The role of influenza, RSV and other common respiratory viruses in severe acute respiratory infections and influenza-like illness in a population with a high HIV sero-prevalence, South Africa 2012–2015
Section snippets
Background
Pneumonia is a leading cause of childhood mortality globally, with about 1.6 million new cases per year, of which 1.2 million occur in the developing world [1] and approximately 10% are severe enough to require hospitalization [1]. Before the worldwide availability of vaccines, Streptococcus pneumoniae (pneumococcus) and Haemophilus influenzae type b were identified as the main bacterial causes of pneumonia [1], [2]. Now, viruses are more commonly detected in patients with acute respiratory
Objectives
To the attributable fraction of 10 common respiratory viruses among patients hospitalized with severe acute respiratory illness (SARI) and outpatients with influenza-like illness (ILI) compared to control subjects.
Study design and population
SARI surveillance: Study samples were obtained from participants enrolled in a prospective hospital-based surveillance program for SARI initiated in February 2009. The methodology and case definition of this study has been previously described [8], [19]. For this study participants were enrolled at 3 public hospitals in 2 provinces of South Africa (Edendale Hospital, KwaZulu-Natal Province; and Klerksdorp and Tshepong Hospitals, North West Province) from May 2012 through April 2015.
ILI and
Characteristics of the study population and detection of respiratory viruses
Over the study period, we enrolled 1959 SARI cases, 3784 ILI cases and 1793 controls. Children <5 years of age accounted for 73% (1431/1953); 28% (1075/3783) and 37% (658/1135) of SARI cases, ILI cases and controls, respectively. The HIV serostatus was known for 79% (1550/1959) of SARI cases, 87% (3280/3784) of ILI cases, and 92% (1643/1793) of controls. Among individuals with known HIV serostatus, the HIV prevalence was 26% (410/1550) among SARI cases, 30% (974/3280) among ILI cases, and 43%
Discussion
We assessed the association between virus detection and mild or severe illness relative to controls. The estimated detection rate attributable to illness reported in this study reflects a more accurate description of the prevalence of viruses causing respiratory disease in both children and adults in South Africa than reporting viral detection rates alone. Most of the viral pathogens evaluated in this study were found to be associated with mild or severe disease irrespective of HIV status.
Funding
Funding provided by co-operative agreement 5U51/IP000155 with the Centers for Disease Control and Prevention, Atlanta, Georgia, USA.
Conflicts of interest
None of the authors has a financial or personal conflict of interest related to this study. All the authors fulfill the uniform requirements criteria, and no assistance other than copy editing was provided in the preparation of the manuscript. The corresponding author has full access to all data in the study and final responsibility for the decision to submit this publication.
Ethical considerations
The SARI and ILI/control protocols was reviewed and approved by the University of the Witwatersrand Human Research Ethics Committee (HREC) and the University of KwaZulu-Natal Human Biomedical Research Ethics Committee (BREC) protocol numbers M081042, BF157/08 and BF 080/12 respectively. This surveillance was deemed non-research by the U.S. Centers for Disease Control and Prevention.
Disclaimer
The findings and conclusions in this report are those of the authors and do not necessarily represent the official position of the US Centers for Disease Control and Prevention.
Acknowledgements
This surveillance study has been funded by a co-operative agreement 5U51/IP000155 with the Centers for Disease Control and Prevention, Atlanta, Georgia, USA. We would like to thank the following Units and individuals at the National Institute for Communicable Diseases a division of the National Health Laboratory Service: Centre for Respiratory Diseases and Meningitis: Amelia Buys, Cardia Fourie, Xolisa Stuurman. Chris Hani Baragwanath Hospital: Andrew Black. Department of Science and
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