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

Journal of General Virology

Volumn 95, Issue PART 1, 2014, Pages 66-70

  Edwards, Victoria C ^a   Patrick McClure, C ^a   Brown, Richard J P ^a   Thompson, Emma ^b   Irving, William L ^a   Ball, Jonathan K ^a  

^a UNIVERSITY OF NOTTINGHAM   (United Kingdom)

^b MRC UNIVERSITY OF GLASGOW CENTRE FOR VIRUS RESEARCH   (United Kingdom)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CLINICAL ARTICLE; CONTROLLED STUDY; DNA FINGERPRINTING; DNA FLANKING REGION; EGYPT; HEALTH CARE PERSONNEL; HEPATITIS C; HEPATITIS C VIRUS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS INFECTION; MALE; MIXED INFECTION; MOLECULAR EPIDEMIOLOGY; NONHUMAN; PHYLOGENY; PRIORITY JOURNAL; SEQUENCE ANALYSIS; SHORT TANDEM REPEAT; VALIDATION STUDY;

EID: 84890277181     PISSN: 00221317     EISSN: 14652099     Source Type: Journal    
DOI: 10.1099/vir.0.057828-0     Document Type: Article

References (15)

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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
11. Ramia, S. & Eid-Fares, J. (2006). Distribution of hepatitis C virus genotypes in the Middle East. Int J Infect Dis 10, 272-277.
12. Saitou, N. & Nei, M. (1987). The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 4, 406-425.
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.
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.
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.