1
|
Adhiambo M, Makwaga O, Adungo F, Kimani H, Mulama DH, Korir JC, Mwau M. Human immunodeficiency virus (HIV) type 1 genetic diversity in HIV positive individuals on antiretroviral therapy in a cross-sectional study conducted in Teso, Western Kenya. Pan Afr Med J 2021; 38:335. [PMID: 34046145 PMCID: PMC8140725 DOI: 10.11604/pamj.2021.38.335.26357] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Accepted: 04/01/2021] [Indexed: 11/16/2022] Open
Abstract
Introduction high HIV-1 infection rates and genetic diversity especially in African population pose significant challenges in HIV-1 clinical management and drug design and development. HIV-1 is a major health challenge in Kenya and causes mortality and morbidity in the country as well as straining the healthcare system and the economy. This study sought to identify HIV-1 genetic subtypes circulating in Teso, Western Kenya which borders the Republic of Uganda. Methods a cross-sectional study was conducted in January 2019 to December 2019. Sequencing of the partial pol gene was carried out on 80 HIV positive individuals on antiretroviral therapy. Subtypes and recombinant forms were generated using the jumping profile hidden Markov model. Alignment of the sequences was done using ClustalW program and phylogenetic tree constructed using MEGA7 neighbor-joining method. Results sixty three samples were successful sequenced. In the analysis of these sequences, it was observed that HIV-1 subtype A1 was predominant 43 (68.3%) followed by D 8 (12.7%) and 1 (1.6%) each of C, G and B and inter-subtype recombinants A1-D 3 (4.8%), A1-B 2 (3.2%) and 1 (1.6%) each of A1-A2, A1-C, BC and BD. Phylogenetic analysis of these sequences showed close clustering of closely related and unrelated sequences with reference sequences. Conclusion there was observed increased genetic diversity of HIV-1 subtypes which not only pose a challenge in disease control and management but also drug design and development. Therefore, there is need for continued surveillance to enhance future understanding of the geographical distribution and transmission patterns of the HIV epidemic.
Collapse
Affiliation(s)
- Maureen Adhiambo
- Department of Biological Sciences, Masinde Muliro University of Science and Technology, Kakamega, Kenya.,Department of Infectious Diseases Control Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Olipher Makwaga
- Department of Biological Sciences, Masinde Muliro University of Science and Technology, Kakamega, Kenya.,Department of Infectious Diseases Control Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Ferdinard Adungo
- Department of Infectious Diseases Control Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Humphrey Kimani
- Department of Infectious Diseases Control Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - David Hughes Mulama
- Department of Biological Sciences, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Jackson Cheruiyot Korir
- Department of Biological Sciences, Masinde Muliro University of Science and Technology, Kakamega, Kenya
| | - Matilu Mwau
- Department of Infectious Diseases Control Research, Kenya Medical Research Institute, Nairobi, Kenya
| |
Collapse
|
2
|
Application of a Sanger-Based External Quality Assurance Strategy for the Transition of HIV-1 Drug Resistance Assays to Next Generation Sequencing. Viruses 2020; 12:v12121456. [PMID: 33348705 PMCID: PMC7766986 DOI: 10.3390/v12121456] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Accepted: 12/15/2020] [Indexed: 01/05/2023] Open
Abstract
The National Institute of Allergy and Infectious Diseases (NIAID) Virology Quality Assurance (VQA) established a robust proficiency testing program for Sanger sequencing (SS)-based HIV-1 drug resistance (HIVDR) testing in 2001. While many of the lessons learned during the development of such programs may also apply to next generation sequencing (NGS)-based HIVDR assays, challenges remain for the ongoing evaluation of NGS-based testing. These challenges include a proper assessment of assay accuracy and the reproducibility of low abundance variant detection, intra- and inter-assay performance comparisons among laboratories using lab-defined tests, and different data analysis pipelines designed for NGS. In collaboration with the World Health Organization (WHO) Global HIVDR Laboratory Network and the Public Health Agency of Canada, the Rush VQA program distributed archived proficiency testing panels to ten laboratories to evaluate internally developed NGS assays. Consensus FASTA files were submitted using 5%, 10%, and 20% variant detection thresholds, and scored based on the same criteria used for SS. This small study showed that the SS External Quality Assurance (EQA) approach can be used as a transitional strategy for using NGS to generate SS-like data and for ongoing performance while using NGS data from the same quality control materials to further evaluate NGS assay performance.
Collapse
|
3
|
Villalobos C, Ceballos ME, Ferrés M, Palma C. Drug resistance mutations in proviral DNA of HIV-infected patients with low level of viremia. J Clin Virol 2020; 132:104657. [PMID: 33049643 DOI: 10.1016/j.jcv.2020.104657] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 08/27/2020] [Accepted: 10/05/2020] [Indexed: 11/16/2022]
Affiliation(s)
- Camila Villalobos
- Infectious Diseases Department, Escuela de Medicina, Pontificia Universidad Católica de Chile, Chile; Infectious Diseases Service, Hospital Naval Almirante Nef, Chile.
| | - María Elena Ceballos
- Infectious Diseases Department, Escuela de Medicina, Pontificia Universidad Católica de Chile, Chile.
| | - Marcela Ferrés
- Pediatric Infectious Diseases and Inmunology Department, Escuela de Medicina, Pontificia Universidad Católica de Chile, Chile; Infectology and Molecular Virology Laboratory, Red Salud UC CHRISTUS, Chile.
| | - Carlos Palma
- Infectology and Molecular Virology Laboratory, Red Salud UC CHRISTUS, Chile.
| |
Collapse
|
4
|
Tien TV, Pho DC, Hong LT, Ba HP, Nam LV, Hung PN. Antiretroviral drug resistance mutations among patients failing first-line treatment in Hanoi, Vietnam. Infect Drug Resist 2019; 12:1237-1242. [PMID: 31190911 PMCID: PMC6522650 DOI: 10.2147/idr.s196448] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2018] [Accepted: 02/13/2019] [Indexed: 01/31/2023] Open
Abstract
Objectives: To study the prevalence of drug resistance and genotype testing for HIV drug resistance on HIV/AIDS patients with first-line antiretroviral treatment failure at Dong Da Hospital, Hanoi, Vietnam. Patients and methods: Forty-seven patients in Dong Da Hospital, Hanoi, with confirmation of first-line antiretroviral therapy (ART) failure were enrolled in this study from June 2006 to December 2016. Both the protease and reverse transcriptase genes were amplified and sequenced using Trugene® HIV-1 Genotyping Kit and OpenGene® DNA system at the biomolecular laboratory of the National Institute of Hygiene and Epidemiology, Vietnam. The Stanford HIV database algorithm was used for interpretation of resistance data and genotyping. Results: Drug resistance mutations were 90.7% in patients with first-line treatment failure. Amongst patients with drug resistance mutation, 97.7% resisted to non-nucleoside reverse transcriptase inhibitors (NNRTIs), followed by nucleoside reverse transcriptase inhibitors (NRTIs, 95.3%) and protease inhibitors (PIs, 11.6%). Amongst the genetic mutations resistant to NNRTIs, G190S mutation was the highest (51.2%), K101HQ mutation was 39.5% and Y181I mutation was 34.9%. In genetic mutations to NRTIs, M184V mutation was 88.4%. In thymidine analogue mutations, K70R mutation was the most common (37.2%), followed by D67N, T215F and T69N mutations (27.9%, 27.9% and 25.6%, respectively). In genetic mutations in PIs, M36I and K20R mutations made up 9.3%. In NNRTIs, the prevalence of nevirapine resistance was 55.8%, and that of efavirenz resistance was 4.7%. In NRTIs, the ratio of lamivudine resistance was 93.0%, and that of zidovudine resistance was 9.3%. No lopinavir/ritonavir resistance was recorded. Conclusions: Drug resistance mutations in patients with first-line ART failure had a high prevalence of NNRTI and NRTI resistance but still susceptible to PIs.
Collapse
Affiliation(s)
- Tran Viet Tien
- Department of Infectious Diseases, Military Hospital 103, Vietnam Military Medical University, Hanoi City, Vietnam
| | - Dinh Cong Pho
- Faculty of Medicine, Vietnam Military Medical University, Ha Dong District, Hanoi City, Vietnam
| | - Le Thu Hong
- Department of Microbiology, Military Hospital 103, Vietnam Military Medical University, Hanoi City, Vietnam
| | - Hien Pham Ba
- Department of Infectious Diseases, Dong Da Hospital, Hanoi City, Vietnam
| | - Le Van Nam
- Department of Infectious Diseases, Military Hospital 103, Vietnam Military Medical University, Hanoi City, Vietnam
| | - Pham Ngoc Hung
- Department of Epidemiology, Vietnam Military Medical University, Hanoi City, Vietnam.,Department of Training, Vietnam Military Medical University, Hanoi City, Vietnam
| |
Collapse
|
5
|
Sepúlveda-Torres LDC, Rishishwar L, Rogers ML, Ríos-Olivares E, Boukli N, Jordan IK, Cubano LA. A decade of viral mutations and associated drug resistance in a population of HIV-1+ Puerto Ricans: 2002-2011. PLoS One 2017; 12:e0177452. [PMID: 28493944 PMCID: PMC5426751 DOI: 10.1371/journal.pone.0177452] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 04/27/2017] [Indexed: 12/14/2022] Open
Abstract
Puerto Rico has one of the highest rates of HIV/AIDS seen for any US state or territory, and antiretroviral therapy has been a mainstay of efforts to mitigate the HIV/AIDS public health burden on the island. We studied the evolutionary dynamics of HIV-1 mutation and antiretroviral drug resistance in Puerto Rico by monitoring the population frequency of resistance-associated mutations from 2002 to 2011. Whole blood samples from 4,475 patients were analyzed using the TRUGENE HIV-1 Genotyping Kit and OpenGene DNA Sequencing System in the Immunoretrovirus Research Laboratory at Universidad Central del Caribe. Results show that 64.0% of female and 62.9% of male patients had HIV-1 mutations that confer resistance to at least one antiretroviral medication. L63P and M184V were the dominant mutations observed for the protease (PRO) and reverse transcriptase (RT) encoding genes, respectively. Specific resistance mutations, along with their associated drug resistance profiles, can be seen to form temporal clusters that reveal a steadily changing landscape of resistance trends over time. Both women and men showed resistance mutations for an average of 4.8 drugs over the 10-year period, further underscoring the strong selective pressure exerted by antiretrovirals along with the rapid adaptive response of HIV. Nevertheless, both female and male patients showed a precipitous decrease for overall drug resistance, and for PRO mutations in particular, over the entire course of the study, with the most rapid decrease in frequency seen after 2006. The reduced HIV-1 mutation and drug resistance trends that we observed are consistent with previous reports from multi-year studies conducted around the world. Reduced resistance can be attributed to the use of more efficacious antiretroviral drug therapy, including the introduction of multi-drug combination therapies, which limited the ability of the virus to mount rapid adaptive responses to antiretroviral selection pressure.
