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Li Y, Han L, Wang Y, Wang X, Jia L, Li J, Han J, Zhao J, Li H, Li L. Establishment and application of a method of tagged-amplicon deep sequencing for low-abundance drug resistance in HIV-1. Front Microbiol 2022; 13:895227. [PMID: 36071961 PMCID: PMC9444182 DOI: 10.3389/fmicb.2022.895227] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 07/29/2022] [Indexed: 11/16/2022] Open
Abstract
In the latest HIV-1 global drug resistance report released by WHO, countries are advised to strengthen pre-treatment monitoring of drug resistance in AIDS patients. In this study, we established an NGS-based segmented amplification HIV-1 drug resistance mutation detection method. The pol region of HIV-1 was divided into three short fragments for NGS. The entire amplification and sequencing panel were more cost-effective and batched by using the barcode sequence corresponding to the sample. Each parameter was evaluated using samples with known resistance variants frequencies. The nucleotide sequence error rate, amino acid error rate, and noise value of the NGS-based segmented amplification method were both less than 1%. When the threshold was 2%, the consensus sequences of the HIV-1 NL4-3 strain were completely consistent with the Sanger sequences. This method can detect the minimum viral load of the sample at 102 copies/ml, and the input frequency and detection frequency of HIV-1 resistance mutations within the range of 1%–100% had good conformity (R2 = 0.9963; R2 = 0.9955). This method had no non-specific amplification for Hepatitis B and C. Under the 2% threshold, the incidence of surveillance drug resistance mutations in ART-naive HIV-infected patients was 20.69%, among which NRTIs class resistance mutations were mainly.
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Affiliation(s)
- Yang Li
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Leilei Han
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- School of Public Health, North China University of Science and Technology, Tangshan, Hebei, China
| | - Yanglan Wang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- College of Life Science and Technology, Beijing University of Chemical Technology, Beijing, China
| | - Xiaolin Wang
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Lei Jia
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingyun Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jingwan Han
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
| | - Jin Zhao
- Shenzhen Center for Disease Control and Prevention, Shenzhen, Guangdong, China
| | - Hanping Li
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- *Correspondence: Hanping Li,
| | - Lin Li
- School of Basic Medical Sciences, Anhui Medical University, Hefei, Anhui, China
- Department of Virology, State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
- Lin Li,
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Application of next generation sequencing in HIV drug resistance studies in Africa, 2005–2019: A systematic review. SCIENTIFIC AFRICAN 2021. [DOI: 10.1016/j.sciaf.2021.e00829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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Abstract
PURPOSE OF REVIEW The purpose of this review is to describe recent clinical trial, laboratory and observational findings that highlight both the progress that can be achieved in elimination of new pediatric infections in international clinical trial settings among HIV-infected breastfeeding women while also describing recent safety concerns related to currently used antiretroviral regimens. The article will also address the ongoing adherence challenges for HIV-infected mothers in taking their antiretroviral drugs. This information is timely and relevant as new regimens are being considered for both prevention of mother-to-child transmission (PMTCT) of HIV and HIV treatment options worldwide. RECENT FINDINGS The main themes described in this article include both efficacy of different antiretroviral therapy (ART) regimens currently being rolled out internationally for PMTCT as well as safety findings from recent research including a large multisite international trial, PROMISE. SUMMARY The findings from the IMPAACT PROMISE trial as well as other recent trial and observational findings suggest that while progress has been steady in reducing PMTCT worldwide, the goal of virtual elimination of pediatric HIV worldwide will require careful attention to optimizing safety of new regimens which are less dependent on maternal daily ART adherence and safer in preventing certain toxicities.
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Affiliation(s)
- Mary G Fowler
- Department of Pathology, Johns Hopkins U. School of Medicine, Baltimore, Maryland
| | - Patricia Flynn
- Department of Infectious Diseases, St. Jude Children's Research Hospital, Memphis, Tennessee
| | - Jim Aizire
- Department of Epidemiology, Johns Hopkins U. Bloomberg School of Public Health, Baltimore, Maryland, USA
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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.
