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Zhang X, Lam C, Martinez E, Sim E, Crighton T, Marais BJ, Sintchenko V. Genomic markers of drug resistance in Mycobacterium tuberculosis populations with minority variants. J Clin Microbiol 2023; 61:e0048523. [PMID: 37750734 PMCID: PMC10595065 DOI: 10.1128/jcm.00485-23] [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] [Received: 04/18/2023] [Accepted: 07/17/2023] [Indexed: 09/27/2023] Open
Abstract
Minority variants of Mycobacterium tuberculosis harboring mutations conferring resistance can become dominant populations during tuberculosis (TB) treatment, leading to treatment failure. Our understanding of drug-resistant within-host subpopulations and the frequency of resistance-conferring mutations in minority variants remains limited. M. tuberculosis sequences recovered from liquid cultures of culture-confirmed TB cases notified between January 2017 and December 2021 in New South Wales, Australia were examined. Potential drug resistance-conferring minority variants were identified using LoFreq, and mixed populations of different M. tuberculosis strains (≥100 SNPs apart) were examined using QuantTB. A total of 1831 routinely sequenced M. tuberculosis strains were included in the analysis. Drug resistance-conferring minority variants were detected in 3.5% (65/1831) of sequenced cultures; 84.6% (55/65) had majority strains that were drug susceptible and 15.4% (10/65) had majority strains that were drug resistant. Minority variants with high-confidence drug resistance-conferring mutations were 1.5 times more common when the majority strains were drug resistant. Mixed M. tuberculosis strain populations were documented in 10.0% (183/1831) of specimens. Minority variants with high-confidence drug resistance-conferring mutations were more frequently detected in mixed M. tuberculosis strain populations (2.7%, 5/183) than in single strain populations (0.6%, 10/1648; P = 0.01). Drug-resistant minority variants require monitoring in settings that implement routine M. tuberculosis sequencing. The frequency with which drug-resistant minority variants are detected is likely influenced by pre-culture requirement. Culture-independent sequencing methods should provide a more accurate reflection of drug-resistant subpopulations.
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Affiliation(s)
- Xiaomei Zhang
- Centre for Research Excellence in Tuberculosis (TB-CRE), Centenary Institute, Sydney, New South Wales, Australia
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, New South Wales, Australia
| | - Connie Lam
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, New South Wales, Australia
| | - Elena Martinez
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, New South Wales, Australia
- NSW Mycobacterium Reference Laboratory,Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, New South Wales, Australia
| | - Eby Sim
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, New South Wales, Australia
| | - Taryn Crighton
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, New South Wales, Australia
- NSW Mycobacterium Reference Laboratory,Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, New South Wales, Australia
| | - Ben J. Marais
- Centre for Research Excellence in Tuberculosis (TB-CRE), Centenary Institute, Sydney, New South Wales, Australia
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Research Excellence in Tuberculosis (TB-CRE), Centenary Institute, Sydney, New South Wales, Australia
- Sydney Infectious Diseases Institute (Sydney ID), The University of Sydney, Sydney, New South Wales, Australia
- Centre for Infectious Diseases and Microbiology-Public Health, Westmead Hospital, Sydney, New South Wales, Australia
- NSW Mycobacterium Reference Laboratory,Centre for Infectious Diseases and Microbiology-Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, New South Wales, Australia
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Laubscher F, Cordey S, Friedlaender A, Schweblin C, Noetzlin S, Simand PF, Bordry N, De Sousa F, Pigny F, Baggio S, Getaz L, Dietrich PY, Kaiser L, Vu DL. SARS-CoV-2 Evolution among Oncological Population: In-Depth Virological Analysis of a Clinical Cohort. Microorganisms 2021; 9:2145. [PMID: 34683466 PMCID: PMC8540785 DOI: 10.3390/microorganisms9102145] [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] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Revised: 09/30/2021] [Accepted: 10/06/2021] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Oncological patients have a higher risk of prolonged SARS-CoV-2 shedding, which, in turn, can lead to evolutionary mutations and emergence of novel viral variants. The aim of this study was to analyze biological samples of a cohort of oncological patients by deep sequencing to detect any significant viral mutations. METHODS High-throughput sequencing was performed on selected samples from a SARS-CoV-2-positive oncological patient cohort. Analysis of variants and minority variants was performed using a validated bioinformatics pipeline. RESULTS Among 54 oncological patients, we analyzed 12 samples of 6 patients, either serial nasopharyngeal swab samples or samples from the upper and lower respiratory tracts, by high-throughput sequencing. We identified amino acid changes D614G and P4715L as well as mutations at nucleotide positions 241 and 3037 in all samples. There were no other significant mutations, but we observed intra-host evolution in some minority variants, mainly in the ORF1ab gene. There was no significant mutation identified in the spike region and no minority variants common to several hosts. CONCLUSIONS There was no major and rapid evolution of viral strains in this oncological patient cohort, but there was minority variant evolution, reflecting a dynamic pattern of quasi-species replication.
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Affiliation(s)
- Florian Laubscher
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (F.L.); (S.C.); (C.S.); (F.P.); (L.K.)
| | - Samuel Cordey
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (F.L.); (S.C.); (C.S.); (F.P.); (L.K.)
- Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (S.B.); (L.G.); (P.-Y.D.)
| | - Alex Friedlaender
- Department of Oncology, Geneva University Hospitals, 1205 Geneva, Switzerland; (A.F.); (S.N.); (P.-F.S.); (N.B.); (F.D.S.)
| | - Cecilia Schweblin
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (F.L.); (S.C.); (C.S.); (F.P.); (L.K.)
| | - Sarah Noetzlin
- Department of Oncology, Geneva University Hospitals, 1205 Geneva, Switzerland; (A.F.); (S.N.); (P.-F.S.); (N.B.); (F.D.S.)
| | - Pierre-François Simand
- Department of Oncology, Geneva University Hospitals, 1205 Geneva, Switzerland; (A.F.); (S.N.); (P.-F.S.); (N.B.); (F.D.S.)
| | - Natacha Bordry
- Department of Oncology, Geneva University Hospitals, 1205 Geneva, Switzerland; (A.F.); (S.N.); (P.-F.S.); (N.B.); (F.D.S.)
| | - Filipe De Sousa
- Department of Oncology, Geneva University Hospitals, 1205 Geneva, Switzerland; (A.F.); (S.N.); (P.-F.S.); (N.B.); (F.D.S.)
| | - Fiona Pigny
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (F.L.); (S.C.); (C.S.); (F.P.); (L.K.)
| | - Stephanie Baggio
- Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (S.B.); (L.G.); (P.-Y.D.)
- Division of Prison Health, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Laurent Getaz
- Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (S.B.); (L.G.); (P.-Y.D.)
- Division of Prison Health, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Pierre-Yves Dietrich
- Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (S.B.); (L.G.); (P.-Y.D.)
- Department of Oncology, Geneva University Hospitals, 1205 Geneva, Switzerland; (A.F.); (S.N.); (P.-F.S.); (N.B.); (F.D.S.)
| | - Laurent Kaiser
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (F.L.); (S.C.); (C.S.); (F.P.); (L.K.)
- Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (S.B.); (L.G.); (P.-Y.D.)
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
- Center for Emerging Viruses, Geneva University Hospitals, 1205 Geneva, Switzerland
| | - Diem-Lan Vu
- Laboratory of Virology, Division of Laboratory Medicine, Geneva University Hospitals, 1205 Geneva, Switzerland; (F.L.); (S.C.); (C.S.); (F.P.); (L.K.)
- Faculty of Medicine, University of Geneva, 1206 Geneva, Switzerland; (S.B.); (L.G.); (P.-Y.D.)
- Division of Infectious Diseases, Geneva University Hospitals, 1205 Geneva, Switzerland
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Mbunkah HA, Bertagnolio S, Hamers RL, Hunt G, Inzaule S, Rinke De Wit TF, Paredes R, Parkin NT, Jordan MR, Metzner KJ. Low-Abundance Drug-Resistant HIV-1 Variants in Antiretroviral Drug-Naive Individuals: A Systematic Review of Detection Methods, Prevalence, and Clinical Impact. J Infect Dis 2021; 221:1584-1597. [PMID: 31809534 DOI: 10.1093/infdis/jiz650] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2019] [Accepted: 12/04/2019] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND The presence of high-abundance drug-resistant HIV-1 jeopardizes success of antiretroviral therapy (ART). Despite numerous investigations, the clinical impact of low-abundance drug-resistant HIV-1 variants (LA-DRVs) at levels <15%-25% of the virus population in antiretroviral (ARV) drug-naive individuals remains controversial. METHODS We systematically reviewed 103 studies assessing prevalence, detection methods, technical and clinical detection cutoffs, and clinical significance of LA-DRVs in antiretroviral drug-naive adults. RESULTS In total, 14 919 ARV drug-naive individuals were included. Prevalence of LA-DRVs (ie, proportion of individuals harboring LA-DRVs) was 0%-100%. Technical detection cutoffs showed a 4 log range (0.001%-10%); 42/103 (40.8%) studies investigating the impact of LA-DRVs on ART; 25 studies included only individuals on first-line nonnucleoside reverse transcriptase inhibitor-based ART regimens. Eleven of those 25 studies (44.0%) reported a significantly association between preexisting LA-DRVs and risk of virological failure whereas 14/25 (56.0%) did not. CONCLUSIONS Comparability of the 103 studies is hampered by high heterogeneity of the studies' designs and use of different methods to detect LA-DRVs. Thus, evaluating clinical impact of LA-DRVs on first-line ART remains challenging. We, the WHO HIVResNet working group, defined central areas of future investigations to guide further efforts to implement ultrasensitive resistance testing in routine settings.
