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Volume 20, Number 7—July 2014

CME ACTIVITY - Research

Epidemiology of Influenza Virus Types and Subtypes in South Africa, 2009–20121

Adam L. CohenComments to Author , Orienka Hellferscee, Marthi Pretorius, Florette Treurnicht, Sibongile Walaza, Shabir Madhi, Michelle Groome, Halima Dawood, Ebrahim Variava, Kathleen Kahn, Nicole Wolter, Anne von Gottberg, Stefano Tempia, Marietjie Venter, and Cheryl Cohen
Author affiliations: Centers for Disease Control and Prevention, Atlanta, Georgia, USA, and Pretoria, South Africa (A.L. Cohen, S. Tempia, M. Venter); National Institute for Communicable Diseases, Sandringham, South Africa (O. Hellferscee, M. Pretorius, F. Treurnicht, S. Walaza, N. Wolter, A. von Gottberg, S. Tempia, M. Venter, C. Cohen); University of the Witwatersrand, Johannesburg, South Africa (S. Madhi, M. Groome, N. Wolter, A. von Gottberg, C. Cohen); Medical Research Council: Respiratory and, Meningeal Pathogens Research Unit, Johannesburg (S. Madhi, M. Groome); Pietermaritzburg Metropolitan Hospital Complex, Pietermaritzburg, South Africa (H. Dawood); University of KwaZulu-Natal, Durban, South Africa (H. Dawood); Klerksdorp Tshepong Hospital, Klerksdorp, South Africa (E. Variava); University of the Witwatersrand, Johannesburg (K. Kahn); Umeå University, Umeå, Sweden (K. Kahn); INDEPTH Network, Accra, Ghana (K. Kahn); University of Pretoria, Pretoria, (M. Venter)

Main Article

Table 1

Characteristics of patients hospitalized with influenza-associated severe acute respiratory illness, by virus type and subtype, 4 sites, South Africa, 2009–2012*

A(H3N2) (reference) A(H1N1)pdm09 B
No. pos/no. tested 
(% pos)

No. pos/no. tested (% pos)
Adjusted RRR (95% CI)

No. pos/no. tested (% pos)
Adjusted RRR (95% CI)
Age group, y
<5 265/463 (57.2) 167/338 (49.4) Reference 171/418 (40.9) Reference
5–24 35/463 (7.6) 49/338 (14.5) 2.3 (1.4–3.8) 43/418 (10.3) 2.0 (1.2–3.4)
25–44 96/463 (20.7) 78/338 (23.1) 1.3 (0.9–2.0) 128/418 (30.6) 1.5 (1.0–2.1)†
45–64 44/463 (9.5) 35/338 (10.4) 1.4 (0.9–2.4) 55/418 (13.2) 1.4 (0.9–2.2)
>65
23/463 (5.0)

9/338 (2.7)
0.6 (0.2–1.3)

21/418 (5.0)
1.1 (0.6–2.2)
Male
207/461 (44.9)

149/336 (44.4)


177/417 (42.5)

Black African
452/460 (98.3)

327/336 (97.3)


407/416 (97.8)

Year
2009 194/463 (41.9) 160/338 (47.3) Reference 25/418 (6.0) Reference
2010 72/463 (15.6) 37/338 (11.0) 0.6 (0.4–1.0)† 164/418 (39.2) 16.8 (10.1–27.9)
2011 98/463 (21.2) 140/338 (41.4) 1.7 (1.2–2.5) 124/418 (29.7) 9.5 (5.7–15.6)
2012
99/463 (21.4)

1/338 (0.3)
0.0 (0.0–0.1)

105/418 (25.1)
7.8 (4.7–13.0)
Co-infections and underlying medical conditions
HIV infection 112/311 (36.0) 110/271 (40.6) 170/352 (48.3)
Tuberculosis 42/458 (9.2) 34/335 (10.2) 38/411 (9.3)
Underlying medical condition excluding tuberculosis, HIV‡ 34/460 (7.4) 31/336 (9.2) 38/417 (9.1)
Pregnancy 3/251 (1.2) 2/187 (1.1) 3/24 (1.3)
Pneumococcal co-infection detected by PCR
23/310 (7.4)

25/286 (8.7)


32/325 (9.9)

Clinical presentation and course
Temperature >38°C 181/364 (49.7) 141/287 (49.1) 138/407 (33.9)
Cough§ 255/264 (96.6) 162/167 (97.0) 163/170 (95.9)
Tachypnea§ 99/250 (39.6) 73/161 (45.3) 62/159 (39.0)
Difficulty breathing§ 188/264 (71.2) 125/167 (74.9) 111/170 (65.3)
Chest wall indrawing§ 96/264 (36.4) 77/167 (46.1) 56/170 (32.9)
Stridor§ 30/264 (11.4) 20/167 (12.0) 36/170 (21.2)
Symptoms ≥3 d before admission 206/452 (45.6) 153/335 (45.7) 239/415 (57.6)
Admitted to ICU 4/457 (0.9) 3/336 (0.9) 4/411 (1.0)
Mechanical ventilation needed 3/457 (0.7) 1/336 (0.3) 4/411 (1.0)
Supplemental oxygen needed 138/457 (30.2) 117/336 (34.8) 144/411 (35.0)
Antimicrobial drugs prescribed on admission 402/421 (95.7) 321/335 (95.8) 384/395 (97.2)
Hospitalized for >2 d
319/451 (70.7)

255/332 (76.8)


323/407 (79.4)

No. deaths/no. patients (case-fatality ratio) 13/459 (2.8) 5/334 (1.5) 16/412 (3.9)

*Pos, positive; RRR, relative risk ratio; ICU, intensive care unit. An expanded version of this table is available in the Technical Appendix.
†p<0.05.
‡Asthma, other chronic lung disease, chronic heart disease (valvular heart disease, coronary artery disease, or heart failure excluding hypertension), liver disease (cirrhosis or liver failure), renal disease (nephrotic syndrome, chronic renal failure), diabetes mellitus, immunocompromising conditions excluding HIV infection (organ transplant, immunosuppressive therapy, immunoglobulin deficiency, malignancy), neurologic disease (cerebrovascular accident, spinal cord injury, seizures, neuromuscular conditions), or pregnancy. Concurrent conditions were considered absent for patients for whom the medical records stated that the patient had no underlying medical condition or when there was no direct reference to that condition.
§Patients <5 y of age.

Main Article

1This information has been presented at Options for the Control of Influenza VIII, Cape Town, South Africa, September 5–9, 2013.

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