Seasonal Influenza 2010



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Consolidated Influenza Surveillance Weekly Report
Updated 2 June 2010 25 July, 2010
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Data presented are provisional as reported to date. The number of consultations is reported by date of consultation and specimens are analysed by date of collection.
Source: SARI surveillance, Viral Watch surveillance and Hospital Consultations Netcare
Data may be freely reproduced provided due acknowledgement is given to the NICD
More information can be found at: http://www.nicd.ac.za

Severe acute respiratory illness (SARI) surveillance


Reporting period: 01/01/2010 to 18/07/2010   Results until end of epidemiologic week 2010: 28


Figure 1. Number of positive samples* by influenza types and subtypes and detection rate by week

*Specimens from patients hospitalised with severe acute respiratory infections at 4 sentinel sites in 3 provinces
**Detection rate calculated on specimens tested at NICD only, not shown before onset of season


Table 1. Cumulative number of identified influenza types and subtypes and total number of samples collected by hospital
Hospital
B
A unsubtyped
Seasonal A (H1N1)
Pandemic A (H1N1)
A (H3N2)
Total samples
Chris Hani Baragwanath (GP)
47
0
0
0
25
1909
Edendale (KZ)
3
0
0
0
0
102
Klerksdorp-Tshepong (NW)
2
0
0
0
1
53
Mapulaneng (MP)
3
0
0
0
0
142
Matikwane (MP)
2
0
0
0
0
159
Total:
57
0
0
0
26
2365
*Gauteng (GP), KwaZulu Natal (KZ), North West (NW), Mpumalanga (MP)


Influenza-like illness (ILI) surveillance (Viral Watch)


Reporting period: 01/01/2010 to 18/07/2010   Results until end of epidemiologic week 2010: 28


Figure 2. Number of positive samples* by influenza types and subtypes and detection rate** by week

*Specimens from patients with Influenza-like illnesses at 223 sentinel sites in 9 provinces
**Detection rate calculated on specimens tested at NICD only, not shown before onset of season

Table 2. Cumulative number of influenza type and subtype and total number of samples collected by province
Province
B
A unsubtyped
Seasonal A (H1N1)
Pandemic A (H1N1)
A (H3N2)
Total samples
Eastern Cape
3
0
0
0
1
44
Free State
0
0
0
0
0
29
Gauteng
75
0
0
6
83
595
KwaZulu-Natal
2
0
0
0
1
30
Limpopo
5
0
0
0
2
59
Mpumalanga
6
0
0
0
2
28
Northern Cape
8
0
0
0
0
30
North West
0
0
0
0
1
18
Western Cape
3
0
0
1
0
101
Total:
102
0
0
7
90
934


Private hospital consultations


Reporting period: 01/01/2010 to 13/06/2010   Results until end of epidemiologic week 2010: 23


Figure 3. Number of private hospital outpatient consultations* with a discharge diagnosis of pneumonia and influenza (P&I) and viral isolates**
* Hospital outpatient data from weekly reports of consultations to the Netcare hospital group. Discharge diagnosis is according to International Statistical Classification of Diseases and Related Health Problems coding/ICD by clinicians and does not represent laboratory confirmation of aetiology
** Influenza positive specimens from the Viral Watch surveillance programme

Figure 4. Number of private hospital admissions* with a discharge diagnosis of pneumonia and influenza (P&I) and viral isolates**

*Hospitalisation admission data from weekly reports of consultations to the Netcare hospital group. Discharge diagnosis is according to International Statistical Classification of diseases and Related Health Problems /ICD by clinicians and does not represent laboratory confirmation of aetiology
** Influenza positive specimens from the SARI surveillance programme

Influenza Viral Watch Sentinel Surveillance weekly update

NOTE: As of 14 August 2009 we have amended the format for weekly reporting of influenza surveillance. The epidemic curve reporting data from all sources will now include specimens tested at other laboratories and reported to the NICD. Breakdown of specimens received by province will only be provided for Viral Watch Data.

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Influenza Viral Watch sentinel surveillance *

Update: to end of week 8 (week ending 28 February)


*Virological surveillance at 256 sentinel sites in 9 provinces
**Detection rate calculated on specimens tested at NICD only, not shown before onset of season.