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Affiliation(s)
- Herbert A Mbunkah
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zürich, Switzerland.,Institute of Medical Virology, University of Zurich, Zürich, Switzerland.,Paul-Ehrlich-Institut, Langen, Germany
| | | | - Raph L Hamers
- Amsterdam Institute for Global Health and Development, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands.,Eijkman-Oxford Clinical Research Unit, Faculty of Medicine, Universitas Indonesia, Jakarta, Indonesia.,Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Gillian Hunt
- National Institute for Communicable Diseases, Johannesburg, South Africa
| | - Seth Inzaule
- Amsterdam Institute for Global Health and Development, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Tobias F Rinke De Wit
- Amsterdam Institute for Global Health and Development, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Roger Paredes
- Infectious Diseases Service and IrsiCaixa AIDS Research Institute for AIDS Research, Hospital Universitari Germans Trias i Pujol, Badalona, Catalonia, Spain
| | | | - Michael R Jordan
- Division of Geographic Medicine and Infectious Disease, Tufts University School of Medicine, Tufts Medical Center, Boston, Massachusetts, USA
| | - Karin J Metzner
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, University of Zurich, Zürich, Switzerland.,Institute of Medical Virology, University of Zurich, Zürich, Switzerland
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Sili U, Aksu B, Tekin A, Hasdemir U, Soyletir G, Korten V. Assessment of Transmitted HIV-1 Drug Resistance Mutations Using Ultra- Deep Pyrosequencing in a Turkish Cohort. Curr HIV Res 2019; 16:216-221. [PMID: 30198436 DOI: 10.2174/1570162x16666180910130112] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Revised: 08/11/2018] [Accepted: 09/03/2018] [Indexed: 11/22/2022]
Abstract
BACKGROUND Antiretroviral treatment (ART) reduces morbidity and mortality caused by human immunodeficiency virus (HIV) infection; however, the emergence of drug-resistant strains poses an important obstacle to treatment success. Using conventional sequencing methods to determine antiretroviral resistance, mutations present in ≥20% of quasispecies can be identified, but drug-resistant minority variants can lead to virologic failure. OBJECTIVE We aimed to assess transmitted drug resistance mutations (TDRMs) within minority variants using ultra-deep pyrosequencing (UDPS). METHOD Treatment-naive adult patients were included in this observational study. Surveillance TDRMs were classified as ≥20% or at minority variant level (≥2% - <20%). Genotypic sensitivity score calculated by using all pre-treatment drug resistance mutations (PDRMs) was also evaluated. RESULTS Thirty-six patients were analyzed. Any TDRM at ≥20% level was detected in 8.3% of the patients (n=3). This prevalence increased to 30.6% (n=11) with the inclusion of minority variants. All non-nucleoside reverse transcriptase inhibitor and protease inhibitor-related TDRMs were within minority variants. The genotypic sensitivity score of rilpivirine-based regimens was considerably diminished when minority variants were included in the PDRM analysis. CONCLUSION UDPS was used for the first time to assess TDRM in a Turkish HIV cohort and uncovered several mutations hidden within minority variants. UDPS may be preferred to detect PDRMs for avoiding virologic failure with rilpivirine-based ART regimens.
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Affiliation(s)
- Uluhan Sili
- Department of Infectious Diseases and Clinical Microbiology, School of Medicine, Marmara University, Istanbul, Turkey
| | - Burak Aksu
- Department of Medical Microbiology, School of Medicine, Marmara University, Istanbul, Turkey
| | - Aysun Tekin
- Department of Infectious Diseases and Clinical Microbiology, School of Medicine, Marmara University, Istanbul, Turkey
| | - Ufuk Hasdemir
- Department of Medical Microbiology, School of Medicine, Marmara University, Istanbul, Turkey
| | - Guner Soyletir
- Department of Medical Microbiology, School of Medicine, Marmara University, Istanbul, Turkey
| | - Volkan Korten
- Department of Infectious Diseases and Clinical Microbiology, School of Medicine, Marmara University, Istanbul, Turkey
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Said Mohammed K, Kibinge N, Prins P, Agoti CN, Cotten M, Nokes D, Brand S, Githinji G. Evaluating the performance of tools used to call minority variants from whole genome short-read data. Wellcome Open Res 2018; 3:21. [PMID: 30483597 PMCID: PMC6234735 DOI: 10.12688/wellcomeopenres.13538.2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/03/2018] [Indexed: 01/06/2023] Open
Abstract
Background: High-throughput whole genome sequencing facilitates investigation of minority virus sub-populations from virus positive samples. Minority variants are useful in understanding within and between host diversity, population dynamics and can potentially assist in elucidating person-person transmission pathways. Several minority variant callers have been developed to describe low frequency sub-populations from whole genome sequence data. These callers differ based on bioinformatics and statistical methods used to discriminate sequencing errors from low-frequency variants. Methods: We evaluated the diagnostic performance and concordance between published minority variant callers used in identifying minority variants from whole-genome sequence data from virus samples. We used the ART-Illumina read simulation tool to generate three artificial short-read datasets of varying coverage and error profiles from an RSV reference genome. The datasets were spiked with nucleotide variants at predetermined positions and frequencies. Variants were called using FreeBayes, LoFreq, Vardict, and VarScan2. The variant callers' agreement in identifying known variants was quantified using two measures; concordance accuracy and the inter-caller concordance. Results: The variant callers reported differences in identifying minority variants from the datasets. Concordance accuracy and inter-caller concordance were positively correlated with sample coverage. FreeBayes identified the majority of variants although it was characterised by variable sensitivity and precision in addition to a high false positive rate relative to the other minority variant callers and which varied with sample coverage. LoFreq was the most conservative caller. Conclusions: We conducted a performance and concordance evaluation of four minority variant calling tools used to identify and quantify low frequency variants. Inconsistency in the quality of sequenced samples impacts on sensitivity and accuracy of minority variant callers. Our study suggests that combining at least three tools when identifying minority variants is useful in filtering errors when calling low frequency variants.
