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Ouyang F, Yuan D, Zhai W, Liu S, Zhou Y, Yang H. HIV-1 Drug Resistance Detected by Next-Generation Sequencing among ART-Naïve Individuals: A Systematic Review and Meta-Analysis. Viruses 2024; 16:239. [PMID: 38400015 PMCID: PMC10893194 DOI: 10.3390/v16020239] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 12/31/2023] [Accepted: 01/30/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND There are an increasing number of articles focused on the prevalence and clinical impact of pretreatment HIV drug resistance (PDR) detected by Sanger sequencing (SGS). PDR may contribute to the increased likelihood of virologic failure and the emergence of new resistance mutations. As SGS is gradually replaced by next-generation sequencing (NGS), it is necessary to assess the levels of PDR using NGS in ART-naïve patients systematically. NGS can detect the viral variants (low-abundance drug-resistant HIV-1 variants (LA-DRVs)) of virus quasi-species at levels below 20% that SGS may fail to detect. NGS has the potential to optimize current HIV drug resistance surveillance methods and inform future research directions. As the NGS technique has high sensitivity, it is highly likely that the level of pretreatment resistance would be underestimated using conventional techniques. METHODS For the systematic review and meta-analysis, we searched for original studies published in PubMed, Web of Science, Scopus, and Embase before 30 March 2023 that focused exclusively on the application of NGS in the detection of HIV drug resistance. Pooled prevalence estimates were calculated using a random effects model using the 'meta' package in R (version 4.2.3). We described drug resistance detected at five thresholds (>1%, 2%, 5%, 10%, and 20% of virus quasi-species). Chi-squared tests were used to analyze differences between the overall prevalence of PDR reported by SGS and NGS. RESULTS A total of 39 eligible studies were selected. The studies included a total of 15,242 ART-naïve individuals living with HIV. The prevalence of PDR was inversely correlated with the mutation detection threshold. The overall prevalence of PDR was 29.74% at the 1% threshold, 22.43% at the 2% threshold, 15.47% at the 5% threshold, 12.95% at the 10% threshold, and 11.08% at the 20% threshold. The prevalence of PDR to INSTIs was 1.22% (95%CI: 0.58-2.57), which is the lowest among the values for all antiretroviral drugs. The prevalence of LA-DRVs was 9.45%. At the 2% and 20% detection threshold, the prevalence of PDR was 22.43% and 11.08%, respectively. Resistance to PIs and INSTIs increased 5.52-fold and 7.08-fold, respectively, in those with a PDR threshold of 2% compared with those with PDR at 20%. However, resistance to NRTIs and NNRTIs increased 2.50-fold and 2.37-fold, respectively. There was a significant difference between the 2% and 5% threshold for detecting HIV drug resistance. There was no statistically significant difference between the results reported by SGS and NGS when using the 20% threshold for reporting resistance mutations. CONCLUSION In this study, we found that next-generation sequencing facilitates a more sensitive detection of HIV-1 drug resistance than SGS. The high prevalence of PDR emphasizes the importance of baseline resistance and assessing the threshold for optimal clinical detection using NGS.
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Affiliation(s)
- Fei Ouyang
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China; (F.O.); (D.Y.); (W.Z.); (S.L.)
| | - Defu Yuan
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China; (F.O.); (D.Y.); (W.Z.); (S.L.)
| | - Wenjing Zhai
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China; (F.O.); (D.Y.); (W.Z.); (S.L.)
| | - Shanshan Liu
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China; (F.O.); (D.Y.); (W.Z.); (S.L.)
| | - Ying Zhou
- Department of HIV/STD Control and Prevention, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing 210009, China
| | - Haitao Yang
- Key Laboratory of Environmental Medicine Engineering of Ministry of Education, Department of Epidemiology and Health Statistics, School of Public Health, Southeast University, Nanjing 210009, China; (F.O.); (D.Y.); (W.Z.); (S.L.)