Collapse
Affiliation(s)
- Lycely del C. Sepúlveda-Torres
- Department of Microbiology and Immunology, Universidad Central del Caribe, Bayamón, Puerto Rico, United States of America
| | - Lavanya Rishishwar
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
- Applied Bioinformatics Laboratory, Atlanta, Georgia, United States of America
| | - Maria Luisa Rogers
- Natural Sciences Department, Sacred Heart University, San Juan, Puerto Rico, United States of America
| | - Eddy Ríos-Olivares
- Department of Microbiology and Immunology, Universidad Central del Caribe, Bayamón, Puerto Rico, United States of America
| | - Nawal Boukli
- Department of Microbiology and Immunology, Universidad Central del Caribe, Bayamón, Puerto Rico, United States of America
| | - I. King Jordan
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, Georgia, United States of America
- PanAmerican Bioinformatics Institute, Cali, Valle del Cauca, Colombia
- Applied Bioinformatics Laboratory, Atlanta, Georgia, United States of America
| | - Luis A. Cubano
- Department of Microbiology and Immunology, Universidad Central del Caribe, Bayamón, Puerto Rico, United States of America
| |
Collapse
|
6
|
Parikh UM, McCormick K, van Zyl G, Mellors JW. Future technologies for monitoring HIV drug resistance and cure. Curr Opin HIV AIDS 2017; 12:182-189. [PMID: 28059958 PMCID: PMC6738332 DOI: 10.1097/coh.0000000000000344] [Citation(s) in RCA: 36] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
PURPOSE OF REVIEW Sensitive, scalable and affordable assays are critically needed for monitoring the success of interventions for preventing, treating and attempting to cure HIV infection. This review evaluates current and emerging technologies that are applicable for both surveillance of HIV drug resistance (HIVDR) and characterization of HIV reservoirs that persist despite antiretroviral therapy and are obstacles to curing HIV infection. RECENT FINDINGS Next-generation sequencing (NGS) has the potential to be adapted into high-throughput, cost-efficient approaches for HIVDR surveillance and monitoring during continued scale-up of antiretroviral therapy and rollout of preexposure prophylaxis. Similarly, improvements in PCR and NGS are resulting in higher throughput single genome sequencing to detect intact proviruses and to characterize HIV integration sites and clonal expansions of infected cells. SUMMARY Current population genotyping methods for resistance monitoring are high cost and low throughput. NGS, combined with simpler sample collection and storage matrices (e.g. dried blood spots), has considerable potential to broaden global surveillance and patient monitoring for HIVDR. Recent adaptions of NGS to identify integration sites of HIV in the human genome and to characterize the integrated HIV proviruses are likely to facilitate investigations of the impact of experimental 'curative' interventions on HIV reservoirs.
Collapse
Affiliation(s)
- Urvi M Parikh
- aDivision of Infectious Diseases, Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA bDivision of Medical Virology, Stellenbosch University and NHLS Tygerberg, Cape Town, South Africa
| | | | | | | |
Collapse
|
7
|
Praparattanapan J, Tragoolpua Y, Wongtrakul J, Kotarathitithum W, Chaiwarith R, Nuntachit N, Sirisanthana T, Supparatpinyo K. Comparison of in-house HIV-1 genotypic drug resistant test with commercial HIV-1 genotypic test kit. ASIAN BIOMED 2017. [DOI: 10.5372/1905-7415.0502.032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Abstract
Background: The use of combination antiretroviral therapy (cART) has become a standard of care in the treatment of HIV infection. However, antiretroviral drug resistance occurs in a substantial number of patients. In resource-limited settings, genotypic resistance assay using a commercial kit is costly.
Objective: Focus on the validation of an in-house HIV-1 specific genotypic drug resistance assay in Thai patients failing cART.
Materials and methods: Results of HIV-1 genotypic drug resistance assay was evaluated by comparing an inhouse method to a commercial test. The TRUGENE HIV-1 genotyping kit was used in 79 plasma specimens (49 from HIV patients failing cART therapy and 30 from proficiency testing panels).
Results: The results from the in-house assay were comparable to those obtained from the TRUGENE HIV-1 genotyping kit with >99.0% codon-to-codon agreement. The lower limit of detection by the in-house assay was approximately 100 copies/mL of HIV-1 RNA. In addition, this in-house assay would allow testing of samples from patients infected with HIV-1 subtype other than B.
Conclusion: The in-house HIV-1 genotypic drug resistance assay may be used as an alternative to commercial kits, particularly in resource limited settings.
Collapse
Affiliation(s)
- Jutarat Praparattanapan
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand Thailand
- Department of Medicine, Faculty of Medicine; Chiang Mai University, Chiang Mai 50200, Thailand
| | - Yingmanee Tragoolpua
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Jeerang Wongtrakul
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Wilai Kotarathitithum
- Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Romanee Chaiwarith
- Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Nontakan Nuntachit
- Department of Medicine, Faculty of Medicine, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Thira Sirisanthana
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| | - Khuanchai Supparatpinyo
- Correspondence to: Department of Medicine, Faculty of Medicine Chiang Mai University, Chiang Mai 50200, Thailand Thailand
- Research Institute for Health Sciences, Chiang Mai University, Chiang Mai 50200, Thailand
| |
Collapse
|
8
|
Jenabian MA, Talla F, Talla P, Mbopi-Kéou FX, Charpentier C, Kane CT, Bélec L. Pitfalls of antiretroviral drug resistance genotyping of HIV-1 Group M and Group N from Cameroon by sequenced-based assays. Niger Med J 2016; 56:420-4. [PMID: 26903701 PMCID: PMC4743293 DOI: 10.4103/0300-1652.171613] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Background: HIV-1 genotyping for antiretroviral drug resistance mutations (DRMs) were developed based basically on subtype B HIV-1 Group M, which represents only 10% of HIV strains worldwide. In sub-Saharan Africa, non-B subtypes HIV-1 largely predominate and HIV-1 genetic diversity could affect the performance of drug resistance genotyping assays. We compared prospectively the performance of the ViroSeq® and Trugene® genotyping assays to detect DRM in HIV-1-infected adult patients living in Douala, Cameroun. Materials and Methods: DRM in protease (P) and reverse transcriptase (RT) genes were assessed in parallel using both ViroSeq® and Trugene® assays in plasma samples from 45 first-line antiretroviral treatment-experienced patients in Douala, Cameroon. Results: Trugene HIV-1 Genotyping Assay® (Siemens Health Care Diagnostics, NY, USA) and ViroSeq HIV-1 Genotyping System®(Celera Diagnostics, CA, USA) assessed equivalently antiretroviral DRMs in P and RT genes from non-B HIV-1 Group M in 44 Cameroonian adults in virological failure; Trugene® was slightly more sensitive than ViroSeq® (100% vs. 91%). One patient infected by HIV-1 Group N was successfully amplified only by the Trugene HIV-1 Genotyping assay®, while ViroSeq HIV-1 Genotyping System v2.0® assay could not. Conclusion: Results showed the higher performance of the Trugene® system to detected and amplify P and RT genes targeting DRM to the principal antiretroviral drugs used in sub-Saharan Africa. Discrepancies between the results of HIV viral load assays and molecular tests should alert clinicians and virologists to the possibility of infection by an atypical variant virus, especially in Central Africa where very broad HIV-1 genetic diversity exists.
Collapse
Affiliation(s)
- Mohammad-Ali Jenabian
- Department of Biological Science and Bio Med Research Centre, University of Quebec at Montreal (UQAM), Montreal, QC, Canada
| | - Frédéric Talla
- Laboratory of Bio-Medical Analysis Litto-Labo, Douala, Cameroon
| | - Perrine Talla
- Laboratory of Bio-Medical Analysis Litto-Labo, Douala, Cameroon
| | - François-Xavier Mbopi-Kéou
- Department of Laboratories and Blood Safety, Ministry of Public Health and University of Yaounde I, Yaounde, Cameroon
| | - Charlotte Charpentier
- IAME, UMR 1137, University of Paris Diderot, Sorbonne Paris Cité, and Bichat-Claude Bernard Hospital, Virology Laboratory, Paris, France
| | - Coumba Toure Kane
- Bacteriology and Virology Laboratory, CHU Aristide Le Dantec, Dakar, Senegal
| | - Laurent Bélec
- Faculty of Medicine, Paris Descartes University Paris Descartes (Paris V), Sorbonne Paris Cité, Paris and Georges Pompidou European Hospital, Paris, France
| |
Collapse
|
9
|
Fu X, Cheng Z, Yu J, Choo P, Chen L, Choo J. A SERS-based lateral flow assay biosensor for highly sensitive detection of HIV-1 DNA. Biosens Bioelectron 2015; 78:530-537. [PMID: 26669705 DOI: 10.1016/j.bios.2015.11.099] [Citation(s) in RCA: 226] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2015] [Revised: 11/29/2015] [Accepted: 11/30/2015] [Indexed: 11/26/2022]
Abstract
User-friendly lateral flow (LF) strips have been extensively used for point-of-care (POC) self-diagnostics, but they have some limitations in their detection sensitivity and quantitative analysis because they only identify the high cut-off value of a biomarker by utilizing color changes that are detected with the naked eye. To resolve these problems associated with LF strips, we developed a novel surface-enhanced Raman scattering (SERS)-based LF assay for the quantitative analysis of a specific biomarker in the low concentration range. Herein, human immunodeficiency virus type 1 (HIV-1) DNA was chosen as the specific biomarker. Raman reporter-labeled gold nanoparticles (AuNPs) were employed as SERS nano tags for targeting and detecting the HIV-1 DNA marker, as opposed to using bare AuNPs in LF strips. It was possible to quantitatively analyze HIV-1 DNA with high sensitivity by monitoring the characteristic Raman peak intensity of the DNA-conjugated AuNPs. Under optimized conditions, the detection limit of our SERS-based lateral flow assay was 0.24 pg/mL, which was at least 1000 times more sensitive compared to colorimetric or fluorescent detection methods. These results demonstrate the potential feasibility of the proposed SERS-based lateral flow assay to quantitatively detect a broad range of genetic diseases with high sensitivity.
Collapse
Affiliation(s)
- Xiuli Fu
- Department of Bionano Technology, Hanyang University, Ansan 426-791, South Korea
| | - Ziyi Cheng
- Department of Bionano Technology, Hanyang University, Ansan 426-791, South Korea
| | - Jimin Yu
- Department of Bionano Technology, Hanyang University, Ansan 426-791, South Korea
| | - Priscilla Choo
- Department of Chemistry, Indiana University, Bloomington, IN 47405-102, USA
| | - Lingxin Chen
- Key Laboratory of Coastal Environmental Processes and Ecological Remediation, Yantai Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Jaebum Choo
- Department of Bionano Technology, Hanyang University, Ansan 426-791, South Korea.
| |
Collapse
|
10
|
Shafiee H, Wang S, Inci F, Toy M, Henrich TJ, Kuritzkes DR, Demirci U. Emerging technologies for point-of-care management of HIV infection. Annu Rev Med 2014; 66:387-405. [PMID: 25423597 DOI: 10.1146/annurev-med-092112-143017] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The global HIV/AIDS pandemic has resulted in 39 million deaths to date, and there are currently more than 35 million people living with HIV worldwide. Prevention, screening, and treatment strategies have led to major progress in addressing this disease globally. Diagnostics is critical for HIV prevention, screening and disease staging, and monitoring antiretroviral therapy (ART). Currently available diagnostic assays, which include polymerase chain reaction (PCR), enzyme-linked immunosorbent assay (ELISA), and western blot (WB), are complex, expensive, and time consuming. These diagnostic technologies are ill suited for use in low- and middle-income countries, where the challenge of the HIV/AIDS pandemic is most severe. Therefore, innovative, inexpensive, disposable, and rapid diagnostic platform technologies are urgently needed. In this review, we discuss challenges associated with HIV management in resource-constrained settings and review the state-of-the-art HIV diagnostic technologies for CD4(+) T lymphocyte count, viral load measurement, and drug resistance testing.
