Contribution of intra- and interhost dynamics to norovirus evolution

Journal of Virology

Volumn 86, Issue 6, 2012, Pages 3219-3229

  Bull, Rowena A ^a   Eden, John Sebastian ^a   Luciani, Fabio ^a   McElroy, Kerensa ^a   Rawlinson, William D ^a,b   White, Peter A ^a  

^a UNIVERSITY OF NEW SOUTH WALES   (Australia)

^b Virology Division   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

PROTEIN VP1;

ACUTE NOROVIRUS INFECTION; ARTICLE; CASE REPORT; CHILD; CHRONIC NOROVIRUS INFECTION; GENE CLUSTER; GENE MUTATION; GENETIC VARIABILITY; HUMAN; IMMUNOCOMPROMISED PATIENT; MALE; MICROBIAL DIVERSITY; MICROBIAL POPULATION DYNAMICS; NONHUMAN; NOROVIRUS; NUCLEOTIDE SEQUENCE; PHYLOGENY; POPULATION DISTRIBUTION; PRESCHOOL CHILD; PRIORITY JOURNAL; RNA VIRUS INFECTION; SEQUENCE ANALYSIS; VIRAL GENETICS; VIRUS CELL INTERACTION; VIRUS TRANSMISSION;

CALICIVIRIDAE INFECTIONS; CHILD; COHORT STUDIES; EVOLUTION, MOLECULAR; FEMALE; GASTROENTERITIS; GENETIC VARIATION; HUMANS; INFANT; MALE; MIDDLE AGED; MOLECULAR SEQUENCE DATA; NOROVIRUS; PHYLOGENY;

NOROVIRUS; RNA VIRUSES;

EID: 84857961991     PISSN: 0022538X     EISSN: 10985514     Source Type: Journal    
DOI: 10.1128/JVI.06712-11     Document Type: Article

References (72)