- Jiangsu Health Development Research Center, Nanjing 210029, China
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2
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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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3
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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: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [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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4
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Cevallos C, Culasso ACA, Urquiza J, Ojeda D, Sued O, Figueroa MI, Avila MM, Delpino MV, Quarleri JF. In vivo drug resistance mutation dynamics from the early to chronic stage of infection in antiretroviral-therapy-naïve HIV-infected men who have sex with men. Arch Virol 2020; 165:2915-2919. [PMID: 32978684 DOI: 10.1007/s00705-020-04823-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 08/25/2020] [Indexed: 01/18/2023]
Abstract
Human immunodeficiency virus type 1 (HIV) primary drug resistance mutations (DRMs) influence the long-term therapeutic effects of antiretroviral treatment (ART). Drug-resistance genotyping based on polymerase gene sequences obtained by next-generation sequencing (NGS) was performed using samples from 10 ART-naïve HIV-infected men who have sex with men (MSM; P1-P10) from the acute/early to chronic stage of infection. Three of the 10 subjects exhibited the presence of major (abundance, ≥ 20%) viral populations carrying DRM at early/acute stage that later, at the chronic stage, dropped drastically (V106M) or remained highly abundant (E138A). Four individuals exhibited additional DRMs (M46I/L; I47A; I54M, L100V) as HIV minority populations (abundance, 2-20%) that emerged during the chronic stage but ephemerally.
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Affiliation(s)
- Cintia Cevallos
- Instituto de Investigaciones Biomédicas en Retrovirus Y Sida (INBIRS), Facultad de Medicina, Universidad de Buenos Aires (UBA), Paraguay 2155-Piso 11 (1121), Buenos Aires, Argentina
| | - Andrés C A Culasso
- Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET) Instituto de Bacteriología Y Virología Molecular (IBaViM) Facultad de Farmacia Y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Buenos Aires, Argentina
| | - Javier Urquiza
- Instituto de Investigaciones Biomédicas en Retrovirus Y Sida (INBIRS), Facultad de Medicina, Universidad de Buenos Aires (UBA), Paraguay 2155-Piso 11 (1121), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Buenos Aires, Argentina
| | - Diego Ojeda
- Instituto de Investigaciones Biomédicas en Retrovirus Y Sida (INBIRS), Facultad de Medicina, Universidad de Buenos Aires (UBA), Paraguay 2155-Piso 11 (1121), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Buenos Aires, Argentina
| | - Omar Sued
- Fundación Huésped, Pasaje Angel Peluffo 3932 (C1202ABB), Ciudad Autónoma de Buenos Aires, Argentina
| | - María I Figueroa
- Fundación Huésped, Pasaje Angel Peluffo 3932 (C1202ABB), Ciudad Autónoma de Buenos Aires, Argentina
| | - María M Avila
- Instituto de Investigaciones Biomédicas en Retrovirus Y Sida (INBIRS), Facultad de Medicina, Universidad de Buenos Aires (UBA), Paraguay 2155-Piso 11 (1121), Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Buenos Aires, Argentina
| | - M Victoria Delpino
- Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Buenos Aires, Argentina
- Instituto de Inmunología, Genética Y Metabolismo (INIGEM), Universidad de Buenos Aires. CONICET, Buenos Aires, Argentina
| | - Jorge F Quarleri
- Instituto de Investigaciones Biomédicas en Retrovirus Y Sida (INBIRS), Facultad de Medicina, Universidad de Buenos Aires (UBA), Paraguay 2155-Piso 11 (1121), Buenos Aires, Argentina.
- Consejo Nacional de Investigaciones Científicas Y Técnicas (CONICET), Buenos Aires, Argentina.
