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Cao G, Yang N, Xiong Y, Shi M, Wang L, Nie F, Huo D, Hou C. Completely Free from PAM Limitations: Asymmetric RPA with CRISPR/Cas12a for Nucleic Acid Assays. ACS Sens 2023; 8:4655-4663. [PMID: 38010352 DOI: 10.1021/acssensors.3c01686] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Experimentally, Cas12a can recognize multiple protospacer adjacent motif (PAM) sequences and is not restricted to the "TTTN". However, the application of the CRISPR/Cas12a system is still limited by the PAM for double-stranded DNA (dsDNA). Here, we developed asymmetric RPA (Asy-RPA) to completely break the limitations of PAM. Asy-RPA not only achieved efficient amplification but also converted dsDNA to single-stranded DNA (ssDNA) without complicated steps. The ssDNA products activated the trans-cleavage activity of Cas12a, outputting signals. The application of Asy-RPA completely freed Cas12a from the PAM, which can be more widely used in nucleic acid detection, such as lumpy skin disease virus, with an actual detection limit as low as 1.21 × 101 copies·μL-1. More importantly, Cas12a was intolerant to mutations on ssDNA. This provided technical support for the detection and identification of wild-type Mycobacterium tuberculosis (WT-TB) and rifampin-resistant mutant-type M. tuberculosis (MT-TB). The detection limit was as low as 1 fM for 1% mixed samples. The detection and availability of different treatment options for treatment-resistant and WT-TB were significant for the elimination of TB. In summary, the platform consisting of Asy-RPA and CRISPR/Cas12a was suitable for the detection of various viruses and bacteria and was a boon for the detection of dsDNA without recognizable PAM.
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Affiliation(s)
- Gaihua Cao
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
- State Key Laboratory of Cattle Diseases Detection (Chongqing) of Customs. Diagnosis and Testing Laboratory of Lumpy Skin Disease, Chongqing Customs Technology Center, Chongqing 400020, PR China
| | - Nannan Yang
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
- State Key Laboratory of Cattle Diseases Detection (Chongqing) of Customs. Diagnosis and Testing Laboratory of Lumpy Skin Disease, Chongqing Customs Technology Center, Chongqing 400020, PR China
| | - Yifan Xiong
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
- State Key Laboratory of Cattle Diseases Detection (Chongqing) of Customs. Diagnosis and Testing Laboratory of Lumpy Skin Disease, Chongqing Customs Technology Center, Chongqing 400020, PR China
| | - Meimei Shi
- State Key Laboratory of Cattle Diseases Detection (Chongqing) of Customs. Diagnosis and Testing Laboratory of Lumpy Skin Disease, Chongqing Customs Technology Center, Chongqing 400020, PR China
| | - Lin Wang
- Science and Technology Research Center of China Customs, Beijing 100730, PR China
| | - Fuping Nie
- State Key Laboratory of Cattle Diseases Detection (Chongqing) of Customs. Diagnosis and Testing Laboratory of Lumpy Skin Disease, Chongqing Customs Technology Center, Chongqing 400020, PR China
| | - Danqun Huo
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
| | - Changjun Hou
- Key Laboratory for Biorheological Science and Technology of Ministry of Education, Bioengineering College of Chongqing University, Chongqing 400044, PR China
- Chongqing Key Laboratory of Bio-perception & Intelligent Information Processing, School of Microelectronics and Communication Engineering, Chongqing University, Chongqing 400044, PR China
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Novitsky V, Nyandiko W, Vreeman R, DeLong AK, Manne A, Scanlon M, Ngeresa A, Aluoch J, Sang F, Ashimosi C, Jepkemboi E, Orido M, Hogan JW, Kantor R. Added Value of Next Generation over Sanger Sequencing in Kenyan Youth with Extensive HIV-1 Drug Resistance. Microbiol Spectr 2022; 10:e0345422. [PMID: 36445146 PMCID: PMC9769539 DOI: 10.1128/spectrum.03454-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 11/16/2022] [Indexed: 12/03/2022] Open
Abstract
HIV-1 drug resistance testing in children and adolescents in low-resource settings is both important and challenging. New (more sensitive) drug resistance testing technologies may improve clinical care, but evaluation of their added value is limited. We assessed the potential added value of using next-generation sequencing (NGS) over Sanger sequencing for detecting nucleoside reverse transcriptase inhibitor (NRTI) and nonnucleoside reverse transcriptase inhibitor (NNRTI) drug resistance mutations (DRMs). Participants included 132 treatment-experienced Kenyan children and adolescents with diverse HIV-1 subtypes and with already high levels of drug resistance detected by Sanger sequencing. We examined overall and DRM-specific resistance and its predicted impact on antiretroviral therapy and evaluated the discrepancy between Sanger sequencing and six NGS thresholds (1%, 2%, 5%, 10%, 15%, and 