Source identification in two criminal cases using phylogenetic analysis of HIV-1 DNA sequences
- 15 November 2010
- journal article
- research article
- Published by Proceedings of the National Academy of Sciences in Proceedings of the National Academy of Sciences of the United States of America
- Vol. 107 (50), 21242-21247
- https://doi.org/10.1073/pnas.1015673107
Abstract
Phylogenetic analysis has been widely used to test the a priori hypothesis of epidemiological clustering in suspected transmission chains of HIV-1. Among studies showing strong support for relatedness between HIV samples obtained from infected individuals, evidence for the direction of transmission between epidemiologically related pairs has been lacking. During transmission of HIV, a genetic bottleneck occurs, resulting in the paraphyly of source viruses with respect to those of the recipient. This paraphyly establishes the direction of transmission, from which the source can then be inferred. Here, we present methods and results from two criminal cases, State of Washington v Anthony Eugene Whitfield, case number 04-1-0617-5 (Superior Court of the State of Washington, Thurston County, 2004) and State of Texas v Philippe Padieu, case numbers 219-82276-07, 219-82277-07, 219-82278-07, 219-82279-07, 219-82280-07, and 219-82705-07 (219th Judicial District Court, Collin County, TX, 2009), which provided evidence that direction can be established from blinded case samples. The observed paraphyly from each case study led to the identification of an inferred source (i.e., index case), whose identity was revealed at trial to be that of the defendant.Keywords
This publication has 41 references indexed in Scilit:
- Mechanisms of change in gene copy numberNature Reviews Genetics, 2009
- Quantitating the Multiplicity of Infection with Human Immunodeficiency Virus Type 1 Subtype C Reveals a Non-Poisson Distribution of Transmitted VariantsJournal of Virology, 2009
- The emerging role of nuclear architecture in DNA repair and genome maintenanceNature Reviews Molecular Cell Biology, 2009
- The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian InferenceSystematic Biology, 2009
- Identification and characterization of transmitted and early founder virus envelopes in primary HIV-1 infectionProceedings of the National Academy of Sciences of the United States of America, 2008
- HIV phylogeneticsBMJ, 2007
- Encoded evidence: DNA in forensic analysisNature Reviews Genetics, 2004
- HIV-1 Dynamics in Vivo: Virion Clearance Rate, Infected Cell Life-Span, and Viral Generation TimeScience, 1996
- Rapid turnover of plasma virions and CD4 lymphocytes in HIV-1 infectionNature, 1995
- Viral dynamics in human immunodeficiency virus type 1 infectionNature, 1995