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5
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Mbisa JL, Kirwan P, Tostevin A, Ledesma J, Bibby DF, Brown A, Myers R, Hassan AS, Murphy G, Asboe D, Pozniak A, Kirk S, Gill ON, Sabin C, Delpech V, Dunn DT. Determining the Origins of Human Immunodeficiency Virus Type 1 Drug-resistant Minority Variants in People Who Are Recently Infected Using Phylogenetic Reconstruction. Clin Infect Dis 2020; 69:1136-1143. [PMID: 30534981 PMCID: PMC6743824 DOI: 10.1093/cid/ciy1048] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2018] [Accepted: 12/06/2018] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Drug-resistant minority variants (DRMinVs) detected in patients who recently acquired human immunodeficiency virus type 1 (HIV-1) can be transmitted, generated de novo through virus replication, or technical errors. The first form is likely to persist and result in treatment failure, while the latter two could be stochastic and transient. METHODS Ultradeep sequencing of plasma samples from 835 individuals with recent HIV-1 infection in the United Kingdom was performed to detect DRMinVs at a mutation frequency between 2% and 20%. Sequence alignments including >110 000 HIV-1 partial pol consensus sequences from the UK HIV Drug Resistance Database (UK-HDRD), linked to epidemiological and clinical data from the HIV and AIDS Reporting System, were used for transmission cluster analysis. Transmission clusters were identified using Cluster Picker with a clade support of >90% and maximum genetic distances of 4.5% or 1.5%, the latter to limit detection to likely direct transmission events. RESULTS Drug-resistant majority variants (DRMajVs) were detected in 66 (7.9%) and DRMinVs in 84 (10.1%) of the recently infected individuals. High levels of clustering to sequences in UK-HDRD were observed for both DRMajV (n = 48; 72.7%) and DRMinV (n = 63; 75.0%) sequences. Of these, 43 (65.2%) with DRMajVs were in a transmission cluster with sequences that harbored the same DR mutation compared to only 3 (3.6%) sequences with DRMinVs (P < .00001, Fisher exact test). Evidence of likely direct transmission of DRMajVs was observed for 25/66 (37.9%), whereas none were observed for the DRMinVs (P < .00001). CONCLUSIONS Using a densely sampled HIV-infected population, we show no evidence of DRMinV transmission among recently infected individuals.
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Affiliation(s)
- Jean L Mbisa
- National Infection Service, Public Health England, London, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, United Kingdom
| | - Peter Kirwan
- National Infection Service, Public Health England, London, United Kingdom
| | - Anna Tostevin
- Institute for Global Health, University College London, London, United Kingdom
| | - Juan Ledesma
- National Infection Service, Public Health England, London, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, United Kingdom
| | - David F Bibby
- National Infection Service, Public Health England, London, United Kingdom
| | - Alison Brown
- National Infection Service, Public Health England, London, United Kingdom
| | - Richard Myers
- National Infection Service, Public Health England, London, United Kingdom
| | - Amin S Hassan
- HIV/STI Group, Kenya Medical Research Institute (KEMRI)/Wellcome Trust Research Programme, Kilifi, Kenya
| | - Gary Murphy
- National Infection Service, Public Health England, London, United Kingdom
| | - David Asboe
- Chelsea and Westminster Hospital, London, United Kingdom
| | - Anton Pozniak
- Chelsea and Westminster Hospital, London, United Kingdom
| | - Stuart Kirk
- University College London Hospital, London, United Kingdom
| | - O Noel Gill
- National Infection Service, Public Health England, London, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, United Kingdom
| | - Caroline Sabin
- National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, United Kingdom.,Institute for Global Health, University College London, London, United Kingdom
| | - Valerie Delpech
- National Infection Service, Public Health England, London, United Kingdom.,National Institute for Health Research Health Protection Research Unit in Blood Borne and Sexually Transmitted Infections, London, United Kingdom
| | - David T Dunn
- Institute for Global Health, University College London, London, United Kingdom
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6
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Geretti AM, White E, Orkin C, Tostevin A, Tilston P, Chadwick D, Leen C, Sabin C, Dunn DT. Virological outcomes of boosted protease inhibitor-based first-line ART in subjects harbouring thymidine analogue-associated mutations as the sole form of transmitted drug resistance. J Antimicrob Chemother 2020; 74:746-753. [PMID: 30544247 PMCID: PMC6376847 DOI: 10.1093/jac/dky468] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2018] [Revised: 10/06/2018] [Accepted: 10/13/2018] [Indexed: 12/13/2022] Open
Abstract
