The pilot study of the features of HIV-1 resistant variants spread using molecular clusters
Introduction. As a result of routine testing of HIV-1 drug resistance (DR), a significant amount of viral nucleotide sequences and epidemiological data of HIV-infected individuals have been collected. Combined with the increasing use of bioinformatics methods in practice, it has become possible to s...
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| Format: | Article |
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Central Research Institute for Epidemiology
2024-11-01
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| Series: | Журнал микробиологии, эпидемиологии и иммунобиологии |
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| Online Access: | https://microbiol.crie.ru/jour/article/viewFile/18680/1515 |
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| author | Alina A. Kirichenko Dmitry E. Kireev Yulia N. Sidorina Natalia D. Abashina Elena E. Brusentseva Vasily G. Akimkin |
| author_facet | Alina A. Kirichenko Dmitry E. Kireev Yulia N. Sidorina Natalia D. Abashina Elena E. Brusentseva Vasily G. Akimkin |
| author_sort | Alina A. Kirichenko |
| collection | DOAJ |
| description | Introduction. As a result of routine testing of HIV-1 drug resistance (DR), a significant amount of viral nucleotide sequences and epidemiological data of HIV-infected individuals have been collected. Combined with the increasing use of bioinformatics methods in practice, it has become possible to study the features of HIV-1 resistant variants spread using molecular clustering analysis.
The aim of the study was to validate the molecular clustering analysis in a pilot region of Russia using a significant number of nucleotide sequences to study the features of the spread of HIV-1 resistant variants.
Materials and methods. HIV-1 nucleotide sequences were obtained from 899 HIV-infected patients who were registered at the Oryol AIDS Center in 2016–2021. HIV-1 genetic variants were determined using the Stanford University database, REGA and HIV BLAST. Resistance mutations and prognostic HIV-1 DR were determined using the Stanford University database. Phylogenetic analysis was carried out using the MEGA program. HIV-1 molecular clusters were identified using Cluster Picker software.
Results. In the pilot region, sub-subtype A6 dominated (85.7%); an increase in the share of CRF63_02A6 was noted. HIV-1 resistance was found in 13.6% of patients without antiretroviral therapy (ART) experience and in 52.0% with ART experience. Molecular clusters were more often formed by HIV-1 nucleotide sequences from ART-naïve patients. HIV-1 DR variants were less likely to fall into molecular clusters. The sources of transmitted mutations were more often patients with ART experience. The most actively and efficiently transmitted mutations were K103N, V179E/T, Y181C and G190S, associated with virus resistance to efavirenz and nevirapine. |
| format | Article |
| id | doaj-art-73b2573588ec4e4d8eb038c84008a04e |
| institution | Kabale University |
| issn | 0372-9311 2686-7613 |
| language | Russian |
| publishDate | 2024-11-01 |
| publisher | Central Research Institute for Epidemiology |
| record_format | Article |
| series | Журнал микробиологии, эпидемиологии и иммунобиологии |
| spelling | doaj-art-73b2573588ec4e4d8eb038c84008a04e2025-01-09T20:09:08ZrusCentral Research Institute for EpidemiologyЖурнал микробиологии, эпидемиологии и иммунобиологии0372-93112686-76132024-11-01101558159310.36233/0372-9311-5652780The pilot study of the features of HIV-1 resistant variants spread using molecular clustersAlina A. Kirichenko0https://orcid.org/0000-0002-7116-0138Dmitry E. Kireev1https://orcid.org/0000-0002-7896-2379Yulia N. Sidorina2https://orcid.org/0009-0003-0888-113XNatalia D. Abashina3https://orcid.org/0009-0007-5078-8026Elena E. Brusentseva4https://orcid.org/0009-0008-8358-6145Vasily G. Akimkin5https://orcid.org/0000-0003-4228-9044Central Research Institute for EpidemiologyCentral Research Institute for EpidemiologyOryol AIDS CenterOryol AIDS CenterOryol AIDS CenterCentral Research Institute for EpidemiologyIntroduction. As a result of routine testing of HIV-1 drug resistance (DR), a significant amount of viral nucleotide sequences and epidemiological data of HIV-infected individuals have been collected. Combined with the increasing use of bioinformatics methods in practice, it has become possible to study the features of HIV-1 resistant variants spread using molecular clustering analysis. The aim of the study was to validate the molecular clustering analysis in a pilot region of Russia using a significant number of nucleotide sequences to study the features of the spread of HIV-1 resistant variants. Materials and methods. HIV-1 nucleotide sequences were obtained from 899 HIV-infected patients who were registered at the Oryol AIDS Center in 2016–2021. HIV-1 genetic variants were determined using the Stanford University database, REGA and HIV BLAST. Resistance mutations and prognostic HIV-1 DR were determined using the Stanford University database. Phylogenetic analysis was carried out using the MEGA program. HIV-1 molecular clusters were identified using Cluster Picker software. Results. In the pilot region, sub-subtype A6 dominated (85.7%); an increase in the share of CRF63_02A6 was noted. HIV-1 resistance was found in 13.6% of patients without antiretroviral therapy (ART) experience and in 52.0% with ART experience. Molecular clusters were more often formed by HIV-1 nucleotide sequences from ART-naïve patients. HIV-1 DR variants were less likely to fall into molecular clusters. The sources of transmitted mutations were more often patients with ART experience. The most actively and efficiently transmitted mutations were K103N, V179E/T, Y181C and G190S, associated with virus resistance to efavirenz and nevirapine.https://microbiol.crie.ru/jour/article/viewFile/18680/1515hiv-1drug resistanceresistance mutationsantiretroviral therapymolecular clusterstransmission clusterssurveillancegenomic surveillance |
| spellingShingle | Alina A. Kirichenko Dmitry E. Kireev Yulia N. Sidorina Natalia D. Abashina Elena E. Brusentseva Vasily G. Akimkin The pilot study of the features of HIV-1 resistant variants spread using molecular clusters Журнал микробиологии, эпидемиологии и иммунобиологии hiv-1 drug resistance resistance mutations antiretroviral therapy molecular clusters transmission clusters surveillance genomic surveillance |
| title | The pilot study of the features of HIV-1 resistant variants spread using molecular clusters |
| title_full | The pilot study of the features of HIV-1 resistant variants spread using molecular clusters |
| title_fullStr | The pilot study of the features of HIV-1 resistant variants spread using molecular clusters |
| title_full_unstemmed | The pilot study of the features of HIV-1 resistant variants spread using molecular clusters |
| title_short | The pilot study of the features of HIV-1 resistant variants spread using molecular clusters |
| title_sort | pilot study of the features of hiv 1 resistant variants spread using molecular clusters |
| topic | hiv-1 drug resistance resistance mutations antiretroviral therapy molecular clusters transmission clusters surveillance genomic surveillance |
| url | https://microbiol.crie.ru/jour/article/viewFile/18680/1515 |
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