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Epidemiology of Influenza Virus Types and Subtypes in South Africa, 2009–20121 - Volume 20, Number 7—July 2014 - Emerging Infectious Disease journal - CDC

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Epidemiology of Influenza Virus Types and Subtypes in South Africa, 2009–20121 - Volume 20, Number 7—July 2014 - Emerging Infectious Disease journal - CDC


Volume 20, Number 7—July 2014


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)


To determine clinical and epidemiologic differences between influenza caused by different virus types and subtypes, we identified patients and tested specimens. Patients were children and adults hospitalized with confirmed influenza and severe acute respiratory illness (SARI) identified through active, prospective, hospital-based surveillance from 2009–2012 in South Africa. Respiratory specimens were tested, typed, and subtyped for influenza virus by PCR. Of 16,005 SARI patients tested, 1,239 (8%) were positive for influenza virus. Patient age and co-infections varied according to virus type and subtype, but disease severity did not. Case-patients with influenza B were more likely than patients with influenza A to be HIV infected. A higher proportion of case-patients infected during the first wave of the 2009 influenza pandemic were 5–24 years of age (19%) than were patients infected during the second wave (9%). Although clinical differences exist, treatment recommendations do not differ according to subtype; prevention through vaccination is recommended.
Most influenza in humans is caused by 2 types of influenza virus: A and B. On the basis of the hemagglutinin and neuraminidase proteins on the surface of the virus, influenza A viruses are further subdivided into subtypes, 2 of which have commonly caused disease in humans over the past century: H3N2 and H1N1. The proportion of these 3 types and subtypes of influenza virus—A(H3N2), A(H1N1), and B—that circulate among humans varies each year. In 2009, a novel pandemic strain of influenza A(H1N1) virus, now called influenza A(H1N1)pdm09 virus, became the dominant H1N1 virus strain circulating worldwide (1).
It is generally not possible to distinguish infection caused by different influenza types and subtypes by clinical features (2,3), although differences in severity have been observed (46). Analyses of vital statistics data from the United States and South Africa have suggested that the numbers of excess deaths associated with influenza are higher in years when influenza A(H3N2) virus is circulating than when influenza B or prepandemic influenza A(H1N1) virus is circulating (4,7). Some studies have suggested that influenza A(H1N1)pdm09 virus infection led to more severe outcomes than did other types and subtypes (8,9). In the first 3 months after influenza A(H1N1)pdm09 virus was identified in South Africa, 91 deaths among 12,331 patients with laboratory-confirmed cases were identified; rates of HIV infection and pregnancy among those who died were high (10). After the influenza pandemic, studies showed that A(H1N1)pdm09 virus was more likely than previously circulating virus types and subtypes to affect children and young adults and that severe disease was associated with clinical characteristics such as obesity (11,12). The data conflict with regard to whether severity of disease increases with subsequent waves of A(H1N1)pdm09 virus infection (1317).
Little data have been reported from Africa on clinical and epidemiologic differences caused by different influenza virus types and subtypes. The objective of our study was 2-fold. First, we sought to compare the demographic and clinical characteristics, factors associated with infection, and disease severity among case-patients hospitalized with severe acute respiratory illness (SARI) associated with influenza A(H1N1)pdm09, A(H3N2), and B viruses in South Africa during 2009–2012. Second, we sought to compare the characteristics of case-patients infected during the first wave of influenza A(H1N1)pdm09 infection in 2009 with those of case-patients infected during the subsequent wave in 2011. Because this surveillance was started in 2009, we did not include prepandemic A(H1N1) virus strains in this study.

Dr Cohen is a pediatrician, medical epidemiologist, and director of the Influenza Program at the Centers for Disease Control and Prevention–South Africa, Pretoria, South Africa. His research interests involve public health in the fields of pneumonia and global child health.


This work was supported by the Centers for Disease Control and Prevention, Atlanta, Georgia, USA, and the National Institute for Communicable Diseases, Johannesburg, South Africa.


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Technical Appendix

Suggested citation for this article: Cohen AL, Hellferscee O, Pretorius M, Treurnicht F, Walaza S, Madhi S, et al. Epidemiology of influenza virus types and subtypes in South Africa, 2009–2012. Emerg Infect Dis [Internet]. 2014 Jul [date cited].
DOI: 10.3201/eid2007.131869
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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