Objectives In subjects with transmitted thymidine analogue mutations (TAMs), boosted PIs (PI/b) are often chosen to overcome possible resistance to the NRTI backbone. However, data to guide treatment selection are limited. Our aim was to obtain firmer guidance for clinical practice using real-world cohort data. Methods We analysed 1710 subjects who started a PI/b in combination with tenofovir or abacavir plus emtricitabine or lamivudine, and compared their virological outcomes with those of 4889 patients who started an NNRTI (predominantly efavirenz), according to the presence of ≥1 TAM as the sole form of transmitted drug resistance. Results Participants with ≥1 TAM comprised predominantly MSM (213 of 269, 79.2%), subjects of white ethnicity (206 of 269, 76.6%) and HIV-1 subtype B infections (234 of 269, 87.0%). Most (203 of 269, 75.5%) had singleton TAMs, commonly a revertant of T215Y or T215F (112 of 269, 41.6%). Over a median of 2.5 years of follow-up, 834 of 6599 (12.6%) subjects experienced viraemia (HIV-1 RNA >50 copies/mL). The adjusted HR for viraemia was 2.17 with PI/b versus NNRTI-based therapy (95% CI 1.88–2.51; P < 0.001). Other independent predictors of viraemia included injecting drug use, black ethnicity, higher viral load and lower CD4 cell count at baseline, and receiving abacavir instead of tenofovir. Resistance showed no overall impact (adjusted HR 0.77 with ≥1 TAM versus no resistance; 95% CI 0.54–1.10; P = 0.15). Conclusions In this cohort, patients harbouring ≥1 TAM as the sole form of transmitted drug resistance gained no apparent virological advantage from starting first-line ART with a PI/b.
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Affiliation(s)
- Anna Maria Geretti
- Institute of Infection & Global Health, University of Liverpool, Liverpool, UK
| | - Ellen White
- MRC Clinical Trials Unit at University College London, London, UK
| | - Chloe Orkin
- Department of Infection & Immunity, Barts Health NHS Trust, London, UK
| | - Anna Tostevin
- Institute for Global Health, University College London, London, UK
| | - Peter Tilston
- Department of Clinical Virology, Manchester Royal Infirmary, Manchester, UK
| | - David Chadwick
- Department of Infectious Diseases, South Tees Hospitals NHS Trust, Middlesbrough, UK
| | - Clifford Leen
- Regional Infectious Diseases Unit, NHS Lothian, Edinburgh, UK
| | - Caroline Sabin
- Institute for Global Health, University College London, London, UK
| | - David T Dunn
- Institute for Global Health, University College London, London, UK
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7
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Matías-Florentino M, Chaillon A, Ávila-Ríos S, Mehta SR, Paz-Juárez HE, Becerril-Rodríguez MA, del Arenal-Sánchez SJ, Piñeirúa-Menéndez A, Ruiz V, Iracheta-Hernández P, Macías-González I, Tena-Sánchez J, Badial-Hernández F, González-Rodríguez A, Reyes-Terán G. Pretreatment HIV drug resistance spread within transmission clusters in Mexico City. J Antimicrob Chemother 2020; 75:656-667. [PMID: 31819984 PMCID: PMC7021100 DOI: 10.1093/jac/dkz502] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2019] [Revised: 10/28/2019] [Accepted: 11/05/2019] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Pretreatment HIV drug resistance (HIVDR) to NNRTIs has consistently increased in Mexico City during the last decade. OBJECTIVES To infer the HIV genetic transmission network in Mexico City to describe the dynamics of the local HIV epidemic and spread of HIVDR. PATIENTS AND METHODS HIV pol sequences were obtained by next-generation sequencing from 2447 individuals before initiation of ART at the largest HIV clinic in Mexico City (April 2016 to June 2018). Pretreatment HIVDR was estimated using the Stanford algorithm at a Sanger-like threshold (≥20%). Genetic networks were inferred with HIV-TRACE, establishing putative transmission links with genetic distances <1.5%. We examined demographic associations among linked individuals with shared drug resistance mutations (DRMs) using a ≥ 2% threshold to include low-frequency variants. RESULTS Pretreatment HIVDR reached 14.8% (95% CI 13.4%-16.2%) in the cohort overall and 9.6% (8.5%-10.8%) to NNRTIs. Putative links with at least one other sequence were found for 963/2447 (39%) sequences, forming 326 clusters (2-20 individuals). The inferred network was assortative by age and municipality (P < 0.001). Clustering individuals were younger [adjusted OR (aOR) per year = 0.96, 95% CI 0.95-0.97, P < 0.001] and less likely to include women (aOR = 0.46, 95% CI 0.28-0.75, P = 0.002). Among clustering individuals, 175/963 (18%) shared DRMs (involving 66 clusters), of which 66/175 (38%) shared K103N/S (24 clusters). Eight municipalities (out of 75) harboured 65% of persons sharing DRMs. Among all persons sharing DRMs, those sharing K103N were younger (aOR = 0.93, 95% CI 0.88-0.98, P = 0.003). CONCLUSIONS Our analyses suggest age- and geographically associated transmission of DRMs within the HIV genetic network in Mexico City, warranting continuous monitoring and focused interventions.