Collapse
Affiliation(s)
- Hadi Shafiee
- Division of Biomedical Engineering, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts 02115
| | | | | | | | | | | | | |
Collapse
|
11
|
Sungkanuparph S, Pasomsub E, Chantratita W. Surveillance of transmitted HIV drug resistance in antiretroviral-naive patients aged less than 25 years, in Bangkok, Thailand. J Int Assoc Provid AIDS Care 2013; 13:12-4. [PMID: 23708678 DOI: 10.1177/2325957413488200] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Emergence of transmitted HIV drug resistance (TDR) is a concern after global scale-up of antiretroviral therapy (ART). World Health Organization had developed threshold survey method for surveillance of TDR in resource-limited countries. ART in Thailand has been scaling up for >10 years. To evaluate the current TDR in Thailand, a cross-sectional study was conducted among antiretroviral-naive HIV-infected patients aged <25 years who newly visited infectious disease clinic in a university hospital, in 2011. HIV genotypic-resistance test was performed. World Health Organization 2009 surveillance drug-resistance mutations were used to define TDR. Of 50 patients, the prevalence of TDR was 4%. Of 2 patients with TDR, 1 had K103N and the other had Y181C mutations. Transmitted HIV drug resistance is emerging in Thailand after a decade of rapid scale-up of ART. Interventions to prevent TDR at the population level are essentially needed in Thailand. Surveillance for TDR in Thailand has to be regularly performed.
Collapse
Affiliation(s)
- Somnuek Sungkanuparph
- Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | | | | |
Collapse
|
12
|
Chew KK, Ng KY, Khong WX, Kaur P, Yap JK, Chua A, Tan MT, Koh YL, Thoon KC, Leo YS, Ng OT. Clinical Evaluation of an In-House Human Immunodeficiency Virus (HIV) Genotyping Assay for the Detection of Drug Resistance Mutations in HIV-1 Infected Patients in Singapore. ANNALS OF THE ACADEMY OF MEDICINE, SINGAPORE 2012. [DOI: 10.47102/annals-acadmedsg.v41n12p553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Introduction: Human immunodeficiency virus type 1 (HIV-1) genotyping resistance test (GRT) is essential for monitoring HIV-1 drug resistance mutations (DRMs). High cost and HIV-1 genetic variability are challenges to assay availability in Singapore. An in-house Sanger sequencing-based GRT method was developed at the Communicable Disease Centre (CDC), Singapore’s HIV national treatment reference centre for both subtype B and non-subtype B HIV-1. Materials and Methods: The in-house GRT sequenced the first 99 codons of protease (PR) and 244 codons of reverse transcriptase (RT) in the pol gene. The results were compared with the Food and Drug Administration (FDA)-approved ViroSeqTM HIV-1 Genotyping System. Results: Subtype assignment for the 46 samples were as follows: 31 (67.4%) CRF01_AE, 14 (30.5%) subtype B and 1 (2.1%) subtype C. All 46 samples had viral load of ≥500 copies/mL, and were successfully amplified by the in-house primer sets. Compared to the ViroSeqTM test, our in-house assay showed drug-resistance conferring codon concordance of 99.9% at PR and 98.9% at RT, and partial concordance of 0.1% at PR and 1.1% at RT. No discordant result was observed. Conclusion: The assay successfully identifi ed DRMs in both subtype AE and B, making it suitable for the efficient treatment monitoring in genetically diverse population. At less than half of the running cost compared to the ViroSeqTM assay, the broadly sensitive in-house assay could serve as a useful addition to the currently limited HIV genotyping assay options for resource-limited settings, thereby enhancing the DRM surveillance and monitoring in the region.
Key words: Drug resistance mutations, Genotypic resistance test, HIV-1
Collapse
|
13
|
Parkin N, Bremer J, Bertagnolio S. Genotyping external quality assurance in the World Health Organization HIV drug resistance laboratory network during 2007-2010. Clin Infect Dis 2012; 54 Suppl 4:S266-72. [PMID: 22544186 DOI: 10.1093/cid/cir992] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The World Health Organization (WHO) has developed a global laboratory network to support human immunodeficiency virus drug resistance genotyping for public health surveillance in resource-limited countries. Blinded proficiency panels are an essential part of a genotyping quality-assurance program and are used to monitor the reliability of genotyping data in the WHO laboratory network. Laboratories in Europe, North America, Asia, Africa, and the Caribbean have tested panels annually since 2007; 103 of 131 submissions (79%) had >99% nucleotide sequence identity and resistance mutation concordance, compared with consensus. Most errors were associated with mixtures in the test specimen, leading to subjectivity in base-calling or amplification bias. Overall, genotyping assays used by the WHO laboratory network are reliable.
Collapse
Affiliation(s)
- Neil Parkin
- HIV Department, World Health Organization, Geneva, Switzerland.
| | | | | |
Collapse
|
14
|
Abstract
The efficacy of an antiretroviral (ARV) treatment regimen depends on the activity of the regimen's individual ARV drugs and the number of HIV-1 mutations required for the development of resistance to each ARV - the genetic barrier to resistance. ARV resistance impairs the response to therapy in patients with transmitted resistance, unsuccessful initial ARV therapy and multiple virological failures. Genotypic resistance testing is used to identify transmitted drug resistance, provide insight into the reasons for virological failure in treated patients, and help guide second-line and salvage therapies. In patients with transmitted drug resistance, the virological response to a regimen selected on the basis of standard genotypic testing approaches the responses observed in patients with wild-type viruses. However, because such patients are at a higher risk of harbouring minority drug-resistant variants, initial ARV therapy in this population should contain a boosted protease inhibitor (PI) - the drug class with the highest genetic barrier to resistance. In patients receiving an initial ARV regimen with a high genetic barrier to resistance, the most common reasons for virological failure are nonadherence and, potentially, pharmacokinetic factors or minority transmitted drug-resistant variants. Among patients in whom first-line ARVs have failed, the patterns of drug-resistance mutations and cross-resistance are often predictable. However, the extent of drug resistance correlates with the duration of uncontrolled virological replication. Second-line therapy should include the continued use of a dual nucleoside/nucleotide reverse transcriptase inhibitor (NRTI)-containing backbone, together with a change in the non-NRTI component, most often to an ARV belonging to a new drug class. The number of available fully active ARVs is often diminished with each successive treatment failure. Therefore, a salvage regimen is likely to be more complicated in that it may require multiple ARVs with partial residual activity and compromised genetic barriers of resistance to attain complete virological suppression. A thorough examination of the patient's ARV history and prior resistance tests should be performed because genotypic and/or phenotypic susceptibility testing is often not sufficient to identify drug-resistant variants that emerged during past therapies and may still pose a threat to a new regimen. Phenotypic testing is also often helpful in this subset of patients. ARVs used for salvage therapy can be placed into the following hierarchy: (i) ARVs belonging to a previously unused drug class; (ii) ARVs belonging to a previously used drug class that maintain significant residual antiviral activity; (iii) NRTI combinations, as these often appear to retain in vivo virological activity, even in the presence of reduced in vitro NRTI susceptibility; and rarely (iv) ARVs associated with previous virological failure and drug resistance that appear to have possibly regained their activity as a result of viral reversion to wild type. Understanding the basic principles of HIV drug resistance is helpful in guiding individual clinical decisions and the development of ARV treatment guidelines.
Collapse
Affiliation(s)
- Michele W Tang
- Stanford University, Division of Infectious Diseases, Stanford, CA 94305-5107, USA.
| | | |
Collapse
|
15
|
Sungkanuparph S, Win MM, Kiertiburanakul S, Phonrat B, Maek-a-nantawat W. HIV-1 drug resistance at virological failure versus immunological failure among patients failing first-line antiretroviral therapy in a resource-limited setting. Int J STD AIDS 2012; 23:316-8. [PMID: 22648883 DOI: 10.1258/ijsa.2011.011337] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Antiretroviral treatment failure has been defined by immunological failure (IF) in some resource-limited settings whereas defining by virological failure (VF) has been widely used in developed countries. There is limited comparison of the levels of HIV-1 drug resistance between using VF and IF for the diagnosis of treatment failure. A retrospective cohort study was conducted among HIV-1-infected patients failing first-line antiretroviral therapy (ART). Of 95 patients, median CD4 and HIV-1 RNA were 158 cells/mm(3) and 10,200 copies/mL, respectively. Patients in the IF group had higher HIV-1 RNA than those in VF group (23,820 versus 9510 copies/mL, P = 0.008). Nucleoside reverse transcriptase inhibitor (NRTI)-, non-NRTI- and protease inhibitor-resistance-associated mutations (RAMs) were observed in 57.9%, 94.7% and 5.3%, respectively. Q151M, a multidrug RAM, was more commonly observed in the IF group (14.8% versus 2.9%, P = 0.032). Using IF to diagnose treatment failure is associated with higher HIV-1 RNA levels and a higher rate of Q151M, which can limit the options for second-line ART.
Collapse
Affiliation(s)
- S Sungkanuparph
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand.
| | | | | | | | | |
Collapse
|
16
|
Köser CU, Ellington MJ, Cartwright EJP, Gillespie SH, Brown NM, Farrington M, Holden MTG, Dougan G, Bentley SD, Parkhill J, Peacock SJ. Routine use of microbial whole genome sequencing in diagnostic and public health microbiology. PLoS Pathog 2012; 8:e1002824. [PMID: 22876174 PMCID: PMC3410874 DOI: 10.1371/journal.ppat.1002824] [Citation(s) in RCA: 361] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Affiliation(s)
- Claudio U Köser
- Department of Medicine, University of Cambridge, Addenbrooke's Hospital, Cambridge, United Kingdom.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Sungkanuparph S, Sukasem C, Kiertiburanakul S, Pasomsub E, Chantratita W. Emergence of HIV-1 drug resistance mutations among antiretroviral-naïve HIV-1-infected patients after rapid scaling up of antiretroviral therapy in Thailand. J Int AIDS Soc 2012; 15:12. [PMID: 22410286 PMCID: PMC3334685 DOI: 10.1186/1758-2652-15-12] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 03/12/2012] [Indexed: 12/02/2022] Open
Abstract
Background After rapid scaling up of antiretroviral therapy in HIV-1-infected patients, the data of primary HIV-1 drug resistance in Thailand is still limited. This study aims to determine the prevalence and associated factors of primary HIV-1 drug resistance in Thailand. Methods A prospective observational study was conducted among antiretroviral-naïve HIV-1-infected Thai patients from 2007 to 2010. HIV-1 subtypes and mutations were assayed by sequencing a region of HIV-1 pol gene. Surveillance drug resistance mutations recommended by the World Health Organization for surveillance of transmitted HIV-1 drug resistance in 2009 were used in all analyses. Primary HIV-1 drug resistance was defined as the presence of one or more surveillance drug resistance mutations. Results Of 466 patients with a mean age of 38.8 years, 58.6% were males. Risks of HIV-1 infection included heterosexual (77.7%), homosexual (16.7%), and intravenous drug use (5.6%). Median (IQR) CD4 cell count and HIV-1 RNA were 176 (42-317) cells/mm3 and 68,600 (19,515-220,330) copies/mL, respectively. HIV-1 subtypes were CRF01_AE (86.9%), B (8.6) and other recombinants (4.5%). The prevalence of primary HIV-1 drug resistance was 4.9%; most of these (73.9%) had surveillance drug resistance mutations to only one class of antiretroviral drugs. The prevalence of patients with NRTI, NNRTI, and PI surveillance drug resistance mutations was 1.9%, 2.8% and 1.7%, respectively. From logistic regression analysis, there was no factor significantly associated with primary HIV-1 drug resistance. There was a trend toward higher prevalence in females [odds ratio 2.18; 95% confidence interval 0.896-5.304; p = 0.086]. Conclusions There is a significant emergence of primary HIV-1 drug resistance in Thailand after rapid scaling up of antiretroviral therapy. Although HIV-1 genotyping prior to antiretroviral therapy initiation is not routinely recommended in Thailand, our results raise concerns about the risk of early treatment failure in patients with primary HIV-1 drug resistance. Interventions to prevent the transmission of HIV-1 drug resistance and continuation of surveillance for primary HIV-1 drug resistance in Thailand are indicated.
