Genetic diversity of the human immunodeficiency virus (HIV-1) in the Kaliningrad region

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Abstract

Introduction. As is currently known, the epidemic process in the Kaliningrad Region was mainly associated with the spread of the recombinant form of HIV-1 (CRF03_AB); however, regular HIV importations from other countries and continents has created favorable conditions for emergence and spread of various recombinant forms of the virus.

The most complete information on the diversity of recombinant forms in the region is also necessary to understand the structure of drug resistance (DR).

The aim of the study was to explore the HIV-1 genetic diversity in the Kaliningrad Region.

Materials and methods. We studied 162 blood plasma samples obtained from patients from the Kaliningrad Region, both with confirmed virological failure of antiretroviral therapy (ART) and with newly diagnosed HIV infection. For reverse transcription and amplification of HIV genome fragments, diagnostic «AmpliSense HIVResist-Seq».

Results and discussion. The various recombinants between subtypes A and B (74%) were predominant in study group: recombinant was between CRF03_AB and subtype A (33.95%) and CRF03_AB-like (13.58%) were the most common. Among the “pure” subtypes of the virus, subtype A6 (16.67%). The circulation of subtypes B (3.70%) and G (1.23%) was also noted.

Ninety-six patients (59.26%) were identified with at least one mutation associated with antiretroviral (ARV) drug resistance.

Conclusion. The observed diversity of subtypes and recombinant forms of the virus implies that the new recombinants are actively emerging in the studied region, both between existing recombinant forms and “pure” subtypes, as well as between “pure” subtypes.

About the authors

Alexander N. Shchemelev

FBSI «Saint Petersburg Pasteur Research Institute of Epidemiology and Microbiology» of the Federal Service for Surveillance of Consumer Rights Protection and Human Welfare (Rospotrebnadzor)

Author for correspondence.
Email: tvildorm@gmail.com
ORCID iD: 0000-0002-3139-3674

Junior Researcher, Laboratory of Immunology and Virology of HIV Infection, St. Petersburg Pasteur Research Institute of Epidemiology and Microbiology, Federal Service for Supervision of Consumer Rights Protection and Human Welfare (Rospotrebnadzor)

Russian Federation, 197101, St. Petersburg

Aleksandr V. Semenov

Ekaterinburg Research Institute of Viral Infections of the Federal Research Institute, State Research Center for Virology and Biotechnology “Vector” of the Consumer Rights Protection and Human Welfare (Rospotrebnadzor)

Email: tvildorm@gmail.com
ORCID iD: 0000-0003-3223-8219
Russian Federation, 620030 Ekaterinburg

Yulia V. Ostankova

FBSI «Saint Petersburg Pasteur Research Institute of Epidemiology and Microbiology» of the Federal Service for Surveillance of Consumer Rights Protection and Human Welfare (Rospotrebnadzor)

Email: tvildorm@gmail.com
ORCID iD: 0000-0003-2270-8897
Russian Federation, 197101, St. Petersburg

Ekaterina V. Naidenova

FSSI Russian Research Anti-Plague Institute «Microbe» of the Federal Service for Surveillance of Consumer Rights Protection and Human Welfare (Rospotrebnadzor)

Email: tvildorm@gmail.com
ORCID iD: 0000-0001-6474-3696
Russian Federation, 410005, Saratov

Elena B. Zueva

FBSI «Saint Petersburg Pasteur Research Institute of Epidemiology and Microbiology» of the Federal Service for Surveillance of Consumer Rights Protection and Human Welfare (Rospotrebnadzor)

Email: tvildorm@gmail.com
ORCID iD: 0000-0002-0579-110X
Russian Federation, 197101, St. Petersburg

Diana E. Valutite

FBSI «Saint Petersburg Pasteur Research Institute of Epidemiology and Microbiology» of the Federal Service for Surveillance of Consumer Rights Protection and Human Welfare (Rospotrebnadzor)

Email: tvildorm@gmail.com
ORCID iD: 0000-0002-0931-102X
Russian Federation, 197101, St. Petersburg

Mariia A. Churina

St. Petersburg GBUZ «Botkin Clinical Infectious Diseases Hospital»

Email: tvildorm@gmail.com
ORCID iD: 0000-0003-0424-4654
Russian Federation, 191167, St. Petersburg

Pavel A. Virolainen

FBSI «Saint Petersburg Pasteur Research Institute of Epidemiology and Microbiology» of the Federal Service for Surveillance of Consumer Rights Protection and Human Welfare (Rospotrebnadzor)

Email: tvildorm@gmail.com
ORCID iD: 0000-0001-5918-9395
Russian Federation, 197101, St. Petersburg

Areg A. Totolian

FBSI «Saint Petersburg Pasteur Research Institute of Epidemiology and Microbiology» of the Federal Service for Surveillance of Consumer Rights Protection and Human Welfare (Rospotrebnadzor)

Email: tvildorm@gmail.com
ORCID iD: 0000-0003-4571-8799
Russian Federation, 197101, St. Petersburg

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Supplementary files

Supplementary Files
Action
1. JATS XML
2. Fig. 2. Comparative recombination analysis of samples 2014_80 (CRF03_AB) and 2014_19 (A + B recombinant) in Rega HIV Subtyping Tool v3.0 [21] and Recombinant Identification Program (https://www.hiv.lanl.gov/content/sequence/RIP/RIP.html) a – sample 2014_80 in Rega HIV Subtyping Tool v3.0; b – sample 2014_80 in the Recombinant Identification Program; c – sample 2014_19 in Rega HIV Subtyping Tool v3.0; d – sample 2014_19 in the Recombinant Identification Program [25].

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3. Fig. 3. Results of the study of multiple mutational profiles by constructing line diagrams: a – for NRTI resistance mutations; b – for NNRTI resistance mutations.

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4. Fig. 1. Results of phylogenetic analysis using the Neighbor Joining algorithm. • – reference sequences (table 2); ▲ – recombinant forms between subtypes A and B, not clustered with other recombinants of this group.

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5. Fig. 2. Comparative recombination analysis of samples 2014_80 (CRF03_AB) and 2014_19 (A + B recombinant) in Rega HIV Subtyping Tool v3.0 [21] and Recombinant Identification Program (https://www.hiv.lanl.gov/content/sequence/RIP/RIP.html) a – sample 2014_80 in Rega HIV Subtyping Tool v3.0; b – sample 2014_80 in the Recombinant Identification Program; c – sample 2014_19 in Rega HIV Subtyping Tool v3.0; d – sample 2014_19 in the Recombinant Identification Program [25].

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6. Fig. 3. Results of the study of multiple mutational profiles by constructing line diagrams: a – for NRTI resistance mutations; b – for NNRTI resistance mutations.

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Copyright (c) 2022 Shchemelev A.N., Semenov A.V., Ostankova Y.V., Naidenova E.V., Zueva E.B., Valutite D.E., Churina M.A., Virolainen P.A., Totolian A.A.

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