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Ozhmegova E, Lebedev A, Antonova A, Kuznetsova A, Kazennova E, Kim K, Tumanov A, Bobkova M. Prevalence of HIV drug resistance at antiretroviral treatment failure across regions of Russia. HIV Med 2024; 25:862-872. [PMID: 38584123 DOI: 10.1111/hiv.13642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 03/24/2024] [Indexed: 04/09/2024]
Abstract
BACKGROUND This study aimed to investigate mutations associated with, the causes of, and the conditions that contribute to HIV drug resistance (DR). This research provides crucial insights into the mechanisms through which HIV evades antiretroviral drugs and suggests strategies to counter this phenomenon. Our objective was to assess the prevalence and structure of DR in HIV-1 across various regions in Russia and identify the primary factors influencing the development of HIV DR. METHODS The study used nucleotide sequences from the HIV-1 pol gene obtained from 1369 patients with a history of therapy and virological failure between 2005 and 2019 to analyze the frequency and structure of DR and the factors associated with it. RESULTS The analysed HIV-1 genotypes included viruses resistant to nucleoside reverse transcriptase inhibitors (NRTIs; 11.8%), non-nucleoside reverse transcriptase inhibitors (NNRTIs; 6.4%), and NRTIs + NNRTIs (31.7%). The mutations M184V/I and G190A/S/E were the most prevalent, accounting for 54.5% and 26.6%, respectively. The dominance of multiple DR persisted throughout the entire observation period. The likelihood of encountering drug-resistant variants was increased among men, patients in the late stage of infection, and those with a viral load <30 000 RNA copies/mL. Injection drug use was not associated with DR. CONCLUSION This study has yielded new insights into HIV DR in Russia, offering valuable information to identify clinical or programmatic events warranting closer attention and support.
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Affiliation(s)
- Ekaterina Ozhmegova
- National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya, Moscow, Russia
| | - Aleksey Lebedev
- National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya, Moscow, Russia
| | - Anastasiia Antonova
- National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya, Moscow, Russia
| | - Anna Kuznetsova
- National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya, Moscow, Russia
| | - Elena Kazennova
- National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya, Moscow, Russia
| | - Kristina Kim
- National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya, Moscow, Russia
| | - Aleksandr Tumanov
- National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya, Moscow, Russia
| | - Marina Bobkova
- I. Mechnikov Research Institute for Vaccines and Sera, Moscow, Russia
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Kemp SA, Kamelian K, Cuadros DF, Cheng MTK, Okango E, Hanekom W, Ndung'u T, Pillay D, Bonsall D, Wong EB, Tanser F, Siedner MJ, Gupta RK. HIV transmission dynamics and population-wide drug resistance in rural South Africa. Nat Commun 2024; 15:3644. [PMID: 38684655 PMCID: PMC11059351 DOI: 10.1038/s41467-024-47254-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Accepted: 03/20/2024] [Indexed: 05/02/2024] Open
Abstract
Despite expanded antiretroviral therapy (ART) in South Africa, HIV-1 transmission persists. Integrase strand transfer inhibitors (INSTI) and long-acting injectables offer potential for superior viral suppression, but pre-existing drug resistance could threaten their effectiveness. In a community-based study in rural KwaZulu-Natal, prior to widespread INSTI usage, we enroled 18,025 individuals to characterise HIV-1 drug resistance and transmission networks to inform public health strategies. HIV testing and reflex viral load quantification were performed, with deep sequencing (20% variant threshold) used to detect resistance mutations. Phylogenetic and geospatial analyses characterised transmission clusters. One-third of participants were HIV-positive, with 21.7% having detectable viral loads; 62.1% of those with detectable viral loads were ART-naïve. Resistance to older reverse transcriptase (RT)-targeting drugs was found, but INSTI resistance remained low (<1%). Non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance, particularly to rilpivirine (RPV) even in ART-naïve individuals, was concerning. Twenty percent of sequenced individuals belonged to transmission clusters, with geographic analysis highlighting higher clustering in peripheral and rural areas. Our findings suggest promise for INSTI-based strategies in this setting but underscore the need for RPV resistance screening before implementing long-acting cabotegravir (CAB) + RPV. The significant clustering emphasises the importance of geographically targeted interventions to effectively curb HIV-1 transmission.
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Affiliation(s)
- Steven A Kemp
- Department of Medicine, University of Cambridge, Cambridge, UK
- Pandemic Science Institute, Big Data Institute, University of Oxford, Oxford, UK
| | - Kimia Kamelian
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Diego F Cuadros
- Digital Epidemiology Laboratory, Digital Futures, University of Cincinnati, Cincinnati, OH, USA
| | - Mark T K Cheng
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Elphas Okango
- Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa
| | - Willem Hanekom
- Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa
- University College London, London, UK
| | - Thumbi Ndung'u
- Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa
- University College London, London, UK
| | | | - David Bonsall
- Pandemic Science Institute, Big Data Institute, University of Oxford, Oxford, UK
| | - Emily B Wong
- Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa
| | - Frank Tanser
- University of Stellenbosch, Cape Town, South Africa
| | - Mark J Siedner
- Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa
- Division of Infectious Diseases, Massachusetts General Hospital, Boston, MA, USA
- University of KwaZulu-Natal, Durban, South Africa
- Harvard University, Cambridge, MA, England
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Africa Health Research Institute, KwaZulu-Natal, Durban, South Africa.
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Gupta R, Kemp S, Kamelian K, Cuadros D, Gupta R, Cheng M, Okango E, Hanekom W, Ndung'u T, Pillay D, Bonsall D, Wong E, Tanser F, Siedner M. HIV transmission dynamics and population-wide drug resistance in rural South Africa. RESEARCH SQUARE 2023:rs.3.rs-3640717. [PMID: 38076835 PMCID: PMC10705695 DOI: 10.21203/rs.3.rs-3640717/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Despite the scale-up of antiretroviral therapy (ART) in South Africa, HIV-1 incidence remains high. The anticipated use of potent integrase strand transfer inhibitors and long-acting injectables aims to enhance viral suppression at the population level and diminish transmission. Nevertheless, pre-existing drug resistance could impede the efficacy of long-acting injectable ART combinations, such as rilpivirine (an NNRTI) and cabotegravir (an INSTI). Consequently, a thorough understanding of transmission networks and geospatial distributions is vital for tailored interventions, including pre-exposure prophylaxis with long-acting injectables. However, empirical data on background resistance and transmission networks remain limited. In a community-based study in rural KwaZulu-Natal (2018-2019), prior to the widespread use of integrase inhibitor-based first-line ART, we performed HIV testing with reflex HIV-1 RNA viral load quantification on 18,025 participants. From this cohort, 6,096 (33.9%) tested positive for HIV via ELISA, with 1,323 (21.7%) exhibiting detectable viral loads (> 40 copies/mL). Of those with detectable viral loads, 62.1% were ART-naïve, and the majority of the treated were on an efavirenz + cytosine analogue + tenofovir regimen. Deep sequencing analysis, with a variant abundance threshold of 20%, revealed NRTI resistance mutations such as M184V in 2% of ART-naïve and 32% of treated individuals. Tenofovir resistance mutations K65R and K70E were found in 12% and 5% of ART-experienced individuals, respectively, and in less than 1% of ART-naïve individuals. Integrase inhibitor resistance mutations were notably infrequent (< 1%). Prevalence of pre-treatment drug resistance to NNRTIs was 10%, predominantly consisting of the K103N mutation. Among those with viraemic ART, NNRTI resistance was 50%, with rilpivirine-associated mutations observed in 9% of treated and 6% of untreated individuals. Cluster analysis revealed that 20% (205/1,050) of those sequenced were part of a cluster. We identified 171 groups with at least two linked participants; three quarters of clusters had only two individuals, and a quarter had 3-6 individuals. Integrating phylogenetic with geospatial analyses, we revealed a complex transmission network with significant clustering in specific regions, notably peripheral and rural areas. These findings derived from population scale genomic analyses are encouraging in terms of the limited resistance to DTG, but indicate that transitioning to long-acting cabotegravir + rilpivirine for transmission reduction should be accompanied by prior screening for rilpivirine resistance. Whole HIV-1 genome sequencing allowed identification of significant proportions of clusters with multiple individuals, and geospatial analyses suggesting decentralised networks can inform targeting public health interventions to effectively curb HIV-1 transmission.
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Abdullahi A, Kida IM, Maina UA, Ibrahim AH, Mshelia J, Wisso H, Adamu A, Onyemata JE, Edun M, Yusuph H, Aliyu SH, Charurat M, Abimiku A, Abeler-Dorner L, Fraser C, Bonsall D, Kemp SA, Gupta RK. Limited emergence of resistance to integrase strand transfer inhibitors (INSTIs) in ART-experienced participants failing dolutegravir-based antiretroviral therapy: a cross-sectional analysis of a Northeast Nigerian cohort. J Antimicrob Chemother 2023; 78:2000-2007. [PMID: 37367727 PMCID: PMC10393879 DOI: 10.1093/jac/dkad195] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
BACKGROUND Due to the high prevalence of resistance to NNRTI-based ART since 2018, consolidated recommendations from the WHO have indicated dolutegravir as the preferred drug of choice for HIV treatment globally. There is a paucity of resistance outcome data from HIV-1 non-B subtypes circulating across West Africa. AIMS We characterized the mutational profiles of persons living with HIV from a cross-sectional cohort in North-East Nigeria failing a dolutegravir-based ART regimen. METHODS WGS of plasma samples collected from 61 HIV-1-infected participants following virological failure of dolutegravir-based ART were sequenced using the Illumina platform. Sequencing was successfully completed for samples from 55 participants. Following quality control, 33 full genomes were analysed from participants with a median age of 40 years and median time on ART of 9 years. HIV-1 subtyping was performed using SNAPPy. RESULTS Most participants had mutational profiles reflective of exposure to previous first- and second-line ART regimens comprised NRTIs and NNRTIs. More than half of participants had one or more drug resistance-associated mutations (DRMs) affecting susceptibility to NRTIs (17/33; 52%) and NNRTIs (24/33; 73%). Almost a quarter of participants (8/33; 24.4%) had one or more DRMs affecting tenofovir susceptibility. Only one participant, infected with HIV-1 subtype G, had evidence of DRMs affecting dolutegravir susceptibility-this was characterized by the T66A, G118R, E138K and R263K mutations. CONCLUSIONS This study found a low prevalence of resistance to dolutegravir; the data are therefore supportive of the continual rollout of dolutegravir as the primary first-line regimen for ART-naive participants and the preferred switch to second-line ART across the region. However, population-level, longer-term data collection on dolutegravir outcomes are required to further guide implementation and policy action across the region.
