Molecular Antiretroviral Resistance Markers of Human Immunodeficiency Virus-1 of CRF01_AE Subtype in Bali, Indonesia

Author(s): Nyoman Sri Budayanti, Tuti Parwati Merati, Budiman Bela, Gusti Ngurah Mahardika*.

Journal Name: Current HIV Research

Volume 16 , Issue 5 , 2018

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Graphical Abstract:


Background: Molecular epidemiological study of human immunodeficiency virus drugresistant (HIVDR) markers is challenging in areas where the dominant subtype is non-B.

Objective: Here we provide molecular data for HIVDR in the CRF01_AE subtype in Bali, Indonesia.

Method: Seventy patients were enrolled in this study and grouped into treatment failure and treatment naïve groups. The full-length pol gene was amplified using nested reverse transcriptase polymerase chain reaction and the product was then sequenced. The readable sequence was then subjected to Stanford HIV Drug Resistance Database genotyping.

Results: We found that clinical classification was in accordance with the presence of HIVDR markers in the pol gene. Independent of therapy history, the treatment failure group showed resistance markers against nucleoside reverse transcriptase inhibitors (NRTI) and non-nucleoside reverse transcriptase inhibitors (NNRTI), ranging from 72%–100% of patients. Only a small proportion of naïve patients harbored HIV with drug resistance markers to NNRTI. No protease inhibitor-resistant marker was found in either patient group. Molecular marker mutations, which were found in more than 50% of treatment failure patients, were M184V (100%), T215A/Y/F (88.2%), D67N/G (76.5%), and M41L (58.8%).

Conclusion: The protocol used in this study to determine genetic markers of HIVDR based on subtype B can be applied for the rapid determination of resistance of the CRF01_AE subtype. All patients with progressive clinical signs and increased viral load should be recommended to undergo second-line treatment of the ARV regimen.

Keywords: Human Immunodeficiency Virus (HIV), CRF01_AE, treatment failure, naïve, Bali, nucleoside reverse transcriptase inhibitors (NRTI).

