Variability of non-structural proteins of HIV-1 sub-subtype A6 (Retroviridae: Orthoretrovirinae: Lentivirus: Human immunodeficiency virus-1, sub-subtype A6) variants circulating in different regions of the Russian Federation

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Abstract

Introduction. HIV-1 non-structural proteins are promising targets for vaccine development and for creating approaches to personalized medicine. HIV-1 sub-subtype A6 has become the dominating strain in Russia. However, the geographic, economic and demographic characteristics of the country can contribute to the formation of differences between A6 variants circulating in different regions.

The aim of the study is a comparative analysis of the consensus sequences of non-structural proteins in A6 variants circulating in the Amur Region, in Arkhangelsk, Irkutsk and Murmansk.

Materials and methods. 48 whole blood samples obtained from HIV-infected patients without experience of therapy observed at the AIDS Centers in Arkhangelsk, Irkutsk, Murmansk and Amur Region were analyzed. HIV-1 whole-genome nucleotide sequences were obtained and were subtyped. Consensus sequences of sub-subtype A6 variants non-structural proteins for each analyzed region were formed. Furthermore, reference sequences of sub-subtype A6 non-structural proteins were formed based on whole-genome sequences retrieved from the international Los Alamos database. Comparison of consensus sequences and references was performed using the MEGA v.10.2.2 and the PSIPRED programs.

Results. Vif, Vpr and Nef reference sequences have been obtained for HIV-1 sub-subtype A6. There was not difference in consensus sequences of Vpr in different regions. Characteristic features were found for consensus sequences of Tat, Rev, Vpu, Vif and Nef proteins in different regions.

Conclusion. A limitation of the study is a small sample size. Overall, the results demonstrate the existing diversity of non-structural proteins in sub-subtype A6 variants in different regions and indicate the relevance of studying the polymorphism of non-structural proteins of virus variants in different regions.

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Introduction

The genome of human immunodeficiency virus type 1 (HIV-1) (Retroviridae: Orthoretrovirinae: Lentivirus: Human immunodeficiency virus-1) encodes 6 non-structural proteins: Tat, Rev, Vpu, Vif, Vpr, Nef. The non-structural proteins create the necessary conditions for virus replication and protect the virus from the host immune system [1]. Earlier studies have shown that HIV-1 nonstructural proteins contain epitopes that can be used for vaccine development [2–4]. It was observed that immunization with Tat protein-based constructs promoted restoration of CD4-cell levels and reduction of viral reservoirs [5]. At present, the development of new approaches to stimulate immune response based on non-structural proteins is ongoing [6–8]. In this regard, studying the variability of HIV-1 non-structural proteins is an important objective and provides a basis for such developments. Furthermore, amino acid substitutions have been identified in HIV-1 nonstructural proteins that are associated with both changes in the rate of HIV infection and the development of comorbid diseases in HIV-1-infected patients [1]. Thus, studying the diversity of HIV-1 nonstructural proteins may also become a platform for the development of personalized medicine approaches.

The molecular epidemiology of HIV-1 in Russia has its own characteristic features. Initially, the active spread of HIV infection in Russia was associated with the introduction of the sub-subtype A6 virus among injecting drug users (IDUs) in the 1990s and its subsequent rapid spread within this social group in all regions of the country [9]. A gradual decline in the proportion of IDUs in the HIV-infected population in the Russian Federation was then noted, with a simultaneous increase in the number of cases of transmission through heterosexual contacts [10]. Currently, sub-subtype A6 remains the dominant (82.9%) genetic variant of HIV-1 in Russia, but there is a constant increase in the genetic diversity of the virus [11, 12].

The epidemic process of HIV infection on the territory of the Russian Federation is of great interest and is caused by a number of peculiarities of the country: Russia is the 1st largest country in the world in terms of territory size, it is a multinational and multi-confessional country, which determines the difference in cultures and behavior, lifestyle and mobility patterns of the population. Furthermore, our country borders 18 states, has numerous transportation corridors, which contributes to high genetic diversity and rapid spread of HIV-1 due to migration processes [13, 14]. Thus, it was noted that the proportion and diversity of circulating non-A6 variants can differ significantly between different federal districts of the Russian Federation [12]. It is likely that the geographical location, peculiarities of socioeconomic development of the region and population composition can also influence the selection of circulating genetic variants of the virus within sub-subtype A6.

Taking into account the above, we hypothesized that nonstructural proteins may differ among HIV-1 variants of sub-subtype A6 circulating in different regions of the Russian Federation. To date, there have been no studies on the diversity of nonstructural proteins of HIV-1 sub-subtype A6 variants circulating in different regions of Russia.

The aim of this study was to comparatively analyze the consensus sequences of non-structural HIV-1 sub-subtype A6 proteins in virus variants circulating in different regions of Russia: Amur region, Arkhangelsk, Irkutsk and Murmansk.

