Experience in Utilization of Phylogenetic Analysis for Epidemiological Investigation of HIV Infection Case

Objective of the study was to investigate a criminal case of infection with HIV, applying molecular-genetic analysis of blood plasma samples from an estimated source of an infection and the recipient for evaluation of probability of epidemiological connection between them. Materials and methods. The study involved genotyping and phylogenetic analysis of nucleotide sequences of HIV-1 variants, isolated from patients in the investigated group and the control one (19 nucleotide sequences of the HIV-1 from the patients living in the Saratov region, and 15 nucleotide sequences from GenBank). Genotyping was performed using the commercial ViroSeq HIV-1 Genotyping System. The sub-typing of HIV-1 strains was carried out on-line, through the COMET HIV-1/2 and HCV and REGA HIV-1 Sybtyping Tool programs. Phylogenetic analysis of nucleotide sequences was carried out by Mega software, version 5.2. Phylogenetic trees were constructed; nucleotide distances were calculated by Kimura method (bootstrap level 1000). Results and conclusions. Virus variants, isolated from the studied samples, were defined as HIV-1 A subtype. Performed phylogenetic analysis showed that nucleotide sequences of the studied samples authentically grouped on the phylogenetic tree, forming a common cluster, which mismatched that of control group. Calculation of the genetic distance testifies that the genetic relation between the samples within the investigated group is higher, than between the same samples and those of the control group. Thus, by means of phylogenetic analysis it is shown that the strains received from an estimated source of infection and the recipient are genetically closer to each other, than to the strains from the group of comparison. In this regard, it is possible to claim with a big share of confidence that probability of epidemiological connection between them exists.

заражение ВИЧ-инфекцией, эпидемиологическое расследование, филогенетический анализ, генетическая дистанция, группа сравнения, infection with HIV, epidemiological investigation, phylogenetic analysis, genetic distance, control group

1. Neshumaev D.A., Tat’yanina E.A., Malysheva M.A., Shevchenko N.M., Kokotyukha Yu.A., Meyrmanova E.M., Vinogradova M.N., Ulanova T.I., Zagryadskaya Yu.E. [Experience in shared use of phylogenetic analysis and infection prescription specification in the investigation of a hospitalacquired HIV infection]. In: [Proceedings of the VIII All-Russian Conference with International Participation “Molecular Diagnostics – 2014”]. M.; 2014. Vol. 1. P. 64–5.

2. Sandyreva T.P., Gerasimova N.A., Lopatukhin A.E., Kireev D.E., Kuevda D.A., Shipulin G.A., Podymova A.S. [Phylogenetic analysis in epidemiological investigations of HIV-infection cases]. Epidemiol. Infek. Bol. 2014; 1:17–21.

3. Sandyreva T.P., Gerasimova N.A., Podymova A.S. [Moleculargenetic methods within the system of epidemiological diagnostics of HIV-infection]. In: [Proceedings of the VIII All-Russian Conference with International Participation “Molecular Diagnostics – 2014”]. M.; 2014. Vol. 1. P. 41–2.