PRELIMINARY OBSERVATIONS OF PRELIMINARY OBSERVATIONS OF THE EPIDEMIOLOGY OF SEASONAL THE EPIDEMIOLOGY OF SEASONAL
AND PANDEMIC INFLUENZA A AND PANDEMIC INFLUENZA A (H1N1) IN SOUTH AFRICA, 2009(H1N1) IN SOUTH AFRICA, 2009
BARRY D SCHOUB MD DSc FRCPath EXECUTIVE DIRECTOR
NATIONAL INSTITUTE FOR COMMUNICABLE DISEASES(A Division of the National Health Laboratory Service)
SOUTH AFRICA
IANPHI CONFERENCE NOVEMBER 2009
Western IST bloc
Central IST bloc
East and South IST bloc
Non AFRO countries
Influenza laboratory
National Influenza Centre
IP
IP
IP
IP
INSP
CPC
IP
INRB
EHNRI
CIRMF
NMIMR
KEMRI CDC
UVRI
NRL
NIL
UTH
UCHNIDL
NICD
UCTMSO
LIST OF INFLUENZA LABORATORIES IN THE AFRICAN REGION
VIRAL WATCH, ENHANCED VIRAL WATCH AND SARI SITES : 2009
VW:2
VW:9
VW:104
VW:20
VW:19
VW:5
VW:12
7
VW:65
VW:243
Enhanced VW :10
SARI : 4
INFLUENZA RESULTS BY TYPE & SUBTYPE :
SOUTH AFRICA 2005 - 20082006
0
20
40
60
80
100
120
1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 41 43 45 48
Week
Nu
mb
er o
f is
ola
tes
0
10
20
30
40
50
60
70
Iso
lati
on
rat
e (%
)
A H1N1 A H3N2 B Isolation rate
2007
0
25
50
75
1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 41 43 45 47 49 51
Week
Nu
mb
er is
ola
tes
0
20
40
60
80
100
120
140N
um
ber
Sp
ecim
ens
A H1N1 A H3N2 Influenza B Specimens
2005
0
20
40
60
80
100
120
1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 41 43 45 48
Week
Nu
mb
er o
f is
ola
tes
0
10
20
30
40
50
60
70
Iso
lati
on
rat
e (%
)
A H1N1 A H3N2 B Isolation rate
2008
0
10
20
30
40
50
60
70
1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 41 43 45 47 49 51
Week
Nu
mb
er o
f is
ola
tes
0
10
20
30
40
**Is
ola
tio
n r
ate
(%)
A H1N1 A H3N2 B Isolation rate
ONSET & DURATION OF INFLUENZA SEASON:
1985 - 2007
• Median onset:– Week 23
– Range 15-28
• Median peak:– Week 27
– Range 20-32
• Median duration:– 10 weeks
– Range 7-17
Epidemiological week
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
19851986
198719881989
19901991
19921993
1994
19951996
19971998
1999
20002001
200220032004
2005
2006
Mean onset
2007
Apr May Jun Jul Aug Sep
19841985
19861987
19881989
19901991
19921993
19941995
19961997
19981999
20002001
20022003
20042005
20062007
2008
0
20
40
60
80
100
B A H3N2 A H1N1
INFLUENZA STRAINS DETECTED : SOUTH AFRICA 1984 - 2008
POSITIVE SAMPLES BY INFLUENZA TYPES AND SUBTYPE: VIRAL WATCH SOUTH
AFRICA 2009
Jan Feb Mar Apr May Jun Jul Aug Sep Oct Nov Dec
0
50
100
150
200
250
1 3 5 7 9 11 13 15 17 19 21 23 25 27 29 31 33 35 37 39 41 43 45 47 49 51
Week
Nu
mb
er
0
20
40
60
80
% D
etec
tio
n r
ate
Seasonal A (H1N1) A H3N2 B Pandem ic A(H1N1) Detection rate
Seasonal A(H1N1) : 4 (0.3%)Pandemic A(H1N1) : 532 (36.1%)A H3N2 : 833 (56.5%)Influenza B : 106 (7.2%)