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Affiliation(s)
- Adam Abdullahi
- Department of Medicine, Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Ibrahim Musa Kida
- Department of Infectious Disease and Clinical Immunology, University of Maiduguri, Borno, Nigeria
| | - Umar Abdullahi Maina
- Department of Veterinary Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Maiduguri, Borno, Nigeria
| | | | - James Mshelia
- Department of Infectious Disease and Clinical Immunology, University of Maiduguri, Borno, Nigeria
| | - Haruna Wisso
- Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Abdullahi Adamu
- Department of Veterinary Pharmacology and Toxicology, Faculty of Veterinary Medicine, University of Maiduguri, Borno, Nigeria
| | | | - Martin Edun
- Institute of Human Virology Nigeria, Abuja, Nigeria
| | - Haruna Yusuph
- Department of Infectious Disease and Clinical Immunology, University of Maiduguri, Borno, Nigeria
| | - Sani H Aliyu
- Department of Microbiology, Addenbrooke’s Hospital, Cambridge University Hospitals NHS Foundation Trust, Cambridge, UK
| | - Man Charurat
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, USA
| | | | - Lucie Abeler-Dorner
- Nuffield Department of Medicine, Big Data Institute, University of Oxford, Oxford, UK
| | - Christophe Fraser
- Nuffield Department of Medicine, Big Data Institute, University of Oxford, Oxford, UK
| | - David Bonsall
- Nuffield Department of Medicine, Big Data Institute, University of Oxford, Oxford, UK
| | - Steven A Kemp
- Department of Medicine, Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Nuffield Department of Medicine, Big Data Institute, University of Oxford, Oxford, UK
| | - Ravindra K Gupta
- Department of Medicine, Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Africa Health Research Institute, Durban, South Africa
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Bassi J, Giannini O, Silacci-Fregni C, Pertusini L, Hitz P, Terrot T, Franzosi Y, Muoio F, Saliba C, Meury M, Dellota EA, Dillen JR, Hernandez P, Czudnochowski N, Cameroni E, Beria N, Ventresca M, Badellino A, Lavorato-Hadjeres S, Lecchi E, Bonora T, Mattiolo M, Trinci G, Garzoni D, Bonforte G, Forni-Ogna V, Giunzioni D, Berwert L, Gupta RK, Ferrari P, Ceschi A, Cippà P, Corti D, Lanzavecchia A, Piccoli L. Poor neutralization and rapid decay of antibodies to SARS-CoV-2 variants in vaccinated dialysis patients. PLoS One 2022; 17:e0263328. [PMID: 35143540 PMCID: PMC8830698 DOI: 10.1371/journal.pone.0263328] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 01/14/2022] [Indexed: 12/11/2022] Open
Abstract
Patients on dialysis are at risk of severe course of SARS-CoV-2 infection. Understanding the neutralizing activity and coverage of SARS-CoV-2 variants of vaccine-elicited antibodies is required to guide prophylactic and therapeutic COVID-19 interventions in this frail population. By analyzing plasma samples from 130 hemodialysis and 13 peritoneal dialysis patients after two doses of BNT162b2 or mRNA-1273 vaccines, we found that 35% of the patients had low-level or undetectable IgG antibodies to SARS-CoV-2 Spike (S). Neutralizing antibodies against the vaccine-matched SARS-CoV-2 and Delta variant were low or undetectable in 49% and 77% of patients, respectively, and were further reduced against other emerging variants. The fraction of non-responding patients was higher in SARS-CoV-2-naïve hemodialysis patients immunized with BNT162b2 (66%) than those immunized with mRNA-1273 (23%). The reduced neutralizing activity correlated with low antibody avidity. Patients followed up to 7 months after vaccination showed a rapid decay of the antibody response with an average 21- and 10-fold reduction of neutralizing antibodies to vaccine-matched SARS-CoV-2 and Delta variant, which increased the fraction of non-responders to 84% and 90%, respectively. These data indicate that dialysis patients should be prioritized for additional vaccination boosts. Nevertheless, their antibody response to SARS-CoV-2 must be continuously monitored to adopt the best prophylactic and therapeutic strategy.
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Affiliation(s)
- Jessica Bassi
- Humabs BioMed SA, A Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Olivier Giannini
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Department of Medicine, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | | | - Laura Pertusini
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Paolo Hitz
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
| | - Tatiana Terrot
- Clinical Trial Unit, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Yves Franzosi
- Clinical Trial Unit, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Francesco Muoio
- Humabs BioMed SA, A Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Christian Saliba
- Humabs BioMed SA, A Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Marcel Meury
- Vir Biotechnology, San Francisco, California, United States of America
| | | | - Josh R. Dillen
- Vir Biotechnology, San Francisco, California, United States of America
| | - Patrick Hernandez
- Vir Biotechnology, San Francisco, California, United States of America
| | | | - Elisabetta Cameroni
- Humabs BioMed SA, A Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Nicola Beria
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | | | - Alberto Badellino
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | | | - Elisabetta Lecchi
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Tecla Bonora
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Matteo Mattiolo
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Guido Trinci
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Daniela Garzoni
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Giuseppe Bonforte
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | | | - Davide Giunzioni
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Lorenzo Berwert
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Ravindra K. Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Paolo Ferrari
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Clinical School, University of New South Wales, Sydney, Australia
| | - Alessandro Ceschi
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Clinical Trial Unit, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Division of Clinical Pharmacology and Toxicology, Institute of Pharmacological Science of Southern Switzerland, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Zurich, Switzerland
| | - Pietro Cippà
- Department of Medicine, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Davide Corti
- Humabs BioMed SA, A Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Luca Piccoli
- Humabs BioMed SA, A Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
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Bassi J, Giannini O, Silacci-Fregni C, Pertusini L, Hitz P, Terrot T, Franzosi Y, Muoio F, Saliba C, Meury M, Dellota EA, Dillen JR, Hernandez P, Czudnochowski N, Cameroni E, Beria N, Ventresca M, Badellino A, Lavorato-Hadjeres S, Lecchi E, Bonora T, Mattiolo M, Trinci G, Garzoni D, Bonforte G, Forni-Ogna V, Giunzioni D, Berwert L, Gupta RK, Ferrari P, Ceschi A, Cippà P, Corti D, Lanzavecchia A, Piccoli L. Poor neutralization and rapid decay of antibodies to SARS-CoV-2 variants in vaccinated dialysis patients. PLoS One 2022. [PMID: 35143540 DOI: 10.1101/2021.10.05.21264054v2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2023] Open
Abstract
Patients on dialysis are at risk of severe course of SARS-CoV-2 infection. Understanding the neutralizing activity and coverage of SARS-CoV-2 variants of vaccine-elicited antibodies is required to guide prophylactic and therapeutic COVID-19 interventions in this frail population. By analyzing plasma samples from 130 hemodialysis and 13 peritoneal dialysis patients after two doses of BNT162b2 or mRNA-1273 vaccines, we found that 35% of the patients had low-level or undetectable IgG antibodies to SARS-CoV-2 Spike (S). Neutralizing antibodies against the vaccine-matched SARS-CoV-2 and Delta variant were low or undetectable in 49% and 77% of patients, respectively, and were further reduced against other emerging variants. The fraction of non-responding patients was higher in SARS-CoV-2-naïve hemodialysis patients immunized with BNT162b2 (66%) than those immunized with mRNA-1273 (23%). The reduced neutralizing activity correlated with low antibody avidity. Patients followed up to 7 months after vaccination showed a rapid decay of the antibody response with an average 21- and 10-fold reduction of neutralizing antibodies to vaccine-matched SARS-CoV-2 and Delta variant, which increased the fraction of non-responders to 84% and 90%, respectively. These data indicate that dialysis patients should be prioritized for additional vaccination boosts. Nevertheless, their antibody response to SARS-CoV-2 must be continuously monitored to adopt the best prophylactic and therapeutic strategy.