20%). Depending on the NGS threshold, agreement between the two technologies was 62% to 88% for any DRM, 83% to 92% for NRTI DRMs, and 73% to 94% for NNRTI DRMs, with more DRMs detected at low NGS thresholds. NGS identified 96% to 100% of DRMs detected by Sanger sequencing, while Sanger identified 83% to 99% of DRMs detected by NGS. Higher discrepancy between technologies was associated with higher DRM prevalence. Even in this resistance-saturated cohort, 12% of participants had higher, potentially clinically relevant predicted resistance detected only by NGS. These findings, in a young, vulnerable Kenyan population with diverse HIV-1 subtypes and already high resistance levels, suggest potential benefits of more sensitive NGS over existing technology. Good agreement between technologies at high NGS thresholds supports their interchangeable use; however, the significance of DRMs identified at lower thresholds to patient care should be explored further. IMPORTANCE HIV-1 drug resistance in children and adolescents remains a significant problem in countries facing the highest burden of the HIV epidemic. Surveillance of HIV-1 drug resistance in children and adolescents is an important public health strategy, particularly in resource-limited settings, and yet, it is limited due mostly to cost and infrastructure constraints. Whether newer and more sensitive next-generation sequencing (NGS) adds substantial value beyond traditional Sanger sequencing in detecting HIV-1 drug resistance in real life settings remains an open and debatable question. In this paper, we attempt to address this issue by performing a comprehensive comparison of drug resistance identified by Sanger sequencing and six NGS thresholds. We conducted this study in a well-characterized, vulnerable cohort of children and adolescents living with diverse HIV-1 subtypes in Kenya and, importantly, failing antiretroviral therapy (ART) with already extensive drug resistance. Our findings suggest a potential added value of NGS over Sanger even in this unique cohort.
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Affiliation(s)
- V. Novitsky
- Brown University, Providence, Rhode Island, USA
| | - W. Nyandiko
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
- Moi University, Eldoret, Kenya
| | - R. Vreeman
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Arnhold Institute for Global Health, New York, New York, USA
| | | | - A. Manne
- Brown University, Providence, Rhode Island, USA
| | - M. Scanlon
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Arnhold Institute for Global Health, New York, New York, USA
| | - A. Ngeresa
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - J. Aluoch
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - F. Sang
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - C. Ashimosi
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - E. Jepkemboi
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - M. Orido
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
| | - J. W. Hogan
- Brown University, Providence, Rhode Island, USA
| | - R. Kantor
- Brown University, Providence, Rhode Island, USA
| | - for the RESistance in a PEdiatric CohorT (RESPECT) Study
- Brown University, Providence, Rhode Island, USA
- Academic Model Providing Access to Healthcare (AMPATH), Eldoret, Kenya
- Moi University, Eldoret, Kenya
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
- Arnhold Institute for Global Health, New York, New York, USA
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3
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Kingwara L, Karanja M, Ngugi C, Kangogo G, Bera K, Kimani M, Bowen N, Abuya D, Oramisi V, Mukui I. From Sequence Data to Patient Result: A Solution for HIV Drug Resistance Genotyping With Exatype, End to End Software for Pol-HIV-1 Sanger Based Sequence Analysis and Patient HIV Drug Resistance Result Generation. J Int Assoc Provid AIDS Care 2021; 19:2325958220962687. [PMID: 32990139 PMCID: PMC7536479 DOI: 10.1177/2325958220962687] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Introduction: With the rapid scale-up of antiretroviral therapy (ART) to treat HIV
infection, there are ongoing concerns regarding probable emergence and
transmission of HIV drug resistance (HIVDR) mutations. This scale-up has to
lead to an increased need for routine HIVDR testing to inform the clinical
decision on a regimen switch. Although the majority of wet laboratory
processes are standardized, slow, labor-intensive data transfer and
subjective manual sequence interpretation steps are still required to
finalize and release patient results. We thus set out to validate the
applicability of a software package to generate HIVDR patient results from
raw sequence data independently. Methods: We assessed the performance characteristics of Hyrax Bioscience’s Exatype (a
sequence data to patient result, fully automated sequence analysis software,
which consolidates RECall, MEGA X and the Stanford HIV database) against the
