HIV Genotyping and Phylogenetic Analysis in the System of Virological Monitoring of HIV Infection
The aim of the study was to assess the possibility and effectiveness of using modern molecular-genetic technologies in determining the source of infection and cause-effect relationships in the epidemic focus of HIV infection.
Materials and Methods. Two samples of blood plasma from HIV-positive persons of the tested group and 18 samples from the infected patients of the comparison group have been genotyped. 13 genetically close nucleotide sequences of HIV genome from the GenBank sequence database were also used in our work.
ABI Prism 3100 and ABI 3500XL genetic analyzers (Applied Biosystems, USA), ViroSeq HIV-1 genotyping system (Abbott, USA), and AmpliSense HIV-Resist-Seq reagent kit (Central Research Institute of Epidemiology of Rospotrebnadzor, Russia) were used for genotyping. Subtyping is done online using COMET HIV-1/2 and HCV software and REGA HIV-1 Sybtyping Tool program (v. 3.0). Phylogenetic analysis and calculation of genetic distance were carried out using MEGA 5.2 program, Maximum Likelihood Estimation method, and the Kimura model (bootstrap level 1000).
Results. All examined viral isolates were found to belong to HIV-1 subtype A (A6). The conducted phylogenetic analysis showed that the samples of the tested group were not collected in a separate cluster, for each of them genetically close samples from the comparison group were found. The distance between the nucleotide sequences of the tested group samples was 0.050; but it varied from 0.007 to 0.058 (average 0.032) between the nucleotide sequences of the 2 samples from the tested group and the samples from the comparison group. The distance equal to 0.007 has been found to be between the nucleotide sequences of sample No.1048 of the tested group and sample No.1051 from the comparison group which indicated a high degree of their genetic proximity, confirming the presence of the epidemiological link between them.
Conclusion. The molecular genetic examination did not confirm the genetic relationship between the samples of the tested group. The results obtained were grounds for refusal to make a diagnosis of occupational HIV infection.
The application of modern technologies in the monitoring of HIV infection has demonstrated their practical significance and efficacy.
- Shakhgildyan V.I., Yadrikhinskaya M.S., Safonova A.P., Domonova E.A., Shipulina O.Yu., Alvares-Figeroa M.V., Dolgova E.A., Tishkevich O.A. Pattern of secondary diseases and current approaches to their laboratory diagnosis in patients with HIV infection. Epidemiologiya i infektsionnye bolezni. Aktual’nye voprosy 2015; 1: 24–30.
- Pis’mo Rospotrebnadzora ot 25.11.2014 g. No.01/13850-14-27 “O merakh po preduprezhdeniyu infitsirovaniya VICh pri okazanii meditsinskoy pomoshchi” [Letter of the Rospotrebnadzor dated November 25, 2014 No.01/13850-14-27 “On measures to prevent HIV infection in the provision of medical care”].
- Zaytseva N.N., Efimov E.I., Nosov N.N., Parfenova O.V., Peksheva O.Yu. Modern molecular genetics research methods in epidemiological surveillance of HIV infection. Medial’ 2014; 2(12): 122–134.
- Federal Service for Supervision of the Consumer Rights and Human Well-Being. Metodicheskie ukazaniya MU 3.1.3342-16 “Epidemiologicheskiy nadzor za VICh-infektsiey” [Methodical instructions MU 3.1.3342-16 “Epidemiological surveillance of HIV infection”]. Moscow; 2016. URL: http://www.garant.ru/products/ipo/prime/doc/71263114/.
- VICh-infektsiya i SPID: natsional’noe rukovodstvo [HIV infection and AIDS: a national guide]. Pod red. V.V. Pokrovskogo [Pokrovskiy V.V. (editor)]. Moscow: GEOTAR-Media; 2013; 608 p.
- 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 cases of HIV infection. Epidemiologiya i infektsionnye bolezni 2014; 19(1): 17–21.
