By Dawn Jenkins
Phylogenies, or the historical relationships among organisms, form the backbone of many biological advancements, including the ability to identify the source of a pathogen used to commit a crime. Over the last decade, cases of persons intentionally transmitting HIV have made national headlines. An important piece of these cases has been the admission of phylogenetic analysis, a type of evolutionary analysis that has helped determine the source of transmission in criminal cases in Louisiana, Texas and Washington.
Jeremy Brown, assistant professor of biological sciences and head of LSU’s Computational Phylogenetics, Phylogeography and Molecular Evolution Lab, or Phyleaux Lab, has been awarded a grant from the National Institute of Justice, or NIJ, titled “Extending the Microbial Forensic Toolkit Through Whole-Genome Sequencing and Statistical Phylogenomics.”
In collaboration with Mike Metzker at Baylor College of Medicine, Brown’s Phyleaux team proposes to expand the existing scientific work on HIV forensic studies and develop a “pathogen toolkit” for source identification using whole genome sequences. The toolkit will improve the process of identifying the source of transmitted pathogens using their evolutionary relationships, and provide a foundation for the criminal justice system when attempting to prosecute people who knowingly spread HIV and other deadly diseases.
The application of phylogenetic methods is important from both forensic and medical perspectives. From a forensic standpoint, the phylogenies must be accurate since the outcome of a case may be affected by the genetic evidence, said Brown.
“The ability to rapidly evolve is HIV’s greatest weapon,” he said. “If we ever hope to eradicate the disease, we must understand how the virus evolves and use its evolutionary tendencies against it.”
At the culmination of this project, Brown and his team will be able to provide specific guidelines to forensic scientists regarding which HIV genes to sequence and which statistical methods to apply to effectively test hypotheses about HIV transmission.
In addition to the virus’ extremely high mutation rate, HIV transmission is a perfect test case for microbial forensics due to its rapid response to selection and strict dependence on human hosts. While phylogenetic analysis of the nucleotide variation in specific genes has been used in past forensic studies to assess relationships among pathogens, a large fraction of those genomes remain uncharacterized, ignoring useful information. Additionally, complex evolutionary processes that generate variation in phylogenetic signal across genomes have not been taken into account. These processes include host-specific responses, recombination, and convergent selection. The Phyleaux team plans to use this neglected information to create the “toolkit,” making identification of pathogen sources easier and more accurate.
Brown points out that phylogenetics is not limited to infectious diseases, but could also reveal the history of a cancerous tumor’s formation. Brown also recognizes that his hard-working team of students has been, and continues to be, absolutely critical to the research process.
“My students and postdoc are the driving force behind our current work on HIV transmission. They have really come together as a team and their interactions have generated some insights that I don’t think any of us would have reached on our own,” said Brown.
The LSU phyleauxgenetics team includes Vinson Doyle, postdoctoral researcher who recently received his Ph.D. from the City University of New York; Brad Nelson, graduate student in the Department of Biological Sciences; Sarah Davis, Board of Regents SURE undergraduate majoring in animal science & technology; John Andersen, Ph.D. student in the Department of Biological Sciences; Kristen Jones and Mason Westmoreland, undergraduate students majoring in biochemistry; and Zach Davis and Jacob Peoples, undergraduate students majoring in biology.