Real world analysis of Omicron outbreak in South Africa including vaccine effectiveness - December 2021
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Real world analysis of Omicron outbreak in South Africa including vaccine effectiveness December 2021
Preface
SA scientists from Network for Discovery Health has continuously The National DoH has created
Genomic Surveillance first to announce shared data throughout the pandemic. considerable capacity to vaccinate the
the identification of Omicron variant. South African population at scale. The
insights herein support the priority of
Discovery Health is in an unusual vaccination and the NDoH’s existing
SA is first to experience Omicron- position to avail early insights given the approval of third dose Pfizer-BioNTech
driven outbreak commencing about 3 dominance of the Omicron variant in boosters.
weeks ago. SA, and the availability of member data
spanning demographic details, clinical
and pathology records and vaccination Discovery Health’s insights have been
records. shared with the SA NDoH, the SA
National Institute for Communicable
Diseases (NICD), the US CDC, leading
SA and UK scientists and others
Dataset is derived for the early period of the Omicron outbreak. Consequently
these preliminary insights may change as this Covid-19 wave extends
Panel
Professor Glenda Gray Shirley Collie Dr Ryan Noach
3
Executive summary | Omicron Insights
1. Epidemiological tracking shows steep trajectory of new Covid-19 infections indicating rapid Omicron
spread, but with a flatter trajectory of hospital admissions, indicating likely lower severity
2. Anecdotal observations demonstrate nuanced differences in the clinical features of Omicron both out
of hospital and in hospital
3. Data indicates that the severity of Omicron is 29% lower than D614G (first) wave of Covid-19 infections
in South Africa
4. Vaccine effectiveness of the double dose Pfizer-BioNTech regime:
• Has reduced from 80% in Delta wave to 33% in Omicron wave against Covid-19 infection; and
• Has reduced from 93% in Delta wave to 70% in Omicron wave against severe complications of
Covid-19 (hospital admission)
5. The protective effect of prior infection has reduced over time, and Omicron has eroded that protective
effect further
6. Children experiencing very low test-positivity rate relative to adults, and low Covid-19 admissions in
absolute terms, but appear to be at 20% greater risk of hospitalisation during Omicron wave relative to
D614G wave
4
Background Clinical and Real-world insights
epidemiological into vaccine
observations effectiveness
5
Discovery Health (DH) is uniquely positioned to derive powerful
COVID-19 insights
• Pathology results
DH Electronic • Hospital admissions
Health Record • ICU and ventilation Unique, real-world
data • Underlying disease burden Covid-19 insights
>3.7 million health
Epidemiological
insurance lives tracking &
administered by modelling,,
Discovery Health resilience against
Vitality Member severe disease,
Wellness vaccination Vaccine
Data data effectiveness safety
and side effects
• Underlying wellness • Vaccination status
• Physical activity • Dose adherence
• Mobility data • Vaccine type
Discovery Health beneficiaries are diverse, allowing for relevant real world
insights to be derived
26% of all individuals are living with chronic
Data distributed widely across age groups
illness
Other
9,6%
9,0% Epilepsy 9,0%
Conduction disorder
2,1
8,2%
7,9% Bipolar mood disorder Hypertension
2,
%
7,6%
2%
7,4% 3,1% 29,5%
6,6% HIV
6,1% 6,2% 4,6%
5,9%
5,1% Ischaemic heart disease 4,8%
4,7%
4,4%
3,4% Hypothyroidism 5,6%
2,8%
2,0%
9,2%
1,2% 1,2%
Diabetes 19,2%
0,8%
Hypercholesterolaemia
10,7%
Discovery Health has extensive South Africa-specific, real-world data 10 Dec 2021
We have been tracking and codifying unique member data since the start of the pandemic
Tests Positive Active Repeat Recoveries Members Deaths Vaccines
conducted cases cases cases admitted administered
2,604,385 467,530 28,415 15,580 424,717 61,579 14,398 2,713,122
DH
SA 19,912,714 3,071,064 113,060 2,867,966 90,038 26,781,642
Testing rate COVID proportion % Active Proportion of Recovery rate Proportion Case % Adult
of DH lives repeat positive admitted fatality rate vaccinated
Testing rate Unique Proportion Hospital Proportion
DH entities readmitted mortality rate administered
national
Pfizer vaccine 14 days – 99 days after second dose. Excludes data on members vaccinated in the public sector post September 2021.