Rojas Sanchez P, Holguin A. Drug resistance in the HIV-1-infected paediatric population worldwide: a systematic review. J Antimicrob Chemother 2014; 69(8): 2032-42.
Hamers RL, Kityo C, Lange JM, et al. Global threat from drug resistant HIV in sub-Saharan Africa. BMJ 2012; 344: e4159.
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.
Ferreira ACG, Coelho LE, Grinsztejn E, et al. Transmitted drug resistance in patients with acute/recent HIV infection in Brazil. Braz J Infect Dis 2017; 21(4): 396-401.
Jayaraman GC, Archibald CP, Kim J, et al. A population-based approach to determine the prevalence of transmitted drug-resistant HIV among recent versus established HIV infections: results from the Canadian HIV strain and drug resistance surveillance program. J Acquir Immune Defic Syndr 2006; 42(1): 86-90.
Abecasis AB, Wensing AM, Paraskevis D, et al. HIV-1 subtype distribution and its demographic determinants in newly diagnosed patients in Europe suggest highly compartmentalized epidemics. Retrovirology 2013; 10: 7.
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.
Buonaguro L, Tornesello ML, Buonaguro FM. Human immunodeficiency virus type 1 subtype distribution in the worldwide epidemic: pathogenetic and therapeutic implications. J Virol 2007; 81(19): 10209-19.
Merati TP, Ryan CE, Spelmen T, et al. CRF01_AE dominates the HIV-1 epidemic in Indonesia. Sex Health 2012; 9(5): 414-21.
Sahbandar IN, Takahashi K, Djoerban Z, et al. Current HIV type 1 molecular epidemiology profile and identification of unique recombinant forms in Jakarta, Indonesia. AIDS Res Hum 2009; 25(7): 637-46.
Indriati DW, Kotaki T, Khairunisa SQ, et al. Appearance of drug resistance mutations among the dominant HIV-1 subtype, CRF01_AE in maumere, Indonesia. Curr HIV Res 2018; 16(2): 158-66.
Chan PA, Kantor R. Transmitted drug resistance in nonsubtype B HIV-1 infection. HIV Ther 2009; 3(5): 447-65.
Januraga PP, Wulandari LP, Muliawan P, et al. Sharply rising prevalence of HIV infection in Bali: a critical assessment of the surveillance data. Int J STD AIDS 2013; 24(8): 633-7.
Ford K, Wirawan DN, Sumantera GM, Sawitri AA, Stahre M. Voluntary HIV testing, disclosure, and stigma among injection drug users in Bali, Indonesia. AIDS Educ Prev 2004; 16(6): 487-98.
Sagung Sawitri AA, Sumantera GM, Wirawan DN, Ford K, Lehman E. HIV testing experience of drug users in Bali, Indonesia. AIDS Care 2006; 18(6): 577-88.
Commision INA: Global AIDS Response Progress Reporting Indonesia Country Report 2012-2013. In.: UNAIDS http://www.
Waluyo A, Culbert GJ, Levy J, Norr KF. Understanding HIV-related stigma among Indonesian nurses. JANAC 2015; 26(1): 69-80.
Kozal MJ, Amico KR, Chiarella J, et al. Antiretroviral resistance and high-risk transmission behavior among HIV-positive patients in clinical care. AIDS 2004; 18(16): 2185-9.
Culbert GJ, Earnshaw VA, Wulanyani NM, et al. Correlates and Experiences of HIV Stigma in Prisoners Living With HIV in Indonesia: A Mixed-Method Analysis. JANAC 2015; 26(6): 743-57.
Chen JH, Wong KH, Li PC, et al. In-house human immunodeficiency virus-1 genotype resistance testing to determine highly active antiretroviral therapy resistance mutations in Hong Kong. Hong Kong Med J 2012; 18(1): 20-4.
Tamura K, Dudley J, Nei M, Kumar S. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol 2007; 24(8): 1596-9.
Ghasemi A, Zahediasl S. Normality tests for statistical analysis: a guide for non-statisticians. Int J Endocrinol Metab 2012; 10(2): 486-9.
Viputtijul K, de Souza M, Trichavaroj R, et al. Heterosexually acquired CRF01_AE/B recombinant HIV type 1 found in Thailand. AIDS Res Hum Retroviruses 2002; 18(16): 1235-7.
