1
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Karim F, Riou C, Bernstein M, Jule Z, Lustig G, van Graan S, Keeton RS, Upton JL, Ganga Y, Khan K, Reedoy K, Mazibuko M, Govender K, Thambu K, Ngcobo N, Venter E, Makhado Z, Hanekom W, von Gottberg A, Hoque M, Karim QA, Abdool Karim SS, Manickchund N, Magula N, Gosnell BI, Lessells RJ, Moore PL, Burgers WA, de Oliveira T, Moosa MYS, Sigal A. Clearance of persistent SARS-CoV-2 associates with increased neutralizing antibodies in advanced HIV disease post-ART initiation. Nat Commun 2024; 15:2360. [PMID: 38491050 PMCID: PMC10943233 DOI: 10.1038/s41467-024-46673-2] [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: 08/10/2023] [Accepted: 02/27/2024] [Indexed: 03/18/2024] Open
Abstract
SARS-CoV-2 clearance requires adaptive immunity but the contribution of neutralizing antibodies and T cells in different immune states is unclear. Here we ask which adaptive immune responses associate with clearance of long-term SARS-CoV-2 infection in HIV-mediated immunosuppression after suppressive antiretroviral therapy (ART) initiation. We assembled a cohort of SARS-CoV-2 infected people in South Africa (n = 994) including participants with advanced HIV disease characterized by immunosuppression due to T cell depletion. Fifty-four percent of participants with advanced HIV disease had prolonged SARS-CoV-2 infection (>1 month). In the five vaccinated participants with advanced HIV disease tested, SARS-CoV-2 clearance associates with emergence of neutralizing antibodies but not SARS-CoV-2 specific CD8 T cells, while CD4 T cell responses were not determined due to low cell numbers. Further, complete HIV suppression is not required for clearance, although it is necessary for an effective vaccine response. Persistent SARS-CoV-2 infection led to SARS-CoV-2 evolution, including virus with extensive neutralization escape in a Delta variant infected participant. The results provide evidence that neutralizing antibodies are required for SARS-CoV-2 clearance in HIV-mediated immunosuppression recovery, and that suppressive ART is necessary to curtail evolution of co-infecting pathogens to reduce individual health consequences as well as public health risk linked with generation of escape mutants.
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Affiliation(s)
- Farina Karim
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Catherine Riou
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | | | - Zesuliwe Jule
- Africa Health Research Institute, Durban, South Africa
| | - Gila Lustig
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Strauss van Graan
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Roanne S Keeton
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
| | | | - Yashica Ganga
- Africa Health Research Institute, Durban, South Africa
| | - Khadija Khan
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Kajal Reedoy
- Africa Health Research Institute, Durban, South Africa
| | | | | | | | | | - Elizabeth Venter
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Zanele Makhado
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Willem Hanekom
- Africa Health Research Institute, Durban, South Africa
- Division of Infection and Immunity, University College London, London, UK
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, University of the Witwatersrand, Johannesburg, South Africa
| | - Monjurul Hoque
- KwaDabeka Community Health Centre, KwaDabeka, South Africa
| | - Quarraisha Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, USA
| | - Nithendra Manickchund
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Nombulelo Magula
- Department of Internal Medicine, Nelson R. Mandela School of Medicine, University of Kwa-Zulu Natal, Durban, South Africa
| | - Bernadett I Gosnell
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Richard J Lessells
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | - Penny L Moore
- SAMRC Antibody Immunity Research Unit, School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- National Institute for Communicable Diseases of the National Health Laboratory Service, Johannesburg, South Africa
| | - Wendy A Burgers
- Institute of Infectious Disease and Molecular Medicine, Division of Medical Virology, Department of Pathology, University of Cape Town, Observatory, South Africa
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Observatory, South Africa
| | - Tulio de Oliveira
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
- Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Department of Global Health, University of Washington, Seattle, WA, USA
| | - Mahomed-Yunus S Moosa
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Alex Sigal
- Africa Health Research Institute, Durban, South Africa.