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Affiliation(s)
- Margarita Matías-Florentino
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
| | - Antoine Chaillon
- University of California San Diego, 9500 Gilman Drive 0679, La Jolla, CA 92093, USA
| | - Santiago Ávila-Ríos
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
| | - Sanjay R Mehta
- University of California San Diego, 9500 Gilman Drive 0679, La Jolla, CA 92093, USA
| | - Héctor E Paz-Juárez
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
| | - Manuel A Becerril-Rodríguez
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Silvia J del Arenal-Sánchez
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
| | - Alicia Piñeirúa-Menéndez
- Clínica Especializada Condesa Iztapalapa, Av. Combate de Celaya S/N, Colonia Unidad Habitacional Vicente Guerrero, CP 09730 Mexico City, Mexico
| | - Verónica Ruiz
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Patricia Iracheta-Hernández
- Clínica Especializada Condesa Iztapalapa, Av. Combate de Celaya S/N, Colonia Unidad Habitacional Vicente Guerrero, CP 09730 Mexico City, Mexico
| | - Israel Macías-González
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Jehovani Tena-Sánchez
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Florentino Badial-Hernández
- Clínica Especializada Condesa Iztapalapa, Av. Combate de Celaya S/N, Colonia Unidad Habitacional Vicente Guerrero, CP 09730 Mexico City, Mexico
| | - Andrea González-Rodríguez
- Clínica Especializada Condesa, Gral, Benjamín Hill 24, Hipódromo Condesa, CP 06170 Mexico City, Mexico
| | - Gustavo Reyes-Terán
- Centre for Research in Infectious Diseases, National Institute of Respiratory Diseases, Calzada de Tlalpan 4502, Colonia Sección XVI, CP 14080 Mexico City, Mexico
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Rhee SY, Clutter D, Fessel WJ, Klein D, Slome S, Pinsky BA, Marcus JL, Hurley L, Silverberg MJ, Kosakovsky Pond SL, Shafer RW. Trends in the Molecular Epidemiology and Genetic Mechanisms of Transmitted Human Immunodeficiency Virus Type 1 Drug Resistance in a Large US Clinic Population. Clin Infect Dis 2020; 68:213-221. [PMID: 29846534 PMCID: PMC6321854 DOI: 10.1093/cid/ciy453] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2018] [Accepted: 05/25/2018] [Indexed: 12/20/2022] Open
Abstract
Background There are few large studies of transmitted drug resistance (TDR) prevalence and the drug resistance mutations (DRMs) responsible for TDR in the United States. Methods Human immunodeficiency virus type 1 (HIV-1) reverse transcriptase (RT) and protease sequences were obtained from 4253 antiretroviral therapy (ART)–naive individuals in a California clinic population from 2003 to 2016. Phylogenetic analyses were performed to study linkages between TDR strains and selection pressure on TDR-associated DRMs. Results From 2003 to 2016, there was a significant increase in overall (odds ratio [OR], 1.05 per year [95% confidence interval {CI}, 1.03–1.08]; P < .001) and nonnucleoside RT inhibitor (NNRTI)–associated TDR (OR, 1.11 per year [95% CI, 1.08–1.15]; P < .001). Between 2012 and 2016, TDR rates to any drug class ranged from 15.7% to 19.2%, and class-specific rates ranged from 10.0% to 12.8% for NNRTIs, 4.1% to 8.1% for nucleoside RT inhibitors (NRTIs), and 3.6% to 5.2% for protease inhibitors. The thymidine analogue mutations, M184V/I and the tenofovir-associated DRMs K65R and K70E/Q/G/N/T accounted for 82.9%, 7.3%, and 1.4% of NRTI-associated TDR, respectively. Thirty-seven percent of TDR strains clustered with other TDR strains sharing the same DRMs. Conclusions Although TDR has increased significantly in this large cohort, many TDR strains are unlikely to influence the activity of currently preferred first-line ART regimens. The high proportion of DRMs associated with infrequently used regimens combined with the clustering of TDR strains suggest that some TDR strains are being transmitted between ART-naive individuals.