Materials and methods

Clinical whole blood samples obtained from 48 ART-naïve (antiretroviral therapy), HIV-infected patients from the following regions of Russia: Amur region, Arkhangelsk, Irkutsk and Murmansk served as the material of the present study (Table 1). Blood was collected from patients once in 2012–2014 within the framework of the CHAIN project of the 7th Framework Program of the European Community «Single Network for Antiretroviral Drug Resistance Research» (https://cordis.europa.eu/project/id/223131). All obtained clinical material was used with the informed consent of the patients based on the permission of the Ethical Committee State Research Center of Virology and Biotechnology VECTOR on March 30, 2010.

 

Table 1. Characteristics of HIV-1 infected patients included in the study

Таблица 1. Характеристики ВИЧ-1-инфицированных пациентов, включенных в исследование

Region

Регион

Number of patients

Число пациентов

Date of sampling

Год забора образца

Sex

Пол

Age

Возраст

Route of infection

Путь инфицирования

Stage of HIV-infection*

Стадия заболевания*

male

муж.

female

жен.

IDU

ПИН

hetero

гетеро

2

3

4

unknown

неизвестно

Amur Region

Амурская область

10

2012

8

2

30,8 (18–41)

4

6

4

5

1

Arkhangelsk

Архангельск

12

2013

3

9

30,3 (18–42)

5

7

1

10

1

Murmansk

Мурманск

13

2013–2014

6

7

33 (26–42)

10

3

5

8

Irkutsk

Иркутск

13

2012

10

3

31,9 (23–49)

10

3

7

6

Note. *In according to clinical recommendation [15].

Примечание. *В соответствии с клиническими рекомендациями [15].

 

Samples were analyzed by mass parallel sequencing using the AmpliSense HIV-Resist-NGS kit according to the manufacturer’s instructions (Central Research Institute of Epidemiology of Rospotrebnadzor, Russia). Whole-genome sequencing of samples was performed using MiSeq technology and appropriate MiSeq reagent kits V2 (Illumina, USA) by analyzing 4 overlapping specific fragments (total length of the analyzed fragment 704-9563 by HXB2).

Genetic variants of the obtained whole-genome sequences were determined using the Comet program (https://comet.lih.lu). Pairwise and multiple alignment of nucleotide sequences was performed using the MEGA v.10.2.2. program (megasoftware.net), then the regions encoding the corresponding analyzed HIV-1 nonstructural proteins (Tat, Rev, Vpu, Vif, Vpr, Nef) were excised from the obtained alignments. Phylogenetic analysis was performed for all tat, rev, vpu, vif, vpr, nef gene sequences. Phylogenetic analysis was performed using the Maximum Likelihood (ML) method using the IQ-TREE program (http://www.iqtree.org). The source of reference sequences was the database of the Los Alamos Laboratory, USA (https://www.hiv.lanl.gov/). The nucleotide substitution model was determined in the jModelTest v.2.1.7 program based on the Akaike information criterion (AIC). The model with the lowest criterion value was considered the most appropriate model for further analysis. The validity of the inferred phylogenies was assessed using bootstrap test (bootstrap) and Shimodaira-Hasegawa approximate likelihood ratio test (SH-aLRT) with 1000 post-start iterations. Clusters with SH-aLRT support > 0.9 were considered to be reliably established. Visualization and graphical processing of the results of phylogenetic analysis were performed in the iTOL program (https://itol.embl.de).

In the next step of the study, the obtained nucleotide sequences were translated into amino acid sequences using an online translation tool available at https://www.bioinformatics.org/sms2/translate.html. Then, using the Simple Consensus Maker tool (https://www.hiv.lanl.gov/content/sequence/CONSENSUS/SimpCon.html), consensus sequences for each nonstructural protein (Tat, Rev,Vpu, Vif, Vpr, Nef) for each RF region were generated based on the obtained amino acid sequences.

For further comparative analysis of consensus sequences, reference sequences for each protein were additionally generated. For this purpose, all available whole-genome sequences of HIV-1 sub-subtype A6 (235 sequences as of 08/13/2024) were downloaded from the Los Alamos international database (Main Search Interface of HIV Sequence Database (lanl.gov)). The sequence sample contained no duplicates: only one sequence from a single patient. For each protein, amino acid and nucleotide sequences were simultaneously downloaded. Then, for each protein analyzed, the nucleotide and amino acid sequences were compared with each other in MEGA v.10.2.2. software (megasoftware.net). Sequences encoding an incomplete protein were removed from the analysis. Insertions were not considered in the generation of reference sequences. Reference sequences for each nonstructural protein (Tat, Rev,Vpu, Vif, Vpr, Nef) were generated using the Simple Consensus Maker tool (https://www.hiv.lanl.gov/content/sequence/CONSENSUS/SimpCon.html) based on amino acid sequences.