standard method (RECall and Stanford database). Exatype is a web-based HIV
Drug resistance bioinformatic pipeline available at sanger.exatype.com. To validate the exatype, we used a test set of
135 remnant HIV viral load samples at the National HIV Reference Laboratory
(NHRL). Result: We analyzed, and successfully generated results of 126 sequences out of 135
specimens by both Standard and Exatype software. Result production using
Exatype required minimal hands-on time in comparison to the Standard (6
computation-hours using the standard method versus 1.5 Exatype
computation-hours). Concordance between the 2 systems was 99.8% for 311,227
bases compared. 99.7% of the 0.2% discordant bases, were attributed to
nucleotide mixtures as a result of the sequence editing in Recall. Both
methods identified similar (99.1%) critical antiretroviral
resistance-associated mutations resulting in a 99.2% concordance of
resistance susceptibility interpretations. The Base-calling comparison
between the 2 methods had Cohen’s kappa (0.97 to 0.99), implying an almost
perfect agreement with minimal base calling variation. On a predefined
dataset, RECall editing displayed the highest probability to score mixtures
accurately 1 vs. 0.71 and the lowest chance to inaccurately assign mixtures
to pure nucleotides (0.002–0.0008). This advantage is attributable to the
manual sequence editing in RECall. Conclusion: The reduction in hands-on time needed is a benefit when using the Exatype HIV
DR sequence analysis platform and result generation tool. There is a minimal
difference in base calling between Exatype and standard methods. Although
the discrepancy has minimal impact on drug resistance interpretation,
allowance of sequence editing in Exatype as RECall can significantly improve
its performance.
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Affiliation(s)
- Leonard Kingwara
- National Public Health Laboratory (NPHL), Nairobi, Kenya.,National AIDS and STI Control Program (NASCOP), Nairobi, Kenya
| | - Muthoni Karanja
- National AIDS and STI Control Program (NASCOP), Nairobi, Kenya
| | - Catherine Ngugi
- National AIDS and STI Control Program (NASCOP), Nairobi, Kenya
| | - Geoffrey Kangogo
- National Public Health Laboratory (NPHL), Nairobi, Kenya.,National AIDS and STI Control Program (NASCOP), Nairobi, Kenya
| | - Kipkerich Bera
- National Public Health Laboratory (NPHL), Nairobi, Kenya
| | - Maureen Kimani
- National AIDS and STI Control Program (NASCOP), Nairobi, Kenya
| | - Nancy Bowen
- National Public Health Laboratory (NPHL), Nairobi, Kenya
| | - Dorcus Abuya
- National Public Health Laboratory (NPHL), Nairobi, Kenya.,National AIDS and STI Control Program (NASCOP), Nairobi, Kenya
| | - Violet Oramisi
- National AIDS and STI Control Program (NASCOP), Nairobi, Kenya
| | - Irene Mukui
- National AIDS and STI Control Program (NASCOP), Nairobi, Kenya
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Siriruchatanon M, Liu S, Carlucci JG, Enns EA, Duarte HA. Addressing Pediatric HIV Pretreatment Drug Resistance and Virologic Failure in Sub-Saharan Africa: A Cost-Effectiveness Analysis of Diagnostic-Based Strategies in Children ≥3 Years Old. Diagnostics (Basel) 2021; 11:diagnostics11030567. [PMID: 33801154 PMCID: PMC8004076 DOI: 10.3390/diagnostics11030567] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 11/16/2022] Open
Abstract
Improvement of antiretroviral therapy (ART) regimen switching practices and implementation of pretreatment drug resistance (PDR) testing are two potential approaches to improve health outcomes for children living with HIV. We developed a microsimulation model of disease progression and treatment focused on children with perinatally acquired HIV in sub-Saharan Africa who initiate ART at 3 years of age. We evaluated the cost-effectiveness of diagnostic-based strategies (improved switching and PDR testing), over a 10-year time horizon, in settings without and with pediatric dolutegravir (DTG) availability as first-line ART. The improved switching strategy increases the probability of switching to second-line ART when virologic failure is diagnosed through viral load testing. The PDR testing strategy involves a one-time PDR test prior to ART initiation to guide choice of initial regimen. When DTG is not available, PDR testing is dominated by the improved switching strategy, which has an incremental cost-effectiveness ratio (ICER) of USD 579/life-year gained (LY), relative to the status quo. If DTG is available, improved switching has a similar ICER (USD 591/LY) relative to the DTGstatus quo. Even when substantial financial investment is needed to achieve improved regimen switching practices, the improved switching strategy still has the potential to be cost-effective in a wide range of sub-Saharan African countries. Our analysis highlights the importance of strengthening existing laboratory monitoring systems to improve the health of children living with HIV.