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Affiliation(s)
- Khadija Said Mohammed
- Pwani University, Kilifi, Kenya
- KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
| | - Nelson Kibinge
- KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
| | - Pjotr Prins
- KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
- University Medical Center Utrecht, Utrecht, The Netherlands
| | - Charles N. Agoti
- Pwani University, Kilifi, Kenya
- KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
| | - Matthew Cotten
- Virosciences Department, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - D.J. Nokes
- KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute (SBIDER), University of Warwick, Coventry, UK
| | - Samuel Brand
- School of Life Sciences and Zeeman Institute (SBIDER), University of Warwick, Coventry, UK
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
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Said Mohammed K, Kibinge N, Prins P, Agoti CN, Cotten M, Nokes D, Brand S, Githinji G. Evaluating the performance of tools used to call minority variants from whole genome short-read data. Wellcome Open Res 2018; 3:21. [PMID: 30483597 PMCID: PMC6234735 DOI: 10.12688/wellcomeopenres.13538.1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/06/2018] [Indexed: 01/11/2023] Open
Abstract
Background: High-throughput whole genome sequencing facilitates investigation of minority sub-populations from virus positive samples. Minority variants are useful in understanding within and between host diversity, population dynamics and can potentially help to elucidate person-person transmission chains. Several minority variant callers have been developed to describe the minority variants sub-populations from whole genome sequence data. However, they differ on bioinformatics and statistical approaches used to discriminate sequencing errors from low-frequency variants. Methods: We evaluated the diagnostic performance and concordance between published minority variant callers used in identifying minority variants from whole-genome sequence data. The ART-Illumina read simulation tool was used to generate three artificial short-read datasets of varying coverage and error profiles from an RSV reference genome. The datasets were spiked with nucleotide variants at predetermined positions and frequencies. Variants were called using FreeBayes, LoFreq, Vardict, and VarScan2. The variant callers' agreement in identifying known variants was quantified using two measures; concordance accuracy and the inter-caller concordance. Results: The variant callers reported differences in identifying minority variants from the datasets. Concordance accuracy and inter-caller concordance were positively correlated with sample coverage. FreeBayes identified majority of the variants although it was characterised by variable sensitivity and precision in addition to a high false positive rate relative to the other minority variant callers and which varied with sample coverage. LoFreq was the most conservative caller. Conclusions: We conducted a performance and concordance evaluation of four minority variant calling tools used to identify and quantify low frequency variants. Inconsistency in the quality of sequenced samples impact on sensitivity and accuracy of minority variant callers. Our study suggests that combining at least three tools when identifying minority variants is useful in filtering errors when calling low frequency variants.
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Affiliation(s)
- Khadija Said Mohammed
- Pwani University, Kilifi, Kenya
- KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
| | - Nelson Kibinge
- KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
| | - Pjotr Prins
- KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
- University Medical Center Utrecht, Utrecht, The Netherlands
| | - Charles N. Agoti
- Pwani University, Kilifi, Kenya
- KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
| | - Matthew Cotten
- Virosciences Department, Erasmus Medical Centre, Rotterdam, The Netherlands
| | - D.J. Nokes
- KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
- School of Life Sciences and Zeeman Institute (SBIDER), University of Warwick, Coventry, UK
| | - Samuel Brand
- School of Life Sciences and Zeeman Institute (SBIDER), University of Warwick, Coventry, UK
| | - George Githinji
- KEMRI-Wellcome Trust Research Programme, KEMRI Centre for Geographic Medicine Research – Coast, Kilifi, Kenya
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Patterson EI, Khanipov K, Rojas MM, Kautz TF, Rockx-Brouwer D, Golovko G, Albayrak L, Fofanov Y, Forrester NL. Mosquito bottlenecks alter viral mutant swarm in a tissue and time-dependent manner with contraction and expansion of variant positions and diversity. Virus Evol 2018; 4:vey001. [PMID: 29479479 PMCID: PMC5814806 DOI: 10.1093/ve/vey001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [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] [Indexed: 12/26/2022] Open
Abstract
Viral diversity is theorized to play a significant role during virus infections, particularly for arthropod-borne viruses (arboviruses) that must infect both vertebrate and invertebrate hosts. To determine how viral diversity influences mosquito infection and dissemination Culex taeniopus mosquitoes were infected with the Venezuelan equine encephalitis virus endemic strain 68U201. Bodies and legs/wings of the mosquitoes were collected individually and subjected to multi-parallel sequencing. Virus sequence diversity was calculated for each tissue. Greater diversity was seen in mosquitoes with successful dissemination versus those with no dissemination. Diversity across time revealed that bottlenecks influence diversity following dissemination to the legs/wings, but levels of diversity are restored by Day 12 post-dissemination. Specific minority variants were repeatedly identified across the mosquito cohort, some in nearly every tissue and time point, suggesting that certain variants are important in mosquito infection and dissemination. This study demonstrates that the interaction between the mosquito and the virus results in changes in diversity and the mutational spectrum and may be essential for successful transition of the bottlenecks associated with arbovirus infection.
