1
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Ngo MH, Pankrac J, Ho RCY, Ndashimye E, Pawa R, Ceccacci R, Biru T, Olabode AS, Klein K, Li Y, Kovacs C, Assad R, Jacobson JM, Canaday DH, Tomusange S, Jamiru S, Anok A, Kityamuweesi T, Buule P, Galiwango RM, Reynolds SJ, Quinn TC, Redd AD, Prodger JL, Mann JFS, Arts EJ. Effective and targeted latency reversal in CD4 + T cells from individuals on long term combined antiretroviral therapy initiated during chronic HIV-1 infection. Emerg Microbes Infect 2024; 13:2327371. [PMID: 38444369 DOI: 10.1080/22221751.2024.2327371] [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: 12/03/2023] [Accepted: 03/01/2024] [Indexed: 03/07/2024]
Abstract
To date, an affordable, effective treatment for an HIV-1 cure remains only a concept with most "latency reversal" agents (LRAs) lacking specificity for the latent HIV-1 reservoir and failing in early clinical trials. We assessed HIV-1 latency reversal using a multivalent HIV-1-derived virus-like particle (HLP) to treat samples from 32 people living with HIV-1 (PLWH) in Uganda, US and Canada who initiated combined antiretroviral therapy (cART) during chronic infection. Even after 5-20 years on stable cART, HLP could target CD4+ T cells harbouring latent HIV-1 reservoir resulting in 100-fold more HIV-1 release into culture supernatant than by common recall antigens, and 1000-fold more than by chemotherapeutic LRAs. HLP induced release of a divergent and replication-competent HIV-1 population from PLWH on cART. These findings suggest HLP provides a targeted approach to reactivate the majority of latent HIV-1 proviruses among individuals infected with HIV-1.
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Affiliation(s)
- Minh Ha Ngo
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
- College of Veterinary Medicine, Vietnam National University of Agriculture, Hanoi, Vietnam
| | - Joshua Pankrac
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
| | - Ryan C Y Ho
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
| | - Emmanuel Ndashimye
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
| | - Rahul Pawa
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
| | - Renata Ceccacci
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
| | - Tsigereda Biru
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
- Special Immunology Unit and Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Abayomi S Olabode
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
| | - Katja Klein
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
- Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Yue Li
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
| | - Colin Kovacs
- Maple Leaf Medical Clinic and Division of Infectious Diseases, Department of Medicine, University of Toronto, Toronto, Canada
| | - Robert Assad
- Special Immunology Unit and Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - Jeffrey M Jacobson
- Special Immunology Unit and Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | - David H Canaday
- Special Immunology Unit and Division of Infectious Diseases, Department of Medicine, Case Western Reserve University, Cleveland, OH, USA
| | | | | | - Aggrey Anok
- Rakai Health Sciences Program, Kalisizo, Uganda
| | | | - Paul Buule
- Rakai Health Sciences Program, Kalisizo, Uganda
| | | | - Steven J Reynolds
- Rakai Health Sciences Program, Kalisizo, Uganda
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Thomas C Quinn
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Andrew D Redd
- Division of Infectious Diseases, Johns Hopkins University School of Medicine, Baltimore, MD, USA
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jessica L Prodger
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
| | - Jamie F S Mann
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
- Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Eric J Arts
- Department of Microbiology and Immunology, University of Western Ontario, London, Canada
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2
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Gill EE, Jia B, Murall CL, Poujol R, Anwar MZ, John NS, Richardsson J, Hobb A, Olabode AS, Lepsa A, Duggan AT, Tyler AD, N'Guessan A, Kachru A, Chan B, Yoshida C, Yung CK, Bujold D, Andric D, Su E, Griffiths EJ, Domselaar GV, Jolly GW, Ward HKE, Feher H, Baker J, Simpson JT, Uddin J, Ragoussis J, Eubank J, Fritz JH, Gálvez JH, Fang K, Cullion K, Rivera L, Xiang L, Croxen MA, Shiell M, Prystajecky N, Quirion PO, Bajari R, Rich S, Mubareka S, Moreira S, Cain S, Sutcliffe SG, Kraemer SA, Joly Y, Alturmessov Y, Consortium C, Consortium C, Academic VDP, Network H, Fiume M, Snutch TP, Bell C, Lopez-Correa C, Hussin JG, Joy JB, Colijn C, Gordon PMK, Hsiao WWL, Poon AFY, Knox NC, Courtot M, Stein L, Otto SP, Bourque G, Shapiro BJ, Brinkman FSL. The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology. ArXiv 2024:arXiv:2405.04734v1. [PMID: 38764594 PMCID: PMC11100916] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 05/21/2024]