Foley B, Donegan E, Silitonga N, et al. Importation of multiple HIV type 1 strains into West Papua, Indonesia (Irian Jaya). AIDS Res Hum Retroviruses 2001; 17(17): 1655-9.
Yahi N, Tamalet C, Tourres C, et al. Mutation patterns of the reverse transcriptase and protease genes in human immunodeficiency virus type 1-infected patients undergoing combination therapy: survey of 787 sequences. J Clin Microbiol 1999; 37(12): 4099-106.
Quinones-Mateu ME, Albright JL, Mas A, Soriano V, Arts EJ. Analysis of pol gene heterogeneity, viral quasispecies, and drug resistance in individuals infected with group O strains of human immunodeficiency virus type 1. J Virol 1998; 72(11): 9002-15.
O’Rourke SM, Sutthent R, Phung P, et al. Glycans flanking the hypervariable connecting peptide between the A and B strands of the V1/V2 domain of HIV-1 gp120 confer resistance to antibodies that neutralize CRF01_AE viruses. PLoS One 2015; 10(3): e0119608.
Paydary K, Khaghani P, Emamzadeh-Fard S, Alinaghi SA, Baesi K. The emergence of drug resistant HIV variants and novel anti-retroviral therapy. Asian Pac J Trop Biomed 2013; 3(7): 515-22.
Ghosn J, Galimand J, Raymond S, et al. Cohort ACP: X4 tropic multi-drug resistant quasi-species detected at the time of primary HIV-1 infection remain exclusive or at least dominant far from PHI. PLoS One 2011; 6(8): e23301.
Dybowski JN, Heider D, Hoffmann D. Structure of HIV-1 quasi-species as early indicator for switches of co-receptor tropism. AIDS Res Ther 2010; 7: 41.
Aasa-Chapman MM, Aubin K, Williams I, McKnight A. Primary CCR5 only using HIV-1 isolates does not accurately represent the in vivo replicating quasi-species. Virology 2006; 351(2): 489-96.
Matsushita S, Takahama S, Shibata J, et al. Ex vivo neutralization of HIV-1 quasi-species by a broadly reactive humanized monoclonal antibody KD-247. Hum Antibodies 2005; 14(3-4): 81-8.
Sankale JL, De La Tour RS, Marlink RG, et al. Distinct quasi-species in the blood and the brain of an HIV-2-infected individual. Virology 1996; 226(2): 418-23.
Sabino E, Pan LZ, Cheng-Mayer C, Mayer A. Comparison of in vivo plasma and peripheral blood mononuclear cell HIV-1 quasi-species to short-term tissue culture isolates: an analysis of tat and C2-V3 env regions. AIDS 1994; 8(7): 901-9.
Nagata S, Imai J, Makino G, Tomita M, Kanai A. Evolutionary Analysis of HIV-1 Pol Proteins Reveals Representative Residues for Viral Subtype Differentiation. Front Microbiol 2017; 8: 2151.
Kuiken C, Korber B, Shafer RW. HIV sequence databases. AIDS Rev 2003; 5(1): 52-61.
Liu J, Yue J, Wu S, Yan Y. Polymorphisms and drug resistance analysis of HIV-1 CRF01_AE strains circulating in Fujian Province, China. Arch Virol 2007; 152(10): 1799-805.
Manosuthi W, Butler DM, Perez-Santiago J, et al. Protease polymorphisms in HIV-1 subtype CRF01_AE represent selection by antiretroviral therapy and host immune pressure. AIDS 2010; 24(3): 411-6.
Ariyoshi K, Matsuda M, Miura H, et al. Patterns of point mutations associated with antiretroviral drug treatment failure in CRF01_AE (subtype E) infection differ from subtype B infection. J Acquir Immune Defic Syndr 2003; 33(3): 336-42.
Santa-Marta M, de Brito PM, Godinho-Santos A, Goncalves J. Host factors and HIV-1 replication: Clinical evidence and potential therapeutic approaches. Front Immunol 2013; 4: 343.
Salgado M, Swanson MD, Pohlmeyer CW, et al. HLA-B*57 elite suppressor and chronic progressor HIV-1 isolates replicate vigorously and cause CD4+ T cell depletion in humanized BLT mice. J Virol 2014; 88(6): 3340-52.
Ndzinu JK, Takeuchi H, Saito H, Yoshida T, Yamaoka S. eIF4A2 is a host factor required for efficient HIV-1 replication. Microbes Infect 2018; 20(6): 346-52.
Sharma G, Kaur G, Mehra N. Genetic correlates influencing immunopathogenesis of HIV infection. Indian J Med Res 2011; 134(6): 749-68.