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Affiliation(s)
- Jessica Bassi
- Humabs BioMed SA, A Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Olivier Giannini
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Department of Medicine, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | | | - Laura Pertusini
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Paolo Hitz
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
| | - Tatiana Terrot
- Clinical Trial Unit, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Yves Franzosi
- Clinical Trial Unit, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Francesco Muoio
- Humabs BioMed SA, A Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Christian Saliba
- Humabs BioMed SA, A Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Marcel Meury
- Vir Biotechnology, San Francisco, California, United States of America
| | | | - Josh R Dillen
- Vir Biotechnology, San Francisco, California, United States of America
| | - Patrick Hernandez
- Vir Biotechnology, San Francisco, California, United States of America
| | | | - Elisabetta Cameroni
- Humabs BioMed SA, A Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Nicola Beria
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | | | - Alberto Badellino
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | | | - Elisabetta Lecchi
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Tecla Bonora
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Matteo Mattiolo
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Guido Trinci
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Daniela Garzoni
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Giuseppe Bonforte
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | | | - Davide Giunzioni
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Lorenzo Berwert
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, United Kingdom
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Paolo Ferrari
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Clinical School, University of New South Wales, Sydney, Australia
| | - Alessandro Ceschi
- Faculty of Biomedical Sciences, Università della Svizzera italiana, Lugano, Switzerland
- Clinical Trial Unit, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Division of Clinical Pharmacology and Toxicology, Institute of Pharmacological Science of Southern Switzerland, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, Zurich, Switzerland
| | - Pietro Cippà
- Department of Medicine, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
- Division of Nephrology, Ente Ospedaliero Cantonale, Lugano, Switzerland
- Faculty of Medicine, University of Zurich, Zurich, Switzerland
| | - Davide Corti
- Humabs BioMed SA, A Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Luca Piccoli
- Humabs BioMed SA, A Subsidiary of Vir Biotechnology, Bellinzona, Switzerland
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Umair M, Khan MS, Ahmed F, Baothman F, Alqahtani F, Alian M, Ahmad J. Detection of COVID-19 Using Transfer Learning and Grad-CAM Visualization on Indigenously Collected X-ray Dataset. SENSORS 2021; 21:s21175813. [PMID: 34502702 PMCID: PMC8434081 DOI: 10.3390/s21175813] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 08/11/2021] [Accepted: 08/16/2021] [Indexed: 12/13/2022]
Abstract
The COVID-19 outbreak began in December 2019 and has dreadfully affected our lives since then. More than three million lives have been engulfed by this newest member of the corona virus family. With the emergence of continuously mutating variants of this virus, it is still indispensable to successfully diagnose the virus at early stages. Although the primary technique for the diagnosis is the PCR test, the non-contact methods utilizing the chest radiographs and CT scans are always preferred. Artificial intelligence, in this regard, plays an essential role in the early and accurate detection of COVID-19 using pulmonary images. In this research, a transfer learning technique with fine tuning was utilized for the detection and classification of COVID-19. Four pre-trained models i.e., VGG16, DenseNet-121, ResNet-50, and MobileNet were used. The aforementioned deep neural networks were trained using the dataset (available on Kaggle) of 7232 (COVID-19 and normal) chest X-ray images. An indigenous dataset of 450 chest X-ray images of Pakistani patients was collected and used for testing and prediction purposes. Various important parameters, e.g., recall, specificity, F1-score, precision, loss graphs, and confusion matrices were calculated to validate the accuracy of the models. The achieved accuracies of VGG16, ResNet-50, DenseNet-121, and MobileNet are 83.27%, 92.48%, 96.49%, and 96.48%, respectively. In order to display feature maps that depict the decomposition process of an input image into various filters, a visualization of the intermediate activations is performed. Finally, the Grad-CAM technique was applied to create class-specific heatmap images in order to highlight the features extracted in the X-ray images. Various optimizers were used for error minimization purposes. DenseNet-121 outperformed the other three models in terms of both accuracy and prediction.
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Affiliation(s)
- Muhammad Umair
- Department of Electrical Engineering, HITEC University, Taxila 47080, Pakistan; (M.U.); (M.A.)
| | - Muhammad Shahbaz Khan
- Department of Electrical Engineering, HITEC University, Taxila 47080, Pakistan; (M.U.); (M.A.)
- Correspondence:
| | - Fawad Ahmed
- Department of Biomedical Engineering, HITEC University, Taxila 47080, Pakistan;
| | - Fatmah Baothman
- Faculty of Computing and Information Technology, King Abdul Aziz University, Jeddah 21431, Saudi Arabia;
| | - Fehaid Alqahtani
- Department of Computer Science, King Fahad Naval Academy, Al Jubail 35512, Saudi Arabia;
| | - Muhammad Alian
- Department of Electrical Engineering, HITEC University, Taxila 47080, Pakistan; (M.U.); (M.A.)
| | - Jawad Ahmad
- School of Computing, Edinburgh Napier University, Edinburgh EH10 5DT, UK;
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8
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Xie YN, Zhu FX, Zhong YT, Chen YT, Gao Q, Lai XL, Liu JJ, Huang DD, Zhang YN, Chen X. Distribution characteristics of drug resistance mutations of HIV CRF01_AE, CRF07_BC and CRF08_BC from patients under ART in Ganzhou, China. J Antimicrob Chemother 2021; 76:2975-2982. [PMID: 34402512 DOI: 10.1093/jac/dkab296] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 07/20/2021] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Drug resistance mutation (DRM)-associated virological failure has become a critical issue for ART and the elimination of HIV. OBJECTIVES To investigate the distribution characteristics of DRMs of HIV CRF01_AE, CRF07_BC and CRF08_BC, the predominant subtypes in China. METHODS Patients receiving ART up to 31 August 2020 in Ganzhou in China were recruited. Full-length sequences of the HIV pol gene were amplified from patients with virological failure. DRMs and antiretroviral susceptibility were explored using the Stanford University HIV Drug Resistance Database HIVdb Program. RESULTS Overall, 279 of 2204 patients under ART were found to have virological failure. Nine HIV subtypes were identified among 211 sequences that were amplified successfully and CRF08_BC (37.0%), CRF01_AE (26.1%) and CRF07_BC (25.6%) were the most prevalent, with mutation frequencies of 44.9% (35/78), 52.7% (29/55) and 35.2% (19/54), respectively. The most common DRMs of these three subtypes were K103N and M184V, while the mutation frequencies of M41L, D67N, K70R, K101E, V106M, Y181C, K219E, H221Y and N348I were obviously different among subtypes. The resistance levels and frequencies for antiretroviral drugs for these three subtypes were similar and resistances to nevirapine, efavirenz, lamivudine and emtricitabine were the most frequently observed. Compared with CRF01_AE and CRF07_BC, CRF08_BC had higher proportions of DRMs for NRTIs and lower frequencies of resistance to NRTIs and NNRTIs. CONCLUSIONS The distribution characteristics of DRMs of HIV CRF01_AE, CRF07_BC and CRF08_BC were inconsistent and should be considered when selecting antiretroviral strategies, developing new drugs and controlling HIV strains containing DRMs.
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Affiliation(s)
- Ying-Na Xie
- Department of Pathogenic Biology, School of Basic Medical Sciences, Gannan Medical University, Ganzhou, China
| | - Feng-Xiu Zhu
- Department of Laboratory, Ganzhou Centre for Disease Control and Prevention, Ganzhou, China
| | - You-Tian Zhong
- Department of Pathogenic Biology, School of Basic Medical Sciences, Gannan Medical University, Ganzhou, China
| | - Ya-Ting Chen
- Department of Pathogenic Biology, School of Basic Medical Sciences, Gannan Medical University, Ganzhou, China
| | - Qian Gao
- Department of Laboratory, Ganzhou Centre for Disease Control and Prevention, Ganzhou, China
| | - Xiao-Ling Lai
- Department of Laboratory, Ganzhou Centre for Disease Control and Prevention, Ganzhou, China
| | - Jun-Jie Liu
- Department of Laboratory, Ganzhou Centre for Disease Control and Prevention, Ganzhou, China
| | - Dan-Dan Huang
- Department of Pathogenic Biology, School of Basic Medical Sciences, Gannan Medical University, Ganzhou, China
| | - Yu-Ning Zhang
- Department of Pathogenic Biology, School of Basic Medical Sciences, Gannan Medical University, Ganzhou, China
| | - Xin Chen
- Department of Pathogenic Biology, School of Basic Medical Sciences, Gannan Medical University, Ganzhou, China
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9
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McCallum M, Bassi J, De Marco A, Chen A, Walls AC, Di Iulio J, Tortorici MA, Navarro MJ, Silacci-Fregni C, Saliba C, Sprouse KR, Agostini M, Pinto D, Culap K, Bianchi S, Jaconi S, Cameroni E, Bowen JE, Tilles SW, Pizzuto MS, Guastalla SB, Bona G, Pellanda AF, Garzoni C, Van Voorhis WC, Rosen LE, Snell G, Telenti A, Virgin HW, Piccoli L, Corti D, Veesler D. SARS-CoV-2 immune evasion by the B.1.427/B.1.429 variant of concern. Science 2021; 373:648-654. [PMID: 34210893 PMCID: PMC9835956 DOI: 10.1126/science.abi7994] [Citation(s) in RCA: 296] [Impact Index Per Article: 98.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 06/25/2021] [Indexed: 01/16/2023]
Abstract
A novel variant of concern (VOC) named CAL.20C (B.1.427/B.1.429), which was originally detected in California, carries spike glycoprotein mutations S13I in the signal peptide, W152C in the N-terminal domain (NTD), and L452R in the receptor-binding domain (RBD). Plasma from individuals vaccinated with a Wuhan-1 isolate-based messenger RNA vaccine or from convalescent individuals exhibited neutralizing titers that were reduced 2- to 3.5-fold against the B.1.427/B.1.429 variant relative to wild-type pseudoviruses. The L452R mutation reduced neutralizing activity in 14 of 34 RBD-specific monoclonal antibodies (mAbs). The S13I and W152C mutations resulted in total loss of neutralization for 10 of 10 NTD-specific mAbs because the NTD antigenic supersite was remodeled by a shift of the signal peptide cleavage site and the formation of a new disulfide bond, as revealed by mass spectrometry and structural studies.
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MESH Headings
- 2019-nCoV Vaccine mRNA-1273
- Amino Acid Substitution
- Antibodies, Monoclonal/immunology
- Antibodies, Neutralizing/blood
- Antibodies, Neutralizing/immunology
- Antibodies, Viral/blood
- Antibodies, Viral/immunology
- Antigens, Viral/immunology
- BNT162 Vaccine
- COVID-19/immunology
- COVID-19/virology
- COVID-19 Vaccines/immunology
- Cryoelectron Microscopy
- Humans
- Immune Evasion
- Models, Molecular
- Mutation
- Neutralization Tests
- Protein Conformation
- Protein Domains
- Protein Interaction Domains and Motifs
- Protein Subunits/chemistry
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- SARS-CoV-2/pathogenicity
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
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Affiliation(s)
- Matthew McCallum
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Jessica Bassi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Alex Chen
- Vir Biotechnology, San Francisco, CA 94158, USA
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | | | - Mary-Jane Navarro
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Christian Saliba
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Kaitlin R Sprouse
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | | | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Siro Bianchi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Stefano Jaconi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - John E Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Sasha W Tilles
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | | | - Giovanni Bona
- Clinical Research Unit, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | | | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | - Wesley C Van Voorhis
- Center for Emerging and Re-emerging Infectious Diseases, Division of Allergy and Infectious Diseases, Department of Medicine, University of Washington School of Medicine, Seattle, WA 98195, USA
| | | | | | | | | | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland.