FIRST CONFIRMED CASES OF H1N1
Argentina May 16
Australia May 7
Chile May 17
New Zealand April 28
Uruguay May 27
USA April 17
South Africa June 13
INTERNATIONAL TOURIST ARRIVALS (MILLIONS)
Source: World Tourism Organization (UNWTO)
0
50
100
150
200
250
300
350
400
450
500
1990 1995 2000 2005 2006 2007
EuropeAsia and PacificAmericasAfrica
Epidemic curve showing laboratory confirmed cases of pandemic influenza A(H1N1) 2009 by epidemiological week of specimen
collection, South Africa, 7 September 2009 (n=7606)
13 June ‘09: First confirmed case symptom onset
13 July ‘09: First 100
confirmed cases
28 July ‘09: First confirmed death
EPIDEMIC CURVE ILLUSTRATING THE NUMBER OF LABORATORY-CONFIRMED PANDEMIC INFLUENZA A (H1N1) 2009 CASES AND DEATHS BY WEEK, SOUTH AFRICA, UPDATED 26 OCT 09 (n(cases)=12,598) OF WHICH
25 WITH UNKNOWN DATE; N (DEATHS) = 91, OF WHICH 2 WITH UNKNOWN DATE
TRAVEL HISTORY OF 42 CASES WITHIN THE FIRST 100 INVESTIGATED
North America 6 14% Europe 15 36%
USA 6 Other European Countries 5
South America 5 12% Germany 1
Argentina 2 Greece 1
Brazil 2 Netherlands 1
Chile 1 Sweden 1
Other African Countries 3 7% Turkey 1
Mauritius 2 UK 5
Zimbabwe 1 Asia 8 19%
Australia 5 12% China 2
Singapore 4
Dubai 1
Bali 1
Province
Laboratory-confirmed cases Lab-confirmed H1N1 deathsN Incidence rate
(per 100 000)
Gauteng 5565 52.8 13
Western Cape 2104 39.3 39
KwaZulu Natal 2254 21.6 21
Eastern Cape 682 10.3 10
Limpopo 544 10.4 0
North West 463 13.4 2
Free State 312 10.8 2
Mpumalanga 499 13.8 1
Northern Cape 133 11.6 3
Unknown 42 - 0
SA Total 12598 25.5 91
LABORATORY CONFIRMED
PANDEMIC INFLUENZA
A(H1N1) 2009
28 October 2009
NUMBER OF LABORATORY CONFIRMED PANDEMIC
INFLUENZA A (H1N1) 2009 CASES BY AGE-GROUP,
SOUTH AFRICA, UPDATED 26 OCTOBER 09 (n=12,598,
OF WHICH 134 WITH UNKNOWN AGE)
Age Group (years)
AGE DISTRIBUTION OF PATIENTS WITH SEASONAL A H3N2 AND PANDEMIC
H1N1
0
10
20
30
40
50
<1yr 1-9yr 10-19yr 20-29yr 30-39yr 40-49yr 50-59yr >=60yr
Age group
Per
cen
tag
e
A H3N2 Pandem ic H1N1
AGE DISTRIBUTION OF PATIENTS WITH SEASONAL A H1N1 (2008) AND
PANDEMIC A H1N1
0
10
20
30
40
50
<1yr 1-9yr 10-19yr 20-29yr 30-39yr 40-49yr 50-59yr >=60yr
Age group
Per
cen
tag
e
Seasonal H1N1(2008) Pandem ic H1N1
AGE DISTRIBUTION OF PATIENTS WITH INFLUENZA B AND PANDEMIC H1N1
0
10
20
30
40
50
<1yr 1-9yr 10-19yr 20-29yr 30-39yr 40-49yr 50-59yr >=60yr
Age groups
Per
cen
tag
e
Infuenza B Pandem ic H1N1
FIRST 100 CASES
ASIAN 12
AFRICAN 6
MIXED RACE 5
WHITE 74
UNKNOWN 3
PRELIMINARY FINDINGS FROM INVESTIGATIONS OF THE FIRST 100
CASES
Symptoms experienced by pandemic influenza A(H1N1) 2009 cases, first 100 confirmed case investigation, South Africa (n=100)