Number of influenza isolates made by week, South Africa, 2009
  
Number of influenza isolates made by province, South Africa, 2009
Week (starting)
Influenza
   Province
Influenza
  
A B Total A B Total
1-23(Jan-7 Jun)
304
6
310
Eastern Cape
18
0
18
24 (14 Jun)
178
9
187
Free State
37
4
41
25 (21 Jun)
113
3
116
Gauteng
984
88
1072
26 (28 Jun)
71
0
71
KwaZulu-Natal
68
2
70
27 (5 Jul)
72
1
73
Limpopo
155
12
167
28 (12 Jul)
58
6
64
Mpumalanga
34
0
34
29 (19 Jul)
44
8
52
Northern Cape
55
1
56
30 (26 Jul)
69
12
81
North West
9
0
9
31 (2 Aug)
148
13
161
Western Cape
293
19
312
32 (9 Aug)
259
26
285
Total
1653
126
1779
33 (16 Aug)
117
12
129
34 (23 Aug)
101
5
106
35 (30 Aug)
57
5
62
36 (6 Sep)
35
5
40
37 (13 Sep)
18
6
24
38 (20 Sep)
9
6
15
39 (27 Sep)
0
2
2
40-48 (Oct-Nov)
0
1
1
Total
1653
126
1779

Source: Epidemiology Division, Respiratory Virus and Viral Diagnostics Units, NICD
Data presented are provisional, as reported to date; Isolates are analysed by date of collection.
More information about the Viral Watch programme can be found at: http://www.nicd.ac.za
Data may be freely reproduced provided due acknowledgement is given to the NICD



Severe Acute Respiratory-tract Infections (SARI) Weekly Report



Severe Acute Respiratory Illness (SARI) Surveillance: Influenza Report.

Severe Acute Respiratory Illness (SARI) Surveillance: Respiratory Viruses Report.

Severe Acute Respiratory Illness (SARI) Surveillance: S. Pneumoniae Report.

Respiratory Consultations Surveillance: Report

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Respiratory Consultations Surveillance: Report
Reporting Period: 04/01/2010 to 28/03/2010
Results until End of Epidemiologic week (2010) 12



* Hospitalisations data from weekly reports of admissions to the Netcare hospital group. Discharge diagnosis is according to ICD coding by clinicians and does not represent laboratory confirmation of aetiology
** Viral isolation data from the Viral Watch sentinel surveillance programme


Source: Epidemiology Division, Respiratory Virus and Viral Diagnostics Units, NICD


Data presented are provisional, as reported to date Numbers of admissions are reported by date of admission and viral isolates by date of collection
More information about the Viral Watch and Respiratory Hospitalisations Surveillance Programme can be found at: http://www.nicd.ac.za
Data may be freely reproduced provided due acknowledgement is given to the NICD

Influenza Sentinel Surveillance Background


Influenza surveillance networks are based on sentinel general practitioner networks. These networks report on influenza-like illnesses seen in their practices and also take nasopharyngeal swabs for virus isolation which is a crucial component of the global influenza surveillance programme on which the strain selection for annual influenza vaccines is made. For example, in the USA the network is comprised of over a 1,000 sentinel sites. In Australia the network consist of a few hundred sites and New Zealand nearly a hundred

The South African Viral Watch Influenza Sentinel Surveillance Programme


The South African Viral Watch active influenza surveillance programme was started in 1984 when 10 centres in Gauteng were enrolled. The centres consisted of 3 general practitioners, 4 paediatric out-patient departments, a primary health care clinic, a mine hospital and a hospital staff clinic.

The objectives were to determine the type and pattern of influenza isolations as well as the type and pattern of other respiratory isolates and to provide objective information on timing of the influenza season to the health care system.

Between 1984 and 2004 changes were made from time to time to include different geographical areas and different types of centres, the total number of which ranged between 12 and 20.
In 2004 a decision was made to actively recruit new centres, and in 2005 an additional 73 practitioners at 53 centres were added to the 12 centres retained from the previous years, making a total of 85, mainly general practitioners, at 65 centres.

In 2006 centres in the Eastern Cape, KwaZulu-Natal, and Western Cape were added bringing the total to 129 sites, and in 2007 a further 3 centres in Mpumalanga and one in Limpopo were added.

In 2008 the Northern Cape and North West Province were added with 7 & 6 practitioners respectively. Thus influenza sentinel surveillance sites have been established in all 9 provinces of South Africa. Currently the total number of participating practitioners stands at 170.

Members of the network are required to identify patients with clinical disease suggestive of influenza, fill in a form which contains information on name, age, a tick list of signs and symptoms, and history of influenza vaccine, and submit a throat or nasopharyngeal swab for virus isolation. Materials and forms are supplied free, and specimens are sent to the National Institute for Communicable Diseases (NICD) through the usual pathology laboratory used by the practitioner. Results are phoned/faxed or emailed directly to the health care provider.

