Surveillance

Influenza surveillance report - South Africa
Report compiled on 23 October 2013

  
Influenza surveillance programmes
   

 The data presented in this report are generated from three influenza surveillance programmes: the Viral Watch [influenza-like illness (ILI)], Severe Acute Respiratory Illness (SARI) and the respiratory consultations and hospitalisations surveillance system.
The Viral Watch is a sentinel influenza surveillance programme started in 1984 in Gauteng and expanded from 2005 onward to include all 9 provinces in South Africa. The majority (90%) of the sentinel sites are general practitioners. Respiratory specimens (throat or nasal swabs) are collected from patients of all ages meeting the ILI case definition which is an acute respiratory illness with a measured temperature of ≥ 38 ˚C and cough, with onset within the past 7 days prior to consultation. Specimens are tested for the presence of influenza and other respiratory viruses by RT-PCR.
The Severe Acute Respiratory Illness (SARI) surveillance program is a prospective sentinel hospital-based surveillance program. It was established in 2009 and is currently conducted at 5 sentinel sites (public hospitals) in 4 provinces of South Africa. Hospitalised patients meeting the surveillance case definition of acute respiratory illness are prospectively enrolled. Clinical and epidemiologic data are collected using standardized questionnaires. Information on in-hospital management and outcome is collected. Upper respiratory tract samples (oropharyngeal and nasopharyngeal swabs in cases ≥5 years old or nasopharyngeal aspirate in cases < 5 years of age) are tested for the presence of influenza and other respiratory viruses using RT reverse transcriptase PCR.
The respiratory consultations and hospitalisations surveillance system collects anonymous influenza and pneumonia associated outpatient consultations and hospitalisations data from one private hospital group in 7 provinces (Gauteng, North West, Free State, Mpumalanga, Eastern and Western Cape and KwaZulu- Natal). These data on the number of consultations and hospitalisations are compared to the influenza season as described by the viral watch and SARI programmes.
 
Comment:
The influenza season started in week 17 (week starting 22 April) when the influenza detection rate rose to 17% in the VW programme, and continued to rise in the following weeks. The influenza season is considered to have started when the detection rate rises above 10% and remains above that level for more than two weeks.
ILI programme:In the first 20weeks of 2013,304 specimens were received from 3 ILI sites.  To date influenza (H1N1)pdm09was detected in six, and influenza B in three patients.  The influenza detection rate rose to 21% in week 19 (week starting 6 May).
VW programme:During the same period 255specimens were received from VW sites. Specimens have been received from eight of the nine provinces.Influenza A not subtyped was detected in 13 patients, A(H1N1)pdm09in 48, influenza A(H1N1)pdm09 and A(H3N3) in one patient, and influenza B in three patients.
SARI programme:In this time period,1233patients with SARI were tested at the 5 sentinel sites.  Influenza A not subtypedwas detected in one patient, influenza A(H1N1)pdm09 in 12 patients, influenza A(H1N1)pdm09 and A(H3N3) in one, and influenza B in one patient. In addition 1026 other respiratory viruses were detected in the specimens of 742patients, rhinovirus(387)  accounted for the majority followed by RSV(273).
Please note that these data are from sentinel sites and reflect trends in the areas with participating sites. Numbers reported reflect numbers of patients enrolled into the surveillance programmes and do not reflect total numbers of patients in the community.
 

 



 

Severe acute respiratory illness (SARI) surveillance
 

Reporting period: 01/01/2013 to 13/10/2013   Results until end of epidemiologic week 41 (2013)
 
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 5 sentinel sites in 4 provinces


Table 1. Cumulative number of identified influenza types and subtypes and total number of samples collected by hospital
Clinic A not typed  A (H1N1) pdm09 A (H3N2) B Total samples
Edendale Gateway Clinics (KZ) 7 52 26 11 759
Embalenhle Clinic (NW) 2 22 12 3 454
Alabama Clinic (NW) 0 11 11 1 196
Joubert Clinics (NW) 0 19 8 3 222
Park Street Clinic (NW) 1 3 0 2 90
Tshepong Gateway Clinic (NW) 0 6 1 0 96
Total: 10 113 58 20 1817
*Gauteng (GP), KwaZulu Natal (KZ), North West (NW), Mpumalanga (MP)
 
 

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

 
Reporting period: 01/01/2013 to 13/10/2013   Results until end of epidemiologic week 2009: 41 (2013)
 
 
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  not subtyped A(H1N1)pdm09 A (H3N2) Total samples
Eastern Cape 4 0 28 1 106
Free State 4 0 12 0 46
Gauteng 52 0 263 57 722
KwaZulu-Natal 15 1 90 9 249
Limpopo 8 0 26 5 101
Mpumalanga 2 0 29 3 90
Northern Cape 0 0 26 0 47
North West 0 0 4 0 7
Western Cape 38 0 105 3 280
Total: 123 1 571 78 1648
 


 

Reporting period: 01/01/2013 to 13/10/2013   Results until end of epidemiologic week 41 (2013)
 
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


Table 3. Cumulative number of identified influenza types and subtypes and total number of samples collected by hospital
Clinic A not subtyped  A (H1N1) pdm09 A (H3N2) B Total samples
Chris Hani Baragwanath (GP 1 31 14 6 705
Edendale (KZ) 2 23 12 1 731
Klerksdorp-Tshepong (NW) 0 29 13 6 847
Mapulaneng (MP) 0 8 1 0 145
Matiwane (MP) 0 8 2 1 154
Total: 4 99 42 14 2582
*Gauteng (GP), KwaZulu Natal (KZ), North West (NW), Mpumalanga (MP)



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



Figure 5: Detection rate for inluenza (INF), respiratory syncytial virus (RSV) and pneumococcus (SP) by week



Figure 6 Number of private hospital outpatients consultation* with a discharge diagnosis of pnemonia 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


Figure 7: 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