Genetic diversity of Vif protein in human immunodeficiency virus type 1 variants (Retroviridae: Orthoretrovirinae: Lentivirus: Human immunodeficiency virus-1) that circulated in the Moscow region in 2019–2020

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Abstract

Introduction. The Vif protein counteracts cellular deaminases, APOBEC3, which prevent viral replication. Vif is used for development of therapeutic agents. Natural polymorphisms in Vif can affect its functionality and may be associated with accelerated progression of HIV-infection to the AIDS. The study of Vif features in HIV-1 variants circulating in Russia has not been conducted previously.

The aim of the study: to study the genetic diversity of Vif in the HIV-1 variants that circulated in the Moscow region in 2019–2020.

Materials and methods. 234 whole blood samples obtained from HIV-infected patients without experience of therapy were analyzed. The study design included the following stages: extraction of proviral DNA, amplification of the vif gene, sequencing, identification of genetic variants, followed by a study of consensus sequences of the most common genetic variants of HIV-1, analysis of the conservation and genetic diversity of Vif-A6 (Vif protein of HIV-1 sub-subtype A6 variants) in patients with different stages of the disease, and assessment of genetic diversity of Vif-A6 in the Moscow region.

Results. A high degree of genetic diversity of vif gene was revealed. Consensus sequences of Vif in B and CRF63_02A6 variants were obtained for the first time. Characteristic substitutions in the consensus sequences were determined for the most common HIV-1 variants.

Conclusion. The limitation of this study is the small sample of B and CRF63_02A6. The results obtained may be of interest and may be taken into account in the development of therapeutic agents based on the Vif protein, as well as in the study of the pathogenicity of HIV-1 sub-subtype A6.

About the authors

Anastasiia A. Antonova

D.I. Ivanovsky Institute of Virology of National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya

Email: anastaseika95@mail.ru
ORCID iD: 0000-0002-9180-9846

PhD, Researcher, Laboratory of T-lymphotropic viruses

Russian Federation, 123098, Moscow

Larisa A. Protasova

D.I. Ivanovsky Institute of Virology of National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya

Email: larisa.protasova.03@mail.ru
ORCID iD: 0009-0001-0430-1578

research assistant, Laboratory of T-lymphotropic viruses

Russian Federation, 123098, Moscow

Kristina V. Kim

D.I. Ivanovsky Institute of Virology of National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya

Email: kimsya99@gmail.com
ORCID iD: 0000-0002-4150-2280

junior researcher, Laboratory of T-lymphotropic viruses

Russian Federation, 123098, Moscow

Iana M. Munchak

D.I. Ivanovsky Institute of Virology of National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya

Email: yana_munchak@mail.ru
ORCID iD: 0000-0002-4792-8928

junior researcher, Laboratory of T-lymphotropic viruses

Russian Federation, 123098, Moscow

Ekaterina N. Mezhenskaya

D.I. Ivanovsky Institute of Virology of National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya

Email: belokopytova.01@mail.ru
ORCID iD: 0000-0002-3110-0843

PhD, Researcher, Laboratory of T-lymphotropic viruses

Russian Federation, 123098, Moscow

Elena A. Orlova-Morozova

Center for the Prevention and Control of AIDS and Infectious Diseases

Email: orlovamorozova@gmail.com
ORCID iD: 0000-0003-2495-6501

PhD, Head of outpatient department

Russian Federation, 140053, Moscow region, Kotelniki

Alexander Yu. Pronin

Center for the Prevention and Control of AIDS and Infectious Diseases

Email: alexanderp909@gmail.com
ORCID iD: 0000-0001-9268-4929

PhD, Chief Physician

Russian Federation, 140053, Moscow region, Kotelniki

Alexey G. Prilipov

D.I. Ivanovsky Institute of Virology of National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya

Email: a_prilipov@mail.ru
ORCID iD: 0000-0001-8755-1419

Doctor of Biological Sciences, leading researcher, head of the laboratory of molecular genetics

Russian Federation, 123098, Moscow

Anna I. Kuznetsova

D.I. Ivanovsky Institute of Virology of National Research Center for Epidemiology and Microbiology named after Honorary Academician N.F. Gamaleya

Author for correspondence.
Email: a-myznikova@list.ru
ORCID iD: 0000-0001-5299-3081

Head of laboratory of T-lymphotropic viruses, PhD, leading researcher

Russian Federation, 123098, Moscow

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Supplementary files

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2. Fig. 1. Schematic representation of functional motifs in the Vif protein

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3. Fig. 2. Phylogenetic analysis of nucleotide sequences of the HIV-1 vif gene (n = 257, nucleotide substitution model – GTR + I + G4).

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4. Fig. 3. Consensus sequences of Vif HIV-1 genetic variants most frequently encountered in Russia. The dots indicate amino acid residues (a.a.r.) positions in which the a.a.r. in the consensus corresponded to the reference.

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5. Fig. 4. Conservation of amino acid sequences of the Vif sub-subtype A6 protein in groups of patients with different stages of the disease.

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Copyright (c) 2025 Antonova A.A., Protasova L.A., Kim K.V., Munchak I.M., Mezhenskaya E.N., Orlova-Morozova E.A., Pronin A.Y., Prilipov A.G., Kuznetsova A.I.

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