Abstract
The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2 genomes from patient samples to track viral evolution and inform public health response. Millions of SARS-CoV-2 genome sequences have been deposited in global public repositories. The Canadian COVID-19 Genomics Network (CanCOGeN - VirusSeq), a consortium tasked with coordinating expanded sequencing of SARS-CoV-2 genomes across Canada early in the pandemic, created the Canadian VirusSeq Data Portal, with associated data pipelines and procedures, to support these efforts. The goal of VirusSeq was to allow open access to Canadian SARS-CoV-2 genomic sequences and enhanced, standardized contextual data that were unavailable in other repositories and that meet FAIR standards (Findable, Accessible, Interoperable and Reusable). The Portal data submission pipeline contains data quality checking procedures and appropriate acknowledgement of data generators that encourages collaboration. Here we also highlight Duotang, a web platform that presents genomic epidemiology and modeling analyses on circulating and emerging SARS-CoV-2 variants in Canada. Duotang presents dynamic changes in variant composition of SARS-CoV-2 in Canada and by province, estimates variant growth, and displays complementary interactive visualizations, with a text overview of the current situation. The VirusSeq Data Portal and Duotang resources, alongside additional analyses and resources computed from the Portal (COVID-MVP, CoVizu), are all open-source and freely available. Together, they provide an updated picture of SARS-CoV-2 evolution to spur scientific discussions, inform public discourse, and support communication with and within public health authorities. They also serve as a framework for other jurisdictions interested in open, collaborative sequence data sharing and analyses.
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3
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Sutcliffe SG, Kraemer SA, Ellmen I, Knapp JJ, Overton AK, Nash D, Nissimov JI, Charles TC, Dreifuss D, Topolsky I, Baykal PI, Fuhrmann L, Jablonski KP, Beerenwinkel N, Levy JI, Olabode AS, Becker DG, Gugan G, Brintnell E, Poon AFY, Valieris R, Drummond RD, Defelicibus A, Dias-Neto E, Rosales RA, Tojal da Silva I, Orfanou A, Psomopoulos F, Pechlivanis N, Pipes L, Chen Z, Baaijens JA, Baym M, Shapiro BJ. Tracking SARS-CoV-2 variants of concern in wastewater: an assessment of nine computational tools using simulated genomic data. Microb Genom 2024; 10. [PMID: 38785221 DOI: 10.1099/mgen.0.001249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024] Open
Abstract
Wastewater-based surveillance (WBS) is an important epidemiological and public health tool for tracking pathogens across the scale of a building, neighbourhood, city, or region. WBS gained widespread adoption globally during the SARS-CoV-2 pandemic for estimating community infection levels by qPCR. Sequencing pathogen genes or genomes from wastewater adds information about pathogen genetic diversity, which can be used to identify viral lineages (including variants of concern) that are circulating in a local population. Capturing the genetic diversity by WBS sequencing is not trivial, as wastewater samples often contain a diverse mixture of viral lineages with real mutations and sequencing errors, which must be deconvoluted computationally from short sequencing reads. In this study we assess nine different computational tools that have recently been developed to address this challenge. We simulated 100 wastewater sequence samples consisting of SARS-CoV-2 BA.1, BA.2, and Delta lineages, in various mixtures, as well as a Delta-Omicron recombinant and a synthetic 'novel' lineage. Most tools performed well in identifying the true lineages present and estimating their relative abundances and were generally robust to variation in sequencing depth and read length. While many tools identified lineages present down to 1 % frequency, results were more reliable above a 5 % threshold. The presence of an unknown synthetic lineage, which represents an unclassified SARS-CoV-2 lineage, increases the error in relative abundance estimates of other lineages, but the magnitude of this effect was small for most tools. The tools also varied in how they labelled novel synthetic lineages and recombinants. While our simulated dataset represents just one of many possible use cases for these methods, we hope it helps users understand potential sources of error or bias in wastewater sequencing analysis and to appreciate the commonalities and differences across methods.
