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

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A H1N1 A H3N2 B Isolation rate

2007

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A H1N1 A H3N2 Influenza B Specimens

2005

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A H1N1 A H3N2 B Isolation rate

2008

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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

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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)

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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

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<1yr 1-9yr 10-19yr 20-29yr 30-39yr 40-49yr 50-59yr >=60yr

Age group

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A H3N2 Pandem ic H1N1

AGE DISTRIBUTION OF PATIENTS WITH SEASONAL A H1N1 (2008) AND

PANDEMIC A H1N1

0

10

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<1yr 1-9yr 10-19yr 20-29yr 30-39yr 40-49yr 50-59yr >=60yr

Age group

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Seasonal H1N1(2008) Pandem ic H1N1

AGE DISTRIBUTION OF PATIENTS WITH INFLUENZA B AND PANDEMIC H1N1

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<1yr 1-9yr 10-19yr 20-29yr 30-39yr 40-49yr 50-59yr >=60yr

Age groups

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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