1. Allen DJ, Gray JJ, Gallimore CI, Xerry J, Iturriza-Gomara M. 2008. Analysis of amino acid variation in the P2 domain of the GII-4 norovirus VP1 protein reveals putative variant-specific epitopes. PLoS One 3:e1485.
2. Allen DJ, et al. 2009. Characterisation of a GII-4 norovirus variantspecific surface-exposed site involved in antibody binding. Virol. J. 6:150.
3. Arnold K, Bordoli L, Kopp J, Schwede T. 2006. The SWISS-MODEL workspace: a Web-based environment for protein structure homology modelling. Bioinformatics 22:195-201.
4. Belliot G, et al. 2003. In vitro proteolytic processing of the MD145 norovirus ORF1 nonstructural polyprotein yields stable precursors and products similar to those detected in calicivirus-infected cells. J. Virol. 77: 10957-10974.
5. Bertolotti-Ciarlet A, Crawford SE, Hutson AM, Estes MK. 2003. The 3= end of Norwalk virus mRNA contains determinants that regulate the expression and stability of the viral capsid protein VP1: a novel function for the VP2 protein. J. Virol. 77:11603-11615.
6. Boillat Blanco N, et al. 2011. Chronic norovirus gastroenteritis in a double hematopoietic stem cell and lung transplant recipient. Transpl. Infect. Dis. 13:213-215.
7. Bok K, et al. 2011. Chimpanzees as an animal model for human norovirus infection and vaccine development. Proc. Natl. Acad. Sci. U. S. A. 108: 325-330.
8. Bull RA, Eden JS, Rawlinson WD, White PA. 2010. Rapid evolution of pandemic noroviruses of the GII.4 lineage. PLoS Pathog. 6:e1000831.
9. Bull RA, et al. 2005. Norovirus recombination in ORF1/ORF2 overlap. Emerg. Infect. Dis. 11:1079 -1085.
10. Bull RA, et al. 2011. Sequential bottlenecks drive viral evolution in early acute hepatitis C virus infection. PLoS Pathog. 7:e1002243.
11. Bull RA, Tanaka MM, White PA. 2007. Norovirus recombination. J. Gen. Virol. 88:3347-3359.
12. Cao S, et al. 2007. Structural basis for the recognition of blood group trisaccharides by norovirus. J. Virol. 81:5949 -5957.
13. Capizzi T, Makari-Judson G, Steingart R, Mertens WC. 2011. Chronic diarrhea associated with persistent norovirus excretion in patients with chronic lymphocytic leukemia: report of two cases. BMC Infect. Dis. 11:131.
14. Carlsson B, et al. 2009. Quasispecies dynamics and molecular evolution of human norovirus capsid P region during chronic infection. J. Gen. Virol. 90:432- 441.
15. Ceballos A, et al. 2008. Lack of viral selection in human immunodeficiency virus type 1 mother-to-child transmission with primary infection during late pregnancy and/or breastfeeding. J. Gen. Virol. 89:2773-2782.
16. Cordey S, et al. 2010. Rhinovirus genome evolution during experimental human infection. PLoS One 5:e10588.
17. Coyne KP, Gaskell RM, Dawson S, Porter CJ, Radford AD. 2007. Evolutionary mechanisms of persistence and diversification of a calicivirus within endemically infected natural host populations. J. Virol. 81: 1961-1971.
18. Debbink K, Donaldson EF, Lindesmith LC, Baric RS. 2012. Genetic mapping of a highly variable norovirus GII.4 blockade epitope: potential role in contribution in escape from human herd immunity. J. Virol. 86: 1214-1226.
19. Deng W, et al. 2010. DIVEIN: a Web server to analyze phylogenies, sequence divergence, diversity, and informative sites. Biotechniques 48: 405-408.
20. Dickover RE, Garratty EM, Plaeger S, Bryson YJ. 2001. Perinatal transmission of major, minor, and multiple maternal human immunodeficiency virus type 1 variants in utero and intrapartum. J. Virol. 75:2194- 2203.
21. Eden JS, et al. 2010. Norovirus GII.4 variant 2006b caused epidemics of acute gastroenteritis in Australia during 2007 and 2008. J. Clin. Virol. 49:265-271.
22. Ewing B, Green P. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8:186 -194.
23. Fischer W, et al. 2010. Transmission of single HIV-1 genomes and dynamics of early immune escape revealed by ultra-deep sequencing. PLoS One 5:e12303.
24. Ghedin E, et al. 2011. Deep sequencing reveals mixed infection with 2009 pandemic influenza A (H1N1) virus strains and the emergence of oseltamivir resistance. J. Infect. Dis. 203:168 -174.
25. Gilles A, et al. 2011. Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics 12:245.
26. Go EP, et al. 2011. Characterization of glycosylation profiles of HIV-1 transmitted/founder envelopes by mass spectrometry. J. Virol. 85:8270- 8284.
27. Goonetilleke N, et al. 2009. The first T cell response to transmitted/ founder virus contributes to the control of acute viremia in HIV-1 infection. J. Exp. Med. 206:1253-1272.
28. Guindon S, Gascuel O. 2003. A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood. Syst. Biol. 52:696-704.
29. Hansman GS, et al. 2011. Crystal structures of GII.10 and GII.12 norovirus protruding domains in complex with histo-blood group antigens reveal details for a potential site of vulnerability. J. Virol. 85:6687- 6701.
30. Jiang X, Wang M, Wang K, Estes MK. 1993. Sequence and genomic organization of Norwalk virus. Virology 195:51- 61.
31. Karst SM, Wobus CE, Lay M, Davidson J, Virgin HW, IV. 2003. STAT1-dependent innate immunity to a Norwalk-like virus. Science 299: 1575-1578.
32. Keele BF. 2010. Identifying and characterizing recently transmitted viruses. Curr. Opin. HIV AIDS 5:327-334.
33. Keele BF, et al. 2008. Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infection. Proc. Natl. Acad. Sci. U. S. A. 105:7552-7557.
34. Kiefer F, Arnold K, Kunzli M, Bordoli L, Schwede T. 2009. The SWISSMODEL Repository and associated resources. Nucleic Acids Res. 37: D387-D392.
35. Koboldt DC, et al. 2009. VarScan: variant detection in massively parallel sequencing of individual and pooled samples. Bioinformatics 25:2283- 2285.