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Affiliation(s)
- Edward I Patterson
- Department of Pathology, Institute for Human Infections and Immunity, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0610, USA
| | - Kamil Khanipov
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-0617, USA
| | - Mark M Rojas
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-0617, USA
| | - Tiffany F Kautz
- Department of Pathology, Institute for Human Infections and Immunity, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0610, USA
| | - Dedeke Rockx-Brouwer
- Department of Pathology, Institute for Human Infections and Immunity, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0610, USA
| | - Georgiy Golovko
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-0617, USA
| | - Levent Albayrak
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-0617, USA
| | - Yuriy Fofanov
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX 77555-0617, USA
| | - Naomi L Forrester
- Department of Pathology, Institute for Human Infections and Immunity, University of Texas Medical Branch, 301 University Boulevard, Galveston, TX 77555-0610, USA
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Porter DP, Daeumer M, Thielen A, Chang S, Martin R, Cohen C, Miller MD, White KL. Emergent HIV-1 Drug Resistance Mutations Were Not Present at Low-Frequency at Baseline in Non-Nucleoside Reverse Transcriptase Inhibitor-Treated Subjects in the STaR Study. Viruses 2015; 7:6360-70. [PMID: 26690199 PMCID: PMC4690866 DOI: 10.3390/v7122943] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Revised: 11/19/2015] [Accepted: 11/20/2015] [Indexed: 01/02/2023] Open
Abstract
At Week 96 of the Single-Tablet Regimen (STaR) study, more treatment-naïve subjects that received rilpivirine/emtricitabine/tenofovir DF (RPV/FTC/TDF) developed resistance mutations compared to those treated with efavirenz (EFV)/FTC/TDF by population sequencing. Furthermore, more RPV/FTC/TDF-treated subjects with baseline HIV-1 RNA >100,000 copies/mL developed resistance compared to subjects with baseline HIV-1 RNA ≤100,000 copies/mL. Here, deep sequencing was utilized to assess the presence of pre-existing low-frequency variants in subjects with and without resistance development in the STaR study. Deep sequencing (Illumina MiSeq) was performed on baseline and virologic failure samples for all subjects analyzed for resistance by population sequencing during the clinical study (n = 33), as well as baseline samples from control subjects with virologic response (n = 118). Primary NRTI or NNRTI drug resistance mutations present at low frequency (≥2% to 20%) were detected in 6.6% of baseline samples by deep sequencing, all of which occurred in control subjects. Deep sequencing results were generally consistent with population sequencing but detected additional primary NNRTI and NRTI resistance mutations at virologic failure in seven samples. HIV-1 drug resistance mutations emerging while on RPV/FTC/TDF or EFV/FTC/TDF treatment were not present at low frequency at baseline in the STaR study.
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Affiliation(s)
| | - Martin Daeumer
- Seq-IT GmbH & Co. KG, Pfaffplatz 10, 67655 Kaiserslautern, Germany.
| | | | - Silvia Chang
- Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, USA.
| | - Ross Martin
- Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, USA.
| | - Cal Cohen
- Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, USA.
| | - Michael D Miller
- Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, USA.
| | - Kirsten L White
- Gilead Sciences, 333 Lakeside Drive, Foster City, CA 94404, USA.
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Noguera-Julian M, Cozzi-Lepri A, Di Giallonardo F, Schuurman R, Däumer M, Aitken S, Ceccherini-Silberstein F, D'Arminio Monforte A, Geretti AM, Booth CL, Kaiser R, Michalik C, Jansen K, Masquelier B, Bellecave P, Kouyos RD, Castro E, Furrer H, Schultze A, Günthard HF, Brun-Vezinet F, Metzner KJ, Paredes R; CHAIN Minority HIV-1 Variants Working group. Contribution of APOBEC3G/F activity to the development of low-abundance drug-resistant human immunodeficiency virus type 1 variants. Clin Microbiol Infect 2016; 22:191-200. [PMID: 26482266 DOI: 10.1016/j.cmi.2015.10.004] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2015] [Revised: 09/07/2015] [Accepted: 10/03/2015] [Indexed: 11/20/2022]
Abstract
Plasma drug-resistant minority human immunodeficiency virus type 1 variants (DRMVs) increase the risk of virological failure to first-line non-nucleoside reverse transcriptase inhibitor antiretroviral therapy (ART). The origin of DRMVs in ART-naive patients, however, remains unclear. In a large pan-European case-control study investigating the clinical relevance of pre-existing DRMVs using 454 pyrosequencing, the six most prevalent plasma DRMVs detected corresponded to G-to-A nucleotide mutations (V90I, V106I, V108I, E138K, M184I and M230I). Here, we evaluated if such DRMVs could have emerged from apolipoprotein B mRNA editing enzyme, catalytic polypeptide 3G/F (APOBEC3G/F) activity. Out of 236 ART-naive subjects evaluated, APOBEC3G/F hypermutation signatures were detected in plasma viruses of 14 (5.9%) individuals. Samples with minority E138K, M184I, and M230I mutations, but not those with V90I, V106I or V108I, were significantly associated with APOBEC3G/F activity (Fisher's P < 0.005), defined as the presence of > 0.5% of sample sequences with an APOBEC3G/F signature. Mutations E138K, M184I and M230I co-occurred in the same sequence as APOBEC3G/F signatures in 3/9 (33%), 5/11 (45%) and 4/8 (50%) of samples, respectively; such linkage was not found for V90I, V106I or V108I. In-frame STOP codons were observed in 1.5% of all clonal sequences; 14.8% of them co-occurred with APOBEC3G/F signatures. APOBEC3G/F-associated E138K, M184I and M230I appeared within clonal sequences containing in-frame STOP codons in 2/3 (66%), 5/5 (100%) and 4/4 (100%) of the samples. In a re-analysis of the parent case control study, the presence of APOBEC3G/F signatures was not associated with virological failure. In conclusion, the contribution of APOBEC3G/F editing to the development of DRMVs is very limited and does not affect the efficacy of non-nucleoside reverse transcriptase inhibitor ART.