Collapse
Affiliation(s)
- Somnuek Sungkanuparph
- Division of Infectious Diseases, Department of Medicine, Faculty of Medicine Ramathibodi Hospital, Mahidol University, Bangkok, Thailand.
| | | | | | | | | |
Collapse
|
18
|
Automating HIV drug resistance genotyping with RECall, a freely accessible sequence analysis tool. J Clin Microbiol 2012; 50:1936-42. [PMID: 22403431 DOI: 10.1128/jcm.06689-11] [Citation(s) in RCA: 135] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Genotypic HIV drug resistance testing is routinely used to guide clinical decisions. While genotyping methods can be standardized, a slow, labor-intensive, and subjective manual sequence interpretation step is required. We therefore performed external validation of our custom software RECall, a fully automated sequence analysis pipeline. HIV-1 drug resistance genotyping was performed on 981 clinical samples at the Stanford Diagnostic Virology Laboratory. Sequencing trace files were first interpreted manually by a laboratory technician and subsequently reanalyzed by RECall, without intervention. The relative performances of the two methods were assessed by determination of the concordance of nucleotide base calls, identification of key resistance-associated substitutions, and HIV drug resistance susceptibility scoring by the Stanford Sierra algorithm. RECall is freely available at http://pssm.cfenet.ubc.ca. In total, 875 of 981 sequences were analyzed by both human and RECall interpretation. RECall analysis required minimal hands-on time and resulted in a 25-fold improvement in processing speed (∼150 technician-hours versus ∼6 computation-hours). Excellent concordance was obtained between human and automated RECall interpretation (99.7% agreement for >1,000,000 bases compared). Nearly all discordances (99.4%) were due to nucleotide mixtures being called by one method but not the other. Similarly, 98.6% of key antiretroviral resistance-associated mutations observed were identified by both methods, resulting in 98.5% concordance of resistance susceptibility interpretations. This automated sequence analysis tool provides both standardization of analysis and a significant improvement in data workflow. The time-consuming, error-prone, and dreadfully boring manual sequence analysis step is replaced with a fully automated system without compromising the accuracy of reported HIV drug resistance data.
Collapse
|
19
|
Stürmer M, Reinheimer C. Description of two commercially available assays for genotyping of HIV-1. Intervirology 2012; 55:134-7. [PMID: 22286883 DOI: 10.1159/000332010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
HIV-1 resistance testing is one important part in the diagnostics of antiretroviral treatment and is commonly done by genotyping. Currently, two systems are commercially available and, despite being far from easy to use, these have achieved a high degree of sophistication. Modifications of standard kit protocols might be necessary based on the clinical situation. Although resistance reports based on decision rules are a part of both systems, considerable knowledge and skills are nevertheless required by the user to establish useful clinical data out of detected resistance patterns. Both systems described here have their advantages and disadvantages; a decision for one or the other system needs to be based on individual requirements. The future might lie in so-called 'next-generation sequencing' systems based on pyrosequencing, which enable a high throughput and the detection of minor variants of less than 1%.
Collapse
Affiliation(s)
- Martin Stürmer
- Johann Wolfgang Goethe-University Hospital, Institute for Medical Virology, Frankfurt, Germany.
| | | |
Collapse
|
20
|
Stelzl E, Pröll J, Bizon B, Niklas N, Danzer M, Hackl C, Stabentheiner S, Gabriel C, Kessler HH. Human immunodeficiency virus type 1 drug resistance testing: Evaluation of a new ultra-deep sequencing-based protocol and comparison with the TRUGENE HIV-1 Genotyping Kit. J Virol Methods 2011; 178:94-7. [PMID: 21907239 DOI: 10.1016/j.jviromet.2011.08.020] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2011] [Revised: 08/19/2011] [Accepted: 08/22/2011] [Indexed: 12/27/2022]
Abstract
Genotypic HIV-1 drug resistance testing with standard Sanger sequencing is limited to the detection of mutations with >20% prevalence. A new protocol for variant detection of protease and reverse transcriptase genes of HIV-1 genotype B samples with ultra-deep sequencing on the GS-FLX sequencer (Roche 454 Life Sciences, Branford, CT) was evaluated. The new technology was compared with the standard Sanger sequencing method. For accuracy testing, genotype B samples obtained from proficiency panels were examined with ultra-deep sequencing. Reproducibility was determined by repeat GS-FLX sequencing of 21 clinical samples. Clinical performance was evaluated with 44 samples and the results were compared to the TRUGENE HIV-1 Genotyping Kit (Siemens Healthcare Diagnostics, Tarrytown, NY). Sequences generated with both protocols were analyzed using the Stanford University HIV drug resistance database. When accuracy was tested, 316 of 317 mutation codons included in the analysis of proficiency panels could be identified correctly with ultra-deep sequencing. Reproducibility testing resulted in a correlation value of R(2)=0.969. Analysis of 44 routine clinical samples with the Stanford University HIV drug resistance database revealed a total number of 269 and 171 mutations by the ultra-deep and standard Sanger sequencing, respectively. Drug resistance interpretations showed differences for 11 samples. With ultra-deep sequencing, total time to result was four times longer in comparison to standard Sanger sequencing. Manual work was increased significantly using the new protocol. The ultra-deep sequencing protocol showed good accuracy and reproducibility. However, automation and shorter time to obtain results are essential for use in the routine diagnostic laboratory.
Collapse
Affiliation(s)
- Evelyn Stelzl
- Research Unit Molecular Diagnostics and Molecular Diagnostics Laboratory, IHMEM, Medical University of Graz, Graz, Austria.
| | | | | | | | | | | | | | | | | |
Collapse
|
21
|
Jain V, Sucupira MC, Bacchetti P, Hartogensis W, Diaz RS, Kallas EG, Janini LM, Liegler T, Pilcher CD, Grant RM, Cortes R, Deeks SG, Hecht FM. Differential persistence of transmitted HIV-1 drug resistance mutation classes. J Infect Dis 2011; 203:1174-81. [PMID: 21451005 DOI: 10.1093/infdis/jiq167] [Citation(s) in RCA: 113] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Transmitted human immunodeficiency virus type 1 (HIV-1) drug resistance (TDR) mutations can become replaced over time by emerging wild-type viral variants with improved fitness. The impact of class-specific mutations on this rate of mutation replacement is uncertain. METHODS We studied participants with acute and/or early HIV infection and TDR in 2 cohorts (San Francisco, California, and São Paulo, Brazil). We followed baseline mutations longitudinally and compared replacement rates between mutation classes with use of a parametric proportional hazards model. RESULTS Among 75 individuals with 195 TDR mutations, M184V/I became undetectable markedly faster than did nonnucleoside reverse-transcriptase inhibitor (NNRTI) mutations (hazard ratio, 77.5; 95% confidence interval [CI], 14.7-408.2; P<.0001), while protease inhibitor and NNRTI replacement rates were similar. Higher plasma HIV-1 RNA level predicted faster mutation replacement, but this was not statistically significant (hazard ratio, 1.71 log(10) copies/mL; 95% CI, .90-3.25 log(10) copies/mL; P=.11). We found substantial person-to-person variability in mutation replacement rates not accounted for by viral load or mutation class (P<.0001). CONCLUSIONS The rapid replacement of M184V/I mutations is consistent with known fitness costs. The long-term persistence of NNRTI and protease inhibitor mutations suggests a risk for person-to-person propagation. Host and/or viral factors not accounted for by viral load or mutation class are likely influencing mutation replacement and warrant further study.
Collapse
Affiliation(s)
- Vivek Jain
- HIV/AIDS Division, San Francisco General Hospital, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Jain V, Liegler T, Vittinghoff E, Hartogensis W, Bacchetti P, Poole L, Loeb L, Pilcher CD, Grant RM, Deeks SG, Hecht FM. Transmitted drug resistance in persons with acute/early HIV-1 in San Francisco, 2002-2009. PLoS One 2010; 5:e15510. [PMID: 21170322 PMCID: PMC3000814 DOI: 10.1371/journal.pone.0015510] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2010] [Accepted: 10/06/2010] [Indexed: 11/18/2022] Open
Abstract
Background Transmitted HIV-1 drug resistance (TDR) is an ongoing public health problem, representing 10–20% of new HIV infections in many geographic areas. TDR usually arises from two main sources: individuals on antiretroviral therapy (ART) who are failing to achieve virologic suppression, and individuals who acquired TDR and transmit it while still ART-naïve. TDR rates can be impacted when novel antiretroviral medications are introduced that allow for greater virologic suppression of source patients. Although several new HIV medications were introduced starting in late 2007, including raltegravir, maraviroc, and etravirine, it is not known whether the prevalence of TDR was subsequently affected in 2008–2009. Methodology/Principal Findings We performed population sequence genotyping on individuals who were diagnosed with acute or early HIV (<6 months duration) and who enrolled in the Options Project, a prospective cohort, between 2002 and 2009. We used logistic regression to compare the odds of acquiring drug-resistant HIV before versus after the arrival of new ART (2005–2007 vs. 2008–2009). From 2003–2007, TDR rose from 7% to 24%. Prevalence of TDR was then 15% in 2008 and in 2009. While the odds of acquiring TDR were lower in 2008–2009 compared to 2005–2007, this was not statistically significant (odds ratio 0.65, 95% CI 0.31–1.38; p = 0.27). Conclusions Our study suggests that transmitted drug resistance rose from 2003–2007, but this upward trend did not continue in 2008 and 2009. Nevertheless, the TDR prevalence in 2008–2009 remained substantial, emphasizing that improved management strategies for drug-resistant HIV are needed if TDR is to be further reduced. Continued surveillance for TDR will be important in understanding the full impact of new antiretroviral medications.