Source: Discovery Health Insights https://discv.co/DiscoveryHealthInsights
8
SA has experienced 3 prior waves of COVID-19 and now entering a
fourth wave with rapid rise in cases driven by Omicron variant
National new cases (7-day moving average) DH new cases (7-day moving average)
20 000 3500
15 043 3000
15 000
2500
2000
10 000 1 519 Gauteng Province accounts for
1500
63% of current COVID-19 cases
5 000
1000
nationally, and 67% of Discovery
500
Health cases in fourth wave
- 0
Sep-20
Sep-21
May-20
May-21
Mar-20
Nov-20
Mar-21
Nov-21
Sep-20
Sep-21
Jan-21
May-20
May-21
Nov-20
Nov-21
Jan-21
Mar-20
Mar-21
Jul-20
Jul-21
Jul-20
Jul-21
26% of the national population
Average weekly new DH cases per 100,000 lives for Gauteng (7-day moving average) resides in Gauteng Province.
Upcoming mobility due to high
120
migrant worker base and holiday
100
period pose a risk of imminent
80 spread to other provinces across
60 South Africa
40
20
0
Week ending 20 Nov Week ending 27 Nov Week ending 4 Dec
Source: NICD, Discovery Health Analysis 9
Background Clinical and Real-world insights
epidemiological into vaccine
observations effectiveness
10Omicron-driven fourth wave is developing at a steeper trajectory of new
infections relative to prior waves
National data Discovery Health data
SA daily cases (7-day average) by wave DH daily cases (7-day average) by wave
25 000 4 000
3 500
20 000
3 000
15 000 2 500
2 000 Steeper increase in
10 000 1 500 new infections and
1 000
5 000
500
test positivity rate
- - during the first
three weeks of the
1
7
1
7
13
19
25
31
37
43
49
55
61
67
73
79
85
91
97
13
19
25
31
37
43
49
55
61
67
73
79
85
91
97
103
109
115
121
127
133
139
103
109
115
121
127
133
139
Day from start of wave Day from start of wave fourth wave
indicating highly
SA weekly test positivity rate by wave DH weekly test positivity rate by wave transmissible
40,0%
35,0%
35,0% variant with rapid
30,0%
30,0% community spread
25,0%
25,0%
20,0% 20,0%
15,0% 15,0%
10,0% 10,0%
5,0% 5,0% D614G wave
0,0% 0,0% Beta wave
1
7
1
7
13
19
25
31
37
43
49
55
61
67
73
79
85
91
97
13
19
25
31
37
43
49
55
61
67
73
79
85
91
97
103
109
115
121
127
133
139
103
109
115
121
127
133
139
Delta wave
Day from start of wave Day from start of wave Omicron wave
Source: NICD, Discovery Health AnalysisOmicron variant has displaced Delta and now dominates 04 Dec 2021
new infections in SA
100
Nextclade clades
19B
20A
75
20B
20C
20D
Alpha (10I, V1)
percentage
50
Beta (20H, V2)
Delta (21A)
Delta (21I)
25 Delta (21J)
Eta (21D)
Kappa (21B)
0 Omicron (21K)
1 2 3 4 5 6 7 8 9 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 C,1.2 (20D)
epiweeks in 2021
• Network of virology and genomic laboratories, scientists and academic institutions across South Africa
• Genomic data produced at five sequencing facilities under the guidance of more than 50 investigators
and scientists
• Launched in June 2020 with support of the Department of Science and Innovation and
South African Medical Research Council
Source: Network for Genomic Surveillance in South Africa 12Anecdotal evidence demonstrates nuanced differences in the
clinical presentation
Out-of-hospital acute care Admissions
• Higher reinfections and breakthrough infections • Most hospitalised patients for Covid-19 related disease
than other waves, including vaccinated are unvaccinated
• Shorter incubation period of 3-4 days • High number of hospitalisations in Gauteng for
non-Covid care, present with Covid as an
• Milder illness with reported recoveries within 3 days incidental finding on admission
• Scratchy/sore throat most common early symptom, • Less respiratory distress on presentation
like other waves
• Proportion of High care and ICU admissions lower
• Typical features include nasal congestion, dry cough compared to previous waves
and myalgia, especially lower back pain
• Significantly lower proportion of admitted patients
requiring oxygen support
• Most hypoxic patients requiring oxygenation
are unvaccinated
• 16% of ICU admissions are vaccinated (raw data)
Source: Dr Gerrit De Villiers, Chief Clinical Officer of Mediclinic Southern AfricaFlatter trajectory of hospital admissions, indicating lower severity
Hospital admissions per 1,000 infections
44 131 101 38
D614G Beta Delta Omicron
Hospital admissions by wave at 3 week snapshot
500 DH daily hospital admissions (7-day average) by wave Caveats:
450
• Underlying Covid-19
400 antibody seroprevalence in
SA population high,
350
especially following Delta
300 D614G wave
wave
Beta wave • Covid-19 treatment has
250
Delta wave improved since D614G
200
Omicron wave wave; especially with the
150 introduction of
100 dexamethasone
• Data represents the first 3
50 weeks of Omicron wave,
0 caution in interpretation of
hospital admissions
1
4
7
10
13
16
19
22
25
28
31
34
37
40
43
46
49
52
55
58
61
64
67
70
73
76
79
82
85
88
91
94
97
100
103
106
109
112
115
118
121
124
127
130
133
136
139
Day from start of wave therefore required
Source: Discovery Health Analysis 14Apparent de-linking of infection curve from admission curve
Much steeper increase in new cases during the first three weeks of the Omicron wave compared to the Delta variant
driven third wave. However, admissions and deaths are not increasing as rapidly.