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Affiliation(s)
- Soo-Yon Rhee
- Division of Infectious Diseases, Department of Medicine, Stanford University
| | - Dana Clutter
- Division of Infectious Diseases, Department of Medicine, Stanford University
| | - W Jeffrey Fessel
- Department of Internal Medicine, Kaiser Permanente Northern California, San Francisco
| | - Daniel Klein
- Department of Infectious Diseases, Kaiser Permanente Northern California, San Leandro
| | - Sally Slome
- Department of Infectious Diseases, Kaiser Permanente Northern California, Oakland
| | | | - Julia L Marcus
- Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts
| | - Leo Hurley
- Division of Research, Kaiser Permanente Northern California, Oakland
| | | | | | - Robert W Shafer
- Division of Infectious Diseases, Department of Medicine, Stanford University
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Hani L, Chaillon A, Nere ML, Ruffin N, Alameddine J, Salmona M, Lopez Zaragoza JL, Smith DM, Schwartz O, Lelièvre JD, Delaugerre C, Lévy Y, Seddiki N. Proliferative memory SAMHD1low CD4+ T cells harbour high levels of HIV-1 with compartmentalized viral populations. PLoS Pathog 2019; 15:e1007868. [PMID: 31220191 PMCID: PMC6605680 DOI: 10.1371/journal.ppat.1007868] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2018] [Revised: 07/02/2019] [Accepted: 05/24/2019] [Indexed: 11/24/2022] Open
Abstract
We previously reported the presence of memory CD4+ T cells that express low levels of SAMHD1 (SAMHD1low) in peripheral blood and lymph nodes from both HIV-1 infected and uninfected individuals. These cells are enriched in Th17 and Tfh subsets, two populations known to be preferentially targeted by HIV-1. Here we investigated whether SAMHD1low CD4+ T-cells harbour replication-competent virus and compartimentalized HIV-1 genomes. We sorted memory CD4+CD45RO+SAMHD1low, CD4+CD45RO+SAMHD1+ and naive CD4+CD45RO-SAMHD1+ cells from HIV-1-infected patients on anti-retroviral therapy (c-ART) and performed HIV-1 DNA quantification, ultra-deep-sequencing of partial env (C2/V3) sequences and phenotypic characterization of the cells. We show that SAMHD1low cells include novel Th17 CCR6+ subsets that lack CXCR3 and CCR4 (CCR6+DN). There is a decrease of the % of Th17 in SAMHD1low compartment in infected compared to uninfected individuals (41% vs 55%, p<0.05), whereas the % of CCR6+DN increases (7.95% vs 3.8%, p<0.05). Moreover, in HIV-1 infected patients, memory SAMHD1low cells harbour high levels of HIV-1 DNA compared to memory SAMHD1+ cells (4.5 vs 3.8 log/106cells, respectively, p<0.001), while naïve SAMHD1+ showed significantly lower levels (3.1 log/106cells, p<0.0001). Importantly, we show that SAMHD1low cells contain p24-producing cells. Moreover, phylogenetic analyses revealed well-segregated HIV-1 DNA populations with compartmentalization between SAMHD1low and SAMHD1+ memory cells, and limited viral exchange. As expected, the % of Ki67+ cells was significantly higher in SAMHD1low compared to SAMHD1+ cells. There was positive association between levels of HIV-1 DNA and Ki67+ in memory SAMHD1low cells, but not in memory and naïve SAMHD1+ CD4+ T-cells. Altogether, these data suggest that proliferative memory SAMHD1low cells contribute to viral persistence. In our previous results we reported that memory CD4+ T cells expressing low levels of SAMHD1 (SAMHD1low) are present in peripheral blood and lymph nodes from HIV-1 infected and uninfected individuals. These cells were enriched in Th17 and Tfh, two populations targeted by HIV-1. Here we used purified memory CD4+CD45RO+SAMHD1low, CD4+CD45RO+SAMHD1+ and naive CD4+CD45RO-SAMHD1+ cells from HIV-1-infected and treated patients to perform cell-associated HIV-1 DNA quantification, p24-producing