Update on COVID variant

CAPRISA hosts a MRC HIV-TB Pathogenesis
and Treatment Research Unit
CAPRISA hosts a DoH-MRC Special Initiative
for HIV Prevention Technology
CAPRISA is the UNAIDS Collaborating
Centre for HIV Research and Policy
CAPRISA hosts a
DST-NRF Centre of
Excellence in
HIV Prevention
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
Director: DSI-NRF Centre of Excellence in HIV Prevention
Pro Vice-Chancellor (Research): University of KwaZulu-Natal
Adjunct Professor in Immunology and Infectious Diseases, Harvard University
Adjunct Professor of Medicine: Cornell University
Update on Covid-19 epidemic &
the 501Y.V2 variant in South Africa
18 January 2021

Key questions addressed in this update
1. Is the 501Y.V2 variant in the 2nd wave spreading faster?
– Biological evidence showing that the virus binds more readily and more strongly (higher
affinity) to the human cells
– Epidemiological evidence from areas where the new variant is known to be dominant
2. Is the 501Y.V2 variant more severe?
3. Any new evidence on whether Covid-19 vaccines are effective or not
against the 501Y.V2 variant?
4. Do antibodies from SA’s 1st wave kill the 501Y.V2 variant of the 2nd
wave?
Conclusion & next steps

Covid-19 in South Africa
7-day moving average of new cases, sentinel hospital admissions and
Covid-19 deaths – to 17 Jan 2021
0
500
1000
1500
2000
2500
3000
3500
0
2000
4000
6000
8000
10000
12000
14000
16000
18000
20000
05-Mar 05-Apr 05-May 05-Jun 05-Jul 05-Aug 05-Sep 05-Oct 05-Nov 05-Dec 05-Jan
7-daymovingaverageofdaily
admissionsanddeaths
7-daymovingaverageofdailycases
Hospital admissions
Cases
Deaths
Level 5
doubling:
15 days
Before lockdown
Doubling: 2 days
Level 4
doubling:
12 days
Level 3 doubling –
Up to16/8: 25 days
L2 doubling –
17/8 – 20/9:
206 days
L1 doubling –
21/9 – 28/11:
276 days
Deaths
Hospital
Admissions
(1,337,926)
(37105)
L1 doubling (start of 2nd wave) –
29/11 – 28/12: 64 days
(174,466)
New
cases
L3 adjusted doubling –
29/12 – 17/01
Source of hospital admissions data: Lucille Blumberg, Richard Welch and Waasila Jassat – DATCOV, NICD

• Amino acid changes lead to charge & shape alterations
• By measuring free energy perturbation (FEP), show that binding
of RBD to ACE2 increasing significantly with 501 mutation
• RBD rotates 20o - approaches deeper to the binding site with
ACE2 receptor
RBD = receptor-binding domain of the spike protein; ACE2 = angiotensin converting enzyme-2

2.3%
7.9%
4.7%
1.7%
2.3%
2.5%
2.8%
2.6%
3.1%
4.1%
5.3%
6.5%
8.1%
8.8%
12.7%
14.9%
20.2%
23.9%
26.7%
27.2%
25.8%
24.1%
20.8%
16.3%
13.5%
11.4%
9.8%
9.2%
9.8%
8.6%
8.3%
8.0%
8.1%
7.8%
7.6%
8.6%
9.9%
14.8%
11.7%
15.4%
20.3%
24.0%
31.2%
31.9%
27.1%
22.8%
0.0% 5.0% 10.0% 15.0% 20.0% 25.0% 30.0% 35.0%
Average weekly proportion of tests positive
Average daily tests & proportion of positive tests
103
788
3157
3118
3238
3971
7366
9305
12890
16258
17354
22857
23565
29675
28528
33131
35159
42063
46336
43883
40849
33108
23670
23541
19671
18446
16622
17154
16947
15270
18662
20238
21760
20563
20002
20833
21511
21292
27229
33543
39395
44936
40489
51181
66585
59966
0 10000 20000 30000 40000 50000 60000 70000
07 Mar - 13 Mar
21 Mar - 27 Mar
04 Apr - 10 Apr
18 Apr - 24 Apr
02 May - 08 May
16 May - 22 May
29 May - 04 Jun
12 Jun - 18 Jun
26 Jun- 02 Jul
10 Jul - 16 Jul
24 Jul - 30 Jul
07 Aug - 13 Aug
21 Aug - 27 Aug
4 Sept - 10 Sept
18 Sept - 24 Sept
2 Oct - 8 Oct
16 Oct - 22 Oct
30 Oct - 5 Nov
13 Nov - 19 Nov
27 Nov - 03 Dec
11 Dec - 17 Dec
25 Dec - 31 Dec
08 Jan - 14 Jan
Average daily number of tests each week
Lighter shade is an
incomplete week
Cumulative number tests 4 March - 17 January = 7,433,571