Collapse
Affiliation(s)
- Vivek Jain
- HIV/AIDS Division, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
| | - Teri Liegler
- HIV/AIDS Division, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
| | - Eric Vittinghoff
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Wendy Hartogensis
- HIV/AIDS Division, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
| | - Peter Bacchetti
- Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, California, United States of America
| | - Lauren Poole
- HIV/AIDS Division, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
| | - Lisa Loeb
- HIV/AIDS Division, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
| | - Christopher D. Pilcher
- HIV/AIDS Division, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
| | - Robert M. Grant
- Gladstone Institute for Virology, University of California San Francisco, San Francisco, California, United States of America
| | - Steven G. Deeks
- HIV/AIDS Division, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
| | - Frederick M. Hecht
- HIV/AIDS Division, San Francisco General Hospital, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
| |
Collapse
|
23
|
Stelzl E, Troppan KT, Winkler M, Korn K, Kessler HH. Optimized protocol for detection of HIV-1 drug mutations in patients with low viral load. J Virol Methods 2010; 168:152-4. [DOI: 10.1016/j.jviromet.2010.05.007] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Revised: 04/15/2010] [Accepted: 05/06/2010] [Indexed: 10/19/2022]
|
24
|
Willberg CB, Garrison KE, Jones RB, Meiklejohn DJ, Spotts G, Liegler TJ, Ostrowski MA, Karlsson AC, Hecht FM, Nixon DF. Rapid progressing allele HLA-B35 Px restricted anti-HIV-1 CD8+ T cells recognize vestigial CTL epitopes. PLoS One 2010; 5:e10249. [PMID: 20422053 PMCID: PMC2858076 DOI: 10.1371/journal.pone.0010249] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2010] [Accepted: 02/09/2010] [Indexed: 11/28/2022] Open
Abstract
Background The HLA-B*35-Px allele has been associated with rapid disease progression in HIV-1 infection, in contrast to the HLA-B*35-Py allele. Methodology/Principal Findings Immune responses to two HLA-B*35 restricted HIV-1 specific CTL epitopes and their variants were followed longitudinally during early HIV-1 infection in 16 HLA-B*35+ individuals. Subjects expressing HLA-B*35-Px alleles showed no difference in response to the consensus epitopes compared to individuals with HLA-B*35-Py alleles. Surprisingly, all the HLA-B*35-Px+ individuals responded to epitope-variants even in the absence of a consensus response. Sequencing of the viral population revealed no evidence of variant virus in any of the individuals. Conclusions/Significance This demonstrates a novel phenomenon that distinguishes individuals with the HLA-B*35-Px rapid progressing allele and those with the HLA-B*35-Py slower progressing allele.
Collapse
Affiliation(s)
- Christian B. Willberg
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Keith E. Garrison
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - R. Brad Jones
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Duncan J. Meiklejohn
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Gerald Spotts
- Division of HIV/AIDS, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Teri J. Liegler
- Division of HIV/AIDS, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Mario A. Ostrowski
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada
| | - Annika C. Karlsson
- Department of Microbiology, Tumor and Cell Biology (MTC), Karolinska Institutet, Solna, Sweden
- Department of Virology, The Swedish Institute for Infectious Disease Control, Solna, Sweden
| | - Frederick M. Hecht
- Division of HIV/AIDS, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
| | - Douglas F. Nixon
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, United States of America
- * E-mail:
| |
Collapse
|
25
|
Wallis CL, Papathanasopoulos MA, Lakhi S, Karita E, Kamali A, Kaleebu P, Sanders E, Anzala O, Bekker LG, Stevens G, de Wit TFR, Stevens W. Affordable in-house antiretroviral drug resistance assay with good performance in non-subtype B HIV-1. J Virol Methods 2009; 163:505-8. [PMID: 19917318 DOI: 10.1016/j.jviromet.2009.11.011] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2009] [Revised: 10/20/2009] [Accepted: 11/05/2009] [Indexed: 10/20/2022]
Abstract
The introduction of antiretroviral (ARV) therapy in resource-poor settings is effective in suppressing HIV-1 replication and prolonging life of infected individuals. This has led to a demand for affordable HIV-1 drug resistance assays, since treatment failure due to development of drug resistance is common. This study developed and evaluated an affordable "in-house" genotyping assay to monitor HIV-1 drug resistance in Africa, particularly South Africa. An "in-house" assay using automated RNA extraction, and subtype C specific PCR and sequencing primers was developed and successfully evaluated 396 patient samples (viral load ranges 1000-1.6 million RNA copies/ml). The "in-house" assay was validated by comparing sequence data and drug resistance profiles from 90 patient and 10 external quality control samples to data from the ViroSeq HIV-1 Genotyping kit. The "in-house" assay was more efficient, amplifying all 100 samples, compared to 91 samples using Viroseq. The "in house" sequences were 99.2% homologous to the ViroSeq sequences, and identical drug resistance mutation profiles were observed in 96 samples. Furthermore, the "in-house" assay genotyped 260 of 295 samples from seven African sites, where 47% were non-subtype C. Overall, the newly validated "in-house" drug resistance assay is suited for use in Africa as it overcomes the obstacle of subtype diversity.
Collapse
Affiliation(s)
- Carole L Wallis
- Department of Molecular Medicine and Haematology, University of the Witwatersrand, Johannesburg, South Africa.
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
26
|
Relationship of injection drug use, antiretroviral therapy resistance, and genetic diversity in the HIV-1 pol gene. J Acquir Immune Defic Syndr 2009; 50:381-9. [PMID: 19214121 DOI: 10.1097/qai.0b013e318198a619] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES To determine if a history of injection drug use influences genotypic protease inhibitor (PI) resistance to antiretroviral agents. METHODS We assessed the presence of resistance mutations in PI-naive injection drug users (IDUs) and non-IDUs participating in the Women's Interagency HIV Study. Eighteen HIV-infected participants who reported injection drug use before study enrollment and 32 HIV-infected non-IDUs contributed a total of 34 and 65 person-visits, respectively, to analyses. RESULTS Based on data from multiple clones obtained from different time points from each individual, we determined that primary PI resistance mutations were more frequent among person visits contributed by IDUs (24%) than non-IDUs (8%, P = 0.05). Although neither reached statistical significance, diversity was higher within the protease region among study visits carrying PI-resistant clones at both the nucleotide level (2.66 vs. 2.35; P = 0.08) and at the amino acid level (1.60 vs. 1.32; P = 0.23). Most of the primary resistance mutations could not be detected using the standard population sequencing employed in the clinical setting. Five of 6 individuals in whom clones encoding PI resistance mutations were identified failed PI-containing highly active antiretroviral therapy within 12 months of therapy initiation. CONCLUSIONS Our findings indicate that more aggressive sampling for resistance mutations among viral clones before highly active antiretroviral therapy initiation might permit selection of more effective treatment, particularly in IDUs.
Collapse
|
27
|
Dried-plasma transport using a novel matrix and collection system for human immunodeficiency virus and hepatitis C virus virologic testing. J Clin Microbiol 2009; 47:1491-6. [PMID: 19321732 DOI: 10.1128/jcm.02354-08] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A novel method for the collection and transportation of dried-blood-plasma samples, SampleTanker (ST), was developed and compared to standard shipping protocols for frozen-plasma specimens containing human immunodeficiency virus type 1 (HIV-1) and/or hepatitis C virus (HCV). Matched frozen and dried 1-ml EDTA-containing plasma samples were collected and analyzed by several molecular-based virologic assays. After addition of 1.175 ml of reconstitution buffer, 1.035 ml of dried plasma was recovered. Mean intra-assay variances were 0.05, 0.05, and 0.06 log(10) copies/ml for the Versant, Amplicor, and NucliSens QT HIV-1 load assays, respectively (P, not significant). However, mean HIV-1 viral load was consistently reduced in dried samples by 0.32 to 0.51 log(10) copies/ml, depending on assay type (P < 0.05). Infectious HIV-1 was not recovered from dried ST plasma. There was no significant difference in HIV-1 viral load results obtained using ST after 8 weeks of storage at ambient temperature. Compared to frozen plasma, HIV-1 genotypic results were >99% concordant at the nucleotide and amino acid levels, as well as for resistance-associated mutations. We further demonstrated successful detection of multiple analytes, including HIV-1 viral load, HIV-1 antiretroviral resistance genotype, and HCV genotype, from a single ST unit. Dried plasma collected with ST yielded comparable results to frozen samples for multiple-analyte clinical testing. As such, ST could be a useful alternative for virologic tests and clinical trials worldwide by significantly diminishing transportation cost and the sample volume restrictions associated with dried-blood-spot technology.
Collapse
|
28
|
Nucleoside and nucleotide analogs select in culture for different patterns of drug resistance in human immunodeficiency virus types 1 and 2. Antimicrob Agents Chemother 2008; 53:708-15. [PMID: 19064892 DOI: 10.1128/aac.01109-08] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Recent findings suggest bidirectional antagonisms between the K65R mutation and thymidine analogue mutations in human immunodeficiency virus type 1 (HIV-1)-infected, treatment-experienced patients, yet little is known about HIV-2 in this regard. This study addressed the effects of innate polymorphisms in HIV-2 on emergent resistance to nucleoside/nucleotide analogues. Emergent drug resistance profiles in HIV-2 subtypes A (n = 3) and B (n = 1) were compared to those of HIV-1 subtypes B and C. Drug resistance was evaluated with cord blood mononuclear cells (CBMCs) and MT2 cells, using selective pressure with tenofovir (TFV), zidovudine (ZDV), stavudine (d4T), didanosine (ddI), abacavir (ABC), lamivudine (3TC), emtricitabine (FTC), or various dual-drug combinations. Resistance was evaluated using conventional and ultrasensitive sequencing approaches. In agreement with our previous findings, dual-drug combinations of TFV, ddI, ABC, d4T, ZDV, and 3TC preferentially selected for K65R in HIV-1 subtype C isolates. In HIV-1 subtype B, TFV-3TC and ZDV-3TC selected for M184I and D67N, respectively. In contrast, selections with all four HIV-2 cultures favored the development of M184I in dual-drug combinations that included either 3TC or FTC. Since HIV-2 cultures did not develop K65R, an ultrasensitive allele-specific real-time PCR assay was developed to distinguish the presence of 65R from wild-type K65 after 16 cycles with a discriminatory ability of 0.1% against a population of wild-type virus. These results underscore potential differences in emergent drug resistance pathways in HIV-1 and HIV-2 and show that polymorphisms may influence the development of the resistance pathways that are likely to emerge.
Collapse
|
29
|
Apisarnthanarak A, Jirayasethpong T, Sa-nguansilp C, Thongprapai H, Kittihanukul C, Kamudamas A, Tungsathapornpong A, Mundy LM. Antiretroviral drug resistance among antiretroviral-naïve persons with recent HIV infection in Thailand. HIV Med 2008; 9:322-5. [PMID: 18400079 DOI: 10.1111/j.1468-1293.2008.00562.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
OBJECTIVES To evaluate the prevalence and patterns of antiretroviral (ARV) drug resistance (ARV-DR) among ARV drug-naïve, recently infected persons with HIV in the 4-year interval (2003-2006) after the inception of the National Access to ARV Programme for People who have AIDS in Thailand. METHODS Cross-sectional study of patients with recent HIV infection for HIV risks, ARV-DR risks and baseline ARV-DR. RESULTS Seven of the 305 patients (2%) had baseline ARV-DR. Via contract tracing, all seven patients with transmitted ARV-DR identified sexual partners with prior ARV treatment failure and had documented low (<75%) ARV adherence. Annual ARV-DR increased from 0 to 5.2% (P=0.06) between 2003 and 2006. CONCLUSIONS Report of sexual partners with potential HIV and ARV drug exposures can prompt baseline ARV-DR testing of at-risk individuals, while behavioural interventions for adherence and safer sex are refined to minimize the emergence of resistance to generic, fixed-dose combination stavudine, lamivudine and nevirapine (GPO-VIR) therapy.
