Clinical epidemiology of bocavirus, rhinovirus, two polyomaviruses and four coronaviruses in HIV-infected and HIV-uninfected South African children.
BACKGROUND
Advances in molecular diagnostics have implicated newly-discovered respiratory viruses in the pathogenesis of pneumonia. We aimed to determine the prevalence and clinical characteristics of human bocavirus (hBoV), human rhinovirus (hRV), polyomavirus-WU (WUPyV) and -KI (KIPyV) and human coronaviruses (CoV)-OC43, -NL63, -HKU1 and -229E among children hospitalized with lower respiratory tract infections (LRTI).


METHODS
Multiplex real-time reverse-transcriptase polymerase chain reaction was undertaken on archived nasopharyngeal aspirates from HIV-infected and -uninfected children (<2 years age) hospitalized for LRTI, who had been previously investigated for respiratory syncytial virus, human metapneumovirus, parainfluenza I-III, adenovirus and influenza A/B.


RESULTS
At least one of these viruses were identified in 274 (53.0%) of 517 and in 509 (54.0%) of 943 LRTI-episodes in HIV-infected and -uninfected children, respectively. Human rhinovirus was the most prevalent in HIV-infected (31.7%) and -uninfected children (32.0%), followed by CoV-OC43 (12.2%) and hBoV (9.5%) in HIV-infected; and by hBoV (13.3%) and WUPyV (11.9%) in HIV-uninfected children. Polyomavirus-KI (8.9% vs. 4.8%; p = 0.002) and CoV-OC43 (12.2% vs. 3.6%; p<0.001) were more prevalent in HIV-infected than -uninfected children. Combined with previously-tested viruses, respiratory viruses were identified in 60.9% of HIV-infected and 78.3% of HIV-uninfected children. The newly tested viruses were detected at high frequency in association with other respiratory viruses, including previously-investigated viruses (22.8% in HIV-infected and 28.5% in HIV-uninfected children).


CONCLUSIONS
We established that combined with previously-investigated viruses, at least one respiratory virus was identified in the majority of HIV-infected and HIV-uninfected children hospitalized for LRTI. The high frequency of viral co-infections illustrates the complexities in attributing causality to specific viruses in the aetiology of LRTI and may indicate a synergetic role of viral co-infections in the pathogenesis of childhood LRTI.
Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, Johannesburg, South Africa ; Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
Marta C
MC
Nunes
Stony Brook School of Medicine, Stony Brook University, Stony Brook, New York, United States of America.
Zachary
Z
Kuschner
Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
Zelda
Z
Rabede
Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, Johannesburg, South Africa ; Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
Richard
R
Madimabe
Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, Johannesburg, South Africa ; Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
Nadia
N
Van Niekerk
Molecular and Immunology Division, BioMérieux, Johannesburg, South Africa.
Jackie
J
Moloi
Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, Johannesburg, South Africa ; Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
Locadiah
L
Kuwanda
Department of Medical Microbiology, University Medical Center Groningen, University of Groningen, Groningen, The Netherlands.
John W
JW
Rossen
Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa ; Hubert Department of Global Health, Rollins School of Public Health and Division of Infectious Diseases, Emory University School of Medicine, Atlanta, Georgia, United States of America.
Keith P
KP
Klugman
Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, Johannesburg, South Africa ; Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa.
Peter V
PV
Adrian
Department of Science and Technology/National Research Foundation: Vaccine Preventable Diseases, Johannesburg, South Africa ; Medical Research Council: Respiratory and Meningeal Pathogens Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa ; National Institute for Communicable Diseases: a division of National Health Laboratory Service, Sandringham, South Africa.
Shabir A
SA
Madhi
D000256:Adenoviridae / Q000235:genetics; D052660:Bocavirus / Q000235:genetics; D002675:Child, Preschool; D060085:Coinfection / Q000453:epidemiology* / Q000821:virology; D017934:Coronavirus / Q000235:genetics; D015658:HIV Infections / Q000453:epidemiology* / Q000821:virology; D006760:Hospitalization / Q000706:statistics & numerical data; D006801:Humans; D007223:Infant; D009980:Influenza A virus / Q000235:genetics; D009981:Influenza B virus / Q000235:genetics; D029121:Metapneumovirus / Q000235:genetics; D010252:Paramyxoviridae / Q000235:genetics; D011120:Polyomavirus / Q000235:genetics; D015995:Prevalence; D012136:Respiratory Syncytial Viruses / Q000235:genetics; D012141:Respiratory Tract Infections / Q000453:epidemiology* / Q000821:virology; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012229:Rhinovirus / Q000235:genetics; D013019:South Africa / Q000453:epidemiology; D014777:Virus Diseases / Q000453:epidemiology* / Q000821:virology