Further comparison of the obtained reference and consensus sequences was performed using the MEGA v.10.2.2 program. The positions of amino acids (a.a.) in the consensus sequences that contained amino acid substitutions relative to the reference sequences were determined.

Next, we compared the secondary structures of the consensus sequences obtained for each region with the reference sequences of the analyzed HIV-1 proteins using the PSIPRED program (http://bioinf.cs.ucl.ac.uk/psipred/).

Results

All nucleotide sequences (48) obtained in this study were deposited in the GenBank international genotype database under the following numbers (Table 2).

 

Table 2. GenBank accession numbers for the HIV-1 nucleotide sequences used in the work

Таблица 2. Регистрационные номера GenBank использованных в работе нуклеотидных последовательностей ВИЧ-1

Region of the Russian Federation

Регион РФ

GenBank accession numbers for sequences

Номера последовательностей GenBank

Amur region

Амурская область

MH330347, MH330348, MH330349, MH330350, MH330351, MH330352, MH330353, MH330354, MH330355, MH330356

Arkhangelsk

Архангельск

MG902950, MG902951, MH330337, MH330338, MH330339, MH330340, MH330341, MH330342, MH330343, MH330344, MH330345, MH330346

Murmansk

Мурманск

MH330370, PP816220, MH330371, MH330372, MH330373, MH330374, MH330375, MH330376, MH330377, MH330378, MH330379, MH330380, MH330381

Irkutsk

Иркутск

MH330357, MH330358, MH330359, PP816221, MH330361, PP816222, MH330363, MH330364, MH330365, PP816223, MH330367, PP816224, PP816225

 

According to the results of preliminary subtyping, all nucleotide sequences analyzed belonged to HIV-1 sub-subtype A6. The phylogenetic analysis confirmed the results of preliminary subtyping (Fig. 1).

 

Fig. 1. Phylogenetic analysis of the obtained sequences: tat (A), rev (B), vpu (C), vif (D), vpr (E), nef (F).

Clusters of the most typical HIV-1 genetic variants for the territory of the Russian Federation are marked in color on the phylogenetic trees: pink – HIV-1 sub-subtype A6, blue – subtype B, light green – circulating recombinant forms CRF02_AG and CRF63_02A6; a cluster formed by the reference sequences of HIV-1 sub-subtype A1 is also marked. Within the HIV-1 sub-subtype A6 cluster, the reference sequences are shown in red, the studied sequences are shown in black; all other clusters of HIV-1 of other genetic variants (A1, C, D, F1, F2, G) include exclusively reference sequences (HIV Databases (lanl.gov).

Рис. 1. Филогенетический анализ полученных последовательностей: tat (A), rev (B), vpu (C), vif (D), vpr (E), nef (F).

Цветом на филогенетических деревьях отмечены кластеры наиболее характерных для территории РФ генетических вариантов ВИЧ-1: розовым цветом – ВИЧ-1 суб-субтипа A6, голубым – субтипа B, салатовым – циркулирующих рекомбинантных форм CRF02_AG и CRF63_02A6; также отмечен кластер, образованный референсными последовательностями ВИЧ-1 суб-субтипа A1. Внутри кластера ВИЧ-1 суб-субтипа A6 референсные последовательности обозначены красным цветом, исследуемые последовательности – черным цветом; все остальные кластеры ВИЧ-1 других генетических вариантов (A1, C, D, F1, F2, G) включают исключительно референсные последовательности (HIV Databases (lanl.gov).

 

At the next stage of the study, consensus amino acid sequences of each HIV-1 nonstructural protein (Tat, Rev, Vpu, Vif, Vpr, Nef) were generated for each region: for the Amur region – based on 10 sequences, for Arkhangelsk – 12 sequences, for Murmansk – 13, for Irkutsk – 13. Insertions (amino acid insertions) were not taken into account in their formation. Table 3 shows all insertions and deletions (point mutations associated with the absence of a.a. at a given position) that were detected during analysis.

