y to EC, Garden route, KZN & Cape Town
- ↑ affinity to ACE2 receptor & potential Ab escape
Source: Tyler N et al, Cell 2020
Preliminary results:
501.V2 variant associated with higher viral load
Speculate the following:
• Higher viral load in swabs may translate to
higher efficiency of transmission ie. Higher
transmissibility
• This may translate into a higher R0
• While other viruses are transmitting, this
variant is transmitting faster
• This may translate into a 2nd wave that will
have many more cases than 1st wave
What do & don’t we know about the 501.V2 variant?
1. Unusual for a new variant to contain several mutations – 3 in
RBD incl. N501Y – which alters ACE2 affinity & ?Ab effects
2. N501Y is being reported in other countries (0.2%) e.g. UK
3. Early signs that the new variant is spreading fast –
sometimes faster than 1st wave viruses
4. It is widespread – probably across most of SA by now
1. Where did it come from & why did it form? Why NMB? – we
have a few hypotheses to investigate
2. Is it more severe? – to early to tell
3. Is it re-infecting people who got infected in the 1st wave
4. Will the current vaccines work against this variant?
– currently being studied by KRISP, AHRI, NICD & CAPRISA
What should we do next?
1. There is reason for concern that we have a virus that seems
to be spreading rapidly; but it is something we can deal with.
2. Same prevention measures & treatment work for 501.V2
3. Similar 501 variants are in other countries e.g. Australia, UK
4. Inform key role-players & the public about the 501.V2 variant
5. Publish the data in a prominent journal
6. Urgently increase phylogenetic screening – need to
sequence 100-200 viruses every month from across SA
7. Complete the studies to answer the 4 unknowns –
fortunately, there are vaccine trials underway in SA e.g. J&J

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The 2nd Covid-19 wave in South Africa:

Transmissibility & a 501.V2 variant

Salim S. Abdool Karim, FRS

13000 Hospital admissions (116,335)

admissions to DATCOV sentinel

hospitals and deaths

Western Cape - second wave Western Cape - first wave

KwaZulu-Natal - first wave KwaZulu-Natal - second wave

Excess deaths COVID-19 deaths Cases

• SARS-CoV-2 relatively stable in 1st wave – SA recorded about

Probably originated in NMB – spread

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