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa.
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa.
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2
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Marques AD, Graham-Wooten J, Fitzgerald AS, Sobel Leonard A, Cook EJ, Everett JK, Rodino KG, Moncla LH, Kelly BJ, Collman RG, Bushman FD. SARS-CoV-2 evolution during prolonged infection in immunocompromised patients. mBio 2024; 15:e0011024. [PMID: 38364100 PMCID: PMC10936176 DOI: 10.1128/mbio.00110-24] [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: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/18/2024] Open
Abstract
Prolonged infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in immunocompromised patients provides an opportunity for viral evolution, potentially leading to the generation of new pathogenic variants. To investigate the pathways of viral evolution, we carried out a study on five patients experiencing prolonged SARS-CoV-2 infection (quantitative polymerase chain reaction-positive for 79-203 days) who were immunocompromised due to treatment for lymphoma or solid organ transplantation. For each timepoint analyzed, we generated at least two independent viral genome sequences to assess the heterogeneity and control for sequencing error. Four of the five patients likely had prolonged infection; the fifth apparently experienced a reinfection. The rates of accumulation of substitutions in the viral genome per day were higher in hospitalized patients with prolonged infection than those estimated for the community background. The spike coding region accumulated a significantly greater number of unique mutations than other viral coding regions, and the mutation density was higher. Two patients were treated with monoclonal antibodies (bebtelovimab and sotrovimab); by the next sampled timepoint, each virus population showed substitutions associated with monoclonal antibody resistance as the dominant forms (spike K444N and spike E340D). All patients received remdesivir, but remdesivir-resistant substitutions were not detected. These data thus help elucidate the trends of emergence, evolution, and selection of mutational variants within long-term infected immunocompromised individuals. IMPORTANCE SARS-CoV-2 is responsible for a global pandemic, driven in part by the emergence of new viral variants. Where do these new variants come from? One model is that long-term viral persistence in infected individuals allows for viral evolution in response to host pressures, resulting in viruses more likely to replicate efficiently in humans. In this study, we characterize replication in several hospitalized and long-term infected individuals, documenting efficient pathways of viral evolution.
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Affiliation(s)
- Andrew D. Marques
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jevon Graham-Wooten
- Division of Pulmonary, Allergy, and Critical Care, Philadelphia, Pennsylvania, USA
| | | | - Ashley Sobel Leonard
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Emma J. Cook
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John K. Everett
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kyle G. Rodino
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Louise H. Moncla
- Department of Pathobiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Brendan J. Kelly
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ronald G. Collman
- Division of Pulmonary, Allergy, and Critical Care, Philadelphia, Pennsylvania, USA
| | - Frederic D. Bushman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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3
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Kenney D, O’Connell AK, Tseng AE, Turcinovic J, Sheehan ML, Nitido AD, Montanaro P, Gertje HP, Ericsson M, Connor JH, Vrbanac V, Crossland NA, Harly C, Balazs AB, Douam F. Resolution of SARS-CoV-2 infection in human lung tissues is driven by extravascular CD163+ monocytes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.583965. [PMID: 38496468 PMCID: PMC10942442 DOI: 10.1101/2024.03.08.583965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
The lung-resident immune mechanisms driving resolution of SARS-CoV-2 infection in humans remain elusive. Using mice co-engrafted with a genetically matched human immune system and fetal lung xenograft (fLX), we mapped the immunological events defining resolution of SARS-CoV-2 infection in human lung tissues. Viral infection is rapidly cleared from fLX following a peak of viral replication. Acute replication results in the emergence of cell subsets enriched in viral RNA, including extravascular inflammatory monocytes (iMO) and macrophage-like T-cells, which dissipate upon infection resolution. iMO display robust antiviral responses, are transcriptomically unique among myeloid lineages, and their emergence associates with the recruitment of circulating CD4+ monocytes. Consistently, mice depleted for human CD4+ cells but not CD3+ T-cells failed to robustly clear infectious viruses and displayed signatures of chronic infection. Our findings uncover the transient differentiation of extravascular iMO from CD4+ monocytes as a major hallmark of SARS-CoV-2 infection resolution and open avenues for unravelling viral and host adaptations defining persistently active SARS-CoV-2 infection.