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland.
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA.
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10
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Menéndez-Arias L, Martín-Alonso S, Frutos-Beltrán E. An Update on Antiretroviral Therapy. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1322:31-61. [PMID: 34258736 DOI: 10.1007/978-981-16-0267-2_2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Human immunodeficiency virus (HIV) infection and acquired immune deficiency syndrome (AIDS) still claim many lives across the world. However, research efforts during the last 40 years have led to the approval of over 30 antiretroviral drugs and the introduction of combination therapies that have turned HIV infection into a chronic but manageable disease. In this chapter, we provide an update on current available drugs and treatments, as well as future prospects towards reducing pill burden and developing long-acting drugs and novel antiretroviral therapies. In addition, we summarize efforts to cure HIV, including pharmaceutical strategies focused on the elimination of the virus.
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Affiliation(s)
- Luis Menéndez-Arias
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, Spain.
| | - Samara Martín-Alonso
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, Spain
| | - Estrella Frutos-Beltrán
- Centro de Biología Molecular "Severo Ochoa", Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid, Madrid, Spain
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11
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Delaugerre C, Nere ML, Eymard-Duvernay S, Armero A, Ciaffi L, Koulla-Shiro S, Sawadogo A, Ngom Gueye NF, Ndour CT, Mpoudi Ngolle M, Amara A, Chaix ML, Reynes J. Deep sequencing analysis of M184V/I mutation at the switch and at the time of virological failure of boosted protease inhibitor plus lamivudine or boosted protease inhibitor maintenance strategy (substudy of the ANRS-MOBIDIP trial). J Antimicrob Chemother 2021; 76:1286-1293. [PMID: 33624081 DOI: 10.1093/jac/dkab002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2020] [Accepted: 12/23/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The ANRS12286/MOBIDIP trial showed that boosted protease inhibitor (bPI) plus lamivudine dual therapy was superior to bPI monotherapy as maintenance treatment in subjects with a history of M184V mutation. OBJECTIVES We aimed to deep analyse the detection of M184V/I variants at time of switch and at the time of virological failure (VF). METHODS Ultra-deep sequencing (UDS) was performed on proviral HIV-DNA at inclusion among 265 patients enrolled in the ANRS 12026/MOBIDIP trial, and on plasma from 31 patients experiencing VF. The proportion of M184V/I variants was described and the association between the M184V/I mutation at 1% of threshold and VF was explored with logistic regression models. RESULTS M184V and I mutations were detected in HIV-DNA for 173/252 (69%) and 31/252 (12%) of participants, respectively. Longer duration of first-line treatment, higher plasma viral load at first-line treatment failure and higher baseline HIV-DNA load were associated with the archived M184V. M184I mutation was always associated with a STOP codon, suggesting defective virus. The 48 week estimated probability of remaining free from VF was comparable with or without the M184V/I mutation for dual therapy. At failure, M184V and major PI mutations were detected in 1/17 and 5/15 patients in the bPI arm and in 2/2 and 0/3 in the bPI+lamivudine arm, respectively. CONCLUSIONS Using UDS evidenced that archiving of M184V in HIV-DNA is heterogeneous despite past historical M184V in 96% of cases. The antiviral efficacy of lamivudine-based dual therapy regimens is mainly due to the residual lamivudine activity.
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Affiliation(s)
- Constance Delaugerre
- Department of Virology, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris, Paris, France.,INSERM U944, University of Paris, Paris, France
| | - Marie-Laure Nere
- Department of Virology, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Sabrina Eymard-Duvernay
- TransVIHMI, Institut de Recherche pour le Développement (IRD) - INSERM U1175 University of Montpellier, Montpellier, France
| | - Alix Armero
- Department of Virology, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris, Paris, France
| | - Laura Ciaffi
- TransVIHMI, Institut de Recherche pour le Développement (IRD) - INSERM U1175 University of Montpellier, Montpellier, France
| | - Sinata Koulla-Shiro
- Department of Infectious Diseases, Central Hospital Yaoundé, Yaoundé, Cameroon
| | - Adrien Sawadogo
- Day Care Center, University Hospital Souro Sanou, Bobo Dioulasso, Burkina Faso
| | | | | | | | - Ali Amara
- INSERM U944, University of Paris, Paris, France
| | - Marie-Laure Chaix
- Department of Virology, Hôpital Saint Louis, Assistance Publique-Hôpitaux de Paris, Paris, France.,INSERM U944, University of Paris, Paris, France
| | - Jacques Reynes
- TransVIHMI, Institut de Recherche pour le Développement (IRD) - INSERM U1175 University of Montpellier, Montpellier, France.,Department of Infectious Diseases, Montpellier University Hospital, Montpellier, France
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12
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Collier DA, De Marco A, Ferreira IATM, Meng B, Datir RP, Walls AC, Kemp SA, Bassi J, Pinto D, Silacci-Fregni C, Bianchi S, Tortorici MA, Bowen J, Culap K, Jaconi S, Cameroni E, Snell G, Pizzuto MS, Pellanda AF, Garzoni C, Riva A, Elmer A, Kingston N, Graves B, McCoy LE, Smith KGC, Bradley JR, Temperton N, Ceron-Gutierrez L, Barcenas-Morales G, Harvey W, Virgin HW, Lanzavecchia A, Piccoli L, Doffinger R, Wills M, Veesler D, Corti D, Gupta RK. Sensitivity of SARS-CoV-2 B.1.1.7 to mRNA vaccine-elicited antibodies. Nature 2021; 593:136-141. [PMID: 33706364 DOI: 10.1038/s41586-021-03412-7] [Citation(s) in RCA: 498] [Impact Index Per Article: 166.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 03/01/2021] [Indexed: 02/02/2023]
Abstract
Transmission of SARS-CoV-2 is uncontrolled in many parts of the world; control is compounded in some areas by the higher transmission potential of the B.1.1.7 variant1, which has now been reported in 94 countries. It is unclear whether the response of the virus to vaccines against SARS-CoV-2 on the basis of the prototypic strain will be affected by the mutations found in B.1.1.7. Here we assess the immune responses of individuals after vaccination with the mRNA-based vaccine BNT162b22. We measured neutralizing antibody responses after the first and second immunizations using pseudoviruses that expressed the wild-type spike protein or a mutated spike protein that contained the eight amino acid changes found in the B.1.1.7 variant. The sera from individuals who received the vaccine exhibited a broad range of neutralizing titres against the wild-type pseudoviruses that were modestly reduced against the B.1.1.7 variant. This reduction was also evident in sera from some patients who had recovered from COVID-19. Decreased neutralization of the B.1.1.7 variant was also observed for monoclonal antibodies that target the N-terminal domain (9 out of 10) and the receptor-binding motif (5 out of 31), but not for monoclonal antibodies that recognize the receptor-binding domain that bind outside the receptor-binding motif. Introduction of the mutation that encodes the E484K substitution in the B.1.1.7 background to reflect a newly emerged variant of concern (VOC 202102/02) led to a more-substantial loss of neutralizing activity by vaccine-elicited antibodies and monoclonal antibodies (19 out of 31) compared with the loss of neutralizing activity conferred by the mutations in B.1.1.7 alone. The emergence of the E484K substitution in a B.1.1.7 background represents a threat to the efficacy of the BNT162b2 vaccine.
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MESH Headings
- Aged
- Aged, 80 and over
- Angiotensin-Converting Enzyme 2/metabolism
- Antibodies, Monoclonal/immunology
- Antibodies, Monoclonal/isolation & purification
- Antibodies, Neutralizing/immunology
- Antibodies, Neutralizing/isolation & purification
- Antibodies, Viral/immunology
- Antibodies, Viral/isolation & purification
- COVID-19/immunology
- COVID-19/metabolism
- COVID-19/therapy
- COVID-19/virology
- COVID-19 Vaccines/immunology
- Female
- HEK293 Cells
- Humans
- Immune Evasion/genetics
- Immune Evasion/immunology
- Immunization, Passive
- Male
- Middle Aged
- Models, Molecular
- Mutation
- Neutralization Tests
- SARS-CoV-2/genetics
- SARS-CoV-2/immunology
- Spike Glycoprotein, Coronavirus/chemistry
- Spike Glycoprotein, Coronavirus/genetics
- Spike Glycoprotein, Coronavirus/immunology
- Spike Glycoprotein, Coronavirus/metabolism
- Vaccines, Synthetic/administration & dosage
- Vaccines, Synthetic/immunology
- COVID-19 Serotherapy
- mRNA Vaccines
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Affiliation(s)
- Dami A Collier
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Isabella A T M Ferreira
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Bo Meng
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Rawlings P Datir
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Steven A Kemp
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Jessica Bassi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Siro Bianchi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - John Bowen
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Stefano Jaconi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Matteo S Pizzuto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | | | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, Lugano, Switzerland
| | - Agostino Riva
- Division of Infectious Diseases, Luigi Sacco Hospital, University of Milan, Milan, Italy
| | - Anne Elmer
- NIHR Cambridge Clinical Research Facility, Cambridge, UK
| | | | | | - Laura E McCoy
- Division of Infection and Immunity, University College London, London, UK
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - John R Bradley
- Department of Medicine, University of Cambridge, Cambridge, UK
- NIHR Bioresource, Cambridge, UK
| | | | | | - Gabriela Barcenas-Morales
- Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK
- Laboratorio de Inmunologia, UNAM, Cuautitlán, Mexico
| | - William Harvey
- Institute of Biodiversity, University of Glasgow, Glasgow, UK
| | | | | | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland
| | - Rainer Doffinger
- Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Mark Wills
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, Bellinzona, Switzerland.