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Todesco E, Mercier-Darty M, Jung M, Bottero J, Boyd A, Marcelin AG, Calvez V, Morand-Joubert L. Ultradeep sequencing in the therapeutic management of HIV-1 infection at treatment initiation. J Antimicrob Chemother 2015; 70:1919-20. [PMID: 25637517 DOI: 10.1093/jac/dkv013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Eve Todesco
- Sorbonne Universités, UPMC Univ Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Pitié-Salpêtrière, APHP, Paris, France Department of Virology, Hôpital Saint Antoine, APHP, Paris, France
| | - Mélanie Mercier-Darty
- Department of Virology, Hôpital Henri Mondor, APHP, Université Paris-Est, Créteil, France
| | - Matthieu Jung
- Institut de Biologie Computationnelle, LIRMM, UMR 5506 CNRS-Université Montpellier 2, Montpellier, France
| | - Julie Bottero
- Department of Infectious Diseases, Hôpital Saint Antoine, APHP, Paris, France
| | - Anders Boyd
- INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Universités, UPMC Univ Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Pitié-Salpêtrière, APHP, Paris, France
| | - Vincent Calvez
- Sorbonne Universités, UPMC Univ Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Pitié-Salpêtrière, APHP, Paris, France
| | - Laurence Morand-Joubert
- Sorbonne Universités, UPMC Univ Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Saint Antoine, APHP, Paris, France
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Welkers MRA, Jonges M, Jeeninga RE, Koopmans MPG, de Jong MD. Improved detection of artifactual viral minority variants in high-throughput sequencing data. Front Microbiol 2015; 5:804. [PMID: 25657642 PMCID: PMC4302989 DOI: 10.3389/fmicb.2014.00804] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [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: 10/01/2014] [Accepted: 12/29/2014] [Indexed: 02/05/2023] Open
Abstract
High-throughput sequencing (HTS) of viral samples provides important information on the presence of viral minority variants. However, detection and accurate quantification is limited by the capacity to distinguish biological from artificial variation. In this study, errors related to the Illumina HiSeq2000 library generation and HTS process were investigated by determining minority variant frequencies in an influenza A/WSN/1933(H1N1) virus reverse-genetics plasmid pool. Errors related to amplification and sequencing were determined using the same plasmid pool, by generation of infectious virus using reverse genetics followed by in duplo reverse-transcriptase PCR (RT-PCR) amplification and HTS in the same sequence run. Results showed that after “best practice” quality control (QC), within the plasmid pool, one minority variant with a frequency >0.5% was identified, while 84 and 139 were identified in the RT-PCR amplified samples, indicating RT-PCR amplification artificially increased variation. Detailed analysis showed that artifactual minority variants could be identified by two major technical characteristics: their predominant presence in a single read orientation and uneven distribution of mismatches over the length of the reads. We demonstrate that by addition of two QC steps 95% of the artifactual minority variants could be identified. When our analysis approach was applied to three clinical samples 68% of the initially identified minority variants were identified as artifacts. Our study clearly demonstrated that, without additional QC steps, overestimation of viral minority variants is very likely to occur, mainly as a consequence of the required RT-PCR amplification step. The improved ability to detect and correct for artifactual minority variants, increases data resolution and could aid both past and future studies incorporating HTS. The source code has been made available through Sourceforge (https://sourceforge.net/projects/mva-ngs).
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Affiliation(s)
- Matthijs R A Welkers
- Department of Medical Microbiology, Academic Medical Centre Amsterdam, Netherlands
| | - Marcel Jonges
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment Bilthoven, Netherlands ; Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands
| | - Rienk E Jeeninga
- Department of Medical Microbiology, Academic Medical Centre Amsterdam, Netherlands
| | - Marion P G Koopmans
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment Bilthoven, Netherlands ; Department of Viroscience, Erasmus Medical Center Rotterdam, Netherlands
| | - Menno D de Jong
- Department of Medical Microbiology, Academic Medical Centre Amsterdam, Netherlands
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Todesco E, Rodriguez C, Morand-Joubert L, Mercier-Darty M, Desire N, Wirden M, Girard PM, Katlama C, Calvez V, Marcelin AG. Improved detection of resistance at failure to a tenofovir, emtricitabine and efavirenz regimen by ultradeep sequencing. J Antimicrob Chemother 2015; 70:1503-6. [PMID: 25614045 DOI: 10.1093/jac/dku557] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2014] [Accepted: 12/12/2014] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES Resistant minority variants present before ART can be a source of virological failure. This has been shown for NRTIs, NNRTIs and CCR5 inhibitors. However, very few data are available for the detection of such minority resistant variants that could be selected at virological failure and not detected using classical Sanger sequencing. METHODS We studied 26 patients treated with tenofovir, emtricitabine and efavirenz with their first virological failure (defined as two consecutive viral loads >50 copies/mL). We performed standard Sanger sequencing and ultradeep sequencing (UDS; Roche 454(®) Life Sciences) in plasma at failure. For UDS, mutations >1% were considered. We compared the presence of reverse transcriptase mutations between the two techniques, using the latest ANRS algorithm. RESULTS UDS detected more resistance mutations in 38.5% of cases (10/26 patients) and the genotypic sensitivity score (GSS) was reduced for 6 of them (23.1%). The GSS was impacted more often for NRTIs than for NNRTIs, for which most mutations were already detected by Sanger sequencing. Resistant minority variants were detected even in patients with low viral load at failure. CONCLUSIONS These results strongly argue for the use of next-generation sequencing in patients failing on an NRTI+NNRTI regimen, as UDS has the potential to modify the choice of the subsequent regimen.
