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HIV & AIDS Review. International Journal of HIV-Related Problems
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vol. 17
Research paper

Genotypic characterization of human immunodeficiency virus type 1 isolated in Bali, Indonesia in 2016

Siti Qamariyah Khairunisa
Sri Masyeni
Adiana Mutamsari Witaningrum
Muhammad Qushai Yunifiar M.
Dwi Wahyu Indriati
Tomohiro Kotaki
Shuhei Ueda
Dewa G. Budiyasa
Nasronudin Nasronudin
Masanori Kameoka

HIV AIDS Rev 2018; 17, 2: 81-90
Online publish date: 2018/05/21
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Human immunodeficiency virus type-1 (HIV-1) is the major causative agent of acquired immune deficiency syndrome (AIDS) [1]. The virus is characterized by extensive genetic heterogenicity. Due to this variability, HIV-1 is subdivided into 4 groups: M (major), O (outlying), N (new or non-M, non-O), and P (pending). Viruses in group M, which are responsible for the majority of infections in the worldwide HIV-1 pandemic [2, 3], are further classified into many subtypes or circulating recombinant forms (CRFs). Of these, subtypes A, B, C, D, and G, as well as CRF01_AE and CRF02_AG are the major subtypes and CRFs responsible for the worldwide pandemic. Inter-subtype genetic variability has been reported among subtypes and CRFs; 15-20% of genetic variability is found in the gag gene and 25-35% in the env gene [1].
While subtype B of HIV-1 is the predominant subtype in the Americas, Europe, and Australia [4, 5], and is also present as a minority in Asia [6], a growing epidemic of non-B subtypes and CRFs has been reported in Africa [7] and Asia [8]. CRF01_AE is prevalent throughout Southeast Asia and responsible for more than 90% of infection cases in Indonesia [9]. Furthermore, several recombinant forms between CRF01_AE and subtype B, including CRF33_01B, have emerged in Indonesia [9-13]. Different subtypes and CRFs are considered to show different rates of disease progression, immune responses, responses to antiretroviral therapy (ART), and the development of drug resistance [14]. Therefore, it is important to monitor the global prevalence of subtypes and CRFs for the prevention and control of HIV-1 as well as vaccine development.
Antiretroviral therapy (ART) has markedly reduced the transmission, morbidity, and mortality associated with HIV. In 2013, number of HIV-infected individuals in Indonesia with CD4+ T-cell count less than 500 cells/mm3 were estimated to be 510,000, and these individuals were eligible for ART according to the World Health Organization (WHO) criteria. The Indonesian national ART program enabled 40% of these individuals to access ART in 2011 [15]. The first-line regimen of ART recommended in Indonesia is a combination of two nucleoside reverse-transcriptase inhibitors (NRTIs) and a non-nucleoside reverse-transcriptase inhibitor (NNRTI). Lamivudine (3TC), zidovudine (AZT), tenofovir (TDF), nevirapine (NVP), and efavirenz (EFV) are commonly used. In patients with virological failure and/or adverse effects to the first-line regimen, ritonavir-boosted protease inhibitors in combination with two NRTIs are recommended as the second-line regimen. Other drugs, including didanosine (ddI), etravirine (ETR), and rilpivirine (RPV), are uncommon in the country. Although ART is successful in Indonesia, the emergence of drug resistance has been reported among treatment failure cases as well as ART-naïve individuals [16-19].
Bali is a famous tourism destination in Indonesia, and many international travelers from several foreign countries visit Bali. It is assumed that some of these travelers may be HIV-infected. According to Indonesian Ministry of Health, Bali has the fourth largest number of HIV cases in Indonesia. Previous studies revealed a large number of HIV infection in Bali [20, 21]. However, the genotypes of HIV-1 strains circulating in Bali has not yet been elucidated in detail. In addition, the information on HIVDR in Bali is limited. In order to clarify the circulating HIV-1 subtypes and monitor the emergence of HIVDR in Bali, a genotypic study was conducted on viral genomic fragments derived from peripheral blood samples of ART-experienced or ART-naïve HIV-1-infected individuals residing in Gianyar and Denpasar, Bali.

Material and methods

Ethics statement

This study was conducted with approvals from the Medical Research Ethics Committees of the Faculty of Medicine of Udayana University, Airlangga University, and Kobe University Graduate School of Medicine. All study participants were enrolled after providing written informed consents.