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Affiliation(s)
- Steven G Sutcliffe
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Susanne A Kraemer
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
- Environment and Climate Change Canada, Montreal, QC, Canada
| | - Isaac Ellmen
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Jennifer J Knapp
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Alyssa K Overton
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Delaney Nash
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Jozef I Nissimov
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - Trevor C Charles
- Department of Biology, University of Waterloo, Waterloo, ON, Canada
| | - David Dreifuss
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland
| | - Ivan Topolsky
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland
| | - Pelin I Baykal
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland
| | - Lara Fuhrmann
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland
| | - Kim P Jablonski
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland
| | - Niko Beerenwinkel
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, BS, Switzerland; SIB Swiss Institute of Bioinformatics, Lausanne, VD, Switzerland
| | - Joshua I Levy
- Department of Immunology and Microbiology, The Scripps Research Institute, La Jolla, CA, USA
| | - Abayomi S Olabode
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Devan G Becker
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Gopi Gugan
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Erin Brintnell
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Art F Y Poon
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Renan Valieris
- Computational Biology, A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | - Rodrigo D Drummond
- Computational Biology, A.C. Camargo Cancer Center, São Paulo, SP, Brazil
| | | | | | | | | | - Aspasia Orfanou
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece
| | - Fotis Psomopoulos
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece
| | - Nikolaos Pechlivanis
- Institute of Applied Biosciences, Centre for Research and Technology Hellas, Thermi, 57001, Thessaloníki, Greece
| | - Lenore Pipes
- Department of Integrative Biology, University of California, Berkeley, CA, USA
| | - Zihao Chen
- School of Mathematical Sciences, Peking University, Beijing, BJ, PR China
| | - Jasmijn A Baaijens
- Delft University of Technology, Delft, ZH, Netherlands
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Michael Baym
- Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - B Jesse Shapiro
- Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
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4
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Olabode AS, Mumby MJ, Wild TA, Muñoz-Baena L, Dikeakos JD, Poon AFY. Phylogenetic Reconstruction and Functional Characterization of the Ancestral Nef Protein of Primate Lentiviruses. Mol Biol Evol 2023; 40:msad164. [PMID: 37463439 PMCID: PMC10400143 DOI: 10.1093/molbev/msad164] [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: 03/28/2023] [Revised: 06/19/2023] [Accepted: 07/10/2023] [Indexed: 07/20/2023] Open
Abstract
Nef is an accessory protein unique to the primate HIV-1, HIV-2, and SIV lentiviruses. During infection, Nef functions by interacting with multiple host proteins within infected cells to evade the immune response and enhance virion infectivity. Notably, Nef can counter immune regulators such as CD4 and MHC-I, as well as the SERINC5 restriction factor in infected cells. In this study, we generated a posterior sample of time-scaled phylogenies relating SIV and HIV Nef sequences, followed by reconstruction of ancestral sequences at the root and internal nodes of the sampled trees up to the HIV-1 Group M ancestor. Upon expression of the ancestral primate lentivirus Nef protein within CD4+ HeLa cells, flow cytometry analysis revealed that the primate lentivirus Nef ancestor robustly downregulated cell-surface SERINC5, yet only partially downregulated CD4 from the cell surface. Further analysis revealed that the Nef-mediated CD4 downregulation ability evolved gradually, while Nef-mediated SERINC5 downregulation was recovered abruptly in the HIV-1/M ancestor. Overall, this study provides a framework to reconstruct ancestral viral proteins and enable the functional characterization of these proteins to delineate how functions could have changed throughout evolutionary history.