Daily new cases over last 7 days/100,000
- up to 11 Jan 2021
29 Dec – 4 Jan 5 Jan – 11 Jan
Increase /
decreaseProvince
Population
/100,000
7-day ave
on 1 Jan
Cases
/100,000
/day
7-day ave
on 8 Jan
Cases
/100,000
/day
EC 67 952 14.8 1041 16.3 +8.5%
FS 29 301 9.2 513 17.8 +41.3%
GP 152 3583 23.6 5291 34.7 +32.3%
KZN 113 4498 39.8 5088 45.1 +11.6%
LP 60 777 13.0 1598 25.2 +51.4%
MP 46 555 12.1 1112 24.0 +50.1%
NC 13 157 12.4 285 22.6 +44.9%
NW 41 437 10.7 755 18.4 +42.1%
WC 68 3233 47.2 3075 44.9 -4.9%
National 580 14496 24.2 19042 31.8 +23.9%
Eastern Cape
16.3
Northern Cape
22.6
North West
18.47
Free State
17.8
Mpumalanga
24.0
Limpopo
25.20
Gauteng
34.7
KwaZulu
Natal
45.1
Western Cape
44.9
0-4.99
Cases /100,000 /day
5 - 9.99
10 - 14.99
>15

Daily new cases over last 7 days/100,000
- up to 18 Jan 2021
5 Jan – 11 Jan 12 Jan – 18 Jan
Increase /
decreaseProvince
Population
/100,000
7-day ave
on 8 Jan
Cases
/100,000
/day
7-day ave
on 15 Jan
Cases
/100,000
/day
EC 67 1041 16.3 873 13.0 -19.2%
FS 29 513 17.8 529 18.3 +3.1%
GP 152 5291 34.7 4084 26.2 -29.6%
KZN 113 5088 45.1 4175 35.7 -21.9%
LP 60 1598 25.2 1351 23.2 -18.3%
MP 46 1112 24.0 1097 23.9 -1.37%
NC 13 285 22.6 294 20.9 +3.2%
NW 41 755 18.4 726 18.0 -4.0%
WC 68 3075 44.9 2342 34.2 -31.3%
National 580 19042 31.8 15214 25.7 -25.2%
Eastern Cape
13.0
Northern Cape
20.9
North West
18.0
Free State
18.3
Mpumalanga
23.9.0
Limpopo
23.2
Gauteng
26.2
KwaZulu
Natal
35.7
Western Cape
34.2
0-4.99
Cases /100,000 /day
5 - 9.99
10 - 14.99
>15

KwaZulu-Natal
Gauteng
Eastern Cape
Western Cape
National
0
10
20
30
40
50
60
05-Mar
12-Mar
19-Mar
26-Mar
02-Apr
09-Apr
16-Apr
23-Apr
30-Apr
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
24-Dec
31-Dec
07-Jan
14-Jan
21-Jan
7-daymovingaverageofnationaldailycases
per100,000population
KwaZulu-Natal
Gauteng
Limpopo
Mpumalanga
North West
Eastern Cape
Western Cape
Free State
Northern Cape
National
Confirmed SARS-CoV-2 cases by province
(7-day moving average cases per 100,000 population – up to 17 January 2021)

0
10
20
30
40
50
1
5
9
13
17
21
25
29
33
37
41
45
49
53
57
61
65
69
73
77
81
85
89
93
97
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
Western Cape - first wave
Western Cape - second wave
SARS-CoV-2 cases in 1st & 2nd waves in Western Cape
(7-day moving average cases per 100,000 population – up to 17 January)
First wave
Second wave

Western Cape daily hospital admissions and in-
hospital deaths
(7-day moving average up 17 January 2021)
NumberofAdmissionsandDeaths
Analysis: Amanda Brewer; Data source: Lucille Blumberg, Waasila Jassat & Richard Welch – DATCOV, NICD
0
100
200
300
400
500
600
7-Day moving ave admissions in WC 7-day moving ave deaths in WC

Eastern Cape daily hospital admissions and in-
hospital deaths
0
50
100
150
200
250
300
7-day moving ave admissions in EC 7-day moving ave deaths in EC

