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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 2

Characteristics of patients hospitalized with influenza A(H1N1)pdm09-associated severe acute respiratory illness, by wave, 4 sites, South Africa, 2009–2012*

First wave (2009),
no. pos/no. tested (% pos) Second wave (2011),
no. pos/no. tested (% pos)
Age group, y
<5 87/160 (54.4) 67/140 (47.9) Reference Reference
5–24 31/160 (19.4) 12/140 (8.6) 0.5 (0.2–1.1) 0.6 (0.3–1.4)
25–44 24/160 (15.0) 42/140 (30.0) 2.3 (1.3–4.1) 2.8 (1.5–5.1)
45–64 13/160 (8.1) 16/140 (11.1) 1.6 (0.7–3.6) 2.0 (0.9–4.6)
>65
5/160 (3.1)
3/139 (2.1)
0.8 (0.2–3.4)
1.1 (0.3–5.1)
Male
76/159 (47.8)
57/139 (41.1)
0.8 (0.5–1.2)

Black African
156/159 (98.1)
135/139 (97.1)
1.5 (0.3–7.0)

Site
Soweto 104/160 (65.0) 98/140 (70.0) Reference Reference
Klerksdorp Not applicable 12/140 (8.6) Not calculated Not calculated
Pietermaritzburg 6/160 (3.8) 12/140 (8.6) 0.4 (0.2–0.7) 0.4 (0.2–0.8)
Agincourt
50/160 (31.3)
18/140 (12.9)
2.1 (0.8–5.9)
2.7 (0.96–7.8)
Co-infections and underlying medical conditions
HIV-infected 47/119 (39.5) 49/117 (41.9) 1.1 (0.7–1.9)
Tuberculosis 18/158 (11.4) 12/139 (8.6) 0.7 (0.3–1.6)
Underlying medical condition excluding tuberculosis, HIV 11/159 (6.9) 15/139 (10.8) 1.6 (0.7–3.7)
Pregnancy 2/83 (2.4) 0/82 (0) Not calculated
Bacterial/viral respiratory co-infection
Pneumococcal co-infection 
detected by PCR 15/129 (11.6) 7/127 (5.5) 0.4 (0.2–1.1)
Respiratory syncytial virus 2/153 (1.3) 11/140 (7.9) 6.4 (1.4–29.6)
Adenovirus 0/153 (0) 18/140 (12.9) Not calculated
Parainfluenzavirus 1, 2, or 3 10/160 (6.3) 3/140 (2.1) 0.3 (0.1–1.2)
Human metapneumovirus 6/153 (3.9) 1/140 (0.7) 0.2 (0.0–1.5)
Rhinovirus 16/153 (10.5) 11/140 (7.9) 0.7 (0.3–1.6)
Enterovirus
2/153 (1.3)
2/140 (1.4)
1.1 (0.2–7.9)

Clinical presentation and course
Temperature ≥38°C 76/110 (69.1) 46/139 (33.1) 0.2 (0.1–0.4)
Cough† 83/87 (95.4) 66/67 (98.5) 3.2 (0.3–29.1)
Tachypnea† 32/84 (38.1) 34/65 (52.3) 1.8 (0.9–3.4)
Difficulty breathing† 69/87 (79.3) 45/67 (67.2) 0.5 (0.3–1.1)
Chest wall indrawing† 44/87 (50.6) 25/67 (47.3) 0.6 (0.3–1.1)
Stridor† 4/87 (4.6) 11/67 (16.4) 4.1 (1.2–13.4)
Tachycardia† 44/87 (50.6) 43/67 (64.2) 1.8 (0.9–3.4)
Diarrhea† 16/87 (18.4) 9/67 (13.4) 0.7 (0.3–1.7)
Unable to eat† 29/87 (33.3) 11/67 (6.4) 0.4 (0.2–0.9)
Vomiting † 26/87 (29.9) 22/67 (32.8) 1.1 (0.6–2.3)
Lethargy† 19/87 (21.8) 10/67 (14.9) 0.6 (0.3–1.5)
Symptoms ≥3 d before admission 58/158 (36.7) 74/139 (53.2) 2.0 (1.2–3.1)
Admission to intensive care unit 1/159 (1.0) 2/139 (1.4) 2.3 (0.2–25.7)
Mechanical ventilation needed 0/159 (0) 1/139 (1.0) Not calculated
Supplemental oxygen needed 37/159 (23.3) 61/139 (43.9) 2.6 (1.6–4.2)
Antimicrobial drugs prescribed on admission 151/158 (95.6) 134/139 (96.4) 1.2 (0.4–4.0)
Duration of hospitalization >2 d
117/157 (74.5)
107/138 (77.5)
1.2 (0.7–2.0)

No. deaths/no. patients (case-fatality ratio) 2/158 (1.3) 2/138 (1.5) 1.1 (0.2–8.3)

*Pos, positive; OR, odds ratio.
†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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