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Affiliation(s)
- Mutita Siriruchatanon
- Department of Industrial & Systems Engineering, University of Washington, Seattle, WA 98185, USA; (M.S.); (S.L.)
| | - Shan Liu
- Department of Industrial & Systems Engineering, University of Washington, Seattle, WA 98185, USA; (M.S.); (S.L.)
| | - James G. Carlucci
- Department of Pediatrics, Ryan White Center for Pediatric Infectious Diseases and Global Health, Indiana University School of Medicine, Indianapolis, IN 46202, USA;
| | - Eva A. Enns
- Division of Health Policy and Management, School of Public Health, University of Minnesota, Minneapolis, MN 55408, USA;
| | - Horacio A. Duarte
- Department of Pediatrics, Division of Infectious Diseases, University of Washington, Seattle, WA 98105, USA
- Seattle Children’s Research Institute, Seattle, WA 98101, USA
- Correspondence: ; Tel.: +1-206-884-8233; Fax: +1-206-884-7311
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Raugi DN, Nixon RS, Leong S, Faye K, Diatta JP, Sall F, Smith RA, Sall EI, Malomar JJ, Seydi M, Gottlieb GS. HIV-2 Drug Resistance Genotyping from Dried Blood Spots. J Clin Microbiol 2020; 59:e02303-20. [PMID: 33055182 DOI: 10.1128/JCM.02303-20] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2020] [Accepted: 10/09/2020] [Indexed: 11/20/2022] Open
Abstract
The treatment of HIV-2 in resource-limited settings (RLS) is complicated by the limited availability of HIV-2-active antiretroviral drugs and inadequate access to HIV-2 viral load and drug resistance testing. Dried blood spots (DBS)-based drug resistance testing, widely studied for HIV-1, has not been reported for HIV-2 and could present an opportunity to improve care for HIV-2-infected individuals. We selected 150 DBS specimens from ongoing studies of antiretroviral therapy (ART) for HIV-2 infection in Senegal and subjected them to genotypic drug resistance testing. Total nucleic acid was extracted from DBS, reverse transcribed, PCR amplified, and analyzed by population-based Sanger sequencing, and major drug resistance-associated mutations (RAM) were identified. Parallel samples from plasma and peripheral blood mononuclear cells (PBMC) were also genotyped. We obtained 58 protease/reverse transcriptase genotypes. Plasma viral load was significantly correlated with genotyping success (P < 0.001); DBS samples with corresponding plasma viral load >250 copies/ml had a success rate of 86.8%. In paired DBS-plasma genotypes, 83.8% of RAM found in plasma were also found in DBS, and replicate DBS genotyping revealed that a single test detected 86.7% of known RAM. These findings demonstrate that DBS-based genotypic drug resistance testing for HIV-2 is feasible and can be deployed in RLS with limited infrastructure.