Study site, patient recruitment, and sample collection

Fifty-eight HIV-infected individuals, consisting of 51 ART-experienced and 7 ART-naïve individuals, were recruited from the Sinta HIV Clinic of Sanjiwani Hospital in Gianyar regency and from Puskesmas Denpasar Selatan II at Denpasar municipality in Bali, Indonesia. Eight milliliters whole blood samples were collected from study participants between January and March 2016. Peripheral blood mononuclear cells (PBMC) were isolated by density gradient centrifugation for 10 minutes at 1,800 rpm using the BD Vacutainer® CPT™ Cell Preparation Tube (Becton, Dickinson and Company, Franklin Lakes, NJ, USA). DNA was then extracted from PBMCs using the QIAamp DNA Blood Mini Kit (Qiagen, Hilden, Germany). Demographic, clinical, and hematological data as well as disease severity according to the WHO guidelines of study participants were retrieved from the medical records.

HIV-1 genotypic analysis

The HIV-1 pol gene encoding protease (PR gene) and reverse transcriptase (RT gene) as well as gag and env genes were amplified by nested polymerase chain reaction (PCR) using Gotaq green master mix (Promega, Madison, WI, USA). The primer sets used were as follows. In order to amplify the viral PR gene, the primers DRPRO5, 5´-AGACAGGYTAATTTTTTAGGGA-3´ ((corresponding to nucleotides (nt) 2074-2095 of an HIV-1 reference strain, HXB2 (GenBank accession no. K03455)) and DRPRO2L, 5´-TATGGATTTTCAGGCCCAATTTTTGA-3´ (nt 2716 to 2691) were used for the first PCR, and the primers DRPRO1M, 5´-AGAGCCAACAGCCCCACCAG-3´ (nt 2148 to 2167), and DRPRO6, 5´-ACTTTTGGGCCATCCATTCC-3´ (nt 2611 to 2592) were used for nested PCR. In order to amplify the viral RT gene, RT1L, 5´-ATGATAGGGGGAATTGGAGGTTT-3´ (nt 2388 to 2410) and DRRT4L, 5´-TACTTCTGTTAGTGCTTTGGTTCC-3´ (nt 4402 to 4380) were used for first PCR, and RT7L, 5´-GACCTACACCTGTCAACATAATTGG-3´ (nt 2485 to 2509) and DRRT6L, 5´-TAATCCCTGCATAAATCTGACTTGC-3´ (nt 4309 to 4285) were used for nested PCR. In order to amplify the gag gene encoding Gag p24, the primers for first PCR were H1G777, 5’-TCACCTAGAACTTTGAATGCATGGG-3’ (nt 1231 to 1255) and H1P202, 5’-CTAATACTGTATCATCTGCTCCTGT-3’ (nt 2352 to 2325), while the primers used for nested PCR were H1Gag1584, 5’-AAAGATGGATAATCCTGGG-3’ (nt 1577 to 1595) and G17, 5’-TCCACATTTCCAACAGCCCTTTTT-3’ (nt 2040 to 2017). In order to amplify the C2-V3 regions of env gene, the primers used for first PCR were M5, 5’-CCAATTCCCATACATTATTGTGCCCCAGCTGG-3’ (nt 6858 to 6889) and M10, 5’-CCAATTGTCCCTCATATCTCCTCCTCCAGG-3’ (nt 7661 to 7632), while the primers used for nested PCR were M3, 5’-GTCAGCACAGTACAATGIACACATGG-3’ (nt 6948 to 6973) and M8, 5’-TCCTTGGATGGGAGGGGCATACATTGC-3’ (nt 7547 to 7521). The PCR product amplified at the end-point dilution of DNA templates were subjected to a sequencing analysis in order to examine the genomic fragment of the major viral population in a sample.
The BigDye Terminator version 3.1 Cycle Sequencing kit and ABI PRISM3500Xl genetic analyzer (Applied Biosys­tems, Foster City, CA, USA) were used in the sequencing analysis of amplified HIV-1 gag, pol, and env genes. Data were assembled using Genetyx version 10 software (Genetyx, Tokyo, Japan). HIV-1 subtyping was conducted using the Recombinant Identification Program (RIP) available on the HIV sequence database website (www.hiv.lanl.gov) and jumping profile Hidden Markov Model (jpHMM)-HIV (http://jphmm.gobics.de/submission_hiv). Neighbor-joining trees with a Kimura two-parameter model were constructed using MEGA6.2 software with bootstrap values (1,000 replicates) for relevant nodes being reported on a representative tree. When a discrepancy was found in the subtyping of a sample among the gag, PR, RT, and env genes, it was defined as a unique recombinant form of more than two HIV-1 subtypes and CRFs. The appearance of drug resistant mutations in the 31 PR and 37 RT genes was studied according to the International Antiviral Society-United States of America (IAS-USA) panel [22]. The nucleotide sequences of the PR, RT, gag, and env genes have been registered in the GenBank database under accession numbers KY985644-KY985676 (env genes), KY985677-KY985723 (gag genes), KY985724-KY985760 (RT genes), and KY985761-KY985791 (PR genes).