36. Lindesmith LC, et al. 2012. Monoclonal antibody-based antigenic mapping of norovirus GII.4-2002. J. Virol. 86:873- 883.
37. Lindesmith LC, Donaldson EF, Baric RS. 2011. Norovirus GII.4 strain antigenic variation. J. Virol. 85:231-242.
38. Lindesmith LC, et al. 2008. Mechanisms of GII.4 norovirus persistence in human populations. PLoS Med. 5:e31.
39. Liu BL, et al. 1999. Molecular characterization of a bovine enteric calicivirus: relationship to the Norwalk-like viruses. J. Virol. 73:819-825.
40. Liu CH, et al. 2006. Selective transmission of hepatitis C virus quasi species through a needlestick accident in acute resolving hepatitis. Clin. Infect. Dis. 42:1254 -1259.
41. Lochridge VP, Hardy ME. 2007. A single-amino-acid substitution in the P2 domain of VP1 of murine norovirus is sufficient for escape from antibody neutralization. J. Virol. 81:12316 -12322.
42. Margulies M, et al. 2005. Genome sequencing in microfabricated highdensity picolitre reactors. Nature 437:376 -380.
43. Marionneau S, et al. 2002. Norwalk virus binds to histo-blood group antigens present on gastroduodenal epithelial cells of secretor individuals. Gastroenterology 122:1967-1977.
44. Martella V, et al. 2008. Detection and molecular characterization of a canine norovirus. Emerg. Infect. Dis. 14:1306 -1308.
45. Martin DP, et al. 2010. RDP3: a flexible and fast computer program for analyzing recombination. Bioinformatics 26:2462-2463.
46. Murcia PR, et al. 2010. Intra- and interhost evolutionary dynamics of equine influenza virus. J. Virol. 84:6943- 6954.
47. Nielsen R, Paul JS, Albrechtsen A, Song YS. 2011. Genotype and SNP calling from next-generation sequencing data. Nat. Rev. Genet. 12:443-451.
48. Peitsch MC. 1995. Protein modeling by e-mail. Nat. Biotechnol. 13: 658 - 660.
49. Posada D, Buckley TR. 2004. Model selection and model averaging in phylogenetics: advantages of akaike information criterion and bayesian approaches over likelihood ratio tests. Syst. Biol. 53:793- 808.
50. Prasad BV, et al. 1999. X-ray crystallographic structure of the Norwalk virus capsid. Science 286:287-290.
51. Ramachandran S, et al. 2011. Temporal variations in the hepatitis C virus intrahost population during chronic infection. J. Virol. 85:6369 - 6380.
52. Rockx BH, Bogers WM, Heeney JL, van Amerongen G, Koopmans MP. 2005. Experimental norovirus infections in non-human primates. J. Med. Virol. 75:313-320.
53. Salazar-Gonzalez JF, et al. 2009. Genetic identity, biological phenotype, and evolutionary pathways of transmitted/founder viruses in acute and early HIV-1 infection. J. Exp. Med. 206:1273-1289.
54. Schorn R, et al. 2010. Chronic norovirus infection after kidney transplantation: molecular evidence for immune-driven viral evolution. Clin. Infect. Dis. 51:307-314.
55. Shanker S, et al. 2011. Structural analysis of histo-blood group antigen binding specificity in a norovirus GII.4 epidemic variant: implications for epochal evolution. J. Virol. 85:8635- 8645.
56. Siebenga JJ, et al. 2008. High prevalence of prolonged norovirus shedding and illness among hospitalized patients: a model for in vivo molecular evolution. J. Infect. Dis. 198:994 -1001.
57. Siebenga JJ, et al. 2010. Phylodynamic reconstruction reveals norovirus GII.4 epidemic expansions and their molecular determinants. PLoS Pathog. 6:e1000884.
58. Siebenga JJ, et al. 2007. Epochal evolution of GGII.4 norovirus capsid proteins from 1995 to 2006. J. Virol. 81:9932-9941.
59. Siebenga JJ, et al. 2009. Norovirus illness is a global problem: emergence and spread of norovirus GII.4 variants, 2001-2007. J. Infect. Dis. 200:802- 812.
60. Smith GJ, et al. 2009. Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic. Nature 459:1122-1125.
61. Sukhrie FH, Siebenga JJ, Beersma MF, Koopmans M. 2010. Chronic shedders as reservoir for nosocomial transmission of norovirus. J. Clin. Microbiol. 48:4303- 4305.
62. Takanashi S, et al. 2011. Characterization of emerging GII.g/GII.12 noroviruses from a gastroenteritis outbreak in the United States in 2010. J. Clin. Microbiol. 49:3234 -3244.
63. Tamura K, et al. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol. Biol. Evol. 28:2731-2739.
64. Tan M, et al. 2008. Elucidation of strain-specific interaction of a GII-4 norovirus with HBGA receptors by site-directed mutagenesis study. Virology 379:324 -334.
65. Teunis PF, et al. 2008. Norwalk virus: how infectious is it? J. Med. Virol. 80:1468 -1476.
66. Tu ET, et al. 2008. Norovirus excretion in an aged-care setting. J. Clin. Microbiol. 46:2119 -2121.
67. Wang QH, et al. 2005. Porcine noroviruses related to human noroviruses. Emerg. Infect. Dis. 11:1874 -1881.
68. Wingfield T, et al. 2010. Chronic norovirus infection in an HIVpositive patient with persistent diarrhoea: a novel cause. J. Clin. Virol. 49:219 -222.
69. Wolf S, et al. 2009. Molecular detection of norovirus in sheep and pigs in New Zealand farms. Vet. Microbiol. 133:184 -189.
70. Wright CF, et al. 2011. Beyond the consensus: dissecting within-host viral population diversity of foot-and-mouth disease virus by using nextgeneration genome sequencing. J. Virol. 85:2266 -2275.
71. Xerry J, Gallimore CI, Iturriza-Gomara M, Allen DJ, Gray JJ. 2008. Transmission events within outbreaks of gastroenteritis determined through analysis of nucleotide sequences of the P2 domain of genogroup II noroviruses. J. Clin. Microbiol. 46:947-953.
72. Zagordi O, Bhattacharya A, Eriksson N, Beerenwinkel N. 2011. ShoRAH: estimating the genetic diversity of a mixed sample from nextgeneration sequencing data. BMC Bioinformatics 12:119.