 

Table 3. Insertions and deletions of amino acids (a.a.) in the analyzed sequences*

Таблица 3. Инсерции и делеции аминокислот в анализируемых последовательностях*

HIV-1

protein

Белок ВИЧ-1

Amur region

Амурская область

Arkhangelsk

Архангельск

Murmansk

Мурманск

Irkutsk

Иркутск

insertion

(sequence ID)

инсерция

(N посл-ти)

deletion

(sequence ID)

делеция

(N посл-ти)

insertion

(sequence ID)

инсерция

(N посл-ти)

deletion

(sequence ID)

делеция

(N посл-ти)

insertion

(sequence ID)

инсерция

(N пос-ти)

deletion (sequence ID)

делеция

(N посл-ти)

insertion (sequence ID)

инсерция

(N пос-ти)

deletion (sequence ID)

делеция

(N посл-ти)

Tat

79–80insE (MH330380)

54–55insS (MH330364)

Rev

del97–119 (MH330355, (MH330353)

del93–99 (MH330341), del94–115 (MH330339)

33–34insR (MH330380)

8–9insA (MH330364)

del91–97 (MH330358)

Vpu

del77 (PP816220)

7–8insTIV (PP816225)

del5 (PP816223)

Vif

del109–115 (PP816224)

Vpr

del85–86 (MH330345)

84–85insI/M (MH330371)

del85–86 (PP816225)

Nef

25–26insPA (MH330352,

MH330354),

25–26ins

PAASGVE

(MH330355),

63–64insEE (MH330355)

del8–11 (MH330351), del8–11 (MH330355)

25–26insPA (MH330342, MH330343)

Del8–9 (MG902950)

25–26insPA (MH330371), 25–26insP (MH330370), 25–26insPAAGG[G/V] (MH330378),

25–26ins

PXARRAPE

(MH330380),

63–64insE (PP816220, MH330380)

25–26insPAP

(PP816221),

25–26insPA

(PP816225),

25–26insPAA (MH330363),

63–64insE (MH330358)

del8–11 (PP816221, MH330361), del10 (PP816223)

Note. *The locations of insertions and deletions are shown according to the consensus sequence of the corresponding HIV-1 protein.

Примечание. *Расположение инсерций и делеций указано относительно консенсусной последовательности неструктурного белка ВИЧ-1 соответствующего 

 

Afterwards, reference protein sequences were generated based on the sequences retrieved from the Los Alamos international database. Tat, Rev, Vif, and Vpr protein reference sequences were generated based on 235 sequences and had the following lengths: 101 a.a., 123 a.a., 192 a.a., 96 a.a., respectively. The reference sequence of Vpu protein was generated based on 232 sequences and contained 81 a.a. The reference sequence of Nef protein was generated on the basis of 223 sequences and contained 207 a.a. (Fig. 2).

 

Fig. 2. Reference sequences of the proteins Tat, Rev, Vpu, Vif, Vpr, Nef.

Non-polar amino acids: G (glycine), A (alanine), V (valine), L (leucine), I (isoleucine), P (proline), M (methionine) and F (phenylalanine), – are marked in blue; Polar uncharged, neutral, amino acids: S (serine), T (threonine), C (cysteine), N (asparagine), Q (glutamine) and W (tryptophan) – green; polar acidic, negatively charged, amino acids: D (aspartic acid) and E (glutamic acid), Y (tyrosine) – orange; polar basic, positively charged amino acids: K (lysine), R (arginine) and H (histidine) [16].

Рис. 2. Референсные последовательности белков Tat, Rev, Vpu, Vif, Vpr, Nef.

Неполярные аминокислоты: G (глицин), A (аланин), V (валин), L (лейцин), I (изолейцин), P (пролин), M (метионин) и F (фенилаланин) ‒ отмечены синим цветом; полярные незаряженные, нейтральные, аминокислоты: S (серин), T (треонин), C (цистеин), N (аспарагин), Q (глутамин) и W (триптофан) – зеленым; gполярные кислые, отрицательно заряженные, аминокислоты: D (аспарагиновая кислота) и E (глутаминовая кислота), Y (тирозин) – оранжевым; полярные основные, положительно заряженные, аминокислоты: K (лизин), R (аргинин) и H (гистидин) – красным [16].

 

The obtained consensus sequences of nonstructural proteins were compared with reference sequences. Table 4 shows the positions in which the consensus sequences of HIV-1 nonstructural proteins of individual regions of Russia differed from the reference sequences.

 

Table 4. Amino acid substitutions in the consensus sequences of non-structural proteins of virus variants circulating in the Amur Region, Arkhangelsk, Murmansk, and Irkutsk, relative to the reference sequences*

Таблица 4. Аминокислотные замены в консенсусных последовательностях неструктурных белков вариантов вирусов, циркулирующих в Амурской области, гг. Архангельске, Мурманске, Иркутске, относительно референсных последовательностей*

HIV-1 protein

Белок ВИЧ-1

Amur region

Амурская область

Arkhangelsk

Архангельск

Murmansk

Мурманск

Irkutsk

Иркутск

Tat

P68L, R99P/R

P68L

Rev

K39R

K39R, A68E, V109I

K39R, V109I

Vpu

F16S/A

F16F/S/A

L33V

Y73L

Vif

F39V

E37G, R50K, E92E/K, V125V/L

E37G, R50K, E92R, I98I/V, H127Q

E37G,

R50K/R

Vpr

Nef

I10I/L, K179R

R29T,Y82F, E152E/S, K179R

R29T, I134I/E, Y144Y/F, E152D, K179R, T193T/K

R29P/T, G84A, F136Y, K179R, T193K

Note. *R99P/R indicates that the consensus sequence contained amino acids P and R with equal probability at the position. Substitutions associated with changes in the properties of amino acids, charged/uncharged or polar/non-polar, are highlighted in bold.