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Affiliation(s)
- Abayomi S Olabode
- Department of Pathology & Laboratory Medicine, Western University, London, Canada
| | - Mitchell J Mumby
- Department of Microbiology & Immunology, Western University, London, Canada
| | - Tristan A Wild
- Department of Microbiology & Immunology, Western University, London, Canada
| | - Laura Muñoz-Baena
- Department of Microbiology & Immunology, Western University, London, Canada
| | - Jimmy D Dikeakos
- Department of Microbiology & Immunology, Western University, London, Canada
| | - Art F Y Poon
- Department of Pathology & Laboratory Medicine, Western University, London, Canada
- Department of Microbiology & Immunology, Western University, London, Canada
- Department of Computer Science, Western University, London, Canada
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5
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Affiliation(s)
- Elisa Chao
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Connor Chato
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Reid Vender
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- School of Medicine, Queen’s University, Kingston, Ontario, Canada
| | - Abayomi S. Olabode
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Roux-Cil Ferreira
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
| | - Art F. Y. Poon
- Department of Pathology and Laboratory Medicine, Western University, London, Ontario, Canada
- * E-mail:
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6
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Peng J, Sun J, Yang MI, Gibson RM, Arts EJ, Olabode AS, Poon AFY, Wang X, Wheeler AR, Edwards EA, Peng H. Early Warning Measurement of SARS-CoV-2 Variants of Concern in Wastewaters by Mass Spectrometry. Environ Sci Technol Lett 2022; 9:638-644. [PMID: 37552744 PMCID: PMC9236213 DOI: 10.1021/acs.estlett.2c00280] [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] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Revised: 06/07/2022] [Accepted: 06/15/2022] [Indexed: 05/24/2023]
Abstract
Wastewater surveillance has rapidly emerged as an early warning tool to track COVID-19. However, the early warning measurement of new SARS-CoV-2 variants of concern (VOCs) in wastewaters remains a major challenge. We herein report a rapid analytical strategy for quantitative measurement of VOCs, which couples nested polymerase chain reaction and liquid chromatography-mass spectrometry (nPCR-LC-MS). This method showed a greater selectivity than the current allele-specific quantitative PCR (AS-qPCR) for tracking new VOC and allowed the detection of multiple signature mutations in a single measurement. By measuring the Omicron variant in wastewaters across nine Ontario wastewater treatment plants serving over a three million population, the nPCR-LC-MS method demonstrated a better quantification accuracy than next-generation sequencing (NGS), particularly at the early stage of community spreading of Omicron. This work addresses a major challenge for current SARS-CoV-2 wastewater surveillance by rapidly and accurately measuring VOCs in wastewaters for early warning.
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Affiliation(s)
- Jiaxi Peng
- Department of Chemistry, University of
Toronto, 80 St George Street, Toronto, Ontario M5S 3H6,
Canada
- Donnelly Centre for Cellular and Biomolecular
Research, University of Toronto, 160 College Street, Toronto,
Ontario M5S 3E1, Canada
- Institute of Biomedical Engineering,
University of Toronto, 164 College Street, Toronto, Ontario
M5S 3G9, Canada
| | - Jianxian Sun
- Department of Chemistry, University of
Toronto, 80 St George Street, Toronto, Ontario M5S 3H6,
Canada
| | - Minqing Ivy Yang
- Department of Chemical Engineering and Applied
Chemistry, University of Toronto, 200 College Street, Toronto,
Ontario M5S 3E5, Canada
| | - Richard M. Gibson
- Department of Microbiology and Immunology,
Western University, 1151 Richmond Street, London, Ontario N6A
5C1, Canada
| | - Eric J. Arts
- Department of Microbiology and Immunology,
Western University, 1151 Richmond Street, London, Ontario N6A
5C1, Canada
| | - Abayomi S. Olabode
- Department of Microbiology and Immunology,
Western University, 1151 Richmond Street, London, Ontario N6A
5C1, Canada
| | - Art F. Y. Poon
- Department of Microbiology and Immunology,
Western University, 1151 Richmond Street, London, Ontario N6A
5C1, Canada
| | - Xianyao Wang
- Department of Chemistry, University of
Toronto, 80 St George Street, Toronto, Ontario M5S 3H6,
Canada
| | - Aaron R. Wheeler
- Department of Chemistry, University of
Toronto, 80 St George Street, Toronto, Ontario M5S 3H6,
Canada
- Donnelly Centre for Cellular and Biomolecular
Research, University of Toronto, 160 College Street, Toronto,