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease, Cambridge, UK.
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Department of Haematology, University of Cambridge, Cambridge, UK.
- University of KwaZulu Natal, Durban, South Africa.
- Africa Health Research Institute, Durban, South Africa.
- Department of Infectious Diseases, Cambridge University Hospitals NHS Trust, Cambridge, UK.
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13
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Kemp SA, Collier DA, Datir RP, Ferreira IATM, Gayed S, Jahun A, Hosmillo M, Rees-Spear C, Mlcochova P, Lumb IU, Roberts DJ, Chandra A, Temperton N, Sharrocks K, Blane E, Modis Y, Leigh KE, Briggs JAG, van Gils MJ, Smith KGC, Bradley JR, Smith C, Doffinger R, Ceron-Gutierrez L, Barcenas-Morales G, Pollock DD, Goldstein RA, Smielewska A, Skittrall JP, Gouliouris T, Goodfellow IG, Gkrania-Klotsas E, Illingworth CJR, McCoy LE, Gupta RK. SARS-CoV-2 evolution during treatment of chronic infection. Nature 2021. [PMID: 33545711 DOI: 10.1038/s41586-021-03291-y.33545711] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/15/2023]
Abstract
The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for virus infection through the engagement of the human ACE2 protein1 and is a major antibody target. Here we show that chronic infection with SARS-CoV-2 leads to viral evolution and reduced sensitivity to neutralizing antibodies in an immunosuppressed individual treated with convalescent plasma, by generating whole-genome ultra-deep sequences for 23 time points that span 101 days and using in vitro techniques to characterize the mutations revealed by sequencing. There was little change in the overall structure of the viral population after two courses of remdesivir during the first 57 days. However, after convalescent plasma therapy, we observed large, dynamic shifts in the viral population, with the emergence of a dominant viral strain that contained a substitution (D796H) in the S2 subunit and a deletion (ΔH69/ΔV70) in the S1 N-terminal domain of the spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype were reduced in frequency, before returning during a final, unsuccessful course of convalescent plasma treatment. In vitro, the spike double mutant bearing both ΔH69/ΔV70 and D796H conferred modestly decreased sensitivity to convalescent plasma, while maintaining infectivity levels that were similar to the wild-type virus.The spike substitution mutant D796H appeared to be the main contributor to the decreased susceptibility to neutralizing antibodies, but this mutation resulted in an infectivity defect. The spike deletion mutant ΔH69/ΔV70 had a twofold higher level of infectivity than wild-type SARS-CoV-2, possibly compensating for the reduced infectivity of the D796H mutation. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy, which is associated with the emergence of viral variants that show evidence of reduced susceptibility to neutralizing antibodies in immunosuppressed individuals.
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Affiliation(s)
- Steven A Kemp
- Division of Infection and Immunity, University College London, London, UK
| | - Dami A Collier
- Division of Infection and Immunity, University College London, London, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Rawlings P Datir
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Isabella A T M Ferreira
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Salma Gayed
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Aminu Jahun
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Myra Hosmillo
- Department of Pathology, University of Cambridge, Cambridge, UK
| | - Chloe Rees-Spear
- Division of Infection and Immunity, University College London, London, UK
| | - Petra Mlcochova
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Ines Ushiro Lumb
- NHS Blood and Transplant, Oxford and BRC Haematology Theme, University of Oxford, Oxford, UK
| | - David J Roberts
- NHS Blood and Transplant, Oxford and BRC Haematology Theme, University of Oxford, Oxford, UK
| | - Anita Chandra
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, Canterbury, UK
| | - Katherine Sharrocks
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Elizabeth Blane
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Yorgo Modis
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Kendra E Leigh
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - John A G Briggs
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Marit J van Gils
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam, The Netherlands
| | - Kenneth G C Smith
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - John R Bradley
- Department of Medicine, University of Cambridge, Cambridge, UK
- NIHR Cambridge Bioresource, Cambridge, UK
| | - Chris Smith
- Department of Virology, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Rainer Doffinger
- Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK
| | | | - Gabriela Barcenas-Morales
- Department of Clinical Biochemistry and Immunology, Addenbrooke's Hospital, Cambridge, UK
- FES-Cuautitlán, UNAM, Cuautitlán Izcalli, Mexico
| | - David D Pollock
- Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, CO, USA
| | | | - Anna Smielewska
- Department of Pathology, University of Cambridge, Cambridge, UK
- Department of Virology, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Jordan P Skittrall
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
- Clinical Microbiology and Public Health Laboratory, Addenbrooke's Hospital, Cambridge, UK
| | - Theodore Gouliouris
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | | | | | - Christopher J R Illingworth
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, Cambridge, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Laura E McCoy
- Division of Infection and Immunity, University College London, London, UK
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK.
- Department of Medicine, University of Cambridge, Cambridge, UK.
- Africa Health Research Institute, Durban, South Africa.
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14
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Kemp SA, Collier DA, Datir RP, Ferreira IATM, Gayed S, Jahun A, Hosmillo M, Rees-Spear C, Mlcochova P, Lumb IU, Roberts DJ, Chandra A, Temperton N, Sharrocks K, Blane E, Modis Y, Leigh K, Briggs J, van Gils M, Smith KGC, Bradley JR, Smith C, Doffinger R, Ceron-Gutierrez L, Barcenas-Morales G, Pollock DD, Goldstein RA, Smielewska A, Skittrall JP, Gouliouris T, Goodfellow IG, Gkrania-Klotsas E, Illingworth CJR, McCoy LE, Gupta RK. SARS-CoV-2 evolution during treatment of chronic infection. Nature 2021; 592:277-282. [PMID: 33545711 PMCID: PMC7610568 DOI: 10.1038/s41586-021-03291-y] [Citation(s) in RCA: 630] [Impact Index Per Article: 210.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 01/26/2021] [Indexed: 02/02/2023]
Abstract
The spike protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is critical for virus infection through the engagement of the human ACE2 protein1 and is a major antibody target. Here we show that chronic infection with SARS-CoV-2 leads to viral evolution and reduced sensitivity to neutralizing antibodies in an immunosuppressed individual treated with convalescent plasma, by generating whole-genome ultra-deep sequences for 23 time points that span 101 days and using in vitro techniques to characterize the mutations revealed by sequencing. There was little change in the overall structure of the viral population after two courses of remdesivir during the first 57 days. However, after convalescent plasma therapy, we observed large, dynamic shifts in the viral population, with the emergence of a dominant viral strain that contained a substitution (D796H) in the S2 subunit and a deletion (ΔH69/ΔV70) in the S1 N-terminal domain of the spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype were reduced in frequency, before returning during a final, unsuccessful course of convalescent plasma treatment. In vitro, the spike double mutant bearing both ΔH69/ΔV70 and D796H conferred modestly decreased sensitivity to convalescent plasma, while maintaining infectivity levels that were similar to the wild-type virus.The spike substitution mutant D796H appeared to be the main contributor to the decreased susceptibility to neutralizing antibodies, but this mutation resulted in an infectivity defect. The spike deletion mutant ΔH69/ΔV70 had a twofold higher level of infectivity than wild-type SARS-CoV-2, possibly compensating for the reduced infectivity of the D796H mutation. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy, which is associated with the emergence of viral variants that show evidence of reduced susceptibility to neutralizing antibodies in immunosuppressed individuals.
