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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, Kotaki T, Hidayati AN, Nasronudin, Kameoka M. Subtype Distribution and Drug Resistance Patterns Among HIV-1 Strains Prevalent in Makassar, Indonesia. AIDS Res Hum Retroviruses 2023; 39:124-129. [PMID: 36656663 DOI: 10.1089/aid.2022.0139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) is characterized by a large degree of genetic variability because of high rates of recombination and mutation, sizable population sizes, and rapid replication. Therefore, this study investigated HIV-1 subtype distribution and the appearance of drug resistance mutations (DRMs) in viruses that are prevalent in Makassar, South Sulawesi, Indonesia. The HIV-1 pol, env, and gag genes were amplified from 63 infected individuals and sequenced for a subtyping analysis. CRF01_AE was identified as the predominant HIV-1 circulating recombinant form (CRF) in Makassar, South Sulawesi, Indonesia. Subtype B and recombinant viruses containing CRF01_AE, CRF02_AG, and/or subtype B gene fragments were also detected. Several major DRMs against non-nucleoside reverse transcriptase inhibitors were found among antiretroviral therapy (ART)-experienced subjects, whereas ART-naive subjects did not possess any transmitted drug resistance. The prevalence of DRMs was very high among ART-experienced subjects; therefore, further surveillance is required in this region.
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Affiliation(s)
- Siti Qamariyah Khairunisa
- Doctoral Program-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
| | - 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, Kobe, Japan.,Division of Global Infectious Diseases, Department of Public Health, Kobe University Graduate School of Health Sciences, Kobe, Japan
| | - Tomohiro Kotaki
- Department of Virology, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Afif Nurul Hidayati
- Doctoral Program-Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia.,Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia
| | - Nasronudin
- Doctoral Program-Faculty of Medicine, Universitas Airlangga, Surabaya, Indonesia.,Faculty of Medicine, 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.,Division of Global Infectious Diseases, Department of Public Health, Kobe University Graduate School of Health Sciences, Kobe, Japan
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Ji H, Sandstrom P. Overview of the Analytes Applied in Genotypic HIV Drug Resistance Testing. Pathogens 2022; 11:pathogens11070739. [PMID: 35889985 PMCID: PMC9321895 DOI: 10.3390/pathogens11070739] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/23/2022] [Accepted: 06/28/2022] [Indexed: 01/25/2023] Open
Abstract
The close monitoring of HIV drug resistance using genotypic HIV drug resistance testing (HIVDRT) has become essential for effective HIV/AIDS management at both individual and population levels. Over the years, a broad spectrum of analytes or specimens have been applied or attempted in HIVDRT; however, the suitability and performance of these analytes in HIVDRT and the clinical relevance of the results from them may vary significantly. This article provides a focused overview of the performance, strengths, and weaknesses of various analytes while used in HIVDRT, which may inform the optimal analytes selection in different application contexts.
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Affiliation(s)
- Hezhao Ji
- National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada;
- Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
- Correspondence: ; Tel.: +1-204-789-6521
| | - Paul Sandstrom
- National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada;
- Max Rady College of Medicine, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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