Genotypic Characterization of Human Immunodeficiency Virus Type 1 Derived from Antiretroviral Therapy-Naive Individuals Residing in Sorong, West Papua

Abstract

Papua and West Papua provinces have the highest prevalence rate of human immunodeficiency virus type 1 (HIV-1) infection in Indonesia; however, data on the molecular epidemiology of HIV-1 are limited. We conducted a genotypic study on HIV-1 genes derived from antiretroviral therapy-naive individuals residing in Sorong, West Papua. HIV-1 genomic fragments were amplified from 43 peripheral blood samples, and sequencing analysis of the genes was carried out. Of the 43 samples, 41 protease (PR), 31 reverse transcriptase (RT), 26 gag, and 25 env genes were sequenced. HIV-1 subtyping revealed that CRF01_AE (48.8%, 21/43) and subtype B (41.9%, 18/43) were the major subtypes prevalent in the region, whereas other recombinant forms were also detected. Major drug resistance-associated mutations for PR inhibitors were not detected; however, mutations for the RT inhibitors, A62V and E138A, appeared in a few samples, indicating the possible emergence of transmitted HIV-1 drug resistance in Sorong, West Papua.

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

“…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.…”

“…A study in Malaysia, a neighbor coun-try 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.…”

“…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 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][10][11][12][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].…”

Appearance of Drug Resistance Mutations Among the Dominant HIV-1 Subtype, CRF01_AE in Maumere, Indonesia

“…However, TDR is considered to have a greater impact, and may rapidly deteriorate the effectiveness of first-line regimens at the population level. Since individuals with TDR start ART with a lower genetic barrier to resistance, there is a higher risk of virological failure due to the appearance of drug-resistant mutations early after the initiation of first-line therapy [12,13,14,15,16]. Thus, the effectiveness of ART needs to be monitored.…”