Skip directly to site content Skip directly to page options Skip directly to A-Z link Skip directly to A-Z link Skip directly to A-Z link
Volume 22, Number 4—April 2016
Research

Evaluation of Viremia Frequencies of a Novel Human Pegivirus by Using Bioinformatic Screening and PCR

David Bonsall, William F. Gregory, Camilla L.C. Ip, Sharyne Donfield, James Iles, M. Azim Ansari, Paolo Piazza, Amy Trebes, Anthony Brown, John Frater, Oliver G. Pybus, Phillip Goulder, Paul Klenerman, Rory Bowden, Edward D. Gomperts, Eleanor Barnes, Amit Kapoor, Colin P. Sharp, and Peter SimmondsComments to Author 
Author affiliations: University of Oxford, Oxford, UK (D. Bonsall, C.L.C. Ip, J. Iles, M.A. Ansari, P. Piazza, A. Trebes, A. Brown, J. Frater, O.G. Pybus, P. Goulder, P. Klenerman, R. Bowden, E. Barnes, P. Simmonds); University of Edinburgh Easter Bush, Edinburgh, Scotland, UK (W.F. Gregory, C.P. Sharp); Rho, Inc., Chapel Hill, North Carolina, USA (S. Donfield); The Childrens' Hospital, Los Angeles, California, USA (E.D. Gomperts); The Research Institute at Nationwide Children's Hospital, Columbus, Ohio, USA (A. Kapoor)

Main Article

Figure 1

Maximum-likelihood phylogenetic analysis of complete genome sequences of human pegivirus assembled in this study (black circles) compared with available human hepegivirus (HPgV) sequences of genotypes 1–6 published in GenBank (accession numbers shown). The tree was constructed by using the maximum-likelihood algorithm implemented in the MEGA6 software package (16). For this dataset, the optimum maximum model was general time reversible model (18) with a gamma distribution (5 rates) and invariant

Figure 1. Maximum-likelihood phylogenetic analysis of complete genome sequences of human pegivirus assembled in this study (black circles) compared with available human hepegivirus (HPgV) sequences of genotypes 1–6 published in GenBank (accession numbers shown). The tree was constructed by using the maximum-likelihood algorithm implemented in the MEGA6 software package (16). For this dataset, the optimum maximum model was general time reversible model (18) with a gamma distribution (5 rates) and invariant sites. Phylogenetic analysis of each dataset used 100 bootstrap resamplings to infer the robustness of groupings. Genotypes previously assigned to HPgV sequences are shown on the right with the exception of sequence AB013501 (from the United Kingdom, shown with genotype “?”). Scale bar indicates nucleotide substitutions per site.

