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Khairunisa SQ, Indriati DW, Megasari NLA, Ueda S, Kotaki T, Fahmi M, Ito M, Rachman BE, Hidayati AN, Nasronudin, Kameoka M. Spatial-temporal transmission dynamics of HIV-1 CRF01_AE in Indonesia. Sci Rep 2024; 14:9917. [PMID: 38730038 PMCID: PMC11087524 DOI: 10.1038/s41598-024-59820-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 04/16/2024] [Indexed: 05/12/2024] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) remains a serious health threat in Indonesia. In particular, the CRF01_AE viruses were the predominant HIV-1 strains in various cities in Indonesia. However, information on the dynamic transmission characteristics and spatial-temporal transmission of HIV-1 CRF01_AE in Indonesia is limited. Therefore, the present study examined the spatial-temporal transmission networks and evolutionary characteristics of HIV-1 CRF01_AE in Indonesia. To clarify the epidemiological connection between CRF01_AE outbreaks in Indonesia and the rest of the world, we performed phylogenetic studies on nearly full genomes of CRF01_AE viruses isolated in Indonesia. Our results showed that five epidemic clades, namely, IDN clades 1-5, of CRF01_AE were found in Indonesia. To determine the potential source and mode of transmission of CRF01_AE, we performed Bayesian analysis and built maximum clade credibility trees for each clade. Our study revealed that CRF01_AE viruses were commonly introduced into Indonesia from Southeast Asia, particularly Thailand. The CRF01_AE viruses might have spread through major pandemics in Asian countries, such as China, Vietnam, and Laos, rather than being introduced directly from Africa in the early 1980s. This study has major implications for public health practice and policy development in Indonesia. The contributions of this study include understanding the dynamics of HIV-1 transmission that is important for the implementation of HIV disease control and prevention strategies in Indonesia.
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Affiliation(s)
- Siti Qamariyah Khairunisa
- Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Dwi Wahyu Indriati
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Department of Health, Vocational Faculty, Universitas Airlangga, Surabaya, Indonesia
| | - Ni Luh Ayu Megasari
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Postgraduate School, Universitas Airlangga, Surabaya, Indonesia
| | - Shuhei Ueda
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo, Japan
- Department of Public Health, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Suma-ku, Kobe, Hyogo, 654-0142, Japan
| | - Tomohiro Kotaki
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Department of Public Health, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Suma-ku, Kobe, Hyogo, 654-0142, Japan
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Muhamad Fahmi
- Research Department, Research Institute for Humanity and Nature, Kyoto, Japan
- Research Organization of Science and Technology, Ritsumeikan University, Kusatsu, Japan
| | - Masahiro Ito
- Department of Bioinformatics, College of Life Sciences, Ritsumeikan University, Kusatsu, Japan
| | - Brian Eka Rachman
- Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Afif Nurul Hidayati
- Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Nasronudin
- Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia.
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.
| | - Masanori Kameoka
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia.
- Department of Public Health, Kobe University Graduate School of Health Sciences, 7-10-2 Tomogaoka, Suma-ku, Kobe, Hyogo, 654-0142, Japan.