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Affiliation(s)
- Steven A Kemp
- Division of Infection and Immunity, University College London, London, UK
| | - Dami A Collier
- Division of Infection and Immunity, University College London, London, UK, Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Rawlings P Datir
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Isabella ATM Ferreira
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Salma Gayed
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Aminu Jahun
- Department of Pathology, University of Cambridge, Cambridge
| | - Myra Hosmillo
- Department of Pathology, University of Cambridge, Cambridge
| | - Chloe Rees-Spear
- Division of Infection and Immunity, University College London, London, UK
| | - Petra Mlcochova
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Ines Ushiro Lumb
- NHS Blood and Transplant, Oxford and BRC Haematology Theme, University of Oxford, UK
| | - David J Roberts
- NHS Blood and Transplant, Oxford and BRC Haematology Theme, University of Oxford, UK
| | - Anita Chandra
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK,Department of Medicine, University of Cambridge, Cambridge, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, UK
| | - The CITIID-NIHR BioResource COVID-19 Collaboration BakerStephen23Principal InvestigatorsDouganGordon23Principal InvestigatorsHessChristoph232627Principal InvestigatorsKingstonNathalie2012Principal InvestigatorsLehnerPaul J.23Principal InvestigatorsLyonsPaul A.23Principal InvestigatorsMathesonNicholas J.23Principal InvestigatorsOwehandWillem H.20Principal InvestigatorsSaundersCaroline19Principal InvestigatorsSummersCharlotte3242528Principal InvestigatorsThaventhiranJames E.D.2322Principal InvestigatorsToshnerMark32425Principal InvestigatorsWeekesMichael P.2Principal InvestigatorsBuckeAshlea19CRF and Volunteer Research NursesCalderJo19CRF and Volunteer Research NursesCannaLaura19CRF and Volunteer Research NursesDomingoJason19CRF and Volunteer Research NursesElmerAnne19CRF and Volunteer Research NursesFullerStewart19CRF and Volunteer Research NursesHarrisJulie41CRF and Volunteer Research NursesHewittSarah19CRF and Volunteer Research NursesKennetJane19CRF and Volunteer Research NursesJoseSherly19CRF and Volunteer Research NursesKourampaJenny19CRF and Volunteer Research NursesMeadowsAnne19CRF and Volunteer Research NursesO’BrienCriona41CRF and Volunteer Research NursesPriceJane19CRF and Volunteer Research NursesPublicoCherry19CRF and Volunteer Research NursesRastallRebecca19CRF and Volunteer Research NursesRibeiroCarla19CRF and Volunteer Research NursesRowlandsJane19CRF and Volunteer Research NursesRuffoloValentina19CRF and Volunteer Research NursesTordesillasHugo19CRF and Volunteer Research NursesBullmanBen2Sample LogisticsDunmoreBenjamin J3Sample LogisticsFawkeStuart30Sample LogisticsGräfStefan31220Sample LogisticsHodgsonJosh3Sample LogisticsHuangChristopher3Sample LogisticsHunterKelvin23Sample LogisticsJonesEmma29Sample LogisticsLegchenkoEkaterina3Sample LogisticsMataraCecilia3Sample LogisticsMartinJennifer3Sample LogisticsMesciaFederica23Sample LogisticsO’DonnellCiara3Sample LogisticsPointonLinda3Sample LogisticsPondNicole23Sample LogisticsShihJoy3Sample LogisticsSutcliffeRachel3Sample LogisticsTillyTobias3Sample LogisticsTreacyCarmen3Sample LogisticsTongZhen3Sample LogisticsWoodJennifer3Sample LogisticsWylotMarta36Sample LogisticsBergamaschiLaura23Sample Processing and Data AcquisitionBetancourtAriana23Sample Processing and Data AcquisitionBowerGeorgie23Sample Processing and Data AcquisitionCossettiChiara23Sample Processing and Data AcquisitionDe SaAloka3Sample Processing and Data AcquisitionEppingMadeline23Sample Processing and Data AcquisitionFawkeStuart32Sample Processing and Data AcquisitionGleadallNick20Sample Processing and Data AcquisitionGrenfellRichard31Sample Processing and Data AcquisitionHinchAndrew23Sample Processing and Data AcquisitionHuhnOisin32Sample Processing and Data AcquisitionJacksonSarah3Sample Processing and Data AcquisitionJarvisIsobel3Sample Processing and Data AcquisitionLewisDaniel3Sample Processing and Data AcquisitionMarsdenJoe3Sample Processing and Data AcquisitionNiceFrancesca39Sample Processing and Data AcquisitionOkechaGeorgina3Sample Processing and Data AcquisitionOmarjeeOmmar3Sample Processing and Data AcquisitionPereraMarianne3Sample Processing and Data AcquisitionRichozNathan3Sample Processing and Data AcquisitionRomashovaVeronika23Sample Processing and Data AcquisitionYarkoniNatalia Savinykh3Sample Processing and Data AcquisitionSharmaRahul3Sample Processing and Data AcquisitionStefanucciLuca20Sample Processing and Data AcquisitionStephensJonathan20Sample Processing and Data AcquisitionStrezleckiMateusz31Sample Processing and Data AcquisitionTurnerLori23Sample Processing and Data AcquisitionDe BieEckart M.D.D.3Clinical Data CollectionBunclarkKatherine3Clinical Data CollectionJosipovicMasa40Clinical Data CollectionMackayMichael3Clinical Data CollectionMesciaFederica23Clinical Data CollectionMichaelAlice25Clinical Data CollectionRossiSabrina35Clinical Data CollectionSelvanMayurun3Clinical Data CollectionSpencerSarah15Clinical Data CollectionYongCissy35Clinical Data CollectionAnsaripourAli25Royal Papworth Hospital ICUMichaelAlice25Royal Papworth Hospital ICUMwauraLucy25Royal Papworth Hospital ICUPattersonCaroline25Royal Papworth Hospital ICUPolwarthGary25Royal Papworth Hospital ICUPolgarovaPetra28Addenbrooke’s Hospital ICUdi StefanoGiovanni28Addenbrooke’s Hospital ICUFaheyCodie34Cambridge and Peterborough Foundation TrustMichelRachel34Cambridge and Peterborough Foundation TrustBongSze-How21ANPC and Centre for Molecular Medicine and Innovative TherapeuticsCoudertJerome D.33ANPC and Centre for Molecular Medicine and Innovative TherapeuticsHolmesElaine37ANPC and Centre for Molecular Medicine and Innovative TherapeuticsAllisonJohn2012NIHR BioResourceButcherHelen1238NIHR BioResourceCaputoDaniela1238NIHR BioResourceClapham-RileyDebbie1238NIHR BioResourceDewhurstEleanor1238NIHR BioResourceFurlongAnita1238NIHR BioResourceGravesBarbara1238NIHR BioResourceGrayJennifer1238NIHR BioResourceIversTasmin1238NIHR BioResourceKasanickiMary1228NIHR BioResourceLe GresleyEmma1238NIHR BioResourceLingerRachel1238NIHR BioResourceMeloySarah1238NIHR BioResourceMuldoonFrancesca1238NIHR BioResourceOvingtonNigel1220NIHR BioResourcePapadiaSofia1238NIHR BioResourcePhelanIsabel1238NIHR BioResourceStarkHannah1238NIHR BioResourceStirrupsKathleen E1220NIHR BioResourceTownsendPaul1220NIHR BioResourceWalkerNeil1220NIHR BioResourceWebsterJennifer1238NIHR BioResourceCambridge Clinical Research Centre, NIHR Clinical Research Facility, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UKDepartment of Haematology, University of Cambridge, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UKAustralian National Phenome Centre, Murdoch University, Murdoch, Western Australia WA 6150, AustraliaMRC Toxicology Unit, School of Biological Sciences, University of Cambridge, Cambridge CB2 1QR, UKR&D Department, Hycult Biotech, 5405 PD Uden, The NetherlandsHeart and Lung Research Institute, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UKRoyal Papworth Hospital NHS Foundation Trust, Cambridge Biomedical Campus, Cambridge CB2 0QQ, UKDepartment of Biomedicine, University and University Hospital Basel, 4031Basel, SwitzerlandBotnar Research Centre for Child Health (BRCCH) University Basel & ETH Zurich, 4058 Basel, SwitzerlandAddenbrooke’s Hospital, Cambridge CB2 0QQ, UKDepartment of Veterinary Medicine, Madingley Road, Cambridge, CB3 0ES, UKCambridge Institute for Medical Research, Cambridge Biomedical Campus, Cambridge CB2 0XY, UKCancer Research UK, Cambridge Institute, University of Cambridge CB2 0RE, UKDepartment of Obstetrics & Gynaecology, The Rosie Maternity Hospital, Robinson Way, Cambridge CB2 0SW, UKCentre for Molecular Medicine and Innovative Therapeutics, Health Futures Institute, Murdoch University, Perth, WA, AustraliaCambridge and Peterborough Foundation Trust, Fulbourn Hospital, Fulbourn, Cambridge CB21 5EF, UKDepartment of Surgery, Addenbrooke’s Hospital, Cambridge CB2 0QQ, UKDepartment of Biochemistry, University of Cambridge, Cambridge, CB2 1QW, UKCentre of Computational and Systems Medicine, Health Futures Institute, Murdoch University, Harry Perkins Building, Perth, WA 6150, AustraliaDepartment of Public Health and Primary Care, School of Clinical Medicine, University of Cambridge, Cambridge Biomedical Campus, Cambridge, UKCancer Molecular Diagnostics Laboratory, Department of Oncology, University of Cambridge, Cambridge CB2 0AH, UKMetabolic Research Laboratories, Wellcome Trust-Medical Research Council Institute of Metabolic Science, University of Cambridge, Cambridge CB2 0QQ, UKDepartment of Paediatrics, University of Cambridge, Cambridge Biomedical Campus, Cambridge, CB2 0QQ, UK
| | | | - Katherine Sharrocks
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Elizabeth Blane
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Yorgo Modis
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Kendra Leigh
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - John Briggs
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Marit van Gils
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Kenneth GC Smith
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK,Department of Medicine, University of Cambridge, Cambridge, UK
| | - John R Bradley
- Department of Medicine, University of Cambridge, Cambridge, UK, NIHR Cambridge Clinical Research Facility, Cambridge, UK
| | - Chris Smith
- Department of Virology, Cambridge University NHS Hospitals Foundation Trust
| | - Rainer Doffinger
- Department of Clinical Biochemistry and Immunology, Addenbrookes Hospital
| | | | - Gabriela Barcenas-Morales
- Department of Clinical Biochemistry and Immunology, Addenbrookes Hospital, FES-Cuautitlán, UNAM, Mexico
| | - David D Pollock
- Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | | | - Anna Smielewska
- Department of Pathology, University of Cambridge, Cambridge,Department of Virology, Cambridge University NHS Hospitals Foundation Trust
| | - Jordan P Skittrall
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK,Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK,Clinical Microbiology and Public Health Laboratory, Addenbrookes’ Hospital, Cambridge, UK
| | - Theodore Gouliouris
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | | | | | - Christopher JR Illingworth
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK, MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - Laura E McCoy
- Division of Infection and Immunity, University College London, London, UK
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK,Department of Medicine, University of Cambridge, Cambridge, UK,Africa Health Research Institute, Durban, South Africa
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15
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Abstract
SARS-CoV-2 entry is mediated by the spike (S) glycoprotein which contains the receptor-binding domain (RBD) and the N-terminal domain (NTD) as the two main targets of neutralizing antibodies (Abs). A novel variant of concern (VOC) named CAL.20C (B.1.427/B.1.429) was originally detected in California and is currently spreading throughout the US and 29 additional countries. It is unclear whether antibody responses to SARS-CoV-2 infection or to the prototypic Wuhan-1 isolate-based vaccines will be impacted by the three B.1.427/B.1.429 S mutations: S13I, W152C and L452R. Here, we assessed neutralizing Ab responses following natural infection or mRNA vaccination using pseudoviruses expressing the wildtype or the B.1.427/B.1.429 S protein. Plasma from vaccinated or convalescent individuals exhibited neutralizing titers, which were reduced 3-6 fold against the B.1.427/B.1.429 variant relative to wildtype pseudoviruses. The RBD L452R mutation reduced or abolished neutralizing activity of 14 out of 35 RBD-specific monoclonal antibodies (mAbs), including three clinical-stage mAbs. Furthermore, we observed a complete loss of B.1.427/B.1.429 neutralization for a panel of mAbs targeting the N-terminal domain due to a large structural rearrangement of the NTD antigenic supersite involving an S13I-mediated shift of the signal peptide cleavage site. These data warrant closer monitoring of signal peptide variants and their involvement in immune evasion and show that Abs directed to the NTD impose a selection pressure driving SARS-CoV-2 viral evolution through conventional and unconventional escape mechanisms.