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Affiliation(s)
- Eve Todesco
- Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP Paris, France
| | - Christophe Rodriguez
- Department of Virology, Hôpital Henri Mondor, Université Paris-Est, Créteil, France INSERM U955, Créteil, France
| | - Laurence Morand-Joubert
- Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Saint Antoine, AP-HP Paris, France
| | | | - Nathalie Desire
- Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP Paris, France
| | - Marc Wirden
- Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP Paris, France
| | - Pierre-Marie Girard
- Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Infectious Diseases, Hôpital Saint Antoine, AP-HP Paris, France
| | - Christine Katlama
- Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Infectious Diseases, Hôpital Pitié-Salpêtrière, AP-HP Paris, France
| | - Vincent Calvez
- Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP Paris, France
| | - Anne-Geneviève Marcelin
- Sorbonne Universités, UPMC Univ. Paris 06, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France INSERM, UMR S_1136, Institut Pierre Louis d'Epidémiologie et de Santé Publique, F-75013 Paris, France Department of Virology, Hôpital Pitié-Salpêtrière, AP-HP Paris, France
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Affiliation(s)
- Jonathan Z Li
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
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Abstract
Technologic advances in human immunodeficiency virus type 1 (HIV-1) sequencing have revolutionized the study of antiretroviral drug resistance and are increasingly moving from the laboratory to clinical practice. These techniques are able to detect HIV-1 drug resistance mutations present at low frequencies not detectable by current HIV-1 genotyping assays. For a number of commonly used antiretroviral medications, such as nonnucleoside reverse transcriptase inhibitors, the detection of these drug-resistant minority variants significantly increases the risk of treatment failure. The level of evidence, however, is insufficient to determine the impact of HIV-1 minority variants for several other classes of antiretroviral medications. Clinicians should be aware of the novel technologies that are moving into routine clinical use and the clinical implications of HIV-1 minority variants. Additional studies are needed to determine the optimal platform for clinical application of these new technologies and to provide guidance to clinicians on the type and frequency of clinically important HIV-1 minority variants.
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Affiliation(s)
- Jonathan Z Li
- Division of Infectious Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.
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Nicot F, Saliou A, Raymond S, Sauné K, Delobel P, Izopet J. Variants minoritaires du VIH-1 : détection, quantification et implications cliniques. Virologie (Montrouge) 2012; 16:276-285. [PMID: 33065912 DOI: 10.1684/vir.2012.0465] [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: 06/11/2023]
Abstract
Success to antiretroviral HIV treatment is reduced by the presence of resistant variants. These variants can be present at very low level in the viral population and not detected by conventional assay. High throughput sequencing technologies allow the detection of minority variants present at less than 20 % and their quantification, easily and rapidly. However, the influence of minority variants on the treatment response must be determined. The detection of minority variants resistant to non-nucleoside reverse transcriptase inhibitors (NNRTI) is associated to an increased risk of virological failure in patients with an NNRTI containing treatment. The detection of X4 using variants is also associated to an increased risk of virological failure in patients treated with a CCR5 antagonist. This association was not observed with other antiretroviral classes. Although, these data need to be confirmed in prospective studies, detection of minority variants could help in optimizing NNRTI and CCR5 antagonist containing treatment.
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Affiliation(s)
- Florence Nicot
- CHU de Toulouse, hôpital Purpan, laboratoire de virologie, institut fédératif de biologie de Purpan, 330, avenue de Grande-Bretagne, 31300 Toulouse, France
| | - Adrien Saliou
- Inserm, U1043, centre de physiopathologie de Toulouse-Purpan, BP 3028, 31024 Toulouse, France
| | - Stéphanie Raymond
- CHU de Toulouse, hôpital Purpan, laboratoire de virologie, institut fédératif de biologie de Purpan, 330, avenue de Grande-Bretagne, 31300 Toulouse, France, Inserm, U1043, centre de physiopathologie de Toulouse-Purpan, BP 3028, 31024 Toulouse, France, Université de Toulouse-III - Paul-Sabatier, faculté de médecine Toulouse-Purpan, 37, allées Jules Guesde, 31300 Toulouse, France
| | - Karine Sauné
- CHU de Toulouse, hôpital Purpan, laboratoire de virologie, institut fédératif de biologie de Purpan, 330, avenue de Grande-Bretagne, 31300 Toulouse, France, Inserm, U1043, centre de physiopathologie de Toulouse-Purpan, BP 3028, 31024 Toulouse, France, Université de Toulouse-III - Paul-Sabatier, faculté de médecine Toulouse-Purpan, 37, allées Jules Guesde, 31300 Toulouse, France
| | - Pierre Delobel
- Inserm, U1043, centre de physiopathologie de Toulouse-Purpan, BP 3028, 31024 Toulouse, France, Université de Toulouse-III - Paul-Sabatier, faculté de médecine Toulouse-Purpan, 37, allées Jules Guesde, 31300 Toulouse, France, CHU de Toulouse, hôpital Purpan, service des maladies infectieuses et tropicales, place du Docteur-Baylac, 31300 Toulouse, France
