Assessment of Transmitted HIV-1 Drug Resistance Mutations Using Ultra- Deep Pyrosequencing in a Turkish Cohort

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Abstract

Background: Antiretroviral treatment (ART) reduces morbidity and mortality caused by human immunodeficiency virus (HIV) infection; however, the emergence of drug-resistant strains poses an important obstacle to treatment success. Using conventional sequencing methods to determine antiretroviral resistance, mutations present in ≥20% of quasispecies can be identified, but drug-resistant minority variants can lead to virologic failure.

Objective: We aimed to assess transmitted drug resistance mutations (TDRMs) within minority variants using ultra-deep pyrosequencing (UDPS).

Method: Treatment-naive adult patients were included in this observational study. Surveillance TDRMs were classified as ≥20% or at minority variant level (≥2% – <20%). Genotypic sensitivity score calculated by using all pre-treatment drug resistance mutations (PDRMs) was also evaluated.

Results: Thirty-six patients were analyzed. Any TDRM at ≥20% level was detected in 8.3% of the patients (n=3). This prevalence increased to 30.6% (n=11) with the inclusion of minority variants. All non-nucleoside reverse transcriptase inhibitor and protease inhibitor-related TDRMs were within minority variants. The genotypic sensitivity score of rilpivirine-based regimens was considerably diminished when minority variants were included in the PDRM analysis.

Conclusion: UDPS was used for the first time to assess TDRM in a Turkish HIV cohort and uncovered several mutations hidden within minority variants. UDPS may be preferred to detect PDRMs for avoiding virologic failure with rilpivirine-based ART regimens.

Keywords: Antiretroviral drug resistance, human immunodeficiency virus, minority variants, rilpivirine resistance, transmitted drug resistance, ultra-deep pyrosequencing.

Graphical Abstract

[1]
Gunthard HF, Saag MS, Benson CA, et al. Antiretroviral drugs for treatment and prevention of hiv infection in adults: 2016 recommendations of the international antiviral society-usa panel. JAMA 2016; 316(2): 191-210.
[2]
Arts EJ, Hazuda DJ. HIV-1 antiretroviral drug therapy. Cold Spring Harb Perspect Med 2012; 2(4): a007161.
[3]
Beyrer C, Pozniak A. HIV Drug Resistance - an emerging threat to epidemic control. N Engl J Med 2017; 377(17): 1605-7.
[4]
Hirsch MS, Brun-Vezinet F, Clotet B, et al. Antiretroviral drug resistance testing in adults infected with human immunodeficiency virus type 1: 2003 recommendations of an International AIDS Society-USA Panel. Clin Infect Dis 2003; 37(1): 113-28.
[5]
Clutter DS, Jordan MR, Bertagnolio S, Shafer RW. HIV-1 drug resistance and resistance testing. Infect Genet Evol 2016; 46: 292-307.
[6]
Little SJ, Holte S, Routy JP, et al. Antiretroviral-drug resistance among patients recently infected with HIV. N Engl J Med 2002; 347(6): 385-94.
[7]
Panichsillapakit T, Smith DM, Wertheim JO, Richman DD, Little SJ, Mehta SR. Prevalence of transmitted HIV drug resistance among recently infected persons in san diego, CA 1996-2013. J Acquir Immune Defic Syndr 2016; 71(2): 228-36.
[8]
World Health Organization. Surveillance of HIV drug resistance in adults initiating antiretroviral therapy (pre-treatment HIV drug resistance). [Available from: http://www.who.int/hiv/pub/drug resistance/pretreatment_drugresistance/en/Accessed on 8.4.2018].
[9]
Bennett DE, Myatt M, Bertagnolio S, Sutherland D, Gilks CF. Recommendations for surveillance of transmitted HIV drug resistance in countries scaling up antiretroviral treatment. Antivir Ther 2008; 13(Suppl. 2): 25-36.
[10]
Rhee SY, Blanco JL, Jordan MR, et al. Geographic and temporal trends in the molecular epidemiology and genetic mechanisms of transmitted HIV-1 drug resistance: an individual-patient- and sequence-level meta-analysis. PLoS Med 2015; 12(4): e1001810.
[11]
Sanger F, Nicklen S, Coulson AR. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci USA 1977; 74(12): 5463-7.
[12]
Shafer RW. Low-abundance drug-resistant HIV-1 variants: finding significance in an era of abundant diagnostic and therapeutic options. J Infect Dis 2009; 199(5): 610-2.
[13]
Tang MW, Shafer RW. HIV-1 antiretroviral resistance: scientific principles and clinical applications. Drugs 2012; 72(9): e1-e25.
[14]
Simen BB, Simons JF, Hullsiek KH, et al. Low-abundance drug-resistant viral variants in chronically HIV-infected, antiretroviral treatment-naive patients significantly impact treatment outcomes. J Infect Dis 2009; 199(5): 693-701.
[15]
Johnson JA, Li JF, Wei X, et al. Minority HIV-1 drug resistance mutations are present in antiretroviral treatment-naive populations and associate with reduced treatment efficacy. PLoS Med 2008; 5(7): e158.
[16]
Lecossier D, Shulman NS, Morand-Joubert L, et al. Detection of minority populations of HIV-1 expressing the K103N resistance mutation in patients failing nevirapine. Journal of acquired immune deficiency syndromes 2005; 38(1): 37-42.
[17]
Paredes R, Clotet B. Clinical management of HIV-1 resistance. Antiviral Res 2010; 85(1): 245-65.
[18]
Wensing AM, Calvez V, Gunthard HF, et al. 2017 update of the drug resistance mutations in HIV-1. Top Antivir Med 2017; 24(4): 132-3.
[19]
Bennett DE, Camacho RJ, Otelea D, et al. Drug resistance mutations for surveillance of transmitted HIV-1 drug-resistance: 2009 update. PLoS One 2009; 4(3): e4724.
[20]
Dudley DM, Chin EN, Bimber BN, et al. Low-cost ultra-wide genotyping using Roche/454 pyrosequencing for surveillance of HIV drug resistance. PLoS One 2012; 7(5): e36494.
[21]
Tang MW, Liu TF, Shafer RW. The HIVdb system for HIV-1 genotypic resistance interpretation. Intervirology 2012; 55(2): 98-101.
[22]
Nicot F, Saliou A, Raymond S, et al. Minority variants associated with resistance to HIV-1 nonnucleoside reverse transcriptase inhibitors during primary infection. J Clin Virol 2012; 55(2): 107-13.
[23]
Hofstra LM, Sauvageot N, Albert J, et al. Transmission of HIV drug resistance and the predicted effect on current first-line regimens in europe. Clinical infectious diseases: an official publication of the Infectious Diseases Society of America 2016; 62(5): 655-63.
[24]
Boyd MA, Moore CL, Molina JM, et al. Baseline HIV-1 resistance, virological outcomes, and emergent resistance in the SECOND-LINE trial: an exploratory analysis. Lancet HIV 2015; 2(2): e42-51.
[25]
Sayan M, Willke A, Ozgunes N, Sargin F. HIV-1 subtypes and primary antiretroviral resistance mutations in antiretroviral therapy naive HIV-1 infected individuals in Turkey. Jpn J Infect Dis 2013; 66(4): 306-11.
[26]
Sayan M, Sargin F, Inan D, et al. HIV-1 Transmitted drug resistance mutations in newly diagnosed antiretroviral-naive patients in turkey. AIDS Res Hum Retroviruses 2016; 32(1): 26-31.
[27]
Korten V, Inan D, Yildirmak T, et al. Prevalence of transmitted drug resistance (TDR) in newly diagnosed HIV-1 infected patients in Turkey. 14th European AIDS Conference (EACS). Brussels, Belgium. 2013.
[28]
Kuskucu MA, Midilli K, Yemisen M, Abdelkareem A, Ergin S, Tabak F. Transmitted drug resistance (TDR) prevalance among treatment naive HIV-1 infected patients in Istanbul remained unchanged between 2004 and 2015. 18th Annual Meeting of European Society for Clinical Virology. Edinburgh, UK. 2015.
[29]
Yalcinkaya T, Kose S. Investigation of HIV-1 primary drug resistance mutations in antiretroviral therapy-naive cases. Mikrobiyol Bul 2014; 48(4): 585-95.
[30]
Avila-Rios S, Garcia-Morales C, Matias-Florentino M, et al. Pretreatment HIV-drug resistance in Mexico and its impact on the effectiveness of first-line antiretroviral therapy: a nationally representative 2015 WHO survey. Lancet HIV 2016; 3(12): e579-91.
[31]
Iwuji C, Derache A, Baisley K, et al. Response to first-line ART in adults with drug resistant HIV, ANRS 12249 TasP trial. Conference on Retroviruses and Opportunistic Infections. Boston, Massachusetts. 2017.
[32]
Ji H, Liang B, Li Y, et al. Low abundance drug resistance variants in transmitted HIV drug resistance surveillance specimens identified using tagged pooled pyrosequencing. J Virol Methods 2013; 187(2): 314-20.
[33]
Mardis ER. Next-generation DNA sequencing methods. Annu Rev Genomics Hum Genet 2008; 9: 387-402.
[34]
Shafer RW. Human immunodeficiency virus type 1 drug resistance mutations update. J Infect Dis 2017; 216(Suppl. 9): S843-6.
[35]
European AIDS Clinical Society (EACS) Guideline_v9. Available from: http://www.eacsociety.org/files/guidelines_9.0-english.pdf Accessed on 8.4.2018.
[36]
British HIV Association (BHIVA) guidelines for the treatment of HIV-1-positive adults with antiretroviral therapy. Available from: http://www.bhiva.org/HIV-1-treatment-guidelines.aspx Accessed on 8.4.2018.