Cases, admissions and deaths indexed to the Delta wave, each as a share of Delta peak (%)
100%
90%
80%
70%
Cases
60%
50%
40%
30%
Admissions
20%
10%
Deaths
0%
Apr May Jun Jul Aug Sep Oct Nov Dec
Source: Discovery Health AnalysisPaediatric cases and admissions appear more prevalent than prior waves,
but typically present as mild cases
Paediatric out-of-hospital cases Paediatric admissions
• Higher number of paediatric cases testing positive • Primary diagnoses in children on admission for Covid-19
relative to prior waves related disease in Omicron wave are bronchiolitis and
• Children present with a sore throat, nasal congestion pneumonia
and fever for 2-3 days, and tend to complain of a • Often with associated diarrhoea and vomiting, and
headache dehydration
• Seems to resolve quickly with recovery after 3 days • Incidental Covid-19 diagnosis for multiple paediatric
admissions, exceeding Covid-19 specific admissions
1,80 DH cases and admissions for under 18 year olds indexed to Delta Wave
1,60 Cases
1,40
1,20 Admissions
1,00
0,80
0,60
0,40
0,20
-
Apr May Jun Jul Aug Sep Oct Nov Dec
Source: Dr Gerrit De Villiers, Chief Clinical Officer of Mediclinic Southern Africa; Discovery Health AnalysisIncrease in paediatric admissions, with high number of incidental Covid-19
diagnoses for unrelated admissions
Admission proportion by age band Admission rate by age band Admission risk by age band
Increase in proportion of paediatric To date, children under age 5 have
admissions in the Omicron wave, possibly 60,0% experienced higher admission risk than
driven by incidental Covid-19 diagnosis on adults
admission
50,0%
COVID19 admissions per 1,000 person years
35,0%
35,00
40,0%
30,0%
30,00
25,0%
30,0% 25,00
20,0%
20,00
15,0% 20,0%
15,00
10,0%
10,00
10,0%
5,0% 5,00
0,0% -
0,0%
0-9 10-19 20-34 35-49 50-59 60-79 80+ 0-4 5-12 13-17 Adults
to 04
to 09
to 14
to 19
to 24
to 29
to 34
to 39
to 44
to 49
to 54
to 59
to 64
to 69
to 74
to 79
to 84
85+Risk-adjusted, Omicron may pose risk of increased severity to children
under 18 years of age; very early data which should be carefully followed;
low risk in absolute terms
Risk of admission relative to South Africa's first wave (fully risk-adjusted)
Adult population Child population
1,20
1,2 1,2
1,1 1,1
1,0 1 1,0 1 29% average lower
0,9 0,9 admission risk
0,8 0,8 relative to D614G
0,71 wave. Children, to
0,7 0,7
date, have had a
0,6 0,6 20% higher risk of
0,5 0,5 admission
0,4 0,4
0,3 0,3
0,2 0,2
0,1 0,1
0,0 0,0
D614G wave Beta Wave Delta Wave Omicron Wave
Assessed using a Cox proportional hazard model allowing for days since PCR collection date, age, sex, number of documented risk factors, vaccination status and documented prior infection*
To be submitted for peer review and publication
Source: Discovery Health Insights https://discv.co/DiscoveryHealthInsightsRisk-adjusted data correlates with anecdotal evidence demonstrating lower
severity in current Omicron wave than previous waves
Adults are experiencing 29% lower admission risk of Covid-19 admissions relative to the D614G wave. Those who are
hospitalised also have a lower admission acuity and a lower propensity to be admitted to ICU, relative to prior waves
Admission risk indexed to the first wave Case mix of Covid 19 admissions indexed to the Proportion of admissions in High care and ICU
first wave by wave
1,12 1,18
1,08 5%
1,00 18% 8%
0,94 1,00 21% 22%
0,79 17% 14% 10%
0,71
87%
65% 65% 68%
D614G Beta Delta Omicron D614G Beta Delta Omicron D614G Beta Delta Omicron
ICU High Care Other wards
Assessed using a Cox proportional hazard model allowing for days since PCR collection date, age, sex, number of documented risk factors, vaccination status and documented prior infection*
To be submitted for peer review and publication