KwaZulu-Natal daily hospital admissions and in-
hospital deaths
0
50
100
150
200
250
300
350
400
450
7-day moving ave admissions in KZN 7-day moving ave deaths in KZN

SARS-CoV-2 cases in 1st & 2nd wave in KwaZulu-Natal
(7-day moving average cases per 100,000 population – up to 17 January)
0
10
20
30
40
50
1
5
9
13
17
21
25
29
33
37
41
45
49
53
57
61
65
69
73
77
81
85
89
93
97
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
KwaZulu-Natal - first wave
First wave
Second wave
KwaZulu-Natal - second wave

How much faster is it spreading in SA’s 2nd wave?
• Days to reach 100,000 cases in the 1st & 2nd wave:
– Western Cape: 50% faster 107 vs 54 days
– KwaZulu-Natal: 39% faster 54 vs 33 days
• Caveats: confounding by behaviour, testing, reporting, etc
• 501Y.V2 is 50% more
transmissible than
previous variants
• Assumes minimal
reinfection levels
Source: Cheryl Baxter, CAPRISA

• Comparing SARS-CoV-2 prevalence, Covid-19 hospital admissions,
hospital & ICU bed occupancy in areas with high & low variant prevalence
• The B.1.1.7 variant with the sole RBD mutation at position 501 is
56% more transmissible than pre-existing variants
• No evidence of more severe disease
CCMMID repository
How does 501Y.V2 compare with B.1.1.7 variant?

against the 501Y.V2 variant? Not yet! Working on it
wave?

Is 501Y.V2 associated with increased admissions?
• When the Western Cape and KwaZulu-Natal reached
100,000 cases in 1st & 2nd wave the admission rate
(per 1000 reported cases) was:
Western Cape: 159 vs 147 (15,942 vs 14,796)
KwaZulu-Natal: 110 vs 106 (11,042 vs 10,632)
• Caveats: confounding by reporting, age, lag, etc
Analysis: Cheryl Baxter, CAPRISA; Data source: Lucille Blumberg, Waasila Jassat & Richard Welch – DATCOV, NICD

Wave period
Early wave 1:
<1 June 2020
1968 admissions
Late wave 1:
1 Jun - 31 Aug 2020
7128 admissions
Between waves:
1 Sep – 15 Oct 2020
666 admissions
Wave 2
≥ 16 Oct 2020
3968 admissions
0
10
20
30
40
50
60
70
80
90
100
Admissions Early wave 1 Admissions Late wave 1 Admissions btwn waves Admissions wave 2
0
10
20
30
40
50
60
70
80
90
100
Deaths Early wave 1 Deaths Late wave 1 Deaths btwn waves Deaths wave 2
Male Age group
DM HPT
CKD
COPD Prev
TB
Curr
TB
HIV
Any comorbidity
No notable
difference
admitted (or
deceased)
patients for the
different wave
periods.
Admission disease profile in WC similar in both waves
Source: Mary-Ann Davies – Western Cape DoH

0%
1%
2%
3%
4%
5%
6%
7%
8%
9%
0.0%
5.0%
10.0%
15.0%
20.0%
25.0%
30.0%
Kaplan-Meier
probability of death
among known public
sector adult cases by
30 days since
diagnosis by age &
“wave period”
Note: different y-axis
for age ≥60 years
20-39y 40-49y 50-59y 60-69y ≥70y
No difference in mortality by age group between waves
Wave period from L-R
Early wave 1:
<1 June 2020
Late wave 1:
1 Jun - 31 Aug 2020
Between waves:
1 Sep – 15 Oct 2020
Wave 2
≥ 16 Oct 2020
Risk of dying in the Western Cape public sector by
age and “wave period”
Source: Mary-Ann Davies – Western Cape DoH

Covid-19 in-hospital monthly case-fatality-ratio
by age group shows little change across waves
5 March 2020 - 9 January 2021
Analysis: Juliet Pulliam from SACEMA; Data source: Lucille Blumberg, Waasila Jassat & Richard Welch – DATCOV, NICD

0
2000
4000
6000
8000
10000
12000
14000
16000
18000
20000
04-Mar
11-Mar
18-Mar
25-Mar
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
01-Jul
08-Jul
15-Jul
22-Jul
29-Jul
05-Aug
12-Aug
19-Aug
26-Aug
02-Sep
09-Sep
16-Sep
23-Sep
30-Sep
07-Oct
14-Oct
21-Oct
28-Oct
04-Nov
11-Nov
18-Nov
25-Nov
02-Dec
09-Dec
16-Dec
23-Dec
30-Dec
06-Jan
13-Jan
20-Jan
Excess deaths
Expected & actual all-cause deaths during Covid-19
Predicted deaths Cases
Recorded deaths
Before lockdown
Excess deaths: 210
Covid-19 deaths : 0
L5
Excess deaths: -3,714
Covid-19 deaths: 93
L4
Excess deaths: -3,894
Covid-19 deaths: 667
L3
Excess deaths: 32,815
Covid-19 deaths: 11,483
National cases
L2
Source: Bradshaw D, et al
L1 - 22 Dec
L3 - 29 Dec

against the 501Y.V2 variant? Not yet! Many working on it
wave?