Примечание. *R99P/R обозначает, что в консенсусной последовательности с равной вероятностью в позиции встречались аминокислоты P и R. Жирным шрифтом выделены замены, ассоциированные с изменениями свойств аминокислот: заряженная/незаряженная, полярная/неполярная.

 

The consensus sequences of protein of virus variants circulating in the analyzed regions did not contain substitutions relative to the reference sequences. Therefore, comparative analysis of the secondary structure of the Vpr protein was not performed in the further study.

The results of predicting the secondary structures of the reference sequences of the analyzed HIV-1 proteins are presented in Table 5.

 

Table 5. Predicted arrangement of helical and strand elements in secondary structures of reference sequences of HIV-1 nonstructural proteins

Таблица 5. Спрогнозированное расположение элементов спиралей и цепей во вторичных структурах референсных последовательностей неструктурных белков ВИЧ-1

Secondary structure type

Тип вторичной структуры

Tat (a.a. position / позиция AК)

Rev (a.a. position / позиция AК)

Vpu (a.a. position / позиция AК)

Vif (a.a. position / позиция AК)

Nef

(a.a. position / позиция AК /)

Helix

Спираль

32–33, 36–39, 86–95

9–24, 35–61

3–52, 61–70

15–31, 78–80, 100–110, 117–124, 145–153

13–21, 38–40,50–51, 57–66, 82–94, 106–110, 151–156, 168–171, 188–192, 196–199, 201–204

Strand

Цепь

4–13, 38–41, 50–59, 63–69, 85–91, 93–97, 128–129

102–104, 111–118, 142–148, 181–186

 

Similarly, the secondary structures of consensus sequences of non-structural protein sequences of HIV-1 sub-subtype A6 variants circulating in the analyzed regions of Russia were predicted.

When comparing the predicted secondary structures of consensus sequences with reference sequences, the following differences were found:

‒ a shift of the helix location from position 86–95 to position 85-94 was detected for the Tat protein variant, characteristic of HIV-1 sub-subtype A6 in the Amur region, containing P68L and R99P substitutions;

‒ a shift of the strand location from position 38–41 to position 39–41 was detected for the Vif protein variant, characteristic of HIV-1 sub-subtype A6 in the Amur region. At the same time, a shift in strand location from position 38–41 to position 38–39 was observed for Vif protein variants of HIV-1 sub-subtype A6, circulating in Arkhangelsk, Murmansk, and Irkutsk. Furthermore, a shift of the strand from position 93–97 to position 94–97 was detected for the Vif protein, characteristic of the virus variants in Murmansk, and a lack of strand structure at position 128–129 was found for the Vif protein characteristic of the virus variants in Arkhangelsk;

– a displacement of the helix element from position 13–21 to 14–21 was detected for the Nef protein variants, characteristic of HIV-1 sub-subtype A6 in Arkhangelsk, Murmansk and Irkutsk. Furthermore, a shift of the helix element from position 57–66 to 56–66 was detected for the Nef protein variant of the virus characteristic of Arkhangelsk.

Discussion

Currently, studies of the HIV-1 pol gene are regularly conducted in Russia both in virus variants circulating in individual regions [17–19] and in the whole country [11, 12, 20]. This is explained by the fact that inhibitors of viral enzymes, integrase, protease, and reverse transcriptase, which are encoded by the pol gene [1, 15], are mainly used to treat HIV infection. Accordingly, most antiretroviral drug resistance mutations occur in the pol gene, and the study of this region of the genome is regulated by regulatory documents in clinical practice. Nonstructural protein genes are outside the analyzed region of the genome, and the variability of nonstructural proteins of virus variants circulating in different regions of the country remains unstudied. In a recent study, we showed that some regions of the Tat protein in HIV-1 sub-subtype A6 variants circulating in the Moscow region are less conserved than in the general population of HIV-1 sub-subtype A6 variants [21].

This study was based on the assumption that there is variability in non-structural proteins of HIV-1 sub-subtype A6 variants circulating in different regions of our country. We analyzed the sequences of non-structural proteins of HIV-1 sub-subtype A6 variants obtained by analyzing clinical whole blood samples of naive patients, i.e., those who had not previously received ART, between 2012 and 2014. Patients were under observation at AIDS centers in the Amur region, Arkhangelsk, Murmansk and Irkutsk (Table 1).