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16
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Collier DA, De Marco A, Ferreira IATM, Meng B, Datir R, Walls AC, Kemp S SA, Bassi J, Pinto D, Fregni CS, Bianchi S, Tortorici MA, Bowen J, Culap K, Jaconi S, Cameroni E, Snell G, Pizzuto MS, Pellanda AF, Garzoni C, Riva A, Elmer A, Kingston N, Graves B, McCoy LE, Smith KG, Bradley JR, Temperton N, Ceron-Gutierrez L L, Barcenas-Morales G, Harvey W, Virgin HW, Lanzavecchia A, Piccoli L, Doffinger R, Wills M, Veesler D, Corti D, Gupta RK. SARS-CoV-2 B.1.1.7 sensitivity to mRNA vaccine-elicited, convalescent and monoclonal antibodies. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.01.19.21249840. [PMID: 33619509 PMCID: PMC7899479 DOI: 10.1101/2021.01.19.21249840] [Citation(s) in RCA: 104] [Impact Index Per Article: 34.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) transmission is uncontrolled in many parts of the world, compounded in some areas by higher transmission potential of the B1.1.7 variant now seen in 50 countries. It is unclear whether responses to SARS-CoV-2 vaccines based on the prototypic strain will be impacted by mutations found in B.1.1.7. Here we assessed immune responses following vaccination with mRNA-based vaccine BNT162b2. We measured neutralising antibody responses following a single immunization using pseudoviruses expressing the wild-type Spike protein or the 8 amino acid mutations found in the B.1.1.7 spike protein. The vaccine sera exhibited a broad range of neutralising titres against the wild-type pseudoviruses that were modestly reduced against B.1.1.7 variant. This reduction was also evident in sera from some convalescent patients. Decreased B.1.1.7 neutralisation was also observed with monoclonal antibodies targeting the N-terminal domain (9 out of 10), the Receptor Binding Motif (RBM) (5 out of 31), but not in neutralising mAbs binding outside the RBM. Introduction of the E484K mutation in a B.1.1.7 background to reflect newly emerging viruses in the UK led to a more substantial loss of neutralising activity by vaccine-elicited antibodies and mAbs (19 out of 31) over that conferred by the B.1.1.7 mutations alone. E484K emergence on a B.1.1.7 background represents a threat to the vaccine BNT162b.
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Affiliation(s)
- Dami A Collier
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Anna De Marco
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Isabella A T M Ferreira
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Bo Meng
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Rawlings Datir
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Alexandra C Walls
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Steven A Kemp S
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Division of Infection and Immunity, University College London, London, UK
| | - Jessica Bassi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Dora Pinto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Siro Bianchi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - John Bowen
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Katja Culap
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Stefano Jaconi
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Elisabetta Cameroni
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Matteo S Pizzuto
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | | | - Christian Garzoni
- Clinic of Internal Medicine and Infectious Diseases, Clinica Luganese Moncucco, 6900 Lugano, Switzerland
| | - Agostino Riva
- Division of Infectious Diseases, Luigi Sacco Hospital, University of Milan, Milan, Italy
| | - Anne Elmer
- NIHR Cambridge Clinical Research Facility, Cambridge, UK
| | | | | | - Laura E McCoy
- Division of Infection and Immunity, University College London, London, UK
| | - Kenneth Gc Smith
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - John R Bradley
- Department of Medicine, University of Cambridge, Cambridge, UK
- NIHR Bioresource, Cambridge, UK
| | | | | | - Gabriela Barcenas-Morales
- Department of Clinical Biochemistry and Immunology, Addenbrookes Hospital, UK
- Laboratorio de Inmunologia, S-Cuautitlán, UNAM, Mexico
| | - William Harvey
- Institute of Biodiversity, University of Glasgow, Glasgow, UK
| | | | - Antonio Lanzavecchia
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Luca Piccoli
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Rainer Doffinger
- Department of Clinical Biochemistry and Immunology, Addenbrookes Hospital, UK
| | - Mark Wills
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - David Veesler
- Department of Biochemistry, University of Washington, Seattle, WA 98195, USA
| | - Davide Corti
- Humabs Biomed SA, a subsidiary of Vir Biotechnology, 6500 Bellinzona, Switzerland
| | - Ravindra K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- University of KwaZulu Natal, Durban, South Africa
- Africa Health Research Institute, Durban, South Africa
- Department of Infectious Diseases, Cambridge University Hospitals NHS Trust, Cambridge UK
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17
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Cilento ME, Kirby KA, Sarafianos SG. Avoiding Drug Resistance in HIV Reverse Transcriptase. Chem Rev 2021; 121:3271-3296. [PMID: 33507067 DOI: 10.1021/acs.chemrev.0c00967] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
HIV reverse transcriptase (RT) is an enzyme that plays a major role in the replication cycle of HIV and has been a key target of anti-HIV drug development efforts. Because of the high genetic diversity of the virus, mutations in RT can impart resistance to various RT inhibitors. As the prevalence of drug resistance mutations is on the rise, it is necessary to design strategies that will lead to drugs less susceptible to resistance. Here we provide an in-depth review of HIV reverse transcriptase, current RT inhibitors, novel RT inhibitors, and mechanisms of drug resistance. We also present novel strategies that can be useful to overcome RT's ability to escape therapies through drug resistance. While resistance may not be completely avoidable, designing drugs based on the strategies and principles discussed in this review could decrease the prevalence of drug resistance.
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Affiliation(s)
- Maria E Cilento
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States.,Children's Healthcare of Atlanta, Atlanta, Georgia 30307, United States
| | - Karen A Kirby
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States.,Children's Healthcare of Atlanta, Atlanta, Georgia 30307, United States
| | - Stefan G Sarafianos
- Laboratory of Biochemical Pharmacology, Department of Pediatrics, Emory University School of Medicine, Atlanta, Georgia 30322, United States.,Children's Healthcare of Atlanta, Atlanta, Georgia 30307, United States
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18
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Kemp SA, Collier DA, Datir R, Ferreira I, Gayed S, Jahun A, Hosmillo M, Rees-Spear C, Mlcochova P, Lumb IU, Roberts DJ, Chandra A, Temperton N, Sharrocks K, Blane E, Briggs J, van GM, Smith K, Bradley JR, Smith C, Doffinger R, Ceron-Gutierrez L, Barcenas-Morales G, Pollock DD, Goldstein RA, Smielewska A, Skittrall JP, Gouliouris T, Goodfellow IG, Gkrania-Klotsas E, Illingworth C, McCoy LE, Gupta RK. Neutralising antibodies in Spike mediated SARS-CoV-2 adaptation. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2020:2020.12.05.20241927. [PMID: 33398302 PMCID: PMC7781345 DOI: 10.1101/2020.12.05.20241927] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
SARS-CoV-2 Spike protein is critical for virus infection via engagement of ACE2, and amino acid variation in Spike is increasingly appreciated. Given both vaccines and therapeutics are designed around Wuhan-1 Spike, this raises the theoretical possibility of virus escape, particularly in immunocompromised individuals where prolonged viral replication occurs. Here we report chronic SARS-CoV-2 with reduced sensitivity to neutralising antibodies in an immune suppressed individual treated with convalescent plasma, generating whole genome ultradeep sequences by both short and long read technologies over 23 time points spanning 101 days. Although little change was observed in the overall viral population structure following two courses of remdesivir over the first 57 days, N501Y in Spike was transiently detected at day 55 and V157L in RdRp emerged. However, following convalescent plasma we observed large, dynamic virus population shifts, with the emergence of a dominant viral strain bearing D796H in S2 and ΔH69/ΔV70 in the S1 N-terminal domain NTD of the Spike protein. As passively transferred serum antibodies diminished, viruses with the escape genotype diminished in frequency, before returning during a final, unsuccessful course of convalescent plasma. In vitro, the Spike escape double mutant bearing ΔH69/ΔV70 and D796H conferred decreased sensitivity to convalescent plasma, whilst maintaining infectivity similar to wild type. D796H appeared to be the main contributor to decreased susceptibility, but incurred an infectivity defect. The ΔH69/ΔV70 single mutant had two-fold higher infectivity compared to wild type and appeared to compensate for the reduced infectivity of D796H. Consistent with the observed mutations being outside the RBD, monoclonal antibodies targeting the RBD were not impacted by either or both mutations, but a non RBD binding monoclonal antibody was less potent against ΔH69/ΔV70 and the double mutant. These data reveal strong selection on SARS-CoV-2 during convalescent plasma therapy associated with emergence of viral variants with reduced susceptibility to neutralising antibodies.