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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
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Alvarez P, Fernández McPhee C, Prieto L, Martín L, Obiang J, Avedillo P, Vargas A, Rojo P, Benito A, Ramos JT, Holguín Á. HIV-1 Variants and Drug Resistance in Pregnant Women from Bata (Equatorial Guinea): 2012-2013. PLoS One 2016; 11:e0165333. [PMID: 27798676 PMCID: PMC5087953 DOI: 10.1371/journal.pone.0165333] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 10/10/2016] [Indexed: 12/16/2022] Open
Abstract
Objectives This is the first study describing drug resistance mutations (DRM) and HIV-1 variants among infected pregnant women in Equatorial Guinea (GQ), a country with high (6.2%) and increasing HIV prevalence. Methods Dried blood spots (DBS) were collected from November 2012 to December 2013 from 69 HIV-1 infected women participating in a prevention of mother-to-child transmission program in the Hospital Regional of Bata and Primary Health Care Centre María Rafols, Bata, GQ. The transmitted (TDR) or acquired (ADR) antiretroviral drug resistance mutations at partial pol sequence among naive or antiretroviral therapy (ART)-exposed women were defined following WHO or IAS USA 2015 lists, respectively. HIV-1 variants were identified by phylogenetic analyses. Results A total of 38 of 69 HIV-1 specimens were successfully amplified and sequenced. Thirty (79%) belonged to ART-experienced women: 15 exposed to nucleoside reverse transcriptase inhibitors (NRTI) monotherapy, and 15 to combined ART (cART) as first regimen including two NRTI and one non-NRTI (NNRTI) or one protease inhibitor (PI). The TDR rate was only found for PI (3.4%). The ADR rate was 37.5% for NNRTI, 8.7% for NRTI and absent for PI or NRTI+NNRTI. HIV-1 group M non-B variants caused most (97.4%) infections, mainly (78.9%) recombinants: CRF02_AG (55.2%), CRF22_A101 (10.5%), subtype C (10.5%), unique recombinants (5.3%), and A3, D, F2, G, CRF06_cpx and CRF11_cpx (2.6% each). Conclusions The high rate of ADR to retrotranscriptase inhibitors (mainly to NNRTIs) observed among pretreated pregnant women reinforces the importance of systematic DRM monitoring in GQ to reduce HIV-1 resistance transmission and to optimize first and second-line ART regimens when DRM are present.
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Affiliation(s)
- Patricia Alvarez
- HIV-1 Molecular Epidemiology Laboratory, Microbiology and Parasitology Department, Hospital Universitario Ramón y Cajal, IRYCIS and CIBERESP, Madrid, Spain
| | | | - Luis Prieto
- Pediatrics Department, Hospital Universitario de Getafe, Madrid, Spain
| | - Leticia Martín
- HIV-1 Molecular Epidemiology Laboratory, Microbiology and Parasitology Department, Hospital Universitario Ramón y Cajal, IRYCIS and CIBERESP, Madrid, Spain
| | - Jacinta Obiang
- Pediatrics Department, Hospital Regional de Bata, Ministerio de Sanidad y Bienestar Social, Bata, Equatorial Guinea
| | - Pedro Avedillo
- Centro Nacional de Medicina Tropical, Instituto de Salud Carlos III-Madrid, RICET, Madrid, Spain
| | - Antonio Vargas
- Centro Nacional de Medicina Tropical, Instituto de Salud Carlos III-Madrid, RICET, Madrid, Spain
| | - Pablo Rojo
- Pediatrics Department, Hospital Universitario Doce de Octubre, Madrid, Spain
| | - Agustín Benito
- Centro Nacional de Medicina Tropical, Instituto de Salud Carlos III-Madrid, RICET, Madrid, Spain
| | - José Tomás Ramos
- Pediatrics Department, Hospital Universitario Clínico San Carlos, Madrid, Spain
| | - África Holguín
- HIV-1 Molecular Epidemiology Laboratory, Microbiology and Parasitology Department, Hospital Universitario Ramón y Cajal, IRYCIS and CIBERESP, Madrid, Spain
- * E-mail:
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