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

• Published in: Journal of microbiology, immunology and infection immunology and infection, 2021-08, Vol.54 (4), p.596-605
• Main Authors: Li, Wei-You, Huang, Szu-Wei, Wang, Sheng-Fan, Liu, Hsin-Fu, Chou, Chih-Hung, Wu, Shang-Jung, Huang, Hsien-Da, Lu, Po-Liang, Fann, Cathy S.J., Chen, Marcelo, Chen, Yen-Hsu, Chen, Yi-Ming Arthur
• Format: Article
• Language: English
• Subjects: Bayes Theorem; Forensic science; High-Throughput Nucleotide Sequencing - methods; HIV Infections - transmission; HIV Infections - virology; HIV-1; HIV-1 - classification; HIV-1 - genetics; HIV-1 - isolation & purification; Humans; Intention; Jurisprudence; Phylogenetic tree analysis; Phylogeny; RNA, Viral - genetics; Taiwan; Ultra-deep pyrosequencing
• ISSN: 1684-1182; 1995-9133
• DOI: 10.1016/j.jmii.2019.12.002

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. 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. 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. 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.