Demographic and clinical information of study participants

The demographic information of 58 study participants is shown in Table 1. The mean age of study participants was 36.5 (SD ± 11.66) years old. Study participants had a median CD4 cell count of 52.50 cells/mm3, with an interquartile range (IQR) of 1-480 cells/mm3. Most ethnic group were from Bali (94.8%). The main route of infection was heterosexual intercourse (87.9%). Six individuals were ART-naïve (10.3%), while 52 individuals had been on ART (89.7%). The fixed combination of AZT/3TC/NVP (17.3%), AZT/3TC/EFV (10.3%), TDF/3TC/EFV (44.8%), or TDF/3TC/NVP (17.3%) was used in the treatment of individuals on ART. The mean duration of ART usage was 26.68 (SD ± 17.84) months. Fourteen individuals were in the non-AIDS stage (24.1%), while 44 individuals were in the AIDS stage (75.9%). Fifty-one individuals had developed opportunistic infections (87.9%).

HIV-1 subtyping

The sequencing data of 31 PR genes (297 bp; nt 2253 to 2,549), 37 RT genes (762-bp; nt 2,550 to 3,311), the partial fragments of 47 gag genes encoding Gag p24 (382-bp; nt 1,627 to 2,008), and the partial fragments of 33 env genes spanning the C2-V3 region (389-bp; nt 7,020 to 7,408) were obtained from 55 blood samples, while no sequencing data was available from 3 samples (Table 2). According to RIP and jpHMM-HIV results as well as the phylogenetic tree analysis, CRF01_AE was the dominant subtype in Bali (94.5%) (Table 3). In addition, recombinant viruses containing CRF01_AE and subtype B gene fragments (5.5%) were detected (Table 3). Viral subtyping by RIP, jpHMM-HIV, and phylogenetic trees showed consistent results (data not shown).

Appearance of drug resistance-associated mutations

The appearance of drug resistance-associated mutations was evaluated on successfully sequenced 31 RT and 26 PR genes derived from ART-experienced individuals. Drug resistance-associated major mutations against NRTIs and NNRTIs were found in 8/31 RT genes (25.8%) in integrated proviral DNA derived from ART-experienced individuals (Table 4). In particular, samples H033 and H056 contained several major mutations, including thymidine analogue-associated mutations (TAMs), which confer multi NRTI resistance (Table 4). In PR genes, no drug resistance-associated major mutations were detected (data not shown). However, minor mutations, M36I ((amino acid substitution from methionin (M) to isoleucine (I) at position 36 in PR gene)) (100%), H69K (100%), and L89M (88.5%) were commonly detected in the PR gene (Table 4) [21]. These mutations confer resistance to ritonavir-boosted indinavir (IDV/r), atazanavir (ATV/r), fosamprenavir (FPV/r), lopinavir (LPV/r), tipranavir (TPV/r), and nelfinavir (NFV).


