Analysis of HIV-1 (Human immunodeficiency virus-1, Lentivirus, Orthoretrovirinae, Retroviridae) Nef protein polymorphism of variants circulating in the former USSR countries

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Abstract

Introduction. The human immunodeficiency virus (HIV) Nef protein is one of the key factors determining the infectivity and replicative properties of HIV. With the ability to interact with numerous proteins of the host cell, this protein provides the maximum level of virus production and protects it from the immune system. The main activities of Nef are associated with a decrease in the expression of the CD4 receptor and major histocompatibility complex class I molecules (MHC-I), as well as the rearrangement of the cytoskeleton. These properties of the protein are determined by the structure of several motifs in the structure of the nef gene encoding it, which is quite variable.
Goals and tasks. The main goal of the work was to analyze the characteristics of Nef protein of HIV-1 variant A6, which dominates in the countries of the former USSR. The objective of the work was a comparative analysis of natural polymorphisms in the nef gene of HIV-1 sub-subtypes A6 and A1 and subtype B.
Material and methods. The sequences of the HIV-1 genome obtained during the previous work of the laboratory were used, as well as the reference sequence from GenBank. In this work, Sanger sequencing and new generation sequencing methods, as well as bioinformation analysis methods were used.
Results and discussion. The existence of noticeable differences in the prevalence of Nef natural polymorphisms (A32P, E38D, I43V, A54D, Q104K, H116N, Y120F, Y143F, V168M, H192T, V194R, R35Q, D108E, Y135F, E155K, E182M, R184K and F191L), some of which are characteristic mutations for variant A6, was shown. Conclusion. Characteristic substitutions were found in the Nef structure, potentially capable of weakening the replicative properties of HIV-1 variant A6.

About the authors

K. B. Gromov

National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya

Email: fake@neicon.ru
ORCID iD: 0000-0002-9316-1975
Moscow, 123098 Russian Federation

E. V. Kazennova

National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya

Email: fake@neicon.ru
ORCID iD: 0000-0002-7896-2379
Moscow, 123098 Russian Federation

D. E. Kireev

Central Research Institute of Epidemiology

Email: fake@neicon.ru
ORCID iD: 0000-0002-1390-8021
Moscow, 111123 Russian Federation

A. V. Murzakova

Central Research Institute of Epidemiology

Email: fake@neicon.ru
ORCID iD: 0000-0002-2826-699X
Moscow, 111123 Russian Federation

A. E. Lopatukhin

Central Research Institute of Epidemiology

Email: fake@neicon.ru
ORCID iD: 0000-0002-7912-4270
Moscow, 111123 Russian Federation

M. R. Bobkova

National Research Centre for Epidemiology and Microbiology named after the honorary academician N.F. Gamaleya

Author for correspondence.
Email: mrbobkova@mail.ru
ORCID iD: 0000-0001-5481-8957

MD, PhD, Dr Biol Sci, chirf researcher, head of T-lymphotropoc viruses
laboratory, Ivanovsky Institute of Virology

Moscow, 123098, 18, Gamaleya street, Russia

Russian Federation

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Copyright (c) 2019 Gromov K.B., Kazennova E.V., Kireev D.E., Murzakova A.V., Lopatukhin A.E., Bobkova M.R.

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