Source: Discovery Health Data 19Although national excess natural deaths increased in the last week of Nov,
excess natural deaths are still significantly lower than previous waves
South Africa weekly natural cause excess deaths National weekly excess deaths Oct – Nov 2021
2 076
16 000
1 504
14 000 1 407 1 376
1 134 1 133 1 187
1 091
12 000 804
10 000
3-Oct 10-Oct 17-Oct 24-Oct 31-Oct 7-Nov 14-Nov 21-Nov 28-Nov
8 000
Provincial weekly excess deaths Oct – Nov 2021
600
6 000
500
4 000 400
300
2 000 200
100
0 -
Sep-20
Sep-21
Oct-20
Oct-21
May-21
Nov-20
Nov-21
Mar-21
Dec-20
Apr-21
Jan-21
Jul-20
Aug-20
Jul-21
Aug-21
Feb-21
Jun-21
3-Oct 17-Oct 31-Oct 14-Nov 28-Nov
EC FS GT KZN LM MP NC NW WC
Source: South African Medical Research Council excess natural deaths report
20Background Clinical and Real-world insights
epidemiological into vaccine
observations effectiveness
21Rapid timeline of Omicron research following identification by SA scientists;
accelerated severity & vaccine effectiveness insights through DH collaboration
with SAMRC
24 November First report of B.1.1.529 from South African scientists
26 November WHO designates Omicron a variant of concern
27 November South African clinicians note mildness of cases relative to prior variants
Moderna and Pfizer announce plans for Omicron-specific vaccine
Less than 3 weeks
2 December 250% increase in re-infection for Omicron relative to prior variants in South Africa (Juliet Pulliam et al)
7 December 4 lab neutralisation studies pre-print published with ~40% reduction in neutralization (Sigal et al, Ciesek et al,
Sheward et al, Pfizer-BioNTech study)
10 December First report of clinical vaccine effectiveness for 2 shots and boosters, 3-fold household transmission contact
transmission vs Delta (UKHSA)
Today First real world study at scale on Pfizer-BioNTech vaccine effectiveness. Pre-print published by Discovery
Health and the South African Medical Research Council
Source: Adapted from Eric Topol twitter, with addition in blueOmicron vaccine effectiveness study parameters
study duration
Covid-19 PCR test results for adult population
Pre-Omicron Period Proxy Omicron Period
1 September 15 November
to to
31 October 2021 7 December 2021
63% 37%
of sample of sample
SGTF positive test Gauteng PCR tests PCR test results
results from Lancet amongst symptomatic
Laboratories admitted patients
45% 55% 8%
of sample
of sample of sample
23Omicron vaccine effectiveness study methodology: Test negative design
Method used globally on pathology surveillance data to assess annual influenza vaccine effectiveness
• Method is generalisable to other
specific respiratory conditions
provided vaccination does not have
clinical efficacy for other respiratory
conditions
• Methodology implicitly adjusts for
biases due to health-seeking
behaviour
• Efficacy estimates and associated
confidence intervals are consistent
with randomized control studies
• A number of publications have used a
test-negative design for real world
Covid-19 vaccine effectiveness
studies
De Serres G, Skowronski DM, Wu XW, Ambrose CS. The test-negative design: validity, accuracy and precision of vaccine efficacy estimates compared to the gold standard of randomised placebo-controlled clinical trials . Euro Surveill. 2013;18(37):pii=2058 24Pfizer-BioNTech vaccine 33% effective in reducing Omicron-related
infection
Real-world Pfizer vaccine Waning effectiveness against infection
effectiveness against infection over time
100 100
90 80% 90
Omicron has
80 80 materially reduced
70 70 vaccine
effectiveness
60 60 against new
50 50 infections,
potentially
40 40 compounded by
30 30 waning durability
56%
20 20 37%
25%
10 10
0 0
Unvaccinated Vaccinated 2 to 4 weeks 1 to 2 months 3 to 4 months