Collapse
Affiliation(s)
- A Apisarnthanarak
- Department of Medicine, Division of Infectious Diseases, Thammasat University Hospital, Pratumthani, Thailand.
| | | | | | | | | | | | | | | |
Collapse
|
30
|
Sungkanuparph S, Sukasem C, Manosuthi W, Wiboonchutikul S, Piyavong B, Chantratita W. Tipranavir resistance associated mutations in protease inhibitor-naïve patients with HIV-1 subtype A/E infection. J Clin Virol 2008; 43:284-6. [DOI: 10.1016/j.jcv.2008.07.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2008] [Revised: 07/01/2008] [Accepted: 07/02/2008] [Indexed: 11/30/2022]
|
31
|
Willberg CB, McConnell JJ, Eriksson EM, Bragg LA, York VA, Liegler TJ, Hecht FM, Grant RM, Nixon DF. Immunity to HIV-1 is influenced by continued natural exposure to exogenous virus. PLoS Pathog 2008; 4:e1000185. [PMID: 18949024 PMCID: PMC2562513 DOI: 10.1371/journal.ppat.1000185] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2008] [Accepted: 09/23/2008] [Indexed: 11/18/2022] Open
Abstract
Unprotected sexual intercourse between individuals who are both infected with HIV-1 can lead to exposure to their partner's virus, and potentially to super-infection. However, the immunological consequences of continued exposure to HIV-1 by individuals already infected, has to our knowledge never been reported. We measured T cell responses in 49 HIV-1 infected individuals who were on antiretroviral therapy with suppressed viral loads. All the individuals were in a long-term sexual partnership with another HIV-1 infected individual, who was either also on HAART and suppressing their viral loads, or viremic (>9000 copies/ml). T cell responses to HIV-1 epitopes were measured directly ex-vivo by the IFN-γ enzyme linked immuno-spot assay and by cytokine flow cytometry. Sexual exposure data was generated from questionnaires given to both individuals within each partnership. Individuals who continued to have regular sexual contact with a HIV-1 infected viremic partner had significantly higher frequencies of HIV-1-specific T cell responses, compared to individuals with aviremic partners. Strikingly, the magnitude of the HIV-1-specific T cell response correlated strongly with the level and route of exposure. Responses consisted of both CD4+ and CD8+ T cell subsets. Longitudinally, decreases in exposure were mirrored by a lower T cell response. However, no evidence for systemic super-infection was found in any of the individuals. Continued sexual exposure to exogenous HIV-1 was associated with increased HIV-1-specific T cell responses, in the absence of systemic super-infection, and correlated with the level and type of exposure. Serosorting, the practice of seeking to engage in unprotected sexual activities only with partners who are of the same HIV-1 status, is a growing trend. Unprotected sexual intercourse between two HIV-1 infected individuals can lead to consequences such as HIV-1 super-infection. However, continued exposure to HIV-1 may also have an important influence on the immune response. Here, we explored this influence in a cohort of HIV-1 infected individuals who were in long-term partnerships with other HIV-1 infected individuals. We found that individuals, who regularly engaged in unprotected receptive sexual intercourse with an HIV-1 infected viremic partner, displayed higher T cell responses to HIV proteins compared to those who were not regularly exposed to a viremic partner. None of the individuals within this study showed evidence of systemic super-infection. Exposure had limited impact on general activation or poly-functionality. These results are clearly of importance for HIV-1 infected individuals who chose to engage in unprotected sexual activity with other HIV-1 infected individuals. These data also reveal a more general mechanism that occurs in infectious diseases: immune responses to chronic viruses are influenced not only by the virus within the host, but also by exposure to the virus from without.
Collapse
Affiliation(s)
- Christian B Willberg
- Division of Experimental Medicine, Department of Medicine, University of California San Francisco, San Francisco, California, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
32
|
Genotypic antiretroviral resistance testing for human immunodeficiency virus type 1 integrase inhibitors by use of the TruGene sequencing system. J Clin Microbiol 2008; 46:4087-90. [PMID: 18945845 DOI: 10.1128/jcm.01246-08] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A sequencing assay for detection of mutations conferring resistance to human immunodeficiency virus type 1 (HIV-1) integrase inhibitors raltegravir and elvitegravir was developed using the automated TruGene sequencing system. The assay returned clear sequencing results for samples with >or=500 RNA copies/ml for mutation detection and HIV-1 subtyping across a spectrum of HIV-1 subtypes.
Collapse
|
33
|
Apisarnthanarak A, Mundy LM. Antiretroviral drug resistance among antiretroviral-naive individuals with HIV infection of unknown duration in Thailand. Clin Infect Dis 2008; 46:1630-1. [PMID: 18419506 DOI: 10.1086/587753] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022] Open
|
34
|
Treatment response in acute/early infection versus advanced AIDS: equivalent first and second phases of HIV RNA decline. AIDS 2008; 22:957-62. [PMID: 18453855 DOI: 10.1097/qad.0b013e3282fbd1da] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
OBJECTIVE Compare the initial phases of virologic decay when acute/early and advanced HIV-infected adults are administered the same treatment regimen. DESIGN Mathematical modeling of a previously completed prospective treatment pilot study involving treatment-naive patients with early and advanced immunosuppression. METHODS We analyzed data from a treatment protocol in which 18 individuals with acute or recent HIV-1 seroconversion and six patients with advanced AIDS were administered the same four-drug antiretroviral regimen. Initial treatment responses were compared by fitting a mathematical model to frequent viral load measurements in order to calculate the first and second phase kinetics of viral clearance, and also by comparing viral load suppression over 24 weeks. Patients were also comprehensively compared in terms of protease inhibitor drug levels, HIV-specific immune responses at baseline, and the presence of drug resistance-conferring mutations. RESULTS There was no statistically meaningful difference in first phase clearance of comparable high-level viremia in the two groups, whether protease inhibitor levels were inserted into the model or 100% antiviral drug effectiveness was assumed. In contrast, acute/early patients had inferior sustained responses than advanced patients, reflecting erratic adherence. CONCLUSIONS Despite many years of intervening immune destruction, the initial virologic decay on therapy appears to be the same at the extremes of the HIV disease spectrum.
Collapse
|
35
|
Sukasem C, Churdboonchart V, Chasombat S, Kohreanudom S, Watitpun C, Piroj W, Tiensuwan M, Chantratita W. Prevalence of antiretroviral drug resistance in treated HIV-1 infected patients: under the initiative of access to the NNRTI-based regimen in Thailand. J Chemother 2008; 19:528-35. [PMID: 18073152 DOI: 10.1179/joc.2007.19.5.528] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
Abstract
To determine the prevalence of antiretroviral resistance in treatment-failure HIV-1 infected individuals, under the initiative of the non-nucleoside reverse transcriptase inhibitor (NNRTI)-based regimen in Thailand, plasma samples were collected from 1,376 HIV-1 infected patients, who were failing in their current HAART therapy during 2000-2004. They were stratified into 2 intervals: group one (1), 558 HIV-1 infected patients (2000-2002; before the initiative of access to HAART), and group two (2), 818 HIV-1 infected patients (2003-2004; after the initiative of access to HAART). Genotypic resistance testing was performed. The frequency of antiretroviral drug resistance in treatment-failure HIV-1 infected patients has significantly increased over time from 68.5% (382/558) during 2000-2002 to 74.9% (613/818) during 2003-2004 (P<0.01). Resistance to NNRTI during 2003-2004 (59.2%) was much higher than that during 2000-2002 (36.9%; P<0.001). However, the frequency of nucleoside reverse transcriptase inhibitor (NRTI) drug resistance was not significantly higher (P=0.153). We showed that this correlated with an increase in the NNRTI-based regimen prescribed during 2003-2004, especially the Thai-produced combination pill, GPO-VIR. Our finding also showed that a high level of genotypic drug resistance is associated with GPO-VIR (40.8% lamivudine, 40.6% stavudine, 43.8% nevirapine). In order to avoid the rapid emergence of resistant viruses in a resource-poor setting, a close surveillance of antiretroviral drug resistance is feasible and should be considered.
Collapse
Affiliation(s)
- C Sukasem
- Department of Pathobiology, Faculty of Science, Mahidol University, Bangkok, Thailand.
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Akinsete OO, Sides T, Hirigoyen D, Cartwright C, Boraas C, Davey C, Pessoa-Brandão L, McLaughlin M, Kane E, Hall J, Henry K. Demographic, clinical, and virologic characteristics of African-born persons with HIV/AIDS in a Minnesota hospital. AIDS Patient Care STDS 2007; 21:356-65. [PMID: 17518528 DOI: 10.1089/apc.2006.0074] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Minnesota is currently home to the tenth largest African population and the second largest East African population in the United States. HIV is increasingly being diagnosed in African-born persons in Minnesota. A retrospective survey was conducted on all African-born patients in our HIV clinic between January 1994 and June 2005. We identified 237 patients who were African-born and HIV-positive. They constituted 12% of patients attending the clinic within the study timeframe. There was no significant difference in the ages of the African-born and non-African patients in the HIV clinic. African-born patients were more likely to be women compared with non-African patients (p < 0.001). Forty-three percent of the African-born patients presented with AIDS as defined by CD4(+) T cell counts less than 200 cells per milliliter compared to 33% of antiretroviral naïve non-African HIV patients in the clinic (p < 0.001). Most patients were infected through heterosexual contact and only 4% were diagnosed as a result of routine testing. Seven known HIV subtypes and four unique recombinant forms were identified. The most common opportunistic infection was pulmonary tuberculosis. African immigrants with HIV appear to: (1) access care at later stages of HIV disease than other patients in our clinic; (2) are often infected with non-B subtypes; (3) do not routinely get tested for HIV. Increased awareness to this growing trend is needed for health care providers and public health officials to tailor educational programs and prevention efforts for African immigrants in the United States.
Collapse
Affiliation(s)
- Omobosola O Akinsete
- University of Minnesota/HIV Program Hennepin County Medical Center, Minneapolis, Minnesota 55405, USA.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Sungkanuparph S, Manosuthi W, Kiertiburanakul S, Piyavong B, Chumpathat N, Chantratita W. Options for a Second-Line Antiretroviral Regimen for HIV Type 1-Infected Patients Whose Initial Regimen of a Fixed-Dose Combination of Stavudine, Lamivudine, and Nevirapine Fails. Clin Infect Dis 2007; 44:447-52. [PMID: 17205457 DOI: 10.1086/510745] [Citation(s) in RCA: 150] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2006] [Accepted: 10/12/2006] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND A fixed-dose combination of stavudine, lamivudine, and nevirapine is extensively used as an antiretroviral regimen in developing countries because of its affordability. Virological failure with this regimen has become more common, and a second-line regimen needs to be prepared in the national program. METHODS Genotypic resistance testing was conducted among human immunodeficiency virus type 1 (HIV-1)-infected patients who experienced treatment failure with their first antiretroviral regimen (a fixed-dose combination of stavudine, lamivudine, and nevirapine) during 2003-2005. Patterns of resistance mutations and options for a second-line regimen were studied. RESULTS We studied 98 patients (mean age, 35.2 years), of whom, 63% were male. The median duration of antiretroviral therapy was 20 months. The median HIV-1 RNA load at the time of virological failure detection was 4.1 log copies/mL. The prevalences of patients with > or =1 major mutation conferring drug resistance to nucleoside reverse-transcriptase inhibitors and nonnucleoside reverse-transcriptase inhibitors were 95% and 92%, respectively. M184V was the most common nucleoside reverse-transcriptase inhibitor resistance mutation (observed in 89% of patients). Thymidine analogue mutations, K65R, and Q151M were observed in 37%, 6%, and 8% of patients, respectively. Patients with an HIV-1 RNA load of >4 log copies/mL at the time of treatment failure had higher prevalence of thymidine analogue mutations (P=.041), K65R (P=.031), and Q151M (P=.008) mutations. The second-line regimen was determined in a resource-limited setting where tenofovir and enfuvirtide are not available; the options were limited for 48% of patients. CONCLUSIONS After experiencing treatment failure with a fixed-dose combination of stavudine, lamivudine, and nevirapine, almost all patients have lamivudine and nonnucleoside reverse-transcriptase inhibitor resistance. The options for a second-line regimen are limited for one-half of these patients. In resource-limited settings where availability of antiretroviral agents is limited, strategies for prevention of HIV-1 resistance are crucial. Early detection of virological failure may provide more options and better treatment outcomes.