PRELIMINARY FINDINGS FROM INVESTIGATIONS
OF THE FIRST 100 CASES• Household Secondary Attack Rate (SAR)
estimate:– 65 households included– Susceptible population: 158 individuals– 27 secondary cases found (16 confirmed, 11
suspected)– Household SAR (confirmed + suspected) =
27/158 = 17%– Household SAR (confirmed cases only) =
16/158 = 10%
PRELIMINARY FINDINGS FROM INVESTIGATIONS
OF THE FIRST 100 CASES• Serial interval estimate
among secondary cases:– All secondary cases:
• Confirmed: Mean 2.32 days (range 1-5, SD 1.34)
• Confirmed + ILI: Mean 2.69 days (range 1-4, SD 1.49)
– Household secondary cases:• Confirmed: Mean 2.19 days
(range 1-4, SD 1.22)• Confirmed + ILI: Mean 2.65
days (range 1-6, SD 1.47)
Time series for household contacts
6 51
4
2
3
3
1 1 102468
10
1 2 3 4 5 6 ??
Days
Cases
SuspectedCases
Preliminary reproductive number (R0) estimates based on the initial exponential growth phase of the epidemic and serial interval estimates established from the first 100 case investigation
Epidemic curve of the observed and predicted frequencies of laboratory confirmed pandemic influenza A(H1N1) 2009 case within the selected time
interval (18 July – 31 July ’09), South Africa
Growth rate = 0.24 (95% CI 0.22-0.27; R2 0.81)
R0 = 1.67 (95% CI 1.60-1.76)
PANDEMIC H1N1 DEATHS (28th October 2009)
TOTAL = 91
= 0.185 per 100,000 population (49.32m)
SELECTED CLINICAL CHARACTERISTICS OF PANDEMIC
INFLUENZA A (H1N1) 2009 RELATED DEATHS, SOUTH
AFRICA, UPDATED 28 OCTOBER 09
FACTOR FREQUENCY OF FACTOR
(NUMERATOR)
NUMBER OF CASES WITH DATA AVILABLE
(DENOMINATOR)
%
HIV infected 17 32 tested 53
Pregnant or puerperium 25 88 28
No co-morbidities identified 16 76 21
Diabetes 11 72 15
Obese 16 73 22
Cardiac disease + 9 71 13
Active tuberculosis (TB) 7 72 10
+ Cardiac disease includes: previous stents, mitral stenosis, cardiomyopathy, congestive cardiac failure, previous valvular replacement, recent myocardial infarction, and previous cardiac bypass surgery; excludes hypertension.
CONCLUDING OBSERVATIONS
1. Delayed commencement
2. Epidemiology of early 100 cases similar to other
countries
3. However presentation in developing & deprived
communities still to be determined.
4. HIV – suggestive of major risk factor
5. Pregnancy major risk factor.
6. Pregnancy +HIV - ? Significantly increased risk
7. Viral characterization – still to come
ACKNOWLEDGEMENTSINFLUENZA EPIDEMIOLOGY TEAM
Brett Archer
Dr Lucille Blumberg
Sr Jo McAnerney
Dr Cheryl Cohen Dr Stefano Tempia
Dr Geraldine Timothy
ACKNOWLEDGEMENTSINFLUENZA LABORATORY TEAM
From l to r:• Jack Manamela • Dr Marietjie Venter• Dhamari Naidoo• Professor Adrian Puren
From l to r:• Cardia Fourie• Amelia Buys• Professor Adrian Puren