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Fabeni L, Santoro MM, Lorenzini P, Rusconi S, Gianotti N, Costantini A, Sarmati L, Antinori A, Ceccherini-Silberstein F, d'Arminio Monforte A, Saracino A, Girardi E, On Behalf Of The Icona Foundation Study Cohort. Evaluation of HIV Transmission Clusters among Natives and Foreigners Living in Italy. Viruses 2020; 12:E791. [PMID: 32718024 DOI: 10.3390/v12080791] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Revised: 07/06/2020] [Accepted: 07/08/2020] [Indexed: 02/06/2023] Open
Abstract
We aimed at evaluating the characteristics of HIV-1 molecular transmission clusters (MTCs) among natives and migrants living in Italy, diagnosed between 1998 and 2018. Phylogenetic analyses were performed on HIV-1 polymerase (pol) sequences to characterise subtypes and identify MTCs, divided into small (SMTCs, 2–3 sequences), medium (MMTCs, 4–9 sequences) and large (LMTCs, ≥10 sequences). Among 3499 drug-naïve individuals enrolled in the Italian Cohort Naive Antiretroviral (ICONA) cohort (2804 natives; 695 migrants), 726 (20.8%; 644 natives, 82 migrants) were involved in 228 MTCs (6 LMTCs, 36 MMTCs, 186 SMTCs). Migrants contributed 14.4% to SMTCs, 7.6% to MMTCs and 7.1% to LMTCs, respectively. HIV-1 non-B subtypes were found in 51 MTCs; noteworthy was that non-B infections involved in MTCs were more commonly found in natives (n = 47) than in migrants (n = 4). Factors such as Italian origin, being men who have sex with men (MSM), younger age, more recent diagnosis and a higher CD4 count were significantly associated with MTCs. Our findings show that HIV-1 clustering transmission among newly diagnosed individuals living in Italy is prevalently driven by natives, mainly MSM, with a more recent diagnosis and frequently infected with HIV-1 non-B subtypes. These results can contribute to monitoring of the HIV epidemic and guiding the public health response to prevent new HIV infections.
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Noguera-Julian M, Lee ER, Shafer RW, Kantor R, Ji H. Dry Panels Supporting External Quality Assessment Programs for Next Generation Sequencing-Based HIV Drug Resistance Testing. Viruses 2020; 12:v12060666. [PMID: 32575676 PMCID: PMC7354622 DOI: 10.3390/v12060666] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 06/18/2020] [Accepted: 06/18/2020] [Indexed: 12/18/2022] Open
Abstract
External quality assessment (EQA) is a keystone element in the validation and implementation of next generation sequencing (NGS)-based HIV drug resistance testing (DRT). Software validation and evaluation is a critical element in NGS EQA programs. While the development, sharing, and adoption of wet lab protocols is coupled with the increasing access to NGS technology worldwide, rendering it easy to produce NGS data for HIV-DRT, bioinformatic data analysis remains a bottleneck for most of the diagnostic laboratories. Several computational tools have been made available, via free or commercial sources, to automate the conversion of raw NGS data into an actionable clinical report. Although different software platforms yield equivalent results when identical raw NGS datasets are analyzed for variations at higher abundance, discrepancies arise when variations at lower frequencies are considered. This implies that validation and performance assessment of the bioinformatics tools applied in NGS HIV-DRT is critical, and the origins of the observed discrepancies should be determined. Well-characterized reference NGS datasets with ground truth on the genotype composition at all examined loci and the exact frequencies of HIV variations they may harbor, so-called dry panels, would be essential in such cases. The strategic design and construction of such panels are challenging but imperative tasks in support of EQA programs for NGS-based HIV-DRT and the validation of relevant bioinformatics tools. Here, we present criteria that can guide the design of such dry panels, which were discussed in the Second International Winnipeg Symposium themed for EQA strategies for NGS HIVDR assays.
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Affiliation(s)
- Marc Noguera-Julian
- IrsiCaixa AIDS Research Institute, Hospital Germans Trias i Pujol, s/n, Catalonia, 08196 Badalona, Spain
- Chair in AIDS and Related Illnesses, Centre for Health and Social Care Research (CESS), Faculty of Medicine, University of Vic, Central University of Catalonia, Can Baumann. Ctra. de Roda, 70, 08500 Vic, Spain
- Correspondence:
| | - Emma R. Lee
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (E.R.L.); (H.J.)
| | | | - Rami Kantor
- Division of Infectious Diseases, Brown University Alpert Medical School, Providence, RI 02903, USA;
| | - Hezhao Ji
- National HIV and Retrovirology Laboratories, National Microbiology Laboratory at JC Wilt Infectious Diseases Research Centre, Public Health Agency of Canada, Winnipeg, MB R3E 3R2, Canada; (E.R.L.); (H.J.)