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Nurjannah, Jayanti S, Tanoerahardjo FS, Al Musyahadah US, Sukowati CHC, Massi MN. Major Drug Resistance Mutations on Reverse Transcriptase Gene in Human Immunodeficiency Virus Type-1 in Indonesia: A Systematic Review. Curr HIV/AIDS Rep 2024; 21:31-39. [PMID: 38244171 DOI: 10.1007/s11904-023-00687-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/29/2023] [Indexed: 01/22/2024]
Abstract
PURPOSE OF REVIEW The prevalence of HIV-1 in Indonesia is on a concerning upward trajectory, with a concurrent rise in the development of drug-resistant strains, challenging the efficacy of antiretroviral therapy (ART). Many mutations have been found in the pol gene that makes HIV resistant to ART. We aim to review the major drug resistance mutations (DRMs) of reverse transcriptase (RT) of pol gene in HIV-1 cases in Indonesia. RECENT FINDINGS A total of eleven articles reporting DRMs in HIV-1 subjects from various regions between 2015-2020 in Indonesia are included. The prevalence of major DRMs on the RT gene in studies included varies from 3.4% to 34%. The CRF01_AE subtype stands out as the predominant variant. Notably, the prevalence of major DRMs in ART-experienced individuals is 22.1%, while ART-naïve individuals show a lower rate of 4.4%. Among the RT gene mutations, M184I/V emerges as the most prevalent (10.5%) within the nucleos(t)ide reverse transcriptase inhibitors (NRTI) group, while K103N leads among the non-NRTI (NNRTI) group, with a frequency of 6.4%. Regionally, North Sulawesi records the highest prevalence of major DRMs in the RT gene at 21.1%, whereas Riau and Central Papua exhibit the lowest rates at 3.4%. Significant variations in drug resistance mutations within the RT gene across Indonesian regions highlight the importance of closely monitoring and evaluating the effectiveness of current antiretroviral therapy (ART) regimens. Considerably, more studies are needed to understand better and overcome the emergence of DRMs on HIV-1 patients in Indonesia.
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Affiliation(s)
- Nurjannah
- Postgraduate School, Hasanuddin University, Makassar, 90245, Indonesia
- Ministry of Health of Republic Indonesia, Jakarta Selatan, 12950, Indonesia
| | - Sri Jayanti
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, 16911, Indonesia
| | | | - Ummu Syauqah Al Musyahadah
- Department of Bioinformatics, Faculty of Health Technology, University of Megarezky, Makassar, 90234, Indonesia
| | - Caecilia Hapsari Ceriapuri Sukowati
- Eijkman Research Center for Molecular Biology, National Research and Innovation Agency, Cibinong, 16911, Indonesia
- Liver Cancer Unit, Fondazione Italiana Fegato ONLUS, AREA Science Park, 34149, Trieste, Italy
| | - Muhammad Nasrum Massi
- Department of Clinical Microbiology, Hasanuddin University, Makassar, 90245, Indonesia.
- Microbiology Laboratory, Hasanuddin University Hospital, Makassar, 90245, Indonesia.
- Hasanuddin University Medical Research Center Laboratory, Faculty of Medicine, Hasanuddin University, Makassar, 90245, Indonesia.
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Khairunisa SQ, Megasari NLA, Ueda S, Budiman W, Kotaki T, Nasronudin, Kameoka M. 2018-2019 Update on the Molecular Epidemiology of HIV-1 in Indonesia. AIDS Res Hum Retroviruses 2020; 36:957-963. [PMID: 32799643 DOI: 10.1089/aid.2020.0151] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The HIV type 1 (HIV-1) epidemic has continued to grow in Indonesia; however, continuous updates on the epidemiology of HIV-1 in Indonesia remain challenging because it is the biggest archipelago in the world. Furthermore, the emergence of HIV drug resistance (HIVDR) has had a negative impact on the treatment of infected individuals. In this study, we performed HIV-1 subtyping and the detection of HIVDR in 105 HIV-1-infected individuals residing in various cities in Indonesia during 2018-2019. The results obtained identified CRF01_AE as the major epidemic HIV-1 strain, responsible for 81.9% of infection cases, followed by subtype B (12.4%), CRF02_AG (3.8%), CRF52_01B (1%), and a recombinant between CRF01_AE and CRF02_AG (1.0%). Major drug resistance-associated mutations against reverse transcriptase inhibitors were detected in 20% of samples. These results suggest that CRF01_AE is a major HIV-1 strain in Indonesia, while CRF02_AG is emerging. The prevalence of HIVDR in Indonesia needs to be monitored.
