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Bakri FG, Mukattash HH, Esmeiran H, Schluck G, Storme CK, Broach E, Mebrahtu T, Alhawarat M, Valencia-Ruiz A, M'Hamdi O, Malia JA, Hassen Z, Shafei MMS, Alkhatib AY, Gazo M, Jaradat SA, Gomez Y, McGeehon S, McCauley MD, Moreland SC, Darden JM, Amare M, Crowell TA, Vasan S, Michael NL, Ake JA, Modjarrad K, Scott PT, Peel SA, Hakre S. Clinical, molecular, and drug resistance epidemiology of HIV in Jordan, 2019-2021: A national study. Int J Infect Dis 2024; 145:107079. [PMID: 38697607 DOI: 10.1016/j.ijid.2024.107079] [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] [Received: 01/13/2024] [Revised: 04/01/2024] [Accepted: 04/28/2024] [Indexed: 05/05/2024] Open
Abstract
BACKGROUND Limited epidemiologic studies have been conducted in Jordan describing the HIV epidemic. This study aimed to address this gap to inform HIV prevention and control. METHODS A nationally-representative cross-sectional study was conducted among adults living with HIV in Jordan. Laboratory testing included HIV viral load and next-generation-sequencing-based clinical genotype. Log-binomial regression estimated risk ratios (RRs) and 95% confidence intervals (CIs). RESULTS Among 231 (70%) participants, most were male (184/80%), and from Jordan (217/94%). Among 188 treatment-experienced-participants (>6 months), 165 (88%) were virally suppressed. High-level resistance was most frequent against nucleoside reverse transcriptase inhibitor (13/81%), and integrase-strand transfer inhibitor (INSTI) (10/62%) drugs among viremic (≥1000 HIV copies/mL) treatment-experienced participants with drug-resistant mutations (DRMs, n = 16). Common HIV subtypes (n = 43) were B (6/14%), A1 (5/12%), and CRF01_AE (5/12%); additionally, novel recombinant forms were detected. In multivariate analysis, independently higher risk for late diagnosis (n = 49) was observed with diagnosis through blood donation (vs check-up: RR 2.20, 95%CI 1.16-4.17) and earlier time-period of diagnosis (1986-2014 vs 2015-2021: RR 2.87, 95%CI 1.46-5.62). CONCLUSIONS Late diagnosis and INSTI resistance endanger national HIV prevention and treatment in Jordan-high-level resistance to INSTI suggests therapeutic drug monitoring is needed for treatment efficacy and conservation of treatment options.
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Affiliation(s)
- Faris G Bakri
- Division of Infectious Diseases, Department of Internal Medicine, Jordan University Hospital, Amman, Jordan; Infectious Diseases and Vaccine Center, University of Jordan, Amman, Jordan
| | | | - Hiam Esmeiran
- HJF Medical Research International (HJFMRI), Amman, Jordan
| | - Glenna Schluck
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD
| | - Casey K Storme
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD
| | - Erica Broach
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD
| | - Tsedal Mebrahtu
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD
| | | | - Anais Valencia-Ruiz
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD; Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, MD
| | - Oussama M'Hamdi
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD; Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, MD
| | - Jennifer A Malia
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, MD
| | - Zebiba Hassen
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD
| | - Mah'd M S Shafei
- Central Public Health Laboratory, Ministry of Health, Amman, Jordan
| | - Ala Y Alkhatib
- Voluntary Counselling and Testing Center, Ministry of Health, Amman, Jordan
| | - Mahmoud Gazo
- Central Public Health Laboratory, Ministry of Health, Amman, Jordan
| | - Saied A Jaradat
- Princess Haya Biotechnology Center, Jordan University of Science and Technology, Irbid, Jordan
| | - Yessenia Gomez
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD; Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD
| | - Samantha McGeehon
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD; Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD
| | - Melanie D McCauley
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD; Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD
| | - Sarah C Moreland
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD; Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD
| | - Janice M Darden
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD; Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, MD
| | - Mihret Amare
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD; Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD
| | - Trevor A Crowell
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD
| | - Sandhya Vasan
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD; Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD
| | - Nelson L Michael
- Center for Infectious Diseases Research, Walter Reed Army Institute of Research, Silver Spring, MD
| | - Julie A Ake
- United States Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, MD
| | - Kayvon Modjarrad
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD
| | - Paul T Scott
- Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD
| | - Sheila A Peel
- Diagnostics and Countermeasures Branch, Walter Reed Army Institute of Research, Silver Spring, MD
| | - Shilpa Hakre
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, MD; Emerging Infectious Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD.