HIV-1 genetic diversity is caused by viral mechanisms that elude immune control and drug pressure. The existence of distinct subtypes and CRFs reflects the presence of a dynamic genetic evolutionary process of the virus. The most prominent HIV-1 subtype in Bali found in the present study was CRF01_AE, which is widely prevalent throughout Southeast Asian countries including Indonesia [8, 9, 17]. Previous HIV-1 genotyping studies in Indonesia reported similar findings. Roselinda and Jekti [23] found that CRF01_AE viruses circulated in 7 provinces in Indonesia as the predominant subtype, followed by subtype B and recombinant viruses containing subtypes A and G gene fragments, which were not found in the present study. CRF01_AE was found in 80% of the samples in North Sumatra province and in East Java, while it was only detected in a quarter of samples in the Papua provinces [23, 24]. A study in Malaysia, a neighbor country of Indonesia, reported similar findings for the HIV-1 subtype distribution in that CRF01_AE was the most dominant strain and other subtypes were identified as minorities [25]. In contrast to this study, subtype B (41.9%) was the major subtype prevalent in Sorong, West Papua, Indonesia [11]. Differences in the distribution of the HIV-1 subtype in Indonesia may be caused by many factors such as different high-risk behaviors for HIV-1 infection, genetic and demographic characteristic of individuals residing in each region, geographic, economic, and social factors. Diverse high-risk behaviors sustain HIV-1 transmission in different regions of the world, and multiple transmission routes may be involved in spreading the HIV-1 epidemic within the same region [1]. As an RNA virus, HIV-1 replication is characterized by high mutation rates, leading to diversification of its strains. Intersubtype recombination contributes to HIV-1 sequence diversity, which is generated by the co-circulation of two or more different subtypes and/or CRFs in high-risk populations [26]. Other recombinant forms, such as recombinant viruses between CRF01_AE and subtype B (5.5%) were also detected in the present study. The prevalence of recombinant forms of HIV-1 in Indonesia was reported to be low. Namely, the low prevalence of recombinants between CRF01_AE and subtype B was similar to previous findings in Surabaya (3.0%) and in Sorong (2.3%) [11, 17]. Subtype B is the most prevalent HIV-1 subtype in North America, Western Europe, and Australia; however, Sides et al. found that non-B subtypes were prevalent as the major subtypes among African-born HIV-1-infected individuals in Minnesota, USA [27], suggesting that migration may have affected the subtype distribution in the world. Furthermore, the epidemic of a minor lineage of HIV-1 subtype B (termed subtype B’) occurred in Asia [6]. Therefore, it is important to continuously monitor the prevalence of HIV-1 subtypes and CRFs worldwide.
Genetic variability was found in viral PR and RT genes coding the viral enzymes targeted by antiretroviral drugs. If a drug resistance-associated mutation appears as a result of a genetic polymorphism, it may be selected further by drug-selective pressure, and markedly influence therapeutic outcome [1]. In the present study, drug resistance-associated major mutations were detected in RT genes derived from 8 ART-experienced individuals. In particular, several mutations were detected in 2 individuals treated with the combination of 2 NRTIs and 1 NNRTI. Patient H033 had been treated with 3TC/AZT/EFV for 43 months. Several TAMs (M41L, D67N, K70R, and M184V) and mutations against NNRTIs (K103N, V108I) was found in the viral RT gene derived from the patient. Based on clinical data, this patient had not developed any opportunistic infections, ART side effect, or ART failure (data not shown). The mutations, M184V and K103N are commonly detected as multi-drug resistance mutations leading to the virological failure of a first-line NRTIs- and NNRTI-based regimens [16, 28]. The appearance pattern of these drug resistance mutations was similar with those in previous studies in Indonesia, Malaysia, Taiwan, Turkey, and USA [17, 18-31]. M184V is a common mutation in treated populations; however, it is very rare among ART-naïve individuals. This may be due to that M184V deteriorates viral fitness in the absence of ART. In present study, drug resistance-associated major mutations were not found in RT genes derived from ART-naïve patients, while several TAMs (M41L, D67N, K70R, L210W, T215Y, K219E) were detected in ART-naïve individuals as transmitted drug resistance (TDR) in a previous study conducted in Surabaya, Indonesia [19]. Due to a limited sample size, the emergence of TDR among ART-naïve individuals cannot be evaluated in this study. Since drug resistance-associated mutations have frequently been detected among treatment-failure patients in Indonesia, there may be a risk of TDR among newly infected individuals. This study needs to be continued with a larger sample size, improved sampling quality, and direct sequencing in order to obtain the best TDR estimation in HIV-1-infected individuals in Indonesia. In addition, several minor mutations were found in PR genes derived from most study participants. Although these mutations may also affect clinical manifestations, this was not evaluated in present study. Minor mutations have been detected in PR genes of non-B subtypes, including CRF01_AE, as natural polymorphisms [14]. Drug resistance-associated minor mutations in PR genes have also been reported in other studies in Indonesia [11, 17, 18].


CRF01_AE is the dominant HIV-1 strain prevalent in Bali. The emergence of drug resistance-associated major mutations was evident among patients on ART. The detection of drug resistance-associated mutations in ART-naïve and ART experienced samples, and the combining of data with clinical, immunological, and virological data of HIV-1-infected individuals are needed in order to improve the clinical outcomes of ART in Indonesia.


MK and N conceived and supervised the study; SQK and TK designed experiments; SQK, AMW, MQYM, and DWI performed experiments; SM, DHB, and AC collected samples and clinical information; AQK, SM, AMW, MQYM, DWI, TK, and SU analyzed data; SQK and SM wrote the manuscript; SU and MK made manuscript revisions. This work was supported by the Japan Initiative for the Global Research Network on Infectious Diseases (J-GRID) from the Ministry of Education, Culture, Sport, Science, and Technology in Japan, and the Japan Agency for Medical Research and Development (AMED); and the Institute of Tropical Disease as the Center of Excellence (COE) program by the Ministry for Research and Technology (RISTEK) of Indonesia. The funders had no role in study design, data collection, and analysis, the decision to publish, or preparation of the manuscript. The manuscript was proofread by Medical English Service, Kyoto, Japan.

Conflict of interest

The authors declare no potential conflicts of interest with respect to the research, authorship, and/or publication of this article.


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