When generating consensus sequences for each HIV-1 non-structural protein, sequences containing deletions/insertions were noted (Table 3), with only one sequence (PP816224) containing a deletion (del109–115) in the Vif protein, and the greatest number of deletions/insertions analyzed sequences contained in the Nef protein (Table 3). This result can be explained by the fact that the main function of the Vif protein is to counteract the cellular protein APOBEG3G, whereas the Nef protein has multiple activities and contacts more host cell proteins, which, accordingly, implies a more flexible structure [1].

Reference sequences of HIV-1 sub-subtype A6 non-structural proteins were generated from 235 whole-genome sequences downloaded from the Los Alamos International Database.

The generated Tat protein reference sequence contained histidine (H) at position 54 and 60, glycine (G) at position 57, and the 78QRD80 motif characteristic of HIV-1 sub-subtype A6 [21, 22].

The generated Rev protein reference sequence contained glutamine (Q) at position 41 and, after position 95, a QSQGTET motif characteristic of HIV-1 sub-subtype A6 [23].

The generated Vpu protein reference sequence relative to the previously published Vpu sub-subtype A6 sequence contained tyrosine (Y) instead of leucine (L) at position 73 [24].

The reference sequences of Vif, Vpr, and Nef proteins of HIV-1 sub-subtype A6 were generated and presented for the first time.

Despite the variability characteristic of Vpr protein in the COOH-terminal region reported earlier, the consensus sequences of Vpr protein from different regions of the Russian Federation did not contain substitutions relative to the reference sequence [25].

The consensus sequences of Tat, Rev, Vpu, Vif, and Nef proteins differed from the reference sequences and differed among themselves by the presence of characteristic amino acid substitutions. Some of the identified amino acid substitutions were associated with changes in the chemical properties of the amino acids, and changes in the secondary structure of the protein relative to the reference sequences were detected for Tat, Vif, and Nef proteins.

The results obtained indicate the existence of differences in non-structural proteins in HIV-1 sub-subtype A6 variants, circulating in different regions of the Russian Federation, which can be explained by the founder effect.

This study has a limitation due to the small sample of analyzed sequences. To confirm the results obtained, it is necessary to conduct further studies of the polymorphism of non-structural proteins of HIV-1 sub-subtype A6 variants, circulating in different regions of the country.

Conclusion

A comparative analysis of consensus sequences of non-structural proteins of HIV-1 sub-subtype A6 variants circulating in different regions of the Russian Federation was performed for the first time. The reference sequences of Vif, Vpr, and Nef proteins of HIV-1 sub-subtype A6 were obtained and presented for the first time. The Vpr protein was determined to be the most conserved. In summary, the results obtained indicate the presence of peculiarities in non-structural proteins of HIV-1 sub-subtype A6 variants in different regions of Russia.

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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 in Biology, Researcher, Laboratory of T-lymphotropic viruses

Россия, 123098, Moscow

Aleksey V. Lebedev

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

Email: lebedevalesha236@gmail.com
ORCID iD: 0000-0001-6787-9345

PhD in Biology, Researcher, Laboratory of T-lymphotropic viruses

Россия, 123098, Moscow

Ekaterina N. Ozhmegova

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 in Biology, Researcher, Laboratory of T-lymphotropic viruses