| | - Jacques Izopet
- CHU de Toulouse, hôpital Purpan, laboratoire de virologie, institut fédératif de biologie de Purpan, 330, avenue de Grande-Bretagne, 31300 Toulouse, France, Inserm, U1043, centre de physiopathologie de Toulouse-Purpan, BP 3028, 31024 Toulouse, France, Université de Toulouse-III - Paul-Sabatier, faculté de médecine Toulouse-Purpan, 37, allées Jules Guesde, 31300 Toulouse, France
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Barzon L, Lavezzo E, Militello V, Toppo S, Palù G. Applications of next-generation sequencing technologies to diagnostic virology. Int J Mol Sci 2011; 12:7861-84. [PMID: 22174638 DOI: 10.3390/ijms12117861] [Citation(s) in RCA: 201] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2011] [Revised: 10/20/2011] [Accepted: 11/07/2011] [Indexed: 02/07/2023] Open
Abstract
Novel DNA sequencing techniques, referred to as “next-generation” sequencing (NGS), provide high speed and throughput that can produce an enormous volume of sequences with many possible applications in research and diagnostic settings. In this article, we provide an overview of the many applications of NGS in diagnostic virology. NGS techniques have been used for high-throughput whole viral genome sequencing, such as sequencing of new influenza viruses, for detection of viral genome variability and evolution within the host, such as investigation of human immunodeficiency virus and human hepatitis C virus quasispecies, and monitoring of low-abundance antiviral drug-resistance mutations. NGS techniques have been applied to metagenomics-based strategies for the detection of unexpected disease-associated viruses and for the discovery of novel human viruses, including cancer-related viruses. Finally, the human virome in healthy and disease conditions has been described by NGS-based metagenomics.
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Halvas EK, Wiegand A, Boltz VF, Kearney M, Nissley D, Wantman M, Hammer SM, Palmer S, Vaida F, Coffin JM, Mellors JW. Low frequency nonnucleoside reverse-transcriptase inhibitor-resistant variants contribute to failure of efavirenz-containing regimens in treatment- experienced patients. J Infect Dis 2010; 201:672-80. [PMID: 20102272 PMCID: PMC2835354 DOI: 10.1086/650542] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022] Open
Abstract
BACKGROUND The contribution of low frequency drug-resistant human immunodeficiency virus type 1 (HIV-1) variants to failure of antiretroviral therapy is not well defined in treatment-experienced patients. We sought to detect minor nonnucleoside reverse-transcriptase inhibitor (NNRTI)-resistant variants at the initiation of multidrug efavirenz-containing therapy in both NNRTI-naive and NNRTI-experienced patients and to determine their association with virologic response. METHODS Plasma samples at entry and at time of virologic failure from patients enrolled in the AIDS Clinical Trials Group study 398 were analyzed by standard genotype, single-genome sequencing and allele-specific polymerase chain reaction (K103N and Y181C) to detect and quantify minor NNRTI-resistant variants. RESULTS Minor populations of NNRTI-resistant variants that were missed by standard genotype were detected more often at study entry in NNRTI-experienced patients than NNRTI-naive patients by both single-genome sequencing (8 of 12 vs 3 of 15; P = .022) and allele-specific polymerase chain reaction (11% Y181C, 5 of 22 vs 3 of 72, respectively; P = .016). K103N variants at frequencies 11% were associated with inferior HIV-1 RNA response to efavirenz-containing therapy between entry and week 24 (change in HIV-1 RNA level, +0.5 vs -1.1 log(10) copies/mL; P < .001). CONCLUSIONS Minor NNRTI-resistant variants were more prevalent in NNRTI-experienced patients and were associated with reduced virologic response to efavirenz-containing multidrug regimens.
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Affiliation(s)
- Elias K. Halvas
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania
| | - Ann Wiegand
- HIV Drug Resistance Program, National Cancer Institute, National Institutes of Health, Frederick, Maryland
| | - Valerie F. Boltz
- HIV Drug Resistance Program, National Cancer Institute, National Institutes of Health, Frederick, Maryland
| | - Mary Kearney
- HIV Drug Resistance Program, National Cancer Institute, National Institutes of Health, Frederick, Maryland
| | - Dwight Nissley
- Basic Research Program, SAIC-Frederick, National Cancer Institute, National Institutes of Health, Frederick, Maryland
| | - Michael Wantman
- Center for Biostatistics in AIDS Research, Harvard School of Public Health, Boston Massachusetts
| | - Scott M. Hammer
- Division of Infectious Diseases, Columbia University College of Physicians and Surgeons, New York, New York
| | - Sarah Palmer
- Basic Research Program, SAIC-Frederick, National Cancer Institute, National Institutes of Health, Frederick, Maryland
- Department of Virology, Swedish Institute for Infectious Disease Control, Karolinksa Institute, Solna, Sweden
| | - Florin Vaida
- Department of Family and Preventive Medicine, University of California at San Diego School of Medicine, La Jolla, CA
| | - John M. Coffin
- HIV Drug Resistance Program, National Cancer Institute, National Institutes of Health, Frederick, Maryland
| | - John W. Mellors
- Division of Infectious Diseases, University of Pittsburgh, Pittsburgh, Pennsylvania
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