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Affiliation(s)
- Devin Kenney
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | - Aoife K. O’Connell
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Anna E. Tseng
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Jacquelyn Turcinovic
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Bioinformatics Program, Boston University, Boston, MA, USA
| | - Meagan L. Sheehan
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- These authors contributed equally to the work
| | - Adam D. Nitido
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- These authors contributed equally to the work
| | - Paige Montanaro
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Hans P. Gertje
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Maria Ericsson
- Electron Microscopy Core Facility, Harvard Medical School, Boston, MA, USA
| | - John H. Connor
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
| | | | - Nicholas A. Crossland
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- Department of Pathology and Laboratory Medicine, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
| | - Christelle Harly
- Université de Nantes, INSERM, CNRS, CRCINA, Nantes, France
- LabEx IGO ‘Immunotherapy, Graft, Oncology’, Nantes, France
- These authors contributed equally to the work
| | - Alejandro B. Balazs
- Ragon Institute of MGH, MIT and Harvard, Cambridge, MA, USA
- These authors contributed equally to the work
| | - Florian Douam
- Department of Virology, Immunology, and Microbiology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, USA
- National Emerging Infectious Diseases Laboratories, Boston University, Boston, MA, USA
- These authors contributed equally to the work
- Lead contact
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4
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Höft MA, Burgers WA, Riou C. The immune response to SARS-CoV-2 in people with HIV. Cell Mol Immunol 2024; 21:184-196. [PMID: 37821620 PMCID: PMC10806256 DOI: 10.1038/s41423-023-01087-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Accepted: 09/12/2023] [Indexed: 10/13/2023] Open
Abstract
This review examines the intersection of the HIV and SARS-CoV-2 pandemics. People with HIV (PWH) are a heterogeneous group that differ in their degree of immune suppression, immune reconstitution, and viral control. While COVID-19 in those with well-controlled HIV infection poses no greater risk than that for HIV-uninfected individuals, people with advanced HIV disease are more vulnerable to poor COVID-19 outcomes. COVID-19 vaccines are effective and well tolerated in the majority of PWH, though reduced vaccine efficacy, breakthrough infections and faster waning of vaccine effectiveness have been demonstrated in PWH. This is likely a result of suboptimal humoral and cellular immune responses after vaccination. People with advanced HIV may also experience prolonged infection that may give rise to new epidemiologically significant variants, but initiation or resumption of antiretroviral therapy (ART) can effectively clear persistent infection. COVID-19 vaccine guidelines reflect these increased risks and recommend prioritization for vaccination and additional booster doses for PWH who are moderately to severely immunocompromised. We recommend continued research and monitoring of PWH with SARS-CoV-2 infection, especially in areas with a high HIV burden.
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Affiliation(s)
- Maxine A Höft
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Wendy A Burgers
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa.
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa.
| | - Catherine Riou
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, South Africa.
- Division of Medical Virology, Department of Pathology, University of Cape Town, Cape Town, South Africa.
- Wellcome Centre for Infectious Diseases Research in Africa, University of Cape Town, Cape Town, South Africa.
