Surveillance

Influenza surveillance report - South Africa
Report compiled on 30 September 2014

  
Influenza surveillance programmes
 

The data presented in this report are generated from influenza surveillance programmes: the Influenza-like illness (ILI) at primary health clinics and Viral Watch (VW) sites, Severe Acute Respiratory Illness (SARI) and the respiratory consultations and hospitalisations surveillance system.
 
ILI surveillance at primary health care clinics was started in 2012 at 2 clinics in two provinces, 4 additional clinics were added in 2013.
The Viral Watch (VW) 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, nasal swabs or nasopharyngeal aspirates) 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, or a history of fever, and cough, with onset within the past 10 days prior to consultation.
 
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 4 sentinel sites (public hospitals) in 3 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 standardised 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-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 data presented in this report are generated from influenza surveillance programmes: the Influenza-like illness (ILI) at primary health clinics and Viral Watch (VW) sites, Severe Acute Respiratory Illness (SARI) and the respiratory consultations and hospitalisations surveillance system.
 
ILI surveillance at primary health care clinics was started in 2012 at 2 clinics in two provinces, 4 additional clinics were added in 2013.
The Viral Watch (VW) 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, nasal swabs or nasopharyngeal aspirates) 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, or a history of fever, and cough, with onset within the past 10 days prior to consultation.
 
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 4 sentinel sites (public hospitals) in 3 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 standardised 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-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.
 



 

Severe acute respiratory illness (SARI) surveillance
 

Reporting period: 01/01/2014 to 21/09/2014   Results until end of epidemiologic week 38 (2014)
 
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) 1 7 120 8 831
Embalenhle Clinic (KZ) 1 7 45 8 389
Grace Mokhomo Clinic (NW) 0 1 15 8 305
Joubert Clinic (NW) 1 2 33 16 511
Total: 3 17 213 40 2036
*Gauteng (GP), KwaZulu Natal (KZ), North West (NW), Mpumalanga (MP)
 
 

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

 
Reporting period: 01/01/2014 to 21/09/2014   Results until end of epidemiologic week 2009: 33 (2014)
 
 
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 0 0 11 25 82
Free State 4 0 1 18 48
Gauteng 48 0 18 182 456
KwaZulu-Natal 1 0 0 0 4
Limpopo 3 0 1 20 56
Mpumalanga 3 0 0 38 92
Northern Cape 1 0 0 5 23
North West 0 0 0 1 3
Western Cape 31 0 32 63 232
Total: 91 0 63 352 996
 


 

Reporting period: 01/01/2014 to 06/07/2014   Results until end of epidemiologic week 27 (2014)
 
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
Edendale (KZ) 0 0 13 0 297
Klerksdorp-Tshepong (NW) 1 2 1 1 409
Mapulaneng (MP) 0 0 15 0 96
Matiwane (MP) 0 1 11 0 64
Total: 0 3 14 1 866
*Gauteng (GP), KwaZulu Natal (KZ), North West (NW), Mpumalanga (MP)



Figure 4. Number of specimns  and detection rate for respiratory viruses* by week



Figure 5: Detection rate for influenza (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