HIV-1 Subtype Distribution Determined by Phylogenetic Analysis of pol Gene Sequences and Automated Subtyping Tools among HIV-1 Isolates from the Aegian Region of Turkey

Biçeroğlu, Servet Uluer; Altuğlu, İmre; Zeka, Arzu Nazlı; Gökengin, Deniz; Sertöz, Rüçhan

doi:10.5578/mb.7609

Cited by 3 publications

(2 citation statements)

References 17 publications

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“…Alttip dağılımı, CRF/CPX çeşit-liliği ve sayısındaki artışa karşın, daha önce yapılan çalışmalarla uyumlu görünmekte; ancak daha ayrıntılı analiz ve sürekli takip gerektirmektedir. Afrika, eski Sovyetler Birliği Cumhuriyetleri ve Doğu Avrupa ile bağlantılı olabilecek sonuçlar, ülkemizdeki HIV epidemisinin karmaşıklığına işaret etmektedir 15,[21][22][23] . Rehberlerde ART'ye başlanmadan önce direnç testi yapılması önerilmektedir 4 8 4-8 .…”

Section: Discussionunclassified

“…HIV-1 alttipleri, MEGA 5.2 programı kullanılarak alttip referans dizileri ve NeighbourJoining yöntemiyle oluşturulan fi logenetik ağaçla tanımlandı (Tablo II) 13,14 . İlk aşamada Los Alamos referans dizileri ile tanımlanamayan ve iki ayrı grup oluşturan dizilerden ilk grup, Gen Bankasından JN882655 dizisinin referans dizisi olarak eklenmesiyle rekombinant B/CRF02_AG olarak belirlendi 15 . İkinci grupta yer alan diziler REGA otomatize HIV-1 alttipleme aracıyla rekombinant B, F1 olarak tanımlandı 16 .…”

Section: Mi̇krobi̇yoloji̇ Bülteni̇unclassified

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Investigation of HIV-1 Primary Drug Resistance Mutations in Antiretroviral Therapy-Naive Cases

Yalçinkaya¹,

Köse²

2014

Mikrobiyol Bul

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Section: Discussionunclassified

Section: Mi̇krobi̇yoloji̇ Bülteni̇unclassified

Investigation of HIV-1 Primary Drug Resistance Mutations in Antiretroviral Therapy-Naive Cases

Yalçinkaya¹,

Köse²

2014

Mikrobiyol Bul

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Molecular Epidemiology of HIV-1 Subtypes and Primary Antiretroviral Resistance Profiles in Northern Cyprus: First Data Series

Guler,

Arikan,

Sultanoglu

et al. 2024

AIDS Research and Human Retroviruses

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Diversity of HIV-1 Subtypes and Transmitted Drug-resistance Mutations Among Minority HIV-1 Variants in a Turkish Cohort

Sarınoğlu

Sili

Hasdemir

et al. 2022

CHR

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Background: The World Health Organization (WHO) recommends the surveillance of transmitted drug resistance mutations (TDRMs) to ensure the effectiveness and sustainability of HIV treatment programs. Objective: Our aim was to determine the TDRMs and evaluate the distribution of HIV-1 subtypes using and compared next-generation sequencing (NGS) and Sanger-based sequencing (SBS) in a cohort of 44 antiretroviral treatment-naïve patients. Methods: All samples that were referred to the microbiology laboratory for HIV drug resistance analysis between December 2016 and February 2018 were included in the study. After exclusions, 44 treatment-naive adult patients with a viral load of >1000 copies/mL were analyzed. DNA sequencing for reverse transcriptase and protease regions was performed using both DeepChek ABL single round kit and Sanger-based ViroSeq HIV-1 Genotyping System. The mutations and HIV-1 subtypes were analyzed using the Stanford HIVdb version 8.6.1 Genotypic Resistance software, and TDRMs were assessed using the WHO surveillance drug-resistance mutation database. HIV-1 subtypes were confirmed by constructing a maximum-likelihood phylogenetic tree using Los Alamos IQ-Tree software. Results: NGS identified nucleos(t)ide reverse transcriptase inhibitor (NRTI)-TDRMs in 9.1% of the patients, non-nucleos(t)ide reverse transcriptase inhibitor (NNRTI)-TDRMs in 6.8% of the patients, and protease inhibitor (PI)-TDRMs in 18.2% of the patients at a detection threshold of ≥1%. Using SBS, 2.3% and 6.8% of the patients were found to have NRTI- and NNRTI-TDRMs, respectively, but no major PI mutations were detected. M41L, L74I, K65R, M184V, and M184I related to NRTI, K103N to NNRTI, and N83D, M46I, I84V, V82A, L24I, L90M, I54V to the PI sites were identified using NGS. Most mutations were found in low-abundance (frequency range: 1.0% - 4.7%) HIV-1 variants, except M41L and K103N. The subtypes of the isolates were found as follows; 61.4% subtype B, 18.2% subtype B/CRF02_AG recombinant, 13.6% subtype A, 4.5% CRF43_02G, and 2.3% CRF02_AG. All TDRMs, except K65R, were detected in HIV-1 subtype B isolates.. Conclusion: The high diversity of protease site TDRMs in the minority HIV-1 variants and prevalence of CRFs were remarkable in this study. All minority HIV-1 variants were missed by conventional sequencing. TDRM prevalence among minority variants appears to be decreasing over time at our center.

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HIV-1 Subtype Distribution Determined by Phylogenetic Analysis of pol Gene Sequences and Automated Subtyping Tools among HIV-1 Isolates from the Aegian Region of Turkey

Cited by 3 publications

References 17 publications

Investigation of HIV-1 Primary Drug Resistance Mutations in Antiretroviral Therapy-Naive Cases

Investigation of HIV-1 Primary Drug Resistance Mutations in Antiretroviral Therapy-Naive Cases

Molecular Epidemiology of HIV-1 Subtypes and Primary Antiretroviral Resistance Profiles in Northern Cyprus: First Data Series

Diversity of HIV-1 Subtypes and Transmitted Drug-resistance Mutations Among Minority HIV-1 Variants in a Turkish Cohort

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