Collapse
|
38
|
McClernon DR, Ramsey E, Clair MS. Magnetic silica extraction for low-viremia human immunodeficiency virus type 1 genotyping. J Clin Microbiol 2006; 45:572-4. [PMID: 17122019 PMCID: PMC1829022 DOI: 10.1128/jcm.01731-06] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Nucleic acid extraction and human immunodeficiency virus type 1 (HIV-1) genotyping using the NucliSens miniMAG platform and the TruGene HIV-1 genotyping kit gave HIV-1 sequence data from HIV-1-negative plasma spiked with 100 copies/ml reference HIV-1 RNA and from low-viremia clinical samples (<500 copies/ml) without the need for ultracentrifugation or nested second-round PCR.
Collapse
Affiliation(s)
- D R McClernon
- Clinical Virology Department, GlaxoSmithKline, P.O. Box 13398, Research Triangle Park, NC 27709-3398, USA.
| | | | | |
Collapse
|
39
|
Ntemgwa M, Brenner BG, Oliveira M, Moisi D, Wainberg MA. Natural polymorphisms in the human immunodeficiency virus type 2 protease can accelerate time to development of resistance to protease inhibitors. Antimicrob Agents Chemother 2006; 51:604-10. [PMID: 17116674 PMCID: PMC1797771 DOI: 10.1128/aac.00870-06] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 2 (HIV-2) contains numerous natural polymorphisms in its protease (PR) gene that are implicated in drug resistance in the case of HIV-1. This study evaluated emergent PR resistance in HIV-2. Three HIV-2 isolates were selected for resistance to amprenavir (APV), nelfinavir (NFV), indinavir (IDV), and tipranavir (TPV) in cell culture. Genotypic analysis determined the time to the appearance of protease inhibitor (PI)-associated mutations compared to HIV-1. Phenotypic drug susceptibility assays were used to determine the levels of drug resistance. Within 10 to 15 weeks of serial passage, three major mutations--I54M, I82F, and L90M--arose in HIV-2 viral cultures exposed to APV, NFV, and IDV, whereas I82L was selected with TPV. After 25 weeks, other cultures had developed I50V and I84V mutations. In contrast, no major PI mutations were selected in HIV-1 over this period except for D30N in the context of NFV selective pressure. The baseline phenotypes of wild-type HIV-2 isolates were in the range observed for HIV-1, except for APV and NFV for which a lower degree of sensitivity was seen. The acquisition of the I54M, I84V, L90M, and L99F mutations resulted in multi-PI-resistant viruses, conferring 10-fold to more than 100-fold resistance. Of note, we observed a 62A/99F mutational motif that conferred high-level resistance to PIs, as well as novel secondary mutations, including 6F, 12A, and 21K. Thus, natural polymorphisms in HIV-2 may facilitate the selection of PI resistance. The increasing incidence of such polymorphisms in drug-naive HIV-1- and HIV-2-infected persons is of concern.
Collapse
Affiliation(s)
- Michel Ntemgwa
- McGill University AIDS Centre, Jewish General Hospital, 3755 Cote Ste Catherine Rd., Montreal, Quebec H3T 1E2, Canada
| | | | | | | | | |
Collapse
|
40
|
Marcial M, Lu J, Deeks SG, Ziermann R, Kuritzkes DR. Performance of human immunodeficiency virus type 1 gp41 assays for detecting enfuvirtide (T-20) resistance mutations. J Clin Microbiol 2006; 44:3384-7. [PMID: 16954280 PMCID: PMC1594677 DOI: 10.1128/jcm.00666-06] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The performance of a gp41 assay, created using reagents designed for use with the OpenGene DNA Sequencing System, was evaluated using a panel of plasma samples obtained from enfuvirtide-naive and -experienced human immunodeficiency virus type 1-infected subjects. Resulting sequence data were highly accurate compared to a "home brew" assay and clonal sequence analysis.
Collapse
Affiliation(s)
- Michelle Marcial
- Section of Retroviral Therapeutics, Brigham and Women's Hospital, 65 Landsdowne Street, Room 449, Cambridge, MA 02139, USA
| | | | | | | | | |
Collapse
|
41
|
Ribas SG, Heyndrickx L, Ondoa P, Fransen K. Performance evaluation of the two protease sequencing primers of the Trugene HIV-1 genotyping kit. J Virol Methods 2006; 135:137-42. [PMID: 16777242 DOI: 10.1016/j.jviromet.2006.05.010] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2005] [Revised: 04/11/2006] [Accepted: 05/02/2006] [Indexed: 11/26/2022]
Abstract
This article describes the performance of the two protease sequencing modules available in the Trugene HIV-1 genotyping Kit on a sample population with a high prevalence of HIV-1 non-B subtypes (n=110). The relevance of the algorithm recommended by the kit was also evaluated. The results indicated a high sequencing failure rate of the PR module (34%). Forty-five percent of the failed sequences derived from non-B subtype viruses. Furthermore, no PR sequence could be obtained from any of the HIV-1 subtype A and C infected samples that were tested. In contrast, a sequence could be obtained from the entire panel using the P2 module. The data indicated that the high rate of sequencing failures of the PR module was related to both the HIV-1 non-B subtypes as well as lower levels of RNA viral load. In six out of the 73 samples for which both protease modules were successful, discrepancies between the two protease sequences were observed, which led to discordant resistance reports in two cases. The data highlight the problems and the clinical implications that may occur during resistance genotyping of clinical samples with a high prevalence of HIV-1 non-B subtypes.
Collapse
|
42
|
Gale HB, Kan VL, Shinol RC. Performance of the TruGene human immunodeficiency virus type 1 genotyping kit and OpenGene DNA sequencing system on clinical samples diluted to approximately 100 copies per milliliter. CLINICAL AND VACCINE IMMUNOLOGY : CVI 2006; 13:235-8. [PMID: 16467331 PMCID: PMC1391930 DOI: 10.1128/cvi.13.2.235-238.2006] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
The TruGene human immunodeficiency virus type 1 (HIV-1) genotyping kit/OpenGene DNA sequencing system (Bayer HealthCare, Tarrytown, NY) reliably produced clinically acceptable resistance profiles for reverse transcriptase and protease inhibitors on patient samples diluted to approximately 100 copies/ml following extraction with the QIAamp viral RNA minikit (QIAGEN Inc., Valencia, CA). One modification of the standard protocol was made to guarantee PCR amplification: a centrifugation step to concentrate virus was added before RNA extraction. For genotypic antiretroviral resistance testing, no significant differences in the identification and sensitivity of detection for codon mutations, base mutations, and multibase sites were found between the original and diluted samples.
Collapse
Affiliation(s)
- Howard B Gale
- Infectious Diseases Section (151B), Veterans Affairs Medical Center, 50 Irving Street N.W., Washington, DC 20422, USA.
| | | | | |
Collapse
|
43
|
Gange SJ, Schneider MF, Grant RM, Liegler T, French A, Young M, Anastos K, Wilson TE, Ponath C, Greenblatt R. Genotypic Resistance and Immunologic Outcomes Among HIV-1-Infected Women With Viral Failure. J Acquir Immune Defic Syndr 2006; 41:68-74. [PMID: 16340476 DOI: 10.1097/01.qai.0000174652.40782.4e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVES To describe the prevalence of specific protease inhibitor (PI) and nonnucleoside reverse transcriptase inhibitor (NNRTI) resistance mutations and the relationship between the presence of these mutations and immunologic outcomes following PI/NNRTI initiation among a cohort of HIV-1-infected women. METHODS Viral genotypic resistance testing was done for 366 women enrolled in the Women's Interagency HIV Study at the visit immediately prior to 1st reported use of PI or NNRTI (baseline) and at the visit approximately 1 year after PI/NNRTI initiation. We modeled the changes in CD4+ T-cell counts and HIV RNA levels approximately 1 year after therapy initiation as a function of baseline and follow-up markers, type of antiretroviral therapy used, and resistance mutations. RESULTS At baseline, 52% of women showed only nucleoside reverse transcriptase inhibitor (NRTI) mutations, 38% showed no mutations, and 10% showed PI or NNRTI mutations. Only 40% of women showed viral response (HIV-1 RNA < or = 80 copies/mL) 1 year after initiating a PI or NNRTI. Among those without a viral response, 54% developed PI or NNRTI mutations. NNRTI (among those with baseline NRTI mutations) and PI resistance mutations were associated with better CD4+ cell count changes (mean increase of 118 cells/mm3 and 64 cells/mm3, respectively, as compared with viral nonresponders with no PI or NNRTI mutations). CONCLUSIONS In this population-based cohort, virologic failure with PI or NNRTI resistance was common. Viremia with these resistance mutations was associated with preserved CD4+ T-cell count responses, providing evidence of reduced virulence or viral fitness.
Collapse
Affiliation(s)
- Stephen J Gange
- Department of Epidemiology, Johns Hopkins University Bloomberg School of Public Health, Baltimore, MD 21205, USA.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Taylor-Castillo L, Herrera-Martínez G, León-Bratti MP, Boza R, León-Rodríguez B, Luftig RB, Visoná K. Study of antiretroviral mutants in HIV patients with treatment failures and the effect of risk factors in the virological failures. Rev Inst Med Trop Sao Paulo 2005; 47:327-31. [PMID: 16553322 DOI: 10.1590/s0036-46652005000600004] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
INTRODUCTION: Information about HIV phenotypes of resistant to available ART and the influence of different risk factors on virological failures (VF) in Costa Rican HIV positive patients prior or during HAART is unknown. MATERIALS AND METHODS: Eighty nine samples, 72 VF and 17 basal (before treatment) were analyzed by examining resistant mutants in reverse transcriptase (RT) and protease (PT) regions using Trugene or LIPA genotyping kits. Sixty eight control patients were selected and relevant information was collected in a questionnaire. RESULTS: Poor adherence, presence of resistant mutations and number of treatment's changes were the only significant factors found (p = 0.006, 0.04 and 0.01 respectively). From 66 sequenced samples, 78%, 50% and 50% showed resistance to NRTI (nucleoside reverse transcriptase inhibitors), NNRT (non-nucleoside reverse transcriptase inhibitors) and PI (protease inhibitors), respectively. The most frequent mutations were M41L, M184V, and T215FY in RT and L62PI, L10FIRV and M36I in PT. DISCUSSION: The most important factor related to treatment response in this study was adherence to treatment. Mutations in RT were related to the treatment failure while the ones found in PT were secondary mutations which have been previously described to influence the selection of primary resistance mutations in these regions. The study reveals the urgency to detect resistant mutations in VF to be considered by physicians for selection of treatment schedule, to analyze basal HIV patients for monitoring of the spread of resistant mutations and the importance to reinforce the adherence in the patients for overall treatment outcome.