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Dong Z, Xu Z, Zhou Y, Tian R, Zhou K, Wang D, Ya X, Shen Q. Genetic characterization of HIV-1 viruses among cases with antiretroviral therapy failure in Suzhou City, China. AIDS Res Ther 2023; 20:41. [PMID: 37381002 PMCID: PMC10303762 DOI: 10.1186/s12981-023-00540-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2022] [Accepted: 06/21/2023] [Indexed: 06/30/2023] Open
Abstract
BACKGROUND This retrospective study aimed to characterize the distribution of HIV-1 genotypes and the prevalence of drug resistance mutations in people with antiretroviral treatment (ART) failure in Suzhou City, China. METHODS Pol gene of HIV-1 viruses in blood samples of EDTA anticoagulants from 398 patients with failed antiviral treatment was successfully amplified by using an in-house assay. Drug resistance mutations were analyzed by using the Stanford HIV Drug Resistance Database system ( https://hivdb.stanford.edu/hivdb/by-mutations/ ). HIV-1 genotypes were determined by the REGA HIV subtyping tool (version 3.46, https://www.genomedetective.com/app/typingtool/hiv ). Near full-length genomes (NFLG) of HIV-1 viruses were obtained by next generation sequencing method. RESULTS Sequences analysis of the pol gene revealed that CRF 01_AE (57.29%, 228/398) was the dominant subtype circulating in Suzhou City, followed by CRF 07_BC (17.34%, 69/398), subtype B (7.54%, 30/398), CRF 08_BC (6.53%, 26/398), CRF 67_01B (3.02%, 12/398) and CRF55_01B (2.51%, 10/398). The overall prevalence of drug-resistant mutations in cases with ART failure was 64.57% (257/398), including 45.48% (181/398) for nucleotide reverse transcriptase inhibitors (NRTIs) mutations, 63.32% (252/398) for non-nucleoside reverse transcriptase inhibitors (NNRTIs) mutations, and 3.02% (12/398) for protease inhibitors (PIs) mutations. Ten near full-length genomes (NFLG) of HIV-1 viruses were identified, including six recombinants of CRF 01_AE and subtype B, two recombinants of CRF 01_AE, subtype B and subtype C sequences, one recombinant of CRF 01_AE and subtype C and one recombinant of CRF 01_AE, subtype A1 and subtype C. CONCLUSIONS The high prevalence of drug-resistant HIV-1 viruses was a serious challenge for HIV prevention and treatment of people with HIV infection. Treatment regimens for ART failure patients should be adjusted over time based on the outcome of drug resistance tests. NFLG sequencing facilitates the identification of new recombinants of HIV-1.
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Affiliation(s)
- Zefeng Dong
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Zhihui Xu
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Ying Zhou
- Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, 210003, China
| | - Runfang Tian
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Kai Zhou
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Di Wang
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China
| | - Xuerong Ya
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China.
| | - Qiang Shen
- Suzhou Center for Disease Control and Prevention, Suzhou, 215004, China.
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Mori M, Ode H, Kubota M, Nakata Y, Kasahara T, Shigemi U, Okazaki R, Matsuda M, Matsuoka K, Sugimoto A, Hachiya A, Imahashi M, Yokomaku Y, Iwatani Y. Nanopore Sequencing for Characterization of HIV-1 Recombinant Forms. Microbiol Spectr 2022; 10:e0150722. [PMID: 35894615 PMCID: PMC9431566 DOI: 10.1128/spectrum.01507-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 07/06/2022] [Indexed: 11/23/2022] Open
Abstract
High genetic diversity, including the emergence of recombinant forms (RFs), is one of the most prominent features of human immunodeficiency virus type 1 (HIV-1). Conventional detection of HIV-1 RFs requires pretreatments, i.e., cloning or single-genome amplification, to distinguish them from dual- or multiple-infection variants. However, these processes are time-consuming and labor-intensive. Here, we constructed a new nanopore sequencing-based platform that enables us to obtain distinctive genetic information for intersubtype RFs and dual-infection HIV-1 variants by using amplicons of HIV-1 near-full-length genomes or two overlapping half-length genome fragments. Repeated benchmark tests of HIV-1 proviral DNA revealed consensus sequence inference with a reduced error rate, allowing us to obtain sufficiently accurate sequence data. In addition, we applied the platform for sequence analyses of 9 clinical samples with suspected HIV-1 RF infection or dual infection according to Sanger sequencing-based genotyping tests for HIV-1 drug resistance. For each RF infection case, replicated analyses involving our nanopore sequencing-based platform consistently produced long consecutive analogous consensus sequences with mosaic genomic structures consisting of two different subtypes. In contrast, we detected multiple heterologous sequences in each dual-infection case. These results demonstrate that our new nanopore sequencing platform is applicable to identify the full-length HIV-1 genome structure of intersubtype RFs as well as dual-infection heterologous HIV-1. Since the genetic diversity of HIV-1 continues to gradually increase, this system will help accelerate full-length genome analysis and molecular epidemiological surveillance for HIV-1. IMPORTANCE HIV-1 is characterized by large genetic differences, including HIV-1 recombinant forms (RFs). Conventional genetic analyses require time-consuming pretreatments, i.e., cloning or single-genome amplification, to distinguish RFs from dual- or multiple-infection cases. In this study, we developed a new analytical system for HIV-1 sequence data obtained by nanopore sequencing. The error rate of this method was reduced to ~0.06%. We applied this system for sequence analyses of 9 clinical samples with suspected HIV-1 RF infection or dual infection, which were extracted from 373 cases of HIV patients based on our retrospective analysis of HIV-1 drug resistance genotyping test results. We found that our new nanopore sequencing platform is applicable to identify the full-length HIV-1 genome structure of intersubtype RFs as well as dual-infection heterologous HIV-1. Our protocol will be useful for epidemiological surveillance to examine HIV-1 transmission as well as for genotypic tests of HIV-1 drug resistance in clinical settings.
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Affiliation(s)
- Mikiko Mori
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
- Division of Basic Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Hirotaka Ode
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Mai Kubota
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Yoshihiro Nakata
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
- Division of Basic Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Takaaki Kasahara
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
- Division of Basic Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Urara Shigemi
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Reiko Okazaki
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Masakazu Matsuda
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Kazuhiro Matsuoka
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Atsuko Sugimoto
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Atsuko Hachiya
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Mayumi Imahashi
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Yoshiyuki Yokomaku
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
| | - Yasumasa Iwatani
- Clinical Research Center, National Hospital Organization Nagoya Medical Center, Nagoya, Japan
- Division of Basic Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
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