Россия, 123098, Moscow

Anastasia V. Shlykova

Central Research Institute of Epidemiology

Email: murzakova_a.v@mail.ru
ORCID iD: 0000-0002-1390-8021

Researcher, Central Research Institute of Epidemiology

Россия, Moscow, 111123

Ilya A. Lapavok

Central Research Institute of Epidemiology

Email: i_lapovok@mail.ru
ORCID iD: 0000-0002-6328-1415

PhD in Biology, Senior researcher

Россия, Moscow, 111123

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

PhD in Biology, Leading Researcher, Head of Laboratory of T-lymphotropic viruses

Россия, 123098, Moscow

References

  1. Kuznetsova A.I. The role of HIV-1 polymorphism in the pathogenesis of the disease. VICh-infektsiya i immunosupressii. 2023; 15(3): 26–37. https://doi.org/10.22328/2077-9828-2023-15-3-26-37 https://elibrary.ru/cwjjai (in Russian)
  2. Frahm N., Korber B.T., Adams C.M., Szinger J.J., Draenert R., Addo M.M., et al. Consistent cytotoxic-T-lymphocyte targeting of immunodominant regions in human immunodeficiency virus across multiple ethnicities. J. Virol. 2004; 78(5): 2187–200. https://doi.org/10.1128/jvi.78.5.2187-2200.2004
  3. Mothe B., Hu X., Llano A., Rosati M., Olvera A., Kulkarni V., et al. A human immune data-informed vaccine concept elicits strong and broad T-cell specificities associated with HIV-1 control in mice and macaques. J. Transl. Med. 2015; 13: 60. https://doi.org/10.1186/s12967-015-0392-5
  4. Frahm N., Kiepiela P., Adams S., Linde C.H., Hewitt H.S., Sango K., et al. Control of human immunodeficiency virus replication by cytotoxic T lymphocytes targeting subdominant epitopes. Nat. Immunol. 2006; 7(2): 173–8. https://doi.org/10.1038/ni1281
  5. Sgadari C., Monini P., Tripiciano A., Picconi O., Casabianca A., Orlandi C., et al. Continued decay of HIV proviral DNA upon vaccination with HIV-1 Tat of subjects on long-term ART: An 8-year follow-up study. Front. Immunol. 2019; 10: 233. https://doi.org/10.3389/fimmu.2019.00233
  6. Kardani K., Hashemi A., Bolhassani A. Comparison of HIV-1 Vif and Vpu accessory proteins for delivery of polyepitope constructs harboring Nef, Gp160 and P24 using various cell penetrating peptides. PLoS One. 2019; 14(10): e0223844. https://doi.org/10.1371/journal.pone.0223844
  7. Kardani K., Hashemi A., Bolhassani A. Comparative analysis of two HIV-1 multiepitope polypeptides for stimulation of immune responses in BALB/c mice. Mol. Immunol. 2020; 119: 106–22. https://doi.org/10.1016/j.molimm.2020.01.013
  8. Sadeghi L., Bolhassani A., Mohit E., Baesi K., Aghasadeghi M.R. Heterologous DNA prime/protein boost immunization targeting Nef-Tat fusion antigen induces potent T-cell activity and in vitro anti-SCR HIV-1 effects. Curr. HIV Res. 2024; 22(2): 109–19. https://doi.org/10.2174/011570162X297602240430142231
  9. Lapovok I.A., Lopatukhin A.E., Kireev D.E., Kazennova E.V., Lebedev A.V., Bobkova M.R., et al. Molecular epidemiological analysis of HIV-1 variants circulating in Russia in 1987-2015. Terapevticheskii arkhiv. 2017; 89(11): 44–9. https://doi.org/10.17116/terarkh2017891144-49 https://elibrary.ru/zwosol (in Russian)
  10. Adgamov R.R., Antonova A.A., Ogarkova D.A., Kuznetsova A.I., Pochtovyi A.A., Kleimenov D.A., et al. HIV-infection in the Russian Federation: current diagnostic trends. VICh-infektsiya i immunosupressii. 2024; 16(1): 45–59. https://doi.org/10.22328/2077-9828-2024-16-1-45-59 https://elibrary.ru/rlhujr (in Russian)
  11. Antonova A.A., Kuznetsova A.I., Ozhmegova E.N., Lebedev A.V., Kazennova E.V., Kim K.V., et al. Genetic diversity of HIV-1 at the current stage of the epidemic in the Russian Federation: an increase in the prevalence of recombinant forms. VICh-infektsiya i immunosupressii. 2023; 15(3): 61–72. https://doi.org/10.22328/2077-9828-2023-15-3-61-72 https://elibrary.ru/tpwttn (in Russian)
  12. Antonova A., Kazennova E., Lebedev A., Ozhmegova E., Kuznetsova A., Tumanov A., et al. Recombinant forms of HIV-1 in the last decade of the epidemic in the Russian Federation. Viruses. 2023; 15(12): 2312. https://doi.org/10.3390/v15122312
  13. Grishina E.A. Features of the geographical position of the Russian Federation. Theory and practice of solving complex tasks of the State Final Attestation in Geography. Vestnik nauki i obrazovaniya. 2019; (6-1): 38–42. https://elibrary.ru/zbmuep (in Russian)
  14. Ivshina I.N. Multi-nationality and multi-religiousness as social and cultural prerequisites for the federalization of Russia. Vestnik MGPU. Seriya: Yuridicheskie nauki. 2018; (4): 19–24. https://doi.org/10.25688/2076-9113.2018.32.4.02 https://elibrary.ru/ypwurf (in Russian)
  15. The Rubricator of Clinical Recommendations. Clinical guidelines. HIV infection in adults. Available at: Available at: https://cr.minzdrav.gov.ru/schema/79_1 (in Russian)
  16. Yakubke Kh.D., Eshkait Kh. Amino acids. Peptides. Proteins [Aminokisloty. Peptidy. Belki]. Moscow: Mir; 1985. (in Russian)
  17. Shchemelev A.N., Semenov A.V., Ostankova Yu.V., Naidenova E.V., Zueva E.B., Valutite D.E., et al. Genetic diversity of the human immunodeficiency virus (HIV-1) in the Kaliningrad region. Voprosy virusologii. 2022; 67(4): 310–21. https://doi.org/10.36233/0507-4088-119 https://elibrary.ru/bkswno (in Russian)
  18. Lebedev A., Lebedeva N., Moskaleychik F., Pronin A., Kazennova E., Bobkova M. Human immunodeficiency virus-1 diversity in the Moscow Region, Russia: Phylodynamics of the most common subtypes. Front. Microbiol. 2019; 10: 320. https://doi.org/10.3389/fmicb.2019.00320
  19. Antonova A.A., Tumanov A.S., Lebedev A.V., Kazennova E.V., Glinkina L.N., Kulagin V.V., et al. Genetic profile and characteristics of HIV-1 drug resistance mutation in the Krasnodar region over the 2014 to 2019. VICh-infektsiya i immunosupressii. 2022; 14(2): 20–30. https://doi.org/10.22328/2077-9828-2022-14-2-20-30 https://elibrary.ru/vzklej (in Russian)
  20. Kirichenko A., Kireev D., Lapovok I., Shlykova A., Lopatukhin A., Pokrovskaya A., et al. HIV-1 drug resistance among treatment-naïve patients in Russia: analysis of the national database, 2006–2022. Viruses. 2023; 15(4): 991. https://doi.org/10.3390/v15040991
  21. Kuznetsova A., Kim K., Tumanov A., Munchak I., Antonova A., Lebedev A., et al. Features of Tat protein in HIV-1 sub-subtype A6 variants circulating in the Moscow region, Russia. Viruses. 2023; 15(11): 2212. https://doi.org/10.3390/v15112212
  22. Kuznetsova A.I., Gromov K.B., Kireev D.E., Shlykova A.V., Lopatukhin A.E., Kazennova E.V., et al. Analysis of tat protein characteristics in human immunodeficiency virus type 1 sub-subtype A6 (Retroviridae: Orthoretrovirinae: lentivirus: human immunodeficiency virus-1). Voprosy virusologii. 2021; 66(6): 452–63. https://doi.org/10.36233/0507-4088-83 https://elibrary.ru/cmzgyc (in Russian)
  23. Lebedev A., Kim K., Ozhmegova E., Antonova A., Kazennova E., Tumanov A., et al. Rev protein diversity in HIV-1 group M clades. Viruses. 2024; 16(5): 759. https://doi.org/10.3390/v16050759
  24. Antonova A.A., Lebedev A.V., Kazennova E.V., Kim K.V., Ozhmegova E.N., Tumanov A.S., et al. Variability of VPU protein in HIV-1 sub-subtype A6 in patients with different stages of HIV infection. VICh-infektsiya i immunosupressii. 2024; 16(2): 40–50. https://doi.org/10.22328/2077-9828-2024-16-2-40-50 https://elibrary.ru/lpjxqk (in Russian)
  25. Lapovok I.A. Analysis of polymorphism of non-structural regions in the genome of the HIV-1 variant dominant in Russia: Diss. Moscow; 2009. https://elibrary.ru/nkranl (in Russian)

