Analysis of molecular clusters for assessing the HIV infection epidemic in Altai Krai in 2017-2024
Objective. Molecular cluster analysis (MC analysis) of genomic nucleotide sequences of varying lengths in HIV-1 samples collected in Altai Krai in 2017 and 2022–2024, using different genetic distance thresholds.Lapovok I.A., Kirichenko A.A. , Bayandina S.V., Syrkina A.V., Fomina D.V., Shlykova A.V., Lukyanenko N.V., Asmanova M.A., Safyanova T.V., Safronova A.E., Shevchenko V.V., Kireev D.E.
Materials and methods. A total of 364 nucleotide sequences of the HIV-1 pol gene in samples obtained from people living with HIV (PLHIV) in Altai Krai in 2022–2024. and 82 previously published HIV-1 sample sequences obtained in 2017 were analyzed. Genotyping of nucleotide sequences, phylogenetic analysis, and MK analysis were performed for sequences of different lengths using genetic distance thresholds of 1.5 and 0.5%.
Results. The main HIV-1 genetic variant in the studied collection was CRF63_02A6 (74.22%). A total of 16 clusters were identified, of which only 3 included pairs of samples obtained from PLHIV from different vulnerable groups. For two PLHIV, information on the vulnerable group was clarified. Analysis of longer sequences yielded more reliable results.
Conclusion. Using the analysis of HIV-1 samples from Altai Krai, the effectiveness of molecular cluster analysis for supplementing data on the HIV epidemic in the region was demonstrated. However, there is a need for a more comprehensive analysis of HIV-1 genetic variants in this region using collections of HIV-1 samples continuously collected over a long period.
Keywords
HIV-1
MK analysis
genetic variant
genetic distance
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About the Authors
Ilya A. Lapovok, Cand. Biol. Sci., Senior Researcher, Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being, Moscow, Russia; i_lapovok@mail.ru;https://orcid.org/0000-0002-6328-1415Alina A. Kirichenko, Cand. Med. Sci, Senior Researcher, Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being, Moscow, Russia; kirichenko@cmd.su, https://orcid.org/0000-0002-7116-0138
Svetlana V. Bayandina, Junior Researcher, Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being, Moscow, Russia; bayandina@cmd.su; https://orcid.org/0009-0008-7211-568X
Arina V. Syrkina, Junior Researcher, Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being, Moscow, Russia; syrkina@cmd.su; https://orcid.org/0009-0003-2733-6663
Daria V. Fomina, Cand. Med. Sci., Researcher, Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being; Senior Researcherя, State Research Center – A.I. Burnazyan Federal Medical Biophysical Center of the Federal Medical-Biological Agency of Russia, Moscow, Russia, dasha_saleeva@inbox.ru, http://orcid.org/0000-0002-5870-5594
Anastasia V. Shlykova, Researcher, Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being, Moscow, Russia, murzakova_a.v@mail.ru; https://orcid.org/0000-0002-1390-8021
Professor Natalya V. Lukyanenko, MD, Professor, Department of Epidemiology, Altai State Medical University, Ministry of Health of the Russia, Barnaul, Russia; natvalluk@mail.ru; https://orcid.org/0000-0002-0003-5145
Maria A. Asmanova, Cand. Med. Sci., Associate Professor, Department of Epidemiology, Altai State Medical University, Ministry of Health of the Russia, Barnaul, Russia, latmaria@mail.ru, https://orcid.org/0000-0003-2515-4658
Professor Tatyana V. Safyanova, MD, Head, Department of Epidemiology, Altai State Medical University, Ministry of Health of the Russia, Barnaul, Russia, tvsafyanova@yandex.ru, https://orcid.org/0000-0003-3293-4265
Arina E. Safronova, Lecturer, Department of Epidemiology, Altai State Medical University, Ministry of Health of the Russia, Barnaul, Russia, safariev00@mail.ru, https://orcid.org/0009-0009-7350-6073
Valery V. Shevchenko, Cand. Med. Sci., Chief Freelance Infectiologist, Main Department for Healthcare and Pharmaceutical Activities of Altai Krai; Associate Professor, Altai State Medical University, Ministry of Health of the Russia; Chief Physician, Altai Regional Center for Prevention and Control of AIDS and Infectious Diseases, Barnaul, Russia, infecgepatit@yandex.ru, https://orcid.org/0000-0001-6282-5495
Dmitry E. Kireev, MD, Head, Laboratory of HIV Diagnostics and Molecular Epidemiology, Central Research Institute of Epidemiology, Russian Federal Service for Supervision of Consumer Rights Protection and Human Well-Being, Moscow, Russia, dmitkireev@yandex.ru, https://orcid.org/0000-0002-7896-2379
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