Ontario M5S 3E1, Canada
- Institute of Biomedical Engineering,
University of Toronto, 164 College Street, Toronto, Ontario
M5S 3G9, Canada
| | - Elizabeth A. Edwards
- Department of Chemical Engineering and Applied
Chemistry, University of Toronto, 200 College Street, Toronto,
Ontario M5S 3E5, Canada
| | - Hui Peng
- Department of Chemistry, University of
Toronto, 80 St George Street, Toronto, Ontario M5S 3H6,
Canada
- School of the Environment, University of
Toronto, 80 St George Street, Toronto, Ontario M5S 3H6,
Canada
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7
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Ndashimye E, Li Y, Reyes PS, Avino M, Olabode AS, Kityo CM, Kyeyune F, Nankya I, Quiñones-Mateu ME, Barr SD, Arts EJ. High-level resistance to bictegravir and cabotegravir in subtype A- and D-infected HIV-1 patients failing raltegravir with multiple resistance mutations. J Antimicrob Chemother 2021; 76:2965-2974. [PMID: 34453542 DOI: 10.1093/jac/dkab276] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 07/02/2021] [Indexed: 01/15/2023] Open
Abstract
OBJECTIVES The second-generation integrase strand transfer inhibitor (INSTI) bictegravir is becoming accessible in low- and middle-income countries (LMICs), and another INSTI, cabotegravir, has recently been approved as a long-acting injectable. Data on bictegravir and cabotegravir susceptibility in raltegravir-experienced HIV-1 subtype A- and D-infected patients carrying drug resistance mutations (DRMs) remain very scarce in LMICs. PATIENTS AND METHODS HIV-1 integrase (IN)-recombinant viruses from eight patients failing raltegravir-based third-line therapy in Uganda were genotypically and phenotypically tested for susceptibility to bictegravir and cabotegravir. Ability of these viruses to integrate into human genomes was assessed in MT-4 cells. RESULTS HIV-1 IN-recombinant viruses harbouring single primary mutations (N155H or Y143R/S) or in combination with secondary INSTI mutations (T97A, M50I, L74IM, E157Q, G163R or V151I) were susceptible to both bictegravir and cabotegravir. However, combinations of primary INSTI-resistance mutations such as E138A/G140A/G163R/Q148R or E138K/G140A/S147G/Q148K led to decreased susceptibility to both cabotegravir (fold change in EC50 values from 429 to 1000×) and bictegravir (60 to 100×), exhibiting a high degree of cross-resistance. However, these same IN-recombinant viruses showed impaired integration capacity (14% to 48%) relative to the WT HIV-1 NL4-3 strain in the absence of drug. CONCLUSIONS Though not currently widely accessible in most LMICs, bictegravir and cabotegravir offer a valid alternative to HIV-infected individuals harbouring subtype A and D HIV-1 variants with reduced susceptibility to first-generation INSTIs but previous exposure to raltegravir may reduce efficacy, more so with cabotegravir.
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Affiliation(s)
- Emmanuel Ndashimye
- Department of Microbiology and Immunology, Western University, London, Canada.,Joint Clinical Research Centre, Kampala, Uganda.,Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Yue Li
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Paul S Reyes
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Mariano Avino
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | - Abayomi S Olabode
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | | | - Fred Kyeyune
- Joint Clinical Research Centre, Kampala, Uganda.,Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Immaculate Nankya
- Joint Clinical Research Centre, Kampala, Uganda.,Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | | | - Stephen D Barr
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Eric J Arts
- Department of Microbiology and Immunology, Western University, London, Canada
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8
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Ndashimye E, Avino M, Olabode AS, Poon AFY, Gibson RM, Li Y, Meadows A, Tan C, Reyes PS, Kityo CM, Kyeyune F, Nankya I, Quiñones-Mateu ME, Arts EJ. Accumulation of integrase strand transfer inhibitor resistance mutations confers high-level resistance to dolutegravir in non-B subtype HIV-1 strains from patients failing raltegravir in Uganda. J Antimicrob Chemother 2021; 75:3525-3533. [PMID: 32853364 DOI: 10.1093/jac/dkaa355] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 07/03/2020] [Indexed: 02/03/2023] Open
Abstract