Collapse
Affiliation(s)
- Lizeth Taylor-Castillo
- Louisiana State University, International Center for Medical Research and training, San José, Costa Rica.
| | | | | | | | | | | | | |
Collapse
|
45
|
Hirigoyen DL, Cartwright CP. Use of sequence data generated in the Bayer Tru Gene genotyping assay to recognize and characterize non-subtype-b human immunodeficiency virus type 1 strains. J Clin Microbiol 2005; 43:5263-71. [PMID: 16207993 PMCID: PMC1248470 DOI: 10.1128/jcm.43.10.5263-5271.2005] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2005] [Revised: 07/05/2005] [Accepted: 07/11/2005] [Indexed: 11/20/2022] Open
Abstract
Human immunodeficiency virus type 1 (HIV-1) protease (PR) and reverse transcriptase (RT) gene sequences obtained during antiretroviral resistance testing with a commercial genotyping assay (Tru Gene; Bayer Corp.) were analyzed to assess the utility of these data for detecting and characterizing non-subtype-B HIV-1 strains. A total of 125 viral sequences obtained from patients believed to have acquired their HIV-1 infection in Africa were analyzed, of which 121 were determined to belong to non-B subtypes. Utilizing Tru Gene sequence data alone, 92 (76%) of these viruses could be subtyped by conventional phylogenetic analysis. The addition of supplemental RT sequence data enabled a further 28 (23.1%) viruses to be classified, while one (0.9%) sample could not be classified conclusively. Two internet-accessible databases that generate HIV-1 subtypes from PR and RT sequences (HIV-SEQ and Geno 2 Pheno) were also evaluated, and both achieved 88% concordance (106/120) with phylogenetic analysis. Non-subtype-B and B-subtype HIV-1 sequences could be readily discriminated by tallying silent polymorphisms listed on the Tru Gene research report. The mean number of silent polymorphisms in the non-B HIV-1 sequences identified in this study was 58.3 (95% confidence interval [CI], 41.1 to 75.5), compared with 20.7 (95% CI, 9.9 to 31.5) for the four subtype B viruses in the study cohort and 118 case-matched B-subtype controls. Sequence data generated in the Tru Gene HIV-1 genotyping assay could, therefore, provide a ready means of tracking the prevalence and identity of non-B subtypes in HIV-1-infected populations undergoing routine antiretroviral resistance testing.
Collapse
Affiliation(s)
- Diane L Hirigoyen
- Department of Laboratory Medicine and Pathology, Hennepin County Medical Center, Minneapolis, MN 55415, USA
| | | |
Collapse
|
46
|
Labayru C, Eiros JM, Hernández B, de Lejarazu RO, Torres AR. RNA extraction prior to HIV-1 resistance detection using Line Probe Assay (LiPA): comparison of three methods. J Clin Virol 2005; 32:265-71. [PMID: 15780803 DOI: 10.1016/j.jcv.2004.08.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 07/22/2004] [Accepted: 08/12/2004] [Indexed: 11/21/2022]
Abstract
BACKGROUND Genotyping testing has been accepted as a guidance in the therapeutic management of Human Immunodeficiency virus 1 (HIV-1). However, optimization of the available routine techniques for such purpose has not been fulfilled. OBJECTIVE To evaluate the use of three RNA extraction methods in order to be applied in the genotypic HIV-1 resistance testing by LiPA. STUDY DESIGN Comparative prospective study of three HIV-1 RNA extraction methods. Forty-eight plasma samples were tested for the determination of viral load (VL) by means of Cobas Amplicor HIV-1 Monitor (Roche Diagnostics. Branchburg, NJ, USA), preserving the obtained RNA extracts. RNA was also extracted using two other techniques: "SV Total RNA Isolation System" (Promega Corporation. Madison, WI, USA) and "QIAamp Viral RNA" (QIAGEN Inc., Valencia, CA, USA). The three RNA extracts were processed in parallel for the detection of HIV resistance by LiPA, and bands were recorded comparatively. RESULTS Results obtained by Roche extraction method were superior, followed by those of Qiagen and Promega, in the several studied parameters. First, proportion of amplified samples (75.0% by Promega versus 95.8 by Qiagen and 97.9% by Roche for LiPA RT and 97.7% by Promega versus 100.0% by Roche and Qiagen for LiPA P); second, percentage of combined mutations patterns, and third, differences in band intensity. Thus, for LiPA RT 51.4% and 54.3% of the samples showed greater intensity after Roche and Qiagen extractions, respectively. These percentages dropped to 12.8 and 19.1 for LiPA P. CONCLUSIONS The outcome obtained by LiPA after RNA extraction by Roche methodology was remarkably superior to those of Promega and Qiagen. LiPA technique needs further optimization, especially the sample amplification phase of LiPA RT.
Collapse
Affiliation(s)
- Cristina Labayru
- Microbiology Service, Hospital General Yagüe, Avda. del Cid s/n, 09005 Burgos, Spain
| | | | | | | | | |
Collapse
|
47
|
Nogales MC, Serrano MC, Bernal S, Jarana R, Pérez de la Rosa L, Fernández-Palacín A, Almeida C, Martín-Mazuelos E. [Study of resistance using the TRUGENE HIV-1 genotyping system and analysis of agreement between rule-based algorithms and virtual phenotyping]. Enferm Infecc Microbiol Clin 2005; 23:149-55. [PMID: 15757587 DOI: 10.1157/13072165] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
INTRODUCTION This study attempts to describe the results obtained in the HIV resistance study performed with clinical samples obtained from patients receiving "HAART" therapy and to compare the results using different interpretation algorithms. METHODS 397 samples have been analysed (TRUGENE HIV-1 GENOTYPING kit). The results were interpreted with the algorithms Visible Genetics and Retrogram. The concordance interalgorithm was done for 105 of these samples, including the virtual phenotype interpretation. RESULTS The samples corresponded to multi regimen failure (39%), first and second failure (30.7% and 27.1% respectively). A 27.6% of the samples were wild type. The more frequent mutations to the ITIAN were T215Y/F (37.2%) and M184V (32.9%) following by other NAMS. The 69 insertion and Q151M complex had low representativity. For the ITINN K103N (25.8%), Y181C (11.2%) and G190A (10.9%). For the IP: key mutations L90M (26.1%), M46I (18.1%) and V82AFTS (12.9%); and accessory mutations L63P (50.5%), A71V (27.2%), L10I (25.2%) and M36I (19.2%). Low correlation was observed between interpretation systems, mainly for ITIAN and IP, being the virtual phenotype more flexible in the assignation of resistance. CONCLUSIONS The requests for HIV resistance testing were similar for the three groups of patients. Many of the failures were the consequence of a poor adherence to the therapy. The mutation pattern found corresponded with the "TARGA" therapy. The low correlation found between interpretation systems, makes necessary the elaboration of a consensus algorithm.
Collapse
|
48
|
Chantratita W, Sukeepaisarncharoen W, Chandeying V, Kulpradist S, Israngkura Na Ayudhtaya B, Rugpao S, Sirawaraporn W, Boonshuyar C, Churdboonchart V. Delayed progression to AIDS in volunteers treated with long-term HIV-1 Immunogen (REMUNE) therapy in Thailand. HIV Med 2004; 5:317-25. [PMID: 15369506 DOI: 10.1111/j.1468-1293.2004.00230.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
OBJECTIVES To observe the long-term effects of an immune-based therapy HIV-1 Immunogen (REMUNE; Immune Response Corp., Carlsbad, CA, USA) as a first course of treatment designed to sustain the immune system and thus delay the initiation of therapy with antiretroviral drugs and/or delay disease progression. METHODS In this open-label, multi-institute extended phase II P2101B study, disease progression, CD4 and CD8 T-cell counts, HIV-1 RNA levels, and genotypic antiretroviral drug resistance were examined in 223 asymptomatic HIV-1-infected Thai volunteers receiving REMUNE every 12 weeks over 132 weeks. A subset of subjects was randomly selected by the physicians to receive antiretroviral drugs for 10 months. RESULTS Patients treated with REMUNE demonstrated a low rate of clinical disease progression (0.72 per 100 person-years), higher CD4 and CD8 T-cell counts, higher body weight before and after treatment in the same patient, and stable viral load with no serious adverse events. We found no genotypic evidence of drug resistance in subgroups of patients on REMUNE monotherapy or REMUNE plus antiretrovirals (ARTs). CONCLUSIONS This Thai study, like previous US and European studies, confirms that therapeutic immunization of HIV-infected volunteers modifies disease progression, as evidenced by stabilization of CD4 and CD8 T-cell counts, body weight, and viral load. As the majority of asymptomatic patients demonstrated an objective response to immunization, this study suggests that REMUNE may be utilized prior to initiation of antiviral drug therapy when CD4 cell counts are still above the current ART guidelines. Further work should be carried out to examine its potential use in combination with ART in order to reduce the increasingly common occurrence of drug resistance.
Collapse
Affiliation(s)
- W Chantratita
- Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Barbour JD, Hecht FM, Wrin T, Liegler TJ, Ramstead CA, Busch MP, Segal MR, Petropoulos CJ, Grant RM. Persistence of primary drug resistance among recently HIV-1 infected adults. AIDS 2004; 18:1683-9. [PMID: 15280779 DOI: 10.1097/01.aids.0000131391.91468.ff] [Citation(s) in RCA: 127] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVES Primary, or transmitted, drug resistance is common among treatment naive patients recently infected with HIV-1, and impairs response to anti-retroviral therapy. We previously observed that patients with secondary resistance (developed in response to anti-retroviral treatment) who chose to stop an anti-retroviral regimen experience rapid overgrowth of drug resistant viruses by wild-type virus of higher pol replication capacity. We sought to determine if primary drug resistance would be lost at a rapid rate, and viral pol replication capacity would increase, in the absence of treatment. METHODS We tracked drug resistance phenotype, genotype, viral pol replication capacity (single cycle recombinant assay incorporating a segment of the patient pol gene [pol RC]), plasma HIV-1 RNA, and CD4 T cell counts in the absence of treatment among patients in early HIV-1 infection. RESULTS Six of 22 patients had evidence of primary drug resistance to at least one class of drug; three resistant to protease inhibitors, three resistant to non-nucleoside reverse transcriptase inhibitors, and four resistant to nucleoside reverse transcriptase inhibitors. All six patients maintained evidence of drug resistance for the period of observation. Among patients with baseline primary drug resistance pol RC did not increase over time. CONCLUSION The selection environment of early infection is determined by immune pressure, and stochastic events, not viral pol replication capacity. In contrast to secondary resistant infections that are rapidly overgrown when therapy is stopped, primary drug resistance persists over time. Surveillance and clinical detection of primary resistance is feasible in the first year of infection.
Collapse
Affiliation(s)
- Jason D Barbour
- Gladstone Institute of Virology and Immunology, San Francisco, California 94141-9100, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Germer JJ, Vandenameele JN, Mitchell PS, Harmsen WS, Yao JDC. Automated sample preparation for the TRUGENE HIV-1 genotyping kit using the MagNA pure LC instrument. Diagn Microbiol Infect Dis 2004; 49:59-61. [PMID: 15135502 DOI: 10.1016/j.diagmicrobio.2003.12.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Use of the MagNA Pure LC Total Nucleic Acid Isolation Kit-Large Volume in conjunction with the TRUGENE HIV-1 Genotyping Kit yielded consistent, interpretable sequence data from 1-mL plasma preparations containing HIV-1 RNA concentrations of > or =400 copies/mL. This finding was confirmed in 18 of 24 low-titer clinical specimens.
Collapse
Affiliation(s)
- Jeffrey J Germer
- Division of Clinical Microbiology, Mayo Clinic, Rochester, Minnesota, USA
| | | | | | | | | |
Collapse
|