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Affiliation(s)
- S A Kemp
- Division of Infection and Immunity, University College London, London, UK
| | - D A Collier
- Division of Infection and Immunity, University College London, London, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - R Datir
- Division of Infection and Immunity, University College London, London, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Iatm Ferreira
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - S Gayed
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - A Jahun
- Department of Pathology, University of Cambridge, Cambridge
| | - M Hosmillo
- Department of Pathology, University of Cambridge, Cambridge
| | - C Rees-Spear
- Division of Infection and Immunity, University College London, London, UK
| | - P Mlcochova
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Ines Ushiro Lumb
- NHS Blood and Transplant, Oxford and BRC Haematology Theme, University of Oxford, UK
| | - David J Roberts
- NHS Blood and Transplant, Oxford and BRC Haematology Theme, University of Oxford, UK
| | - Anita Chandra
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - N Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent, UK
| | - K Sharrocks
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - E Blane
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Jag Briggs
- Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Gils Mj van
- Department of Medical Microbiology, Academic Medical Center, University of Amsterdam, Amsterdam Institute for Infection and Immunity, Amsterdam, Netherlands
| | - Kgc Smith
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - J R Bradley
- Department of Medicine, University of Cambridge, Cambridge, UK
- NIHR Cambridge Clinical Research Facility, Cambridge, UK
| | - C Smith
- Department of Virology, Cambridge University NHS Hospitals Foundation Trust
| | - R Doffinger
- Department of Clinical Biochemistry and Immunology, Addenbrookes Hospital
| | - L Ceron-Gutierrez
- Department of Clinical Biochemistry and Immunology, Addenbrookes Hospital
| | - G Barcenas-Morales
- Department of Clinical Biochemistry and Immunology, Addenbrookes Hospital
| | - D D Pollock
- Biochemistry and Molecular Genetics, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - R A Goldstein
- Division of Infection and Immunity, University College London, London, UK
| | - A Smielewska
- Department of Pathology, University of Cambridge, Cambridge
- Department of Virology, Cambridge University NHS Hospitals Foundation Trust
| | - J P Skittrall
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK
- Clinical Microbiology and Public Health Laboratory, Addenbrookes' Hospital, Cambridge, UK
| | - T Gouliouris
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - I G Goodfellow
- Department of Pathology, University of Cambridge, Cambridge
| | - E Gkrania-Klotsas
- Department of Infectious Diseases, Cambridge University NHS Hospitals Foundation Trust, Cambridge, UK
| | - Cjr Illingworth
- Department of Applied Mathematics and Theoretical Physics, University of Cambridge, UK
- MRC Biostatistics Unit, University of Cambridge, Cambridge, UK
| | - L E McCoy
- Division of Infection and Immunity, University College London, London, UK
| | - R K Gupta
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Cambridge, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
- Africa Health Research Institute, Durban, South Africa
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19
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Gupta-Wright A, Fielding K, van Oosterhout JJ, Alufandika M, Grint DJ, Chimbayo E, Heaney J, Byott M, Nastouli E, Mwandumba HC, Corbett EL, Gupta RK. Virological failure, HIV-1 drug resistance, and early mortality in adults admitted to hospital in Malawi: an observational cohort study. Lancet HIV 2020; 7:e620-e628. [PMID: 32890497 PMCID: PMC7487765 DOI: 10.1016/s2352-3018(20)30172-7] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/03/2020] [Accepted: 06/12/2020] [Indexed: 01/19/2023]
Abstract
BACKGROUND Antiretroviral therapy (ART) scale-up in sub-Saharan Africa combined with weak routine virological monitoring has driven increasing HIV drug resistance. We investigated ART failure, drug resistance, and early mortality among patients with HIV admitted to hospital in Malawi. METHODS This observational cohort study was nested within the rapid urine-based screening for tuberculosis to reduce AIDS-related mortality in hospitalised patients in Africa (STAMP) trial, which recruited unselected (ie, irrespective of clinical presentation) adult (aged ≥18 years) patients with HIV-1 at admission to medical wards. Patients were included in our observational cohort study if they were enrolled at the Malawi site (Zomba Central Hospital) and were taking ART for at least 6 months at admission. Patients who met inclusion criteria had frozen plasma samples tested for HIV-1 viral load. Those with HIV-1 RNA of at least 1000 copies per mL had drug resistance testing by ultra-deep sequencing, with drug resistance defined as intermediate or high-level resistance using the Stanford HIVDR program. Mortality risk was calculated 56 days from enrolment. Patients were censored at death, at 56 days, or at last contact if lost to follow-up. The modelling strategy addressed the causal association between HIV multidrug resistance and mortality, excluding factors on the causal pathway (most notably, CD4 cell count, clinical signs of advanced HIV, and poor functional and nutritional status). FINDINGS Of 1316 patients with HIV enrolled in the STAMP trial at the Malawi site between Oct 26, 2015, and Sept 19, 2017, 786 had taken ART for at least 6 months. 252 (32%) of 786 patients had virological failure (viral load ≥1000 copies per mL). Mean age was 41·5 years (SD 11·4) and 528 (67%) of 786 were women. Of 237 patients with HIV drug resistance results available, 195 (82%) had resistance to lamivudine, 128 (54%) to tenofovir, and 219 (92%) to efavirenz. Resistance to at least two drugs was common (196, 83%), and this was associated with increased mortality (adjusted hazard ratio 1·7, 95% CI 1·2-2·4; p=0·0042). INTERPRETATION Interventions are urgently needed and should target ART clinic, hospital, and post-hospital care, including differentiated care focusing on patients with advanced HIV, rapid viral load testing, and routine access to drug resistance testing. Prompt diagnosis and switching to alternative ART could reduce early mortality among inpatients with HIV. FUNDING Joint Global Health Trials Scheme of the Medical Research Council, UK Department for International Development, and Wellcome Trust.
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Affiliation(s)
- Ankur Gupta-Wright
- Department of Infection and Immunity, University College London, London UK; Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi.
| | - Katherine Fielding
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK; School of Public Health, University of the Witwatersrand, Johannesburg, South Africa
| | - Joep J van Oosterhout
- Department of Medicine, University of Malawi College of Medicine, Blantyre, Malawi; Dignitas International, Zomba, Malawi
| | - Melanie Alufandika
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi; Dignitas International, Zomba, Malawi
| | - Daniel J Grint
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London, UK
| | - Elizabeth Chimbayo
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Judith Heaney
- Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Foundation Trust, London, UK
| | - Matthew Byott
- Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Foundation Trust, London, UK
| | - Eleni Nastouli
- Advanced Pathogen Diagnostics Unit, University College London Hospitals NHS Foundation Trust, London, UK
| | - Henry C Mwandumba
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi; Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Elizabeth L Corbett
- Department of Clinical Research, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK; Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
| | - Ravindra K Gupta
- Department of Medicine, University of Cambridge, Cambridge, UK; Africa Health Research Institute, Durban, KwaZulu-Natal, South Africa
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20
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Crowell TA, Danboise B, Parikh A, Esber A, Dear N, Coakley P, Kasembeli A, Maswai J, Khamadi S, Bahemana E, Iroezindu M, Kiweewa F, Owuoth J, Freeman J, Jagodzinski LL, Malia JA, Eller LA, Tovanabutra S, Peel SA, Ake JA, Polyak CS. Pretreatment and Acquired Antiretroviral Drug Resistance Among Persons Living With HIV in Four African Countries. Clin Infect Dis 2020; 73:e2311-e2322. [PMID: 32785695 PMCID: PMC8492117 DOI: 10.1093/cid/ciaa1161] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND Emerging HIV drug resistance (HIVDR) could jeopardize the success of standardized HIV management protocols in resource-limited settings. We characterized HIVDR among antiretroviral therapy (ART)-naive and experienced participants in the African Cohort Study (AFRICOS). METHODS From January 2013 to April 2019, adults with HIV-1 RNA >1000 copies/mL underwent ART history review and HIVDR testing upon enrollment at 12 clinics in Uganda, Kenya, Tanzania, and Nigeria. We calculated resistance scores for specific drugs and tallied major mutations to non-nucleoside reverse transcriptase inhibitors (NNRTIs), nucleoside reverse transcriptase inhibitors (NRTIs), and protease inhibitors (PIs) using Stanford HIVDB 8.8 and SmartGene IDNS software. For ART-naive participants, World Health Organization surveillance drug resistance mutations (SDRMs) were noted. RESULTS HIVDR testing was performed on 972 participants with median age 35.7 (interquartile range [IQR] 29.7-42.7) years and median CD4 295 (IQR 148-478) cells/mm3. Among 801 ART-naive participants, the prevalence of SDRMs was 11.0%, NNRTI mutations 8.2%, NRTI mutations 4.7%, and PI mutations 0.4%. Among 171 viremic ART-experienced participants, NNRTI mutation prevalence was 83.6%, NRTI 67.8%, and PI 1.8%. There were 90 ART-experienced participants with resistance to both efavirenz and lamivudine, 33 (36.7%) of whom were still prescribed these drugs. There were 10 with resistance to both tenofovir and lamivudine, 8 (80.0%) of whom were prescribed these drugs. CONCLUSIONS Participants on failing ART regimens had a high burden of HIVDR that potentially limited the efficacy of standardized first- and second-line regimens. Management strategies that emphasize adherence counseling while delaying ART switch may promote drug resistance and should be reconsidered.
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Affiliation(s)
- Trevor A Crowell
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Brook Danboise
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Ajay Parikh
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Allahna Esber
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Nicole Dear
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Peter Coakley
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Alex Kasembeli
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,HJF Medical Research International, Kericho, Kenya
| | - Jonah Maswai
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,HJF Medical Research International, Kericho, Kenya
| | - Samoel Khamadi
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,HJF Medical Research International, Mbeya, Tanzania
| | - Emmanuel Bahemana
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,HJF Medical Research International, Mbeya, Tanzania
| | - Michael Iroezindu
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,HJF Medical Research International, Abuja, Nigeria
| | | | - John Owuoth
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,HJF Medical Research International, Kisumu, Kenya
| | - Joanna Freeman
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Linda L Jagodzinski
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Jennifer A Malia
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Leigh Ann Eller
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Sodsai Tovanabutra
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
| | - Sheila A Peel
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Julie A Ake
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Christina S Polyak
- US Military HIV Research Program, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA.,Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, USA
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