BACKGROUND Increasing first-line treatment failures in low- and middle-income countries (LMICs) have led to increased use of integrase strand transfer inhibitors (INSTIs) such as dolutegravir. However, HIV-1 susceptibility to INSTIs in LMICs, especially with previous raltegravir exposure, is poorly understood due to infrequent reporting of INSTI failures and testing for INSTI drug resistance mutations (DRMs). METHODS A total of 51 non-subtype B HIV-1 infected patients failing third-line (raltegravir-based) therapy in Uganda were initially selected for the study. DRMs were detected using Sanger and deep sequencing. HIV integrase genes of 13 patients were cloned and replication capacities (RCs) and phenotypic susceptibilities to dolutegravir, raltegravir and elvitegravir were determined with TZM-bl cells. Spearman's correlation coefficient was used to determine cross-resistance between INSTIs. RESULTS INSTI DRMs were detected in 47% of patients. HIV integrase-recombinant virus carrying one primary INSTI DRM (N155H or Y143R/S) was susceptible to dolutegravir but highly resistant to raltegravir and elvitegravir (>50-fold change). Two patients, one with E138A/G140A/Q148R/G163R and one with E138K/G140A/S147G/Q148K, displayed the highest reported resistance to raltegravir, elvitegravir and even dolutegravir. The former multi-DRM virus had WT RC whereas the latter had lower RCs than WT. CONCLUSIONS In HIV-1 subtype A- and D-infected patients failing raltegravir and harbouring INSTI DRMs, there is high-level resistance to elvitegravir and raltegravir. More routine monitoring of INSTI treatment may be advised in LMICs, considering that multiple INSTI DRMs may have accumulated during prolonged exposure to raltegravir during virological failure, leading to high-level INSTI resistance, including dolutegravir resistance.
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Affiliation(s)
- Emmanuel Ndashimye
- Department of Microbiology and Immunology, Western University, London, Canada.,Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Mariano Avino
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | - Abayomi S Olabode
- Department of Pathology and Laboratory Medicine, Western University, London, Canada
| | - Art F Y Poon
- Department of Microbiology and Immunology, Western University, London, Canada.,Department of Pathology and Laboratory Medicine, Western University, London, Canada.,Department of Applied Mathematics, Western University, London, Canada
| | - Richard M Gibson
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Yue Li
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Adam Meadows
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Christine Tan
- Department of Microbiology and Immunology, Western University, London, Canada
| | - Paul S Reyes
- Department of Microbiology and Immunology, Western University, London, Canada
| | | | - Fred Kyeyune
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | - Immaculate Nankya
- Center for AIDS Research Uganda Laboratories, Joint Clinical Research Centre, Kampala, Uganda
| | | | - Eric J Arts
- Department of Microbiology and Immunology, Western University, London, Canada
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9
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Abstract
Many virus-encoded proteins have intrinsically disordered regions that lack a stable, folded three-dimensional structure. These disordered proteins often play important functional roles in virus replication, such as down-regulating host defense mechanisms. With the widespread availability of next-generation sequencing, the number of new virus genomes with predicted open reading frames is rapidly outpacing our capacity for directly characterizing protein structures through crystallography. Hence, computational methods for structural prediction play an important role. A large number of predictors focus on the problem of classifying residues into ordered and disordered regions, and these methods tend to be validated on a diverse training set of proteins from eukaryotes, prokaryotes, and viruses. In this study, we investigate whether some predictors outperform others in the context of virus proteins and compared our findings with data from non-viral proteins. We evaluate the prediction accuracy of 21 methods, many of which are only available as web applications, on a curated set of 126 proteins encoded by viruses. Furthermore, we apply a random forest classifier to these predictor outputs. Based on cross-validation experiments, this ensemble approach confers a substantial improvement in accuracy, e.g., a mean 36 per cent gain in Matthews correlation coefficient. Lastly, we apply the random forest predictor to severe acute respiratory syndrome coronavirus 2 ORF6, an accessory gene that encodes a short (61 AA) and moderately disordered protein that inhibits the host innate immune response. We show that disorder prediction methods perform differently for viral and non-viral proteins, and that an ensemble approach can yield more robust and accurate predictions.
