Source identification of HIV-1 transmission in three lawsuits Using Ultra-Deep pyrosequencing and phylogenetic analysis

Wei You Li, Szu Wei Huang, Sheng Fan Wang, Hsin Fu Liu, Chih Hung Chou, Shang Jung Wu, Hsien Da Huang, Po Liang Lu, Cathy S.J. Fann, Marcelo Chen, Yen Hsu Chen, Yi Ming Arthur Chen

Research output: Contribution to journalArticlepeer-review

3 Citations (Scopus)


Background/purpose: Intentional transmission of HIV-1 is a crime. Identifying the source of transmission between HIV-1 infected cases using phylogenetic analysis has limitations, including delayed examinations after the initiation of infection and ambiguity of phyletic relationships. This study was the first to introduce phylogenetic tree Results as forensic evidence in a trial in Taiwan. Methods: Three lawsuit cases from different district courts in Taiwan were chosen for this study. We identified the source of transmission between individuals in each lawsuit based on the maximum likelihood and Bayesian phylogenetic tree analyses using the HIV-1 sequences from molecular cloning and ultra-deep pyrosequencing (UDPS). Two gene regions of the HIV genome, env and gag, were involved. Results: The results of phylogenetic analysis using sequences from molecular cloning were clear and evidential enough in lawsuits 1 and 3. Due to the delayed sampling time, the result of sequences from molecular cloning in lawsuit 2 was ambiguous. Combined with the analyzed result of sequences from UDPS and epidemiological information, the source of transmission in lawsuit 2 was further identified. Conclusion: Hence phylogenetic analyses cannot exclude the possibility of unsampled intermediaries, the data interpretation should be more careful and conservative, and it should not be considered as the only evidence for the source identification in a trial without epidemiological or serological information. The evaluation of the introduced UDPS method in the identification of transmission source has shown that the validity and evidential effects were still limited and need further optimization.
Original languageEnglish
Pages (from-to)596-605
Number of pages10
JournalJournal of Microbiology, Immunology and Infection
Issue number4
Publication statusPublished - 2020


  • Forensic science
  • HIV-1
  • Phylogenetic tree analysis
  • Ultra-deep pyrosequencing

ASJC Scopus subject areas

  • Immunology and Allergy
  • General Immunology and Microbiology
  • Microbiology (medical)
  • Infectious Diseases


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