Genetic diversity and molecular epidemiology of human rhinoviruses in South Africa

Influenza and other Respiratory Viruses

Volumn 8, Issue 5, 2014, Pages 567-573

  Pretorius, Marthi A ^a,b   Tempia, Stefano ^c,d   Treurnicht, Florette K ^a   Walaza, Sibongile ^a   Cohen, Adam L ^c,d   Moyes, Jocelyn ^a,e   Hellferscee, Orienka ^a   Variava, Ebrahim ^f,g   Dawood, Halima ^h,i   Chhagan, Meera ⁱ   Haffjee, Sumayya ⁱ   Madhi, Shabir A ^a,g,j   Cohen, Cheryl ^a,e   Venter, Marietjie ^a,b,k  

^a NATIONAL INSTITUTE FOR COMMUNICABLE DISEASES   (South Africa)

^b UNIVERSITY OF PRETORIA   (South Africa)

^c CENTERS FOR DISEASE CONTROL AND PREVENTION   (United States)

^d Centers for Disease Control and Prevention South Africa   (South Africa)

^e UNIVERSITY OF THE WITWATERSRAND   (South Africa)

^f Department of Health North West Province   (South Africa)

^g UNIVERSITY OF THE WITWATERSRAND   (South Africa)

^h Pietermaritzburg Metropolitan Hosp   (South Africa)

ⁱ UNIVERSITY OF KWAZULU NATAL   (South Africa)

^j UNIVERSITY OF THE WITWATERSRAND   (South Africa)

^k Global AIDS Programs   (South Africa)

more..

Author keywords

Disease association; Genetic diversity; Rhinovirus; South Africa

Indexed keywords

ADOLESCENT; ADULT; ARTICLE; CHILD; CONTROLLED STUDY; DISEASE ASSOCIATION; DISEASE SEVERITY; DISEASE SURVEILLANCE; FEMALE; FLU LIKE SYNDROME; GENETIC VARIABILITY; HOSPITAL; HUMAN; HUMAN RHINOVIRUS; MAJOR CLINICAL STUDY; MALE; MOLECULAR EPIDEMIOLOGY; OUTPATIENT DEPARTMENT; PHYLOGENY; PREVALENCE; PRIORITY JOURNAL; RHINOVIRUS INFECTION; SEVERE ACUTE RESPIRATORY SYNDROME; SOUTH AFRICA; VIRUS STRAIN; CLASSIFICATION; GENETICS; INFANT; ISOLATION AND PURIFICATION; MIDDLE AGED; MOLECULAR GENETICS; PICORNAVIRIDAE INFECTIONS; PRESCHOOL CHILD; RHINOVIRUS; VIROLOGY; YOUNG ADULT;

ADOLESCENT; ADULT; CHILD; CHILD, PRESCHOOL; FEMALE; GENETIC VARIATION; HUMANS; INFANT; MALE; MIDDLE AGED; MOLECULAR EPIDEMIOLOGY; MOLECULAR SEQUENCE DATA; PHYLOGENY; PICORNAVIRIDAE INFECTIONS; RHINOVIRUS; SOUTH AFRICA; YOUNG ADULT;

EID: 84908058970     PISSN: 17502640     EISSN: 17502659     Source Type: Journal    
DOI: 10.1111/irv.12264     Document Type: Article

References (23)

1. Black RE, Cousens S, Johnson HL et al. Global, regional, and national causes of child mortality in 2008: a systematic analysis. Lancet 2010; 375:1969-1987.
2. Briese T, Renwick N, Venter M et al. Global distribution of novel rhinovirus genotype. Emerg Infect Dis 2008; 14:944-947.
3. Mahony JB. Detection of respiratory viruses by molecular methods. Clin Microbiol Rev 2008; 21:716-747.
4. Miller EK, Edwards KM, Weinberg GA et al. A novel group of rhinoviruses is associated with asthma hospitalizations. J Allergy Clin Immunol 2009; 123:98-104.e1.
5. Pretorius MA, Madhi SA, Cohen C et al. Respiratory viral coinfections identified by a 10-plex real-time reverse-transcription polymerase chain reaction assay in patients hospitalized with severe acute respiratory illness-South Africa, 2009-2010. J Infect Dis 2012; 206(Suppl 1):S159-S165.
6. Fry AM, Chittaganpitch M, Baggett HC et al. The burden of hospitalized lower respiratory tract infection due to respiratory syncytial virus in rural Thailand. PLoS ONE 2010; 5:e15098.
7. Smuts HE, Workman LJ, Zar HJ. Human rhinovirus infection in young African children with acute wheezing. BMC Infect Dis 2011; 11:65.
8. Peltola V, Waris M, Kainulainen L, Kero J, Ruuskanen O. Virus shedding after human rhinovirus infection in children, adults and patients with hypogammaglobulinaemia. Clin Microbiol Infect 2013; 19:E322-E327.
9. Statistics South Africa. Mid-year Population Estimates 2013. Statistics South Africa. Available at www.statssa.gov.za/publications (Accessed 14 November 2013).
10. Cohen C, Moyes J, Tempia S, Groom M, Walaza S, Pretorius M. Severe influenza-associated respiratory infection in high HIV prevalence setting, South Africa, 2009-2011. Emerg Infect Dis 2013; 19:1766-1774.
11. Coiras MT, Aguilar JC, Garcia ML, Casas I, Perez-Brena P. Simultaneous detection of fourteen respiratory viruses in clinical specimens by two multiplex reverse transcription nested-PCR assays. J Med Virol 2004; 72:484-495.
12. Arden KE, McErlean P, Nissen MD, Sloots TP, Mackay IM. Frequent detection of human rhinoviruses, paramyxoviruses, coronaviruses, and bocavirus during acute respiratory tract infections. J Med Virol 2006; 78:1232-1240.
13. Katoh K, Standley DM. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Mol Biol Evol 2013; 30:772-780.
14. Darriba D, Taboada GL, Doallo R, Posada D. jModelTest 2: more models, new heuristics and parallel computing. Nat Methods 2012; 9:772.
15. Guindon S, Gascuel O. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst Biol 2003; 52:696-704.
16. Guindon S, Lethiec F, Duroux P, Gascuel O. PHYML Online-a web server for fast maximum likelihood-based phylogenetic inference. Nucleic Acids Res 2005; 33(Web Server issue):W557-W559.
17. Fry AM, Lu X, Olsen SJ et al. Human rhinovirus infections in rural Thailand: epidemiological evidence for rhinovirus as both pathogen and bystander. PLoS ONE 2011; 6:e17780.
18. Onyango CO, Welch SR, Munywoki PK et al. Molecular epidemiology of human rhinovirus infections in Kilifi, coastal Kenya. J Med Virol 2012; 84:823-831.
19. Lau SKP, Yip CCY, Tsoi H-W et al. Clinical features and complete genome characterization of a distinct human rhinovirus (HRV) genetic cluster, probably representing a previously undetected HRV species, HRV-C, associated with acute respiratory illness in children. J Clin Microbiol 2007; 45:3655-3664.
20. Kotaniemi-Syrjanen A, Vainionpaa R, Reijonen TM, Waris M, Korhonen K, Korppi M. Rhinovirus-induced wheezing in infancy-the first sign of childhood asthma? J Allergy Clin Immunol 2003; 111:66-71.
21. Bizzintino J, Lee WM, Laing IA et al. Association between human rhinovirus C and severity of acute asthma in children. Eur Respir J 2011; 37:1037-1042.
22. Cox DW, Bizzintino J, Ferrari G et al. Human rhinovirus species C infection in young children with acute wheeze is associated with increased acute respiratory hospital admissions. Am J Respir Crit Care Med 2013; 188:1358-1364.
23. Blaschke AJ, Allison MA, Meyers L et al. Non-invasive sample collection for respiratory virus testing by multiplex PCR. J Clin Virol 2011; 52:210-214.