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Affiliation(s)
- Gal Almog
- Department of Pathology & Laboratory Medicine, Western University, Dental Sciences Building, Rm. 4044 London, Ontario, Canada, N6A 5C1
| | - Abayomi S Olabode
- Department of Pathology & Laboratory Medicine, Western University, Dental Sciences Building, Rm. 4044 London, Ontario, Canada, N6A 5C1
| | - Art F Y Poon
- Department of Pathology & Laboratory Medicine, Western University, Dental Sciences Building, Rm. 4044 London, Ontario, Canada, N6A 5C1.,Department of Applied Mathematics, Western University, Middlesex College Room 255, 1151 Richmond Street London, Ontario, Canada, N6A 5B7.,Department of Microbiology & Immunology, Western University, 1151 Richmond Street London, Ontario, Canada, N6A 3K
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10
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Ferreira RC, Wong E, Gugan G, Wade K, Liu M, Baena LM, Chato C, Lu B, Olabode AS, Poon AFY. OUP accepted manuscript. Virus Evol 2021; 7:veab092. [PMID: 37124703 PMCID: PMC10131274 DOI: 10.1093/ve/veab092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Revised: 09/20/2021] [Accepted: 11/05/2021] [Indexed: 11/13/2022] Open
Abstract
Phylogenetics has played a pivotal role in the genomic epidemiology of severe acute respiratory syndrome coronavirus 2, such as tracking the emergence and global spread of variants and scientific communication. However, the rapid accumulation of genomic data from around the world-with over two million genomes currently available in the Global Initiative on Sharing All Influenza Data database-is testing the limits of standard phylogenetic methods. Here, we describe a new approach to rapidly analyze and visualize large numbers of SARS-CoV-2 genomes. Using Python, genomes are filtered for problematic sites, incomplete coverage, and excessive divergence from a strict molecular clock. All differences from the reference genome, including indels, are extracted using minimap2 and compactly stored as a set of features for each genome. For each Pango lineage (https://cov-lineages.org), we collapse genomes with identical features into 'variants', generate 100 bootstrap samples of the feature set union to generate weights, and compute the symmetric differences between the weighted feature sets for every pair of variants. The resulting distance matrices are used to generate neighbor-joining trees in RapidNJ that are converted into a majority-rule consensus tree for each lineage. Branches with support values below 50 per cent or mean lengths below 0.5 differences are collapsed, and tip labels on affected branches are mapped to internal nodes as directly sampled ancestral variants. Currently, we process about 2 million genomes in approximately 9 h on 52 cores. The resulting trees are visualized using the JavaScript framework D3.js as 'beadplots', in which variants are represented by horizontal line segments, annotated with beads representing samples by collection date. Variants are linked by vertical edges to represent branches in the consensus tree. These visualizations are published at https://filogeneti.ca/CoVizu. All source code was released under an MIT license at https://github.com/PoonLab/covizu.
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Affiliation(s)
| | - Emmanuel Wong
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Gopi Gugan
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Kaitlyn Wade
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Molly Liu
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Laura Muñoz Baena
- Department of Microbiology and Immunology, Western University, London, ON, Canada
| | - Connor Chato
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
| | - Bonnie Lu
- Department of Pathology and Laboratory Medicine, Western University, London, ON, Canada
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11
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Abstract
Reconstructing the early dynamics of the HIV-1 pandemic can provide crucial insights into the socioeconomic drivers of emerging infectious diseases in human populations, including the roles of urbanization and transportation networks. Current evidence indicates that the global pandemic comprising almost entirely of HIV-1/M originated around the 1920s in central Africa. However, these estimates are based on molecular clock estimates that are assumed to apply uniformly across the virus genome. There is growing evidence that recombination has played a significant role in the early history of the HIV-1 pandemic, such that different regions of the HIV-1 genome have different evolutionary histories. In this study, we have conducted a dated-tip analysis of all near full-length HIV-1/M genome sequences that were published in the GenBank database. We used a sliding window approach similar to the 'bootscanning' method for detecting breakpoints in inter-subtype recombinant sequences. We found evidence of substantial variation in estimated root dates among windows, with an estimated mean time to the most recent common ancestor of 1922. Estimates were significantly autocorrelated, which was more consistent with an early recombination event than with stochastic error variation in phylogenetic reconstruction and dating analyses. A piecewise regression analysis supported the existence of at least one recombination breakpoint in the HIV-1/M genome with interval-specific means around 1929 and 1913, respectively. This analysis demonstrates that a sliding window approach can accommodate early recombination events outside the established nomenclature of HIV-1/M subtypes, although it is difficult to incorporate the earliest available samples due to their limited genome coverage.