Source: https://ssrn.com/abstract=3725763 & Dejnirattisai W. The antigenic anatomy of SARS-CoV-2 receptor binding domain, 2020 (Pre-print)

Immune responses target 2 main areas of the spike protein:
• Receptor-binding domain (RBD)
• N-terminal domain

Convalescent sera from 4 patients were not able to
neutralize viruses with a 484 mutation, which alters the
charge & shape of the RBD

Note: These are all antibody
binding studies – they do not
factor in T-cell immunity, which is
also likely to play an important
role in preventing reinfection
Study of convalescent sera from 44 South Africans infected in
first wave, >90% showed reduced immunity & 48% had
complete immune escape to 501Y.V2
E484 mutations reduced antibody binding
in 9 of 11 convalescent serum samples,
with some sera >10-fold reduction in
neutralization

 No, not at this stage. Vaccines like Pfizer & Moderna are among most
effective vaccines we have for any disease
 They achieve an important goal – reduce clinical illness & hospitalisation
 There are many unknowns - will take long to resolve and answer fully:
1. Are they free of long-term side effects?
2. Do they prevent asymptomatic infection?
3. Do they prevent viral spread from vaccinees?
4. Do they work against new variants?
 Vaccine rollout is not going to be easy or quick – mammoth logistical task
that needs all hands on deck to vaccinate at least HCWs, elderly, and
patients with hypertension, diabetes and cancer…..
Should this information change vaccine approach?

What have we learnt from this update on the 501Y.V2
variant?
• With some caveats – unpublished data, data quality, etc
• Virus is spreading (~50%) faster in 2nd wave than 1st wave in SA’s
coastal provinces where the 501Y.V2 variant is known to be dominant
• Current data suggests that new variant is not more severe
• Published convalescent serum studies suggest natural antibodies less
effective – viral escape facilitated by 484, 501 & N-terminal mutations
• Vaccine antibodies are different – may or may not be impacted
• No empiric evidence yet on whether vaccines are effective
against the 501Y.V2 variant – studies are underway
• Note: variant is called “501Y.V2” & not “South African” variant just like
“SARS-CoV-2” is not called “China virus”. Many variants in the world.

“The pandemic has exposed the paradox that while we are more
connected, we are also more divided….
“To come out of this crisis better, we have to recover the knowledge that
as a people we have a shared destination. The pandemic has reminded us
that no one is saved alone. What ties us to one another is what we
commonly call solidarity. Solidarity is more than acts of generosity,
important as they are; it is the call to embrace the reality that we are
bound by bonds of reciprocity. On this solid foundation we can build a
better, different, human future.”
- Pope Francis, head of the Catholic Church

Dr Richard Lessels
Senior Infectious Diseases Specialist,
based at the KwaZulu-Natal Research
Innovation & Sequencing Platform
Prof Penny Moore
DSI/NRF South African Research
Chair of Virus-Host Dynamics at WITS
and the NICD
Prof Alex Sigal
Virologist at the Africa Health Research
Institute and a Research Group Leader
at the Max Planck Institute
Prof Koleka Mlisana
Executive Manager of Academic
Affairs, Research & Quality
Assurance at the National Health
Laboratory Services
Prof Mary-Ann Davies
Public Health Medicine Specialist
responsible for epidemiology and
surveillance in the Western Cape
Department of Health
Dr Waasila Jassat
Medical doctor and public health
medicine specialist. She heads the
DATCOV Hospital Surveillance for
COVID-19 at NICD
Prof Willem Hanekom
Leading TB and vaccines expert
who leads the Africa Health
Research Institute
Prof Tulio de Oliveira
Bioinformatician who directs the
KwaZulu-Natal Research and
Innovation Sequencing Platform at
UKZN

Update on COVID variant

Recommended

Recommended

More Related Content

Similar to Update on COVID variant

Similar to Update on COVID variant (20)

More from Preggie Moodley

More from Preggie Moodley (20)

Recently uploaded

Recently uploaded (20)

Update on COVID variant