Pre-Omicron Omicron wave post 2nd dose post 2nd dose 15 Novpost
to 2nd
3 Dec
dose2021
*To be submitted for peer review and publication
Authors have no conflicts of interest direct or in kind
Source: Discovery Health Insights https://discv.co/DiscoveryHealthInsights 25Pfizer-BioNTech vaccine 70% effective in reducing Omicron-related
hospital admissions
Real-world Pfizer-BioNTech vaccine
effectiveness against hospital admission
100 93%
90
80 Real world effectiveness of the
Pfizer-BioNTech vaccine
70
against hospital admission has
60 reduced from 93% in the Delta
50 (pre-Omicron) wave to 70% in
the Omicron wave, continuing
40
to provide substantial
30 protection against hospital
20 admission
10
0
Unvaccinated Vaccinated
Pre-Omicron Omicron wave
* Submitted for peer review and publication with the NEJM
Authors have no conflicts of interest direct or in kind
Source: Discovery Health analysis of Pfizer-BioNTech effectiveness 26Vaccine effectiveness retracts slightly with increasing age but is maintained
across various comorbidities – durability impact confounding
Vaccine effectiveness by age during Omicron Vaccine effectiveness by comorbidity during
period Omicron period
1,00 1,00
92%
0,90 0,90
82%
0,80 75% 0,80
74%
68% 69%
0,70 67% 0,70
63% 64%
59%
0,60 0,60
0,50 0,50
0,40 0,40
0,30 0,30
0,20 0,20
0,10 0,10
- -
Hyper- Ischemic Heart
18-29 30-39 40-49 50-59 60-69 70-79 Diabetes Hypertension
cholesterolamia Disease
*To be submitted for peer review and publication
Authors have no conflicts of interest direct or in kind
Source: Discovery Health analysis of Pfizer-BioNTech effectivenessAlthough prior infection confers reduced risk of re-infection, this is
diminished against Omicron re-infection
D614G Beta Delta
0,73 The protective
effect of prior
0,59 infection has
reduced over time,
0,48 and Omicron has
0,41 eroded that
protective effect
0,29 further
0,27
Odds of reinfection- Omicron period Odds of reinfection Sept/Oct 2021
*To be submitted for peer review and publication, Pre-Omicron period refers to September - October
Source: Discovery Health Insights https://discv.co/DiscoveryHealthInsightsAcknowledgements
Shirley Collie, Jared Champion, Lizelle Steenkamp, Sameera Haneef, Matt Zylstra, Tommy Chen,
Michael Cohen, Ismail Rasool, Thishen Govender
Milani Wolmarans Mary Anne Davies
Andrew Boulle
Petro Rossouw
Reshma Kassanjee
Prof Glenda Gray Prof Linda Gail Bekker
Dr Harry Moultrie Dr Richard Lessels
Prof Cheryl Cohen Tulio de Oliveira
Hendrik van de Venter
John Sole
29Conclusion| Omicron Insights
1. Apparent 29% lower severity based on early data (in high seroprevalence population) and supported by
anecdotal clinical feedback
2. Vaccination remains single most important intervention to mitigate against severe Covid-19, with
double dose of Pfizer-BioNTech vaccine showing 70% effectiveness in reducing risk of hospitalisation
3. Vaccine effectiveness against infection is materially reduced, with high numbers of breakthrough
infections in vaccinated individuals
4. The protective effect of prior infection has reduced over time, and Omicron has eroded that protective
effect further, with high re-infection rates in previously Covid-19 positive individuals
5. Notwithstanding the lower severity, health systems could still be over-run by the sheer volume of cases,
considering Omicron’s rapid community spread
6. Children experiencing very low test positivity rate relative to adults, and low Covid-19 admissions in
absolute terms, but appear to be at 20% greater risk of hospitalisation during Omicron wave relative to
D614G wave
30Real world analysis of omicron outbreak in South Africa including vaccine effectiveness December 2021
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