cells detection, ultra-deep-sequencing of partial env (C2/V3) HIV-1 DNA and further phenotypic characterization. Our results demonstrate that (i) Th17 and CCR6+DN-expressing transcriptional signature of early Th17, two major populations that are susceptible to HIV-1 infection, are present in SAMHD1low cells, and while the former decreased significantly in c-ART HIV-1 infected compared to uninfected individuals, the latter significantly increased; (ii) memory SAMHD1low cells from c-ART patients carry high levels of HIV-1 DNA compared to SAMHD1+ cells, and these levels positively and significantly correlated with Ki67 expression; (iii) memory SAMHD1low cells from patients harbour p24-producing cells; (iv) phylogenetic analyses revealed well-segregated HIV-1 DNA populations with significant compartmentalization between SAMHD1low and SAMHD1+ cells and limited viral exchange. Our data demonstrate that memory SAMHD1low cells contribute to HIV-1 persistence.
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Affiliation(s)
- Lylia Hani
- Inserm, U955 Equipe 16, Créteil, France
- Université Paris Est, Faculté de médecine, Créteil, France
- Vaccine Research Institute (VRI), Créteil, France
| | - Antoine Chaillon
- Vaccine Research Institute (VRI), Créteil, France
- Department of Medicine, University of California San Diego, CA, United States of America
| | - Marie-Laure Nere
- Hôpital Saint Louis, INSERM U944, Université de Paris, Paris, France
| | - Nicolas Ruffin
- Inserm, U955 Equipe 16, Créteil, France
- Université Paris Est, Faculté de médecine, Créteil, France
- Vaccine Research Institute (VRI), Créteil, France
| | - Joudy Alameddine
- Inserm, U955 Equipe 16, Créteil, France
- Université Paris Est, Faculté de médecine, Créteil, France
- Vaccine Research Institute (VRI), Créteil, France
| | - Maud Salmona
- Hôpital Saint Louis, INSERM U944, Université de Paris, Paris, France
| | - José-Luiz Lopez Zaragoza
- Inserm, U955 Equipe 16, Créteil, France
- Université Paris Est, Faculté de médecine, Créteil, France
- Vaccine Research Institute (VRI), Créteil, France
- AP-HP, Hôpital H. Mondor—A. Chenevier, Service d'immunologie clinique et maladies infectieuses, Créteil, France
| | - Davey M. Smith
- Department of Medicine, University of California San Diego, CA, United States of America
| | - Olivier Schwartz
- Vaccine Research Institute (VRI), Créteil, France
- Unité Virus et Immunité, Département de Virologie, Institut Pasteur, Paris, France
| | - Jean-Daniel Lelièvre
- Inserm, U955 Equipe 16, Créteil, France
- Université Paris Est, Faculté de médecine, Créteil, France
- Vaccine Research Institute (VRI), Créteil, France
- AP-HP, Hôpital H. Mondor—A. Chenevier, Service d'immunologie clinique et maladies infectieuses, Créteil, France
| | - Constance Delaugerre
- Vaccine Research Institute (VRI), Créteil, France
- Hôpital Saint Louis, INSERM U944, Université de Paris, Paris, France
| | - Yves Lévy
- Inserm, U955 Equipe 16, Créteil, France
- Université Paris Est, Faculté de médecine, Créteil, France
- Vaccine Research Institute (VRI), Créteil, France
- AP-HP, Hôpital H. Mondor—A. Chenevier, Service d'immunologie clinique et maladies infectieuses, Créteil, France
| | - Nabila Seddiki
- Inserm, U955 Equipe 16, Créteil, France
- Université Paris Est, Faculté de médecine, Créteil, France
- Vaccine Research Institute (VRI), Créteil, France
- * E-mail:
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Bandera A, Gori A, Clerici M, Sironi M. Phylogenies in ART: HIV reservoirs, HIV latency and drug resistance. Curr Opin Pharmacol 2019; 48:24-32. [PMID: 31029861 DOI: 10.1016/j.coph.2019.03.003] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2019] [Revised: 03/07/2019] [Accepted: 03/12/2019] [Indexed: 11/17/2022]