Supplementary files

Supplementary Files
Action
1. JATS XML
2. Fig. 1. Phylogenetic analysis of the obtained sequences: tat (A), rev (B), vpu (C), vif (D), vpr (E), nef (F). Clusters of the most typical HIV-1 genetic variants for the territory of the Russian Federation are marked in color on the phylogenetic trees: pink – HIV-1 sub-subtype A6, blue – subtype B, light green – circulating recombinant forms CRF02_AG and CRF63_02A6; a cluster formed by the reference sequences of HIV-1 sub-subtype A1 is also marked. Within the HIV-1 sub-subtype A6 cluster, the reference sequences are shown in red, the studied sequences are shown in black; all other clusters of HIV-1 of other genetic variants (A1, C, D, F1, F2, G) include exclusively reference sequences (HIV Databases (lanl.gov).

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3. Fig. 2. Reference sequences of the proteins Tat, Rev, Vpu, Vif, Vpr, Nef. Non-polar amino acids: G (glycine), A (alanine), V (valine), L (leucine), I (isoleucine), P (proline), M (methionine) and F (phenylalanine), – are marked in blue; Polar uncharged, neutral, amino acids: S (serine), T (threonine), C (cysteine), N (asparagine), Q (glutamine) and W (tryptophan) – green; polar acidic, negatively charged, amino acids: D (aspartic acid) and E (glutamic acid), Y (tyrosine) – orange; polar basic, positively charged amino acids: K (lysine), R (arginine) and H (histidine) [16].

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Copyright (c) 2024 Antonova A.A., Lebedev A.V., Ozhmegova E.N., Shlykova A.V., Lapavok I.A., Kuznetsova A.I.

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