Lama J, Planelles V. Host factors influencing susceptibility to HIV infection and AIDS progression. Retrovirology 2007; 4: 52.
Candore G, Romano GC, D’Anna C, et al. Biological basis of the HLA-B8, DR3-associated progression of acquired immune deficiency syndrome. Pathobiology 1998; 66(1): 33-7.
Pinching AJ. Factors affecting the natural history of human immunodeficiency virus infection. Immunodefic Rev 1988; 1(1): 23-38.
Ueda S, Witaningrum AM, Khairunisa SQ, et al. Genetic Diversity and Drug Resistance of HIV-1 Circulating in North Sulawesi, Indonesia. AIDS Res Hum Retroviruses 2018. [Epub ahead of print].
El-Khatib Z, Ekstrom AM, Ledwaba J, et al. Viremia and drug resistance among HIV-1 patients on antiretroviral treatment: a cross-sectional study in Soweto, South Africa. AIDS 2010; 24(11): 1679-87.
Almeida FJ, Berezin EN, Rodrigues R, et al. Diversity and prevalence of antiretroviral genotypic resistance mutations among HIV-1-infected children. J Pediatr (Rio J) 2009; 85(2): 104-9.
Machado DM, Fernandes SC, Succi RC, et al. Analysis of HIV- type 1 protease and reverse transcriptase in Brazilian children failing highly active antiretroviral therapy (HAART). Rev Inst Med Trop São Paulo 2005; 47(1): 1-5.
Delaugerre C, Warszawski J, Chaix ML, et al. Prevalence and risk factors associated with antiretroviral resistance in HIV-1-infected children. J Med Virol 2007; 79(9): 1261-9.
Riemenschneider M, Senge R, Neumann U, Hullermeier E, Heider D. Exploiting HIV-1 protease and reverse transcriptase cross-resistance information for improved drug resistance prediction by means of multi-label classification. BioData Min 2016; 9: 10.
Miller V, Larder BA. Mutational patterns in the HIV genome and cross-resistance following nucleoside and nucleotide analogue drug exposure. Antivir Ther 2001; 6(Suppl 3): 25-44.
Ma L, Huang J, Xing H, et al. Genotypic and phenotypic cross-drug resistance of harboring drug-resistant HIV type 1 subtype B′ strains from former blood donors in central Chinese provinces. AIDS Res Hum Retroviruses 2010; 26(9): 1007-13.
Heider D, Senge R, Cheng W, Hullermeier E. Multilabel classification for exploiting cross-resistance information in HIV-1 drug resistance prediction. Bioinformatics 2013; 29(16): 1946-52.
Groschel B, Cinatl J, Perigaud C, et al. S-acyl-2-thioethyl (SATE) pronucleotides are potent inhibitors of HIV-1 replication in T-lymphoid cells cross-resistant to deoxycytidine and thymidine analogs. Antiviral Res 2002; 53(2): 143-52.
Van Laethem K, Witvrouw M, Balzarini J, et al. Patient HIV-1 strains carrying the multiple nucleoside resistance mutations are cross-resistant to abacavir. AIDS 2000; 14(4): 469-71.
Palmer S, Shafer RW, Merigan TC. Highly drug-resistant HIV-1 clinical isolates are cross-resistant to many antiretroviral compounds in current clinical development. AIDS 1999; 13(6): 661-7.
Gu Z, Fletcher RS, Arts EJ, Wainberg MA, Parniak MA. The K65R mutant reverse transcriptase of HIV-1 cross-resistant to 2′, 3′-dideoxycytidine, 2′,3′-dideoxy-3′-thiacytidine, and 2′,3′-dideoxyinosine shows reduced sensitivity to specific dideoxynucleoside triphosphate inhibitors in vitro. J Biol Chem 1994; 269(45): 28118-22.
Clutter DS, Zhou S, Varghese V, et al. Prevalence of drug-resistant minority variants in untreated HIV-1-infected individuals with and those without transmitted drug resistance detected by sanger sequencing. J Infect Dis 2017; 216(3): 387-91.
Li T, Qian F, Yuan T, et al. Drug resistance mutation profiles of the drug-naive and first-line regimen-treated HIV-1-infected population of Suzhou, China. Virol Sin 2017; 32(4): 271-9.