Abstract
Combination antiretroviral therapy (ART) has significantly reduced the morbidity and mortality resulting from HIV infection. ART is, however, unable to eradicate HIV, which persists latently in several cell types and tissues. Phylogenetic analyses suggested that the proliferation of cells infected before ART initiation is mainly responsible for residual viremia, although controversy still exists. Conversely, it is widely accepted that drug resistance mutations (DRMs) do not appear during ART in patients with suppressed viral loads. Studies based on sequence clustering have in fact indicated that, at least in developed countries, HIV-infected ART-naive patients are the major source of drug-resistant viruses. Analysis of longitudinally sampled sequences have also shown that DRMs have variable fitness costs, which are strongly influenced by the viral genetic background.
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Affiliation(s)
- Alessandra Bandera
- Infectious Diseases Unit, Department of Internal Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20090 Milan, Italy; Department of Pathophysiology and Transplantation, School of Medicine and Surgery, University of Milan, 20090 Milan, Italy
| | - Andrea Gori
- Infectious Diseases Unit, Department of Internal Medicine, Fondazione IRCCS Ca' Granda Ospedale Maggiore Policlinico, 20090 Milan, Italy; Department of Pathophysiology and Transplantation, School of Medicine and Surgery, University of Milan, 20090 Milan, Italy
| | - Mario Clerici
- Department of Pathophysiology and Transplantation, School of Medicine and Surgery, University of Milan, 20090 Milan, Italy; IRCCS Fondazione Don Carlo Gnocchi, 20148 Milan, Italy
| | - Manuela Sironi
- Bioinformatics, Scientific Institute, IRCCS E. MEDEA, 23842 Bosisio Parini, Lecco, Italy.
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Abstract
OBJECTIVES Molecular epidemiology is applied to various aspects of HIV transmission analyses. With ultradeep sequencing (UDS), in-depth characterization of transmission episodes involving minority variants is permitted. We explored HIV-1 epidemiological linkage and evaluated characteristics of transmission dynamics and transmitted drug resistance (TDR) detection through the added value of UDS. DESIGN HIV pol gene fragments were sequenced by UDS and Sanger sequencing on samples of 70 HIV-1-infected, treatment-naive recently diagnosed MSM. METHODS Pairwise genetic distances and maximum likelihood phylogenies were computed. Transmission events were identified as clades with branch support at least 70% and intraclade genetic difference less than 4.5%. TDR mutations were recognized from the TDR consensus list. Transmission directionality, directness and inoculum size were inferred from tree topologies. RESULTS Both datasets concurred in the identification of seven transmission pairs and one cluster of three patients. With UDS, direction of transmission was inferred in four out of eight chains. Evidence for multiple founder viruses was found in two out of eight chains. No transmission of minority-resistant variants was evidenced. TDR mutations prevalence in protease and reverse transcriptase fragments was 4.3% with Sanger sequencing and 18.6% with UDS. CONCLUSION Although Sanger sequencing and UDS identified the same transmission chains, UDS provided additional information on founder viruses, direction of transmission and levels of TDR. Nevertheless, topology of clusters was not always consistent across gene fragments, calling for a cautious interpretation of the data. Moreover, unobserved intermediary links cannot be excluded. Phylogenetic analysis use as a forensic technique for HIV transmission investigations is risky.
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