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Affiliation(s)
- Siti Qamariyah Khairunisa
- Indonesian-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Ni Luh Ayu Megasari
- Indonesian-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
| | - Shuhei Ueda
- Indonesian-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo, Japan
- Department of Public Health, Kobe University Graduate School of Health Sciences, Hyogo, Japan
| | | | - Tomohiro Kotaki
- Department of Public Health, Kobe University Graduate School of Health Sciences, Hyogo, Japan
| | - Nasronudin
- Indonesian-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Universitas Airlangga, Surabaya, Indonesia
- Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Masanori Kameoka
- Department of Public Health, Kobe University Graduate School of Health Sciences, Hyogo, Japan
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Ueda S, Witaningrum AM, Khairunisa SQ, Kotaki T, Nasronudin, Kameoka M. Genetic Diversity and Drug Resistance of HIV-1 Circulating in North Sulawesi, Indonesia. AIDS Res Hum Retroviruses 2019; 35:407-413. [PMID: 30229669 DOI: 10.1089/aid.2018.0221] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Manado, the capital city of North Sulawesi, is a unique region in Indonesia because of its religion. We collected peripheral blood samples from 63 individuals on antiretroviral therapy. The amplification of viral genomic fragments, viral subtyping, detection of HIV drug resistance-associated mutations (DRAMs), and phylogenetic analyses were performed. Viral subtyping revealed that the most prevalent HIV type 1 (HIV-1) subtype/circulating recombinant form (CRF) was CRF01_AE (84.1%), followed by subtype B (6.8%) and recombinants between CRF01_AE and CRF02_AG (4.5%). Although no major DRAMs were present in protease genes, they were detected in reverse transcriptase (RT) genes. Nine of 38 samples (23.7%) had major DRAMs against nucleoside RT inhibitors (NRTIs) and/or non-NRTIs. The results of phylogenetic analyses indicated that CRF01_AE in North Sulawesi is related to that in Bali. Therefore, Bali may play an important role in circulating CRF01_AE in North Sulawesi.
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Affiliation(s)
- Shuhei Ueda
- Department of Public Health, Kobe University Graduate School of Health Sciences, Hyogo, Japan
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo, Japan
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Adiana Mutamsari Witaningrum
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Siti Qamariyah Khairunisa
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Tomohiro Kotaki
- Department of Public Health, Kobe University Graduate School of Health Sciences, Hyogo, Japan
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Nasronudin
- Indonesia-Japan Collaborative Research Center for Emerging and Re-emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
- Faculty of Medicine, Airlangga University, Surabaya, Indonesia
- Airlangga Hospital, Surabaya, Indonesia
| | - Masanori Kameoka
- Department of Public Health, Kobe University Graduate School of Health Sciences, Hyogo, Japan
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo, Japan
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Khairunisa SQ, Ueda S, Witaningrum AM, Yunifiar Matondang MQ, Indriati DW, Kotaki T, Nasronudin, Kameoka M. Genotypic Characterization of Human Immunodeficiency Virus Type 1 Prevalent in Kepulauan Riau, Indonesia. AIDS Res Hum Retroviruses 2018; 34:555-560. [PMID: 29589465 DOI: 10.1089/aid.2018.0040] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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.
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Affiliation(s)
- Siti Qamariyah Khairunisa
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Shuhei Ueda
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo, Japan
- Department of International Health, Kobe University Graduate School of Health Sciences, Hyogo, Japan
| | - Adiana Mutamsari Witaningrum
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Muhammad Qushai Yunifiar Matondang
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
| | - Dwi Wahyu Indriati
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
- Department of Health, Faculty of Vocational Studies, Airlangga University, Surabaya, Indonesia
| | - Tomohiro Kotaki
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
- Department of International Health, Kobe University Graduate School of Health Sciences, Hyogo, Japan
| | - Nasronudin
- Indonesian-Japan Collaborative Research Center for Emerging and Re-Emerging Infectious Diseases, Institute of Tropical Disease, Airlangga University, Surabaya, Indonesia
- Faculty of Medicine, Airlangga University, Surabaya, Indonesia
- Airlangga University Hospital, Surabaya, Indonesia
| | - Masanori Kameoka
- Center for Infectious Diseases, Kobe University Graduate School of Medicine, Hyogo, Japan
- Department of International Health, Kobe University Graduate School of Health Sciences, Hyogo, Japan
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Wang L, Xu X, Zhang Z, Zhang D, Liu X, Zhang L. Green sample clean-up based on magnetic multiwalled carbon nanotubes for the determination of lamivudine by high performance liquid chromatography. RSC Adv 2015. [DOI: 10.1039/c5ra00102a] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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