Main Article

References
  1. Lipkin  WI, Anthony  SJ. Virus hunting. Virology. 2015;479–480:1949. DOIPubMedGoogle Scholar
  2. Chiu  CY. Viral pathogen discovery. Curr Opin Microbiol. 2013;16:46878. DOIPubMedGoogle Scholar
  3. Lei  XY, Liu  MM, Yu  XJ. Severe fever with thrombocytopenia syndrome and its pathogen SFTSV. Microbes Infect. 2015;17:14954. DOIPubMedGoogle Scholar
  4. McMullan  LK, Folk  SM, Kelly  AJ, MacNeil  A, Goldsmith  CS, Metcalfe  MG, A new phlebovirus associated with severe febrile illness in Missouri. N Engl J Med. 2012;367:83441. DOIPubMedGoogle Scholar
  5. Lipkin  WI, Firth  C. Viral surveillance and discovery. Curr Opin Virol. 2013;3:199–204.
  6. Kapoor  A, Kumar  A, Simmonds  P, Bhuva  N, Singh  CL, Lee  B, Virome Analysis of transfusion recipients reveals a novel human virus that shares genomic features with hepaciviruses and pegiviruses. MBio. 2015;6:e0146615 . DOIPubMedGoogle Scholar
  7. Petty  TJ, Cordey  S, Padioleau  I, Docquier  M, Turin  L, Preynat-Seauve  O, Comprehensive human virus screening using high-throughput sequencing with a user-friendly representation of bioinformatics analysis: a pilot study. J Clin Microbiol. 2014;52:335161. DOIPubMedGoogle Scholar
  8. Li  L, Deng  X, Mee  ET, Collot-Teixeira  S, Anderson  R, Schepelmann  S, Comparing viral metagenomics methods using a highly multiplexed human viral pathogens reagent. J Virol Methods. 2015;213:13946. DOIPubMedGoogle Scholar
  9. Greninger  AL, Naccache  SN, Federman  S, Yu  G, Mbala  P, Bres  V, Rapid metagenomic identification of viral pathogens in clinical samples by real-time nanopore sequencing analysis. Genome Med. 2015;7:99;0220–9.
  10. Hilgartner  MW, Donfield  SM, Willoughby  A, Contant  CF Jr, Evatt  BL, Gomperts  ED, Hemophilia growth and development study. Design, methods, and entry data. Am J Pediatr Hematol Oncol. 1993;15:20818. DOIPubMedGoogle Scholar
  11. SPARTAC Trial Investigators. Fidler S, Porter K, Ewings F, Frater J, Ramjee G, Cooper D, et al. Short-course antiretroviral therapy in primary HIV infection. N Engl J Med. 2013;368:207–17.
  12. Matthews  PC, Adland  E, Listgarten  J, Leslie  A, Mkhwanazi  N, Carlson  JM, HLA-A*7401-mediated control of HIV viremia is independent of its linkage disequilibrium with HLA-B*5703. J Immunol. 2011;186:567586. DOIPubMedGoogle Scholar
  13. Iles  JC, Abby Harrison  GL, Lyons  S, Djoko  CF, Tamoufe  U, Lebreton  M, Hepatitis C virus infections in the Democratic Republic of Congo exhibit a cohort effect. Infect Genet Evol. 2013;19:38694. DOIPubMedGoogle Scholar
  14. Yang  X, Charlebois  P, Gnerre  S, Coole  MG, Lennon  NJ, Levin  JZ, De novo assembly of highly diverse viral populations. BMC Genomics. 2012;13:475. DOIPubMedGoogle Scholar
  15. Simmonds  P. SSE: a nucleotide and amino acid sequence analysis platform. BMC Res Notes. 2012;5:50. DOIPubMedGoogle Scholar
  16. Tamura  K, Stecher  G, Peterson  D, Filipski  A, Kumar  S. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol. 2013;30:27259. DOIPubMedGoogle Scholar
  17. Simmonds  P, Tuplin  A, Evans  DJ. Detection of genome-scale ordered RNA structure (GORS) in genomes of positive-stranded RNA viruses: Implications for virus evolution and host persistence. RNA. 2004;10:133751. DOIPubMedGoogle Scholar
  18. Tavaré  S. Some probabilistic and statistical problems in the analysis of DNA sequences. In: Miura RM, editor. Lectures on mathematics in the life sciences. Volume 17. Providence (RI): American Mathematical Society; 1986. p. 57–86.
  19. Van Vliet  KE, Muir  P, Echevarria  JM, Klapper  PE, Cleator  GM, Van Loon  AM. Multicenter proficiency testing of nucleic acid amplification methods for the detection of enteroviruses. J Clin Microbiol. 2001;39:33902. DOIPubMedGoogle Scholar
  20. Kircher  M, Sawyer  S, Meyer  M. Double indexing overcomes inaccuracies in multiplex sequencing on the Illumina platform. Nucleic Acids Res. 2012;40:e3. DOIPubMedGoogle Scholar
  21. Kwok  S, Higuchi  R. Avoiding false positives with PCR. Nature. 1989;339:2378. DOIPubMedGoogle Scholar
  22. Scallan  MF, Clutterbuck  D, Jarvis  LM, Scott  GR, Simmonds  P. Sexual transmission of GB virus-C/hepatitis G virus. J Med Virol. 1998;55:2038. DOIPubMedGoogle Scholar
  23. Wu  JC, Sheng  WY, Huang  YH, Hwang  SJ, Lee  SD. Prevalence and risk factor analysis of GBV-C/HGV infection in prostitutes. J Med Virol. 1997;52:835. DOIPubMedGoogle Scholar
  24. Rubio  A, Rey  C, Sanchez Quijano  A, Leal  M, Pineda  JA, Lissen  E, Is hepatitis G virus transmitted sexually? JAMA. 1997;277:5323. DOIPubMedGoogle Scholar
  25. Nerurkar  VR, Chua  PK, Hoffmann  PR, Dashwood  WM, Shikuma  CM, Yanagihara  R. High prevalence of GB virus C hepatitis G virus infection among homosexual men infected with human immunodeficiency virus type 1: Evidence for sexual transmission. J Med Virol. 1998;56:1237. DOIPubMedGoogle Scholar
  26. Dawson  GJ, Schlauder  GG. PilotMatias TJ, Thiele D, Leary TP, Murphy P et al. Prevalence studies of GB virus-C infection using reverse transcriptase polymerase chain reaction. J Med Virol. 1996;50:97–103.
  27. Liu  HF, Goderniaux  E, Burtonboy  G, Goubau  P. Molecular analysis of GB virus C/hepatitis G virus in HIV-1–positive intravenous drug users in Belgium. J Hum Virol. 1999;2:11520 .PubMedGoogle Scholar
  28. Davis  M, Sagan  S, Pezacki  J, Evans  DJ, Simmonds  P. Bioinformatic and physical characterisation of genome-scale ordered RNA structure (GORS) in mammalian RNA viruses. J Virol. 2008;82:1182436. DOIPubMedGoogle Scholar
  29. Sharp  CP, Lail  A, Donfield  S, Gomperts  ED, Simmonds  P. Virologic and clinical features of primary infection with human parvovirus 4 in subjects with hemophilia: frequent transmission by virally inactivated clotting factor concentrates. Transfusion. 2012;52:14829. DOIPubMedGoogle Scholar
  30. Matthews  PC, Malik  A, Simmons  R, Sharp  C, Simmonds  P, Klenerman  P. PARV4: an emerging tetraparvovirus. PLoS Pathog. 2014;10:e1004036. DOIPubMedGoogle Scholar

Main Article

Page created: March 15, 2016
Page updated: March 15, 2016
Page reviewed: March 15, 2016
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
file_external