Genetic diversity and molecular epidemiology of human rhinoviruses in South Africa

Authors

  • Marthi A. Pretorius,

    1. Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
    2. Department of Medical Virology, University of Pretoria, Pretoria, South Africa
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  • Stefano Tempia,

    1. Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
    2. Influenza Division, Centers for Disease Control and Prevention, Pretoria, South Africa
    3. Influenza Programme, Centers for Disease Control and Prevention–South Africa, Pretoria, South Africa
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  • Florette K. Treurnicht,

    1. Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
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  • Sibongile Walaza,

    1. Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
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  • Adam L. Cohen,

    1. Influenza Division, Centers for Disease Control and Prevention, Atlanta, GA, USA
    2. Influenza Division, Centers for Disease Control and Prevention, Pretoria, South Africa
    3. Influenza Programme, Centers for Disease Control and Prevention–South Africa, Pretoria, South Africa
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  • Jocelyn Moyes,

    1. Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
    2. Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
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  • Orienka Hellferscee,

    1. Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
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  • Ebrahim Variava,

    1. Department of Medicine, Klerksdorp Tshepong Hospital, Klerksdorp, South Africa
    2. Department of Medicine, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
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  • Halima Dawood,

    1. Department of Medicine, Pietermaritzburg Metropolitan Hospital, Pietermaritzburg, South Africa
    2. Department of Medicine, University of KwaZulu Natal, Pietermaritzburg, South Africa
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  • Meera Chhagan,

    1. Department of Paediatrics, University of KwaZulu Natal, Pietermaritzburg, South Africa
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  • Sumayya Haffjee,

    1. School of Pathology, University of KwaZulu Natal, Pietermaritzburg, South Africa
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  • Shabir A. Madhi,

    1. Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
    2. Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
    3. Department of Science and Technology/National Research Foundation, Vaccine Preventable Diseases, University of the Witwatersrand, Johannesburg, South Africa
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  • Cheryl Cohen,

    1. Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
    2. Faculty of Health Sciences, School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
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  • Marietjie Venter

    Corresponding author
    1. Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
    2. Department of Medical Virology, University of Pretoria, Pretoria, South Africa
    3. Global Disease Detection, Centres for Disease Control and Prevention, Pretoria, South Africa
    • Correspondence: Marietjie Venter, One Health Program Director, Global Disease Detection, US Centres for Disease Control and Prevention, Pretoria, South Africa. E-mails: yds8@cdc.gov, mventer@cdc.gov

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Abstract

Background

Rhinoviruses (RV) are a well-established cause of respiratory illness. RV-C has been associated with more severe illness. We aimed to characterize and compare the clinical presentations and disease severity of different RV type circulating in South Africa.

Method

We performed two analyses of RV-positive specimens identified through surveillance in South Africa across all age groups. First, RV-positive specimens identified through severe acute respiratory illness (SARI) surveillance in four provinces was randomly selected from 2009 to 2010 for molecular characterization. Second, RV-positive specimens identified through SARI, influenza-like illness (ILI) and control surveillance at hospitals and outpatient clinics in during 2012–2013 were used to determine the association of RV type with severe disease. Selected specimens were sequenced, and phylogenetic analysis was performed.

Results

Among the 599 sequenced specimens from 2009 to 2010 and 2012 to 2013, RV-A (285, 48%) and RV-C (247, 41%) were more commonly identified than RV-B (67, 11%), with no seasonality and a high genetic diversity. A higher prevalence of RV infection was identified in cases with SARI [515/962 (26%); aRRR = 1·6; 95% CI 1·21; 2·2] and ILI [356/962 (28%); aRRR = 1·9; 95% CI 1·37; 2·6] compared with asymptomatic controls (91/962, 22%). There was no difference in disease severity between the different type when comparing SARI, ILI and controls.

Conclusion

All three type of RV were identified in South Africa, although RV-A and RV-C were more common than RV-B. RV was associated with symptomatic respiratory illness; however, there was no association between RV type and disease severity.

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