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Affiliation(s)
- Abayomi S Olabode
- Department of Pathology & Laboratory Medicine, Western University, London, Ontario, Canada
| | - Mariano Avino
- Department of Pathology & Laboratory Medicine, Western University, London, Ontario, Canada
| | - Garway T Ng
- Department of Pathology & Laboratory Medicine, Western University, London, Ontario, Canada
| | - Faisal Abu-Sardanah
- Department of Pathology & Laboratory Medicine, Western University, London, Ontario, Canada
| | - David W Dick
- Department of Applied Mathematics, Western University, London, Ontario, Canada
| | - Art F Y Poon
- Department of Pathology & Laboratory Medicine, Western University, London, Ontario, Canada.,Department of Applied Mathematics, Western University, London, Ontario, Canada.,Department of Microbiology & Immunology, Western University, London, Ontario, Canada
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12
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Abstract
Despite the use of combination antiretroviral drugs for the treatment of HIV-1 infection, the emergence of drug resistance remains a problem. Resistance may be conferred either by a single mutation or a concerted set of mutations. The involvement of multiple mutations can arise due to interactions between sites in the amino acid sequence as a consequence of the need to maintain protein structure. To better understand the nature of such epistatic interactions, we reconstructed the ancestral sequences of HIV-1’s Pol protein, and traced the evolutionary trajectories leading to mutations associated with drug resistance. Using contemporary and ancestral sequences we modelled the effects of mutations (i.e. amino acid replacements) on protein structure to understand the functional effects of residue changes. Although the majority of resistance-associated sequences tend to destabilise the protein structure, we find there is a general tendency for protein stability to decrease across HIV-1’s evolutionary history. That a similar pattern is observed in the non-drug resistance lineages indicates that non-resistant mutations, for example, associated with escape from the immune response, also impacts on protein stability. Maintenance of optimal protein structure therefore represents a major constraining factor to the evolution of HIV-1.
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Affiliation(s)
- Abayomi S Olabode
- Evolution & Genomic Sciences, School of Biological Sciences, University of Manchester, Oxford Road, Manchester, UK
| | - Shaun M Kandathil
- Evolution & Genomic Sciences, School of Biological Sciences, University of Manchester, Oxford Road, Manchester, UK.,Francis Crick Institute & Dept. of Computer Science, University College London, London, UK
| | - Simon C Lovell
- Evolution & Genomic Sciences, School of Biological Sciences, University of Manchester, Oxford Road, Manchester, UK
| | - David L Robertson
- Evolution & Genomic Sciences, School of Biological Sciences, University of Manchester, Oxford Road, Manchester, UK.,MRC-University of Glasgow Centre for Virus Research, Garscube Campus, Glasgow, UK
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13
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Olabode AS, Jiang X, Robertson DL, Lovell SC. Ebolavirus is evolving but not changing: No evidence for functional change in EBOV from 1976 to the 2014 outbreak. Virology 2015; 482:202-7. [PMID: 25880111 PMCID: PMC4503884 DOI: 10.1016/j.virol.2015.03.029] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2015] [Revised: 03/11/2015] [Accepted: 03/15/2015] [Indexed: 01/05/2023]
Abstract
The 2014 epidemic of Ebola virus disease (EVD) has had a devastating impact in West Africa. Sequencing of ebolavirus (EBOV) from infected individuals has revealed extensive genetic variation, leading to speculation that the virus may be adapting to humans, accounting for the scale of the 2014 outbreak. We computationally analyze the variation associated with all EVD outbreaks, and find none of the amino acid replacements lead to identifiable functional changes. These changes have minimal effect on protein structure, being neither stabilizing nor destabilizing, are not found in regions of the proteins associated with known functions and tend to cluster in poorly constrained regions of proteins, specifically intrinsically disordered regions. We find no evidence that the difference between the current and previous outbreaks is due to evolutionary changes associated with transmission to humans. Instead, epidemiological factors are likely to be responsible for the unprecedented spread of EVD.
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Affiliation(s)
- Abayomi S Olabode
- Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, UK
| | - Xiaowei Jiang
- Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, UK; Department of Genetics, University of Cambridge, Cambridge, UK
| | - David L Robertson
- Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, UK.
| | - Simon C Lovell
- Computational and Evolutionary Biology, Faculty of Life Sciences, University of Manchester, Manchester, UK.
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