Use of short tandem repeat fingerprinting to validate sample origins in hepatitis C virus molecular epidemiology studies Open Access

Abstract

Sequence analysis is used to define the molecular epidemiology and evolution of the hepatitis C virus. Whilst most studies have shown that individual patients harbour viruses that are derived from a limited number of highly related strains, some recent reports have shown that some patients can be co-infected with very distinct variants whose frequency can fluctuate greatly. Whilst co-infection with highly divergent strains is possible, an alternative explanation is that such data represent contamination or sample mix-up. In this study, we have shown that DNA fingerprinting techniques can accurately assess sample provenance and differentiate between samples that are truly exhibiting mixed infection from those that harbour distinct virus populations due to sample mix-up. We have argued that this approach should be adopted routinely in virus sequence analyses to validate sample provenance.

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2014-01-01
2024-03-29
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References

  1. Ahmed A., Linacre A. M. T., Mohammed A. A. A., Vanezis P., Goodwin W. 2001; STR population data for 10 STR loci including the GenePrint PowerPlex 1.2 kit from El-Minia (Central Egypt). Forensic Sci Int 117:233–234 [View Article][PubMed]
    [Google Scholar]
  2. Brown R. J., Hudson N., Wilson G., Rehman S. U., Jabbari S., Hu K., Tarr A. W., Borrow P., Joyce M.other authors 2012; Hepatitis C virus envelope glycoprotein fitness defines virus population composition following transmission to a new host. J Virol 86:11956–11966 [View Article][PubMed]
    [Google Scholar]
  3. Bull R. A., Luciani F., McElroy K., Gaudieri S., Pham S. T., Chopra A., Cameron B., Maher L., Dore G. J.other authors 2011; Sequential bottlenecks drive viral evolution in early acute hepatitis C virus infection. PLoS Pathog 7:e1002243 [View Article][PubMed]
    [Google Scholar]
  4. Butler J. M. 2006; Genetics and genomics of core short tandem repeat loci used in human identity testing. J Forensic Sci 51:253–265 [View Article][PubMed]
    [Google Scholar]
  5. Butler J. M., Shen Y., McCord B. R. 2003; The development of reduced size STR amplicons as tools for analysis of degraded DNA. J Forensic Sci 48:1054–1064[PubMed]
    [Google Scholar]
  6. Dusheiko G., Schmilovitz-Weiss H., Brown D., McOmish F., Yap P.-L., Sherlock S., McIntyre N., Simmonds P. 1994; Hepatitis C virus genotypes: an investigation of type-specific differences in geographic origin and disease. Hepatology 19:13–18 [View Article][PubMed]
    [Google Scholar]
  7. Gross A. M., Liberty A. A., Ulland M. M., Kuriger J. K. 2008; Internal validation of the AmpFlSTR Yfiler amplification kit for use in forensic casework. J Forensic Sci 53:125–134 [View Article][PubMed]
    [Google Scholar]
  8. Klintschar M., al-Hammadi N., Reichenpfader B. 1999; Population genetic studies on the tetrameric short tandem repeat loci D3S1358, VWA, FGA, D8S1179, D21S11, D18S51, D5S818, D13S317 and D7S820 in Egypt. Forensic Sci Int 104:23–31 [View Article][PubMed]
    [Google Scholar]
  9. Li H., Stoddard M. B., Wang S., Blair L. M., Giorgi E. E., Parrish E. H., Learn G. H., Hraber P., Goepfert P. A.other authors 2012; Elucidation of hepatitis C virus transmission and early diversification by single genome sequencing. PLoS Pathog 8:e1002880 [View Article][PubMed]
    [Google Scholar]
  10. Opel K. L., Chung D. T., Drábek J., Butler J. M., McCord B. R. 2007; Developmental validation of reduced-size STR Miniplex primer sets. J Forensic Sci 52:1263–1271 [View Article][PubMed]
    [Google Scholar]
  11. Ramia S., Eid-Fares J. 2006; Distribution of hepatitis C virus genotypes in the Middle East. Int J Infect Dis 10:272–277 [View Article][PubMed]
    [Google Scholar]
  12. Saitou N., Nei M. 1987; The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4:406–425[PubMed]
    [Google Scholar]
  13. Smith J. A., Aberle J. H., Fleming V. M., Ferenci P., Thomson E. C., Karayiannis P., McLean A. R., Holzmann H., Klenerman P. 2010; Dynamic coinfection with multiple viral subtypes in acute hepatitis C. J Infect Dis 202:1770–1779 [View Article][PubMed]
    [Google Scholar]
  14. Tamura K., Dudley J., Nei M., Kumar S. 2007; MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 24:1596–1599 [View Article][PubMed]
    [Google Scholar]
  15. Wang G. P., Sherrill-Mix S. A., Chang K.-M., Quince C., Bushman F. D. 2010; Hepatitis C virus transmission bottlenecks analyzed by deep sequencing. J Virol 84:6218–6228 [View Article][PubMed]
    [Google Scholar]
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