- Department of Medical Microbiology and Infectious Diseases, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, MB R3E 0J9, Canada
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8
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Lee ER, Gao F, Sandstrom P, Ji H. External Quality Assessment for Next-Generation Sequencing-Based HIV Drug Resistance Testing: Unique Requirements and Challenges. Viruses 2020; 12:E550. [PMID: 32429382 DOI: 10.3390/v12050550] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/09/2020] [Accepted: 05/14/2020] [Indexed: 12/25/2022] Open
Abstract
Over the past decade, there has been an increase in the adoption of next generation sequencing (NGS) technologies for HIV drug resistance (HIVDR) testing. NGS far outweighs conventional Sanger sequencing as it has much higher throughput, lower cost when samples are batched and, most importantly, significantly higher sensitivities for variants present at low frequencies, which may have significant clinical implications. Despite the advantages of NGS, Sanger sequencing remains the gold standard for HIVDR testing, largely due to the lack of standardization of NGS-based HIVDR testing. One important aspect of standardization includes external quality assessment (EQA) strategies and programs. Current EQA for Sanger-based HIVDR testing includes proficiency testing where samples are sent to labs and the performance of the lab conducting such assays is evaluated. The current methods for Sanger-based EQA may not apply to NGS-based tests because of the fundamental differences in their technologies and outputs. Sanger-based genotyping reports drug resistance mutations (DRMs) data as dichotomous, whereas NGS-based HIVDR genotyping also reports DRMs as numerical data (percent abundance). Here we present an overview of the need to develop EQA for NGS-based HIVDR testing and some unique challenges that may be encountered.
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9
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Brooks RB, Feldman KA, Blythe D, Flynn C. Completeness of HIV nucleotide sequence ascertainment and its potential impact on understanding HIV transmission - Maryland, 2011-2013 .. AIDS Care 2018; 31:621-628. [PMID: 30430842 DOI: 10.1080/09540121.2018.1545983] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
HIV nucleotide sequences generated through routine drug resistance testing (DRT) and reported to Maryland's Molecular HIV Surveillance system are most effective for elucidating transmission patterns and identifying outbreaks if DRT is ordered promptly and sequences are reported completely. Among reported cases of HIV infection newly diagnosed during 2011-2013 in Maryland residents aged ≥13 years, we assessed sequence ascertainment completeness. To better understand which populations were most likely to have a sequence, we examined associations between sequence ascertainment and clinical and demographic characteristics. During 2011-2013, 4423 new HIV infection diagnoses were reported; sequences were ascertained for 1282 (29.0%). Among 3267 cases with complete data, odds for having a sequence ascertained were highest for cases in persons living inside Maryland's Central Region with initial CD4 counts ≤500 cells/mm3 (adjusted odds ratio [aOR] 2.4, 95% confidence interval [CI] 1.9-3.1). Sequence ascertainment did not vary significantly by patient age, sex, race/ethnicity or HIV transmission category. Educational interventions, policy changes and improved processes to increase timely DRT and subsequent sequence reporting with a focus on testing at entry to care, particularly for those with higher CD4 counts and those living outside the Central Region, might improve ascertainment completeness.
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Affiliation(s)
- Richard B Brooks
- a Epidemic Intelligence Service, Division of Scientific Education and Professional Development , Centers for Disease Control and Prevention , Atlanta , GA , USA.,b Infectious Disease Epidemiology and Outbreak Response Bureau , Maryland Department of Health , Baltimore , MD , USA
| | - Katherine A Feldman
- b Infectious Disease Epidemiology and Outbreak Response Bureau , Maryland Department of Health , Baltimore , MD , USA
| | - David Blythe
- b Infectious Disease Epidemiology and Outbreak Response Bureau , Maryland Department of Health , Baltimore , MD , USA
| | - Colin Flynn
- b Infectious Disease Epidemiology and Outbreak Response Bureau , Maryland Department of Health , Baltimore , MD , USA
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Abstract
Combination antiretroviral therapy for HIV-1 infection has resulted in profound reductions in viremia and is associated with marked improvements in morbidity and mortality. Therapy is not curative, however, and prolonged therapy is complicated by drug toxicity and the emergence of drug resistance. Management of clinical drug resistance requires in depth evaluation, and includes extensive history, physical examination and laboratory studies. Appropriate use of resistance testing provides valuable information useful in constructing regimens for treatment-experienced individuals with viremia during therapy. This review outlines the emergence of drug resistance in vivo, and describes clinical evaluation and therapeutic options of the individual with rebound viremia during therapy.
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