Genotypic Characterization of Human Immunodeficiency Virus Type 1 Prevalent in Kepulauan Riau, Indonesia

Abstract

Kepulauan Riau is a famous tourist destination in Indonesia. The epidemic of human immunodeficiency virus type 1 (HIV-1) infection is gradually increasing in this region. We collected peripheral blood samples from 62 antiretroviral therapy-experienced individuals. The amplification of viral genomic fragments, HIV-1 subtyping, and the detection of HIV drug resistance (HIVDR) were performed. Viral subtyping revealed that the most prevalent HIV-1 subtype/circulating recombinant form (CRF) was CRF01_AE (55.6%), followed by recombinants between CRF01_AE and subtype B (17.8%) and then subtype B (15.6%). Recombinants containing CRF02_AG gene fragments were also detected (11.1%). Regarding HIVDR, no drug resistance-associated major mutations were found in pol genes encoding protease, although minor mutations were frequently detected. Furthermore, major mutations, including M184V (2.2%) and Y188L (2.2%), were identified in the viral pol gene encoding reverse transcriptase derived from a study participant, suggesting that the prevalence of HIVDR is low in the region.

Transmission dynamics of HIV-1 subtype B strains in Indonesia

“…To elucidate the epidemiological link between HIV-1B epidemics in Indonesia and those in the remainder of the world, we conducted phylogenetic analyses using our previously identified HIV-1B sequences 7–12 , other reported HIV-1B sequences in Indonesia, and closely related HIV-1B sequences available on the HIV Sequence Database of the Los Alamos National Laboratory (LANL, https://www.hiv.lanl.gov/). HIV-1 subtyping was performed on the gag , pol , and env genes using the Recombination Identification Program (RIP) available on the LANL database in our previous studies 7–12 , and recombinant viruses containing HIV-1B gene fragments were not included in the present study. As Indonesian HIV-1B strains, 32 sequences from our previous studies (Genbank accession no.…”

“…As Indonesian HIV-1B strains, 32 sequences from our previous studies (Genbank accession no. KM212841, KM212867, KM212896, KM212925, KU596470, KU596473, KU596476, KU596479, KU596480 - KU596482, KU596487, KU596495, KU596498, KU596500, KU596502, KU596507, KU596511, KU596514, KU596517, KU596519 - KU596522, KU596527, KU596534, KU596535, KU596537, KU596538, KU596540, KX639376, KX639377, KX639381, KX639383, KX639384, KX639390, KX639391, KX639395, KX639397, KX639398, MG717595, MG717596, MG717603, MG717604, MG717612, MG717620, MG717631, MG717632, MG717637, MG717638, MG717644, MG717650, MG793084, MG793091, MG793095, MG793097, MG793174, MG793177, MG793183, MG793184, MH727252, and MH727285, HIV-1 pol gene sequences encoding viral protease and reverse transcriptase, were separately registered to Genbank) 7–12 and an Indonesian HIV-1B sequence (GenBank accession no. KY927962) from the LANL database were examined in the present study.…”

“…We previously revealed that although circulating recombinant form (CRF) 01_AE is a predominant subtype in Indonesia, HIV-1B is also widely prevalent in this country 7–12 . Eastern parts of Indonesia, such as the Papua and West Papua provinces, have a high prevalence of HIV-1B 7,8,13 .…”

Detection of Human Immunodeficiency Virus Type 1 Transmitted Drug Resistance among Treatment-Naive Individuals Residing in Jakarta, Indonesia

“…Amplification of HIV-1 PR and RT genes were conducted by a nested polymerase chain reaction (PCR) using the Gotaq green master mix (Promega, Madison, WI, USA) or Ex Taq (Takara Bio, Shiga, Japan) and primer sets described previously. 6 Primer sequences are available upon request. We carried out a limiting dilution of DNA samples, and endpoint PCR amplicon which may be from the major population of virus in infected individuals were subjected to sequencing analysis using the BigDye Terminator v3.1 Cycle Sequencing kit (Applied Biosystems, Foster City, CA, USA) and the ABI PRISM 3500 xl genetic analyzer (Applied Biosystems, Foster City, CA, USA).…”

Genotypic Characterization of Human Immunodeficiency Virus Type 1 Isolated from Antiretroviral Treatment-Experienced Individuals in Buleleng Regency, Bali, Indonesia

“…CRF01_AE, the second predominant circulating CRF accounting for 5% of infection cases worldwide in 2004-2007, is responsible for the vast majority of infections in Southeast Asia, including several regions in Indonesia. [3][4][5][6][7] Subtypes and CRFs may differ in the rates of disease progression and viral transmission.…”