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5
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Baker SJC, Nfonsam LE, Leto D, Rutherford C, Smieja M, McArthur AG. Chronic COVID-19 infection in an immunosuppressed patient shows changes in lineage over time: a case report. Virol J 2024; 21:8. [PMID: 38178158 PMCID: PMC10768205 DOI: 10.1186/s12985-023-02278-7] [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: 08/01/2023] [Accepted: 12/25/2023] [Indexed: 01/06/2024] Open
Abstract
BACKGROUND The COVID-19 pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 virus, emerged in late 2019 and spready globally. Many effects of infection with this pathogen are still unknown, with both chronic and repeated COVID-19 infection producing novel pathologies. CASE PRESENTATION An immunocompromised patient presented with chronic COVID-19 infection. The patient had history of Hodgkin's lymphoma, treated with chemotherapy and stem cell transplant. During the course of their treatment, eleven respiratory samples from the patient were analyzed by whole-genome sequencing followed by lineage identification. Whole-genome sequencing of the virus present in the patient over time revealed that the patient at various timepoints harboured three different lineages of the virus. The patient was initially infected with the B.1.1.176 lineage before coinfection with BA.1. When the patient was coinfected with both B.1.1.176 and BA.1, the viral populations were found in approximately equal proportions within the patient based on sequencing read abundance. Upon further sampling, the lineage present within the patient during the final two timepoints was found to be BA.2.9. The patient eventually developed respiratory failure and died. CONCLUSIONS This case study shows an example of the changes that can happen within an immunocompromised patient who is infected with COVID-19 multiple times. Furthermore, this case demonstrates how simultaneous coinfection with two lineages of COVID-19 can lead to unclear lineage assignment by standard methods, which are resolved by further investigation. When analyzing chronic COVID-19 infection and reinfection cases, care must be taken to properly identify the lineages of the virus present.
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Affiliation(s)
- Sheridan J C Baker
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, ON, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada
- Hamilton Regional Laboratory Medicine Program, St Joseph's Healthcare, Hamilton, ON, Canada
| | - Landry E Nfonsam
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, ON, Canada
| | - Daniela Leto
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, ON, Canada
| | - Candy Rutherford
- Hamilton Regional Laboratory Medicine Program, St Joseph's Healthcare, Hamilton, ON, Canada
| | - Marek Smieja
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada
- Hamilton Regional Laboratory Medicine Program, St Joseph's Healthcare, Hamilton, ON, Canada
- Department of Pathology and Molecular Medicine, McMaster University, Hamilton, ON, Canada
- Hamilton Regional Laboratory Medicine Program, Hamilton Health Sciences, Hamilton, ON, Canada
| | - Andrew G McArthur
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, ON, Canada.
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, ON, Canada.
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, ON, Canada.
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6
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Bi H, You R, Bian X, Li P, Zhao X, You Z. A magnetic control enrichment technique combined with terahertz metamaterial biosensor for detecting SARS-CoV-2 spike protein. Biosens Bioelectron 2024; 243:115763. [PMID: 37890389 DOI: 10.1016/j.bios.2023.115763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2023] [Revised: 10/12/2023] [Accepted: 10/15/2023] [Indexed: 10/29/2023]
Abstract
The highly contagious SARS-CoV-2 virus, responsible for the COVID-19 pandemic continues to pose significant challenges to public health. Developing new methods for early detection and diagnosis is crucial in combatting the disease, mitigating its impact and be prepared for future challenges in pandemic diseases. In this study, we propose a terahertz (THz) biosensing technology that capitalizes on the properties of THz metamaterial in conjunction with magnetic nanoparticles. This approach can accurately identify the SARS-CoV-2 spike protein by pinpointing its location on the THz resonance sources grooved surface. The magnetic nanoparticles are employed to selectively bind with target molecules, and migrate towards the THz metamaterial unit cell when exposed to an applied magnetic field. The presence of target molecules in to the metamaterial variation in the frequency, amplitude, and phase of the resonance response, thus enabling swift, accurate and sensitive detection. To assess the effectiveness of the proposed technique, we have conducted a comparative analysis between real samples on platforms controlled by magnetic manipulation and those without the control. It was confirmed that the proposed THz sensing method demonstrated a linear detection range spanning from 0.005 ng mL-1 to 1000 ng mL-1 with a detection limit of 0.002 ng mL-1. Furthermore, it exhibited a frequency shift of 24 GHz and a stability index of 95%. The THz biosensing technique may pave a new avenue in identifying and preempting the spread of potential pandemic diseases.
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Affiliation(s)
- Hao Bi
- Beijing Laboratory of Biomedical Detection Technology and Instrument, Beijing Information