The programme provides the following benefits to participating practitioners:-
  1. Laboratory diagnosis of acute respiratory disease in a patient at no extra cost
  2. Regular contact between NICD and the practitioner which will focus on general feedback, specific influenza information, and on currently circulating viruses
  3. An annual discussion group
  4. Receipt of regular epidemiological updates in the form of 2 publications from the NICD – NICD Infectious Diseases Communiqué (monthly and ad hoc) and NICD Bulletin (quarterly). The latter publication is specifically designed as a continuing medical educational tool in communicable diseases.
  5. Annual participation would earn participants 12 points - this has been approved by the CPD committee at the University of the Witwatersrand.
  6. Annual participation in a national / international influenza symposium
  7. A certificate that could be placed in the waiting area in the practice stating that the practice participates in the WHO/NICD national influenza surveillance network.


Distribution of Viral Watch Practitioners per Province




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Viral Watch Specimen Slip



This data may be freely reproduced provided due acknowledgement is given to the NICD.
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The Respiratory Consultations Surveillance System


The Respiratory Consultations Surveillance System was established in 2005 as collaboration between the private hospital sector and the NICD (however data are available from 2003). The surveillance programme aims to monitor admissions for key diagnoses potentially associated with the influenza season. The specific objectives are to describe seasonal and annual trends in hospital outpatient consultations and admissions for key diagnoses associated with the influenza season and to establish an independent source of data on timing of the influenza season.

Data on numbers of outpatient consultations and hospitalisations and discharge diagnosis are extracted automatically from the database of a private hospital group situated in 4 provinces of South Africa (Gauteng, Western Cape, KwaZulu-Natal and Free State). Data are submitted to the NICD on a weekly basis. There is a one-month delay in reporting of cases as complete numbers are only available one month after the date of admission. Discharge diagnoses are coded according to the International Classification of Diseases version 10 (ICD 10) system and reflect the discharge diagnoses of clinicians for billing purposes. Discharge diagnosis is according to coding by the clinician and does not represent laboratory confirmation of aetiology. The corresponding ICD 10 coded for the diagnosis of Pneumonia and Influenza (P&I) are J10-J18. Weekly numbers of P&I cases are reported on the NICD web page www.nicd.ac.za.

The surveillance project has several limitations. The population of individuals accessing private health care is poorly defined and may be affected by multiple factors e.g. availability of provider in certain geographical areas, personal choice based on perceived quality of care, socioeconomic class etc. Findings may thus not be generalised to other groups and population denominators will not be available. This limits the utility of the system for determination of burden of disease. The public health-care system is not included – however the time of the influenza season would not be expected to differ between public and private hospitals. Delays in reporting of data and use of aggregate data mean that this system would be of limited use for early detection of emerging respiratory infections.


We would like to acknowledge the Netcare Hospital Group for their collaboration.
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Severe Acute Respiratory-tract Infections (SARI) surveillance background



In 2009 a sentinel surveillance programme for severe acute respiratory tract infection was introduced. This programme aims to describe trends in numbers of SARI cases at sentinel surveillance sites and determine the relative contribution of influenza and other respiratory viruses to this disease presentation in a setting with a high prevalence of Human Immunodeficiency Virus (HIV). These data will serve to better inform public health policy regarding SARI management, prevention and control in South Africa. In addition, it will assist in planning for future influenza pandemics and will be essential to the assessment of both influenza and pneumococcal conjugate vaccine strategies in South Africa.

The programme is a prospective hospital-based sentinel surveillance programme. There are three sentinel sites in Gauteng Province (Chris Hani Baragwanath Hospital), KwaZulu-Natal Province (Edendale Hospital) and Limpopo Province (Tintswalo, Mapulaneng and Matikwane Hospitals). Surveillance Officers review the clinical details of all patients admitted to sentinel sites to establish whether cases meet the SARI case definition. Identified cases are approached for inclusion in the sentinel surveillance. Consenting patients are asked to complete a questionnaire by interview on previous medical history and clinical data and to provide a specimen (oropharyngeal and nasopharyngeal swab in cases = 5 years old or nasopharyngeal aspirate in cases < 5 years of age) for diagnosis of respiratory viruses. Specimens are tested for the presence of influenza virus, respiratory syncitial virus, parainfluenza virus 1,2 and 3, adenovirus and human metapneumovirus by viral culture and polymerase chain reaction as appropriate. In addition, results of routine patient investigations such as HIV-serology testing and blood culture results are collected. Data are entered on a centralised database at the National Institute for Communicable Diseases (NICD). Core surveillance indicators are reported to stakeholders weekly in the influenza season and monthly out of season.

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