Andreis S, Basso M, Scaggiante R, et al. Drug resistance in B and non-B subtypes amongst subjects recently diagnosed as primary/recent or chronic HIV-infected over the period 2013-2016: Impact on susceptibility to first-line strategies including integrase strand-transfer inhibitors. J Glob Antimicrob Resist 2017; 10: 106-12.
Paraskevis D, Kostaki E, Magiorkinis G, et al. Prevalence of drug resistance among HIV-1 treatment-naive patients in Greece during 2003-2015: Transmitted drug resistance is due to onward transmissions. Infect Genet Evol 2017; 54: 183-91.
Ghafari S, Memarnejadian A, Samarbaf-Zadeh A, et al. Prevalence of HIV-1 transmitted drug resistance in recently infected, treatment-naive persons in the Southwest of Iran, 2014-2015. Arch Virol 2017; 162(9): 2737-45.
Socias ME, Nosova E, Kerr T, et al. Patterns of transmitted drug resistance and virological response to first-line antiretroviral treatment among HIV-positive people who use illicit drugs in a Canadian setting. Clin Infect Dis 2017; 65(5): 796-802.
Kotaki T, Khairunisa SQ, Witaningrum AM, et al. HIV-1 transmitted drug resistance mutations among antiretroviral therapy-Naive individuals in Surabaya, Indonesia. AIDS Res Ther 2015; 12: 5.
Witaningrum AM, Kotaki T, Khairunisa SQ, et al. Genotypic Characterization of Human Immunodeficiency Virus Type 1 Derived from Antiretroviral Therapy-Naive Individuals Residing in Sorong, West Papua. AIDS Res Hum Retroviruses 2016; 32(8): 812-7.
Roberts JD, Bebenek K, Kunkel TA. The accuracy of reverse transcriptase from HIV-1. Science 1988; 242(4882): 1171-3.
Cuevas JM, Geller R, Garijo R, Lopez-Aldeguer J, Sanjuan R. Extremely High Mutation Rate of HIV-1 In Vivo. PLoS Biol 2015; 13(9): e1002251.
De Luca A, Sidumo ZJ, Zanelli G, et al. Accumulation of HIV-1 drug resistance in patients on a standard thymidine analogue-based first line antiretroviral therapy after virological failure: implications for the activity of next-line regimens from a longitudinal study in Mozambique. BMC infectious diseases 2017; 17(1): 605.
Moscona R, Ram D, Wax M, et al. Comparison between next-generation and Sanger-based sequencing for the detection of transmitted drug-resistance mutations among recently infected HIV-1 patients in Israel, 2000-2014. J Int AIDS Soc 2017; 20(1): 1-9.
Golmohammadi R, Baesi K, Moradi A, et al. The first characterization of HIV-1 subtypes and drug resistance mutations among antiretrovirally treated patients in Kermanshah, Iran. Intervirology 2017; 60(1-2): 33-7.
Cozzi-Lepri A, Ruiz L, Loveday C, et al. Thymidine analogue mutation profiles: factors associated with acquiring specific profiles and their impact on the virological response to therapy. Antivir Ther 2005; 10(7): 791-802.
Rezende LF, Prasad VR. Nucleoside-analog resistance mutations in HIV-1 reverse transcriptase and their influence on polymerase fidelity and viral mutation rates. Int J Biochem Cell Biol 2004; 36(9): 1716-34.
Johnson VA, Brun-Vezinet F, Clotet B, et al. Update of the drug resistance mutations in HIV-1. Top HIV Med 2008; 16(5): 138-45.
Boyer PL, Sarafianos SG, Arnold E, Hughes SH. Selective excision of AZTMP by drug-resistant human immunodeficiency virus reverse transcriptase. J Virol 2001; 75(10): 4832-42.
Demeter LM, D’Aquila R, Weislow O, et al. Interlaboratory concordance of DNA sequence analysis to detect reverse transcriptase mutations in HIV-1 proviral DNA. ACTG Sequencing Working Group. AIDS Clinical Trials Group. J Virol Methods 1998; 75(1): 93-104.
Gall A, Ferns B, Morris C, et al. Universal amplification, next-generation sequencing, and assembly of HIV-1 genomes. J Clin Microbiol 2012; 50(12): 3838-44.

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Year: 2018
Page: [374 - 382]
Pages: 9
DOI: 10.2174/1570162X17666190204101154

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