Replacement and positive evolution of subtype A and B respiratory syncytial virus G-protein genotypes from 1997-2012 in South Africa

Journal of Infectious Diseases

Volumn 208, Issue SUPPL. 3, 2013, Pages

  Pretorius, Marthi A ^a,d   Van Niekerk, Stephanie ^d   Tempia, Stefano ^b   Moyes, Jocelyn ^a   Cohen, Cheryl ^a   Madhi, Shabir A ^a,c,e   Venter, Marietjie ^a,d  

^a NATIONAL INSTITUTE FOR COMMUNICABLE DISEASES   (South Africa)

^b US Centers for Diseases Control and Prevention NICD NHLS   (United States)

^c UNIVERSITY OF THE WITWATERSRAND   (South Africa)

^d UNIVERSITY OF PRETORIA   (South Africa)

^e NATIONAL RESEARCH FOUNDATION   (South Africa)

Author keywords

Evolutionary rate; Genotypes; Positive selection; Respiratory syncytial virus

Indexed keywords

GUANINE NUCLEOTIDE BINDING PROTEIN; G GLYCOPROTEIN, RESPIRATORY SYNCYTIAL VIRUS; VIRUS FUSION PROTEIN;

ADOLESCENT; ADULT; CHILD; CONTROLLED STUDY; EVOLUTION; GENETIC SELECTION; GENOTYPE; HUMAN; MAJOR CLINICAL STUDY; MIDDLE AGED; MOLECULAR PHYLOGENY; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RESPIRATORY SYNCYTIAL PNEUMOVIRUS; RESPIRATORY SYNCYTIAL VIRUS A; RESPIRATORY SYNCYTIAL VIRUS B; REVIEW; SEQUENCE ANALYSIS; SOUTH AFRICA; UNINDEXED SEQUENCE; VIRAL GENETICS; VIRUS DETECTION; VIRUS MUTATION; VIRUS STRAIN; AGED; ARTICLE; CLASSIFICATION; DNA SEQUENCE; EVOLUTIONARY RATE; FEMALE; GENETICS; GENOTYPES; INFANT; ISOLATION AND PURIFICATION; MALE; MOLECULAR EPIDEMIOLOGY; MOLECULAR EVOLUTION; MOLECULAR GENETICS; PHYLOGENY; POSITIVE SELECTION; PRESCHOOL CHILD; RESPIRATORY SYNCYTIAL VIRUS INFECTION; VIROLOGY; YOUNG ADULT; HUMAN RESPIRATORY SYNCYTIAL VIRUS; RESPIRATORY SYNCYTIAL VIRUS INFECTIONS;

EVOLUTIONARY RATE; GENOTYPES; POSITIVE SELECTION; RESPIRATORY SYNCYTIAL VIRUS;

ADOLESCENT; ADULT; AGED; CHILD; CHILD, PRESCHOOL; EVOLUTION, MOLECULAR; FEMALE; GENOTYPE; HUMANS; INFANT; MALE; MIDDLE AGED; MOLECULAR EPIDEMIOLOGY; MOLECULAR SEQUENCE DATA; PHYLOGENY; RESPIRATORY SYNCYTIAL VIRUS INFECTIONS; RESPIRATORY SYNCYTIAL VIRUS, HUMAN; SELECTION, GENETIC; SEQUENCE ANALYSIS, DNA; SOUTH AFRICA; VIRAL FUSION PROTEINS; YOUNG ADULT;

EID: 84893491956     PISSN: 00221899     EISSN: 15376613     Source Type: Journal    
DOI: 10.1093/infdis/jit477     Document Type: Review

References (38)

1. Nair H, Nokes DJ, Gessner BD, et al. Global burden of acute lower respiratory infections due to respiratory syncytial virus in young children: a systematic review and meta-analysis. Lancet 2010; 375:1545-55.
2. Bukreyev A, Yang L, Fricke J, et al. The secreted form of respiratory syncytial virus G glycoprotein helps the virus evade antibody-mediated restriction of replication by acting as an antigen decoy and through effects on Fc receptor-bearing leukocytes. J Virol 2008; 82:12191-204.
3. Agoti CN, Mbisa JL, Bett A, Medley GF, Nokes DJ, Cane PA. Intrapa- tient variation of the respiratory syncytial virus attachment protein gene. J Virol 2010; 84:10425-8.
4. Peret TC, Hall CB, Hammond GW, et al. Circulation patterns of group A and B human respiratory syncytial virus genotypes in 5 communities in North America. J Infect Dis 2000; 181:1891-6.
5. Peret TC, Hall CB, Schnabel KC, Golub JA, Anderson LJ. Circulation patterns of genetically distinct group A and B strains of human respiratory syncytial virus in a community. J Gen Virol 1998; 79(Pt 9):2221-9.
6. van Niekerk S, Venter M. Replacement of previously circulating respiratory syncytial virus subtype B strains with the BA genotype in South Africa. J Virol 2011; 85:8789-97.
7. Venter M, Madhi SA, Tiemessen CT, Schoub BD. Genetic diversity and molecular epidemiology of respiratory syncytial virus over four consecutive seasons in South Africa: identification of new subgroup A and B genotypes. J Gen Virol 2001; 82:2117-24.
8. Zlateva KT, Lemey P, Moes E, Van damme AM, Van Ranst M. Genetic variability and molecular evolution of the human respiratory syncytial virus subgroup B attachment G-protein. J Virol 2005; 79: 9157-67.
9. Zlateva KT, Lemey P, Vandamme A-M, Van Ranst M. Molecular evolution and circulation patterns of human respiratory syncytial virus subgroup A: positively selected sites in the attachment G glycoprotein. J Virol 2004; 78:4675-83.
10. Matheson JW, Rich FJ, Cohet C, et al. Distinct patterns of evolution between respiratory syncytial virus subgroups A and B From New Zealand isolates collected over thirty-seven years. Journal of Medical Virology 2006; 78:1354-64.
11. Papenburg J, Carbonneau J, Hamelin ME, et al. Molecular evolution of respiratory syncytial virus fusion gene, Canada, 2006-2010. Emerg Infect Dis 2012; 18:120-4.
12. Venter M, Collinson M, Schoub BD. Molecular epidemiological analysis of community circulating respiratory syncytial virus in rural South Africa: Comparison of viruses and genotypes responsible for different disease manifestations. J Med Virol 2002; 68:452-61.
13. Trento A, Galiano M, Videla C, et al. Major changes in the G-protein of human respiratory syncytial virus isolates introduced by a duplication of 60 nucleotides. J Gen Virol 2003; 84:3115-20.
14. Trento A, Casas I, Calderon A, et al. Ten years of global evolution of the human respiratory syncytial virus BA genotype with a 60-nudeotide duplication in the G-protein gene. J Virol 2010; 84:7500-12.
15. Dapat IC, Shobugawa Y, Sano Y, et al. New genotypes within respiratory syncytial virus group B genotype BA in Niigata, Japan. J Clin Microbiol 2010; 48:3423-7.
16. Madhi SA, Venter M, Alexandra R, et al Respiratory syncytial virus associated illness in high-risk children and national characterisation of the circulating virus genotype in South Africa. J Clin Virol 2003; 27:180-9.
17. Galiano MC, Palomo C, Videla CM, Arbiza J, Melero JA, Carballal G. Genetic and antigenic variability of human respiratory syncytial virus (groups a and b) isolated over seven consecutive seasons in Argentina (1995 to 2001). J Clin Microbiol 2005; 43:2266-73.
18. Visser A, Delport S, Venter M. Molecular epidemiological analysis of a nosocomial outbreak of respiratory syncytial virus assodated pneumonia in a kangaroo mother care unit in South Africa. J Med Virol 2008; 80:724-32.
19. Pretorius MA, Madhi SA, Cohen C, et al. Respiratory viral co-infections identified by a 10-plex real time polymerase chain reaction assay in patients hospitalised with Severe Acute Respiratory Illness-South Africa, 2009-2010. J Inf Dis 2012; 206 (Suppl 1)S159-65.
20. Trento A, Viegas M, Galiano M, et al Natural history of human respiratory syncytial virus inferred from phylogenetic analysis of the attachment (G) glycoprotein with a 60-nudeotide duplicatioa J Virol 2006; 80:975-84.
21. Sullender WM, Sun L, Anderson LJ. Analysis of respiratory syncytial virus genetic variability with amplified cDNAs. J Clin Microbiol 1993; 31:1224-31.
22. Venter M, Tiemessen C, Collinson M, Schoub B. Molecular epidemiological analysis of community circulating respiratory syncytial virus in rural South Africa: comparison of viruses and genotypes causing different disease manifestations. J Med Virol 2002; 68:452-61.
23. Drummond AJ, Rambaut A. BEAST: Bayesian evolutionary analysis by sampling trees. BMC Evol. Biol 2007; 7:214.
24. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL-X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 1997; 25:4876-82.
25. Hall TA. BioEdit: a user-friendly biological sequence aligment editor and analysis program for Windows 95/98/NT. Nucleic Acids Symp Ser 1999;41:95-8.
26. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0. Molr Biol Evol 2007; 24:1596-9.
27. Kumar S, Nei M, Dudley J, Tamura K. MEGA: a biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinform 2008; 9:299-306.
28. Kosakovsky Pond SL, Frost SDW. Not so different after all: a comparison of methods for detecting amino acid sites under selection. Mol Biol Evol 2005; 22:1208-22.
29. Delport W, Poon AF, Frost SD, Kosakovsky Pond SL. Datamonkey 2010: a suite of phylogenetic analysis tools for evolutionary biology. Bioinformatics 2010; 26:2455-7.
30. Pond SL, Frost SD. Datamonkey: rapid detection of selective pressure on individual sites of codon alignments. Bioinformatics 2005; 21: 2531-3.
31. Nei M, Gojobori T. Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions. Mol Biol Evol 1986; 3:418-26.
32. Eshaghi A, Duwuri VR, Lai R, et al. Genetic variability of human respiratory syncytial virus A strains circulating in ontario: a novel genotype with a 72 nucleotide G gene duplicatioa PLoS One 2012; 7:e32807.
33. Zlateva KT, Vijgen L, Dekeersmaeker N, Naranjo C, Van Ranst M. Subgroup prevalence and genotype circulation patterns of human respiratory syncytial virus in Belgium during ten successive epidemic seasons. J Clin Microbiol 2007; 45:3022-30.
34. Shobugawa Y, Saito R, Sano Y, et al. Emerging genotypes of human respiratory syncytial virus subgroup A among patients in Japan. J Clin Microbiol 2009; 47:2475-82.
35. Yamaguchi M, Sano Y, Dapat IC, et al. High frequency of repeated infections due to emerging genotypes of human respiratory syncytial viruses among children during eight successive epidemic seasons in Japan. J Clin Microbiol 2011; 49:1034-40.
36. Rebuffo-Scheer C, Bose M, He J, et al. Whole genome sequencing and evolutionary analysis of human respiratory syncytial virus A and B from Milwaukee, WI1998-2010. PLoS One 2011; 6:e25468.
37. Botosso VF, Zanotto PM, Ueda M, et al. Positive selection results in frequent reversible amino acid replacements in the G-protein gene of human respiratory syncytial virus. PLoS Pathog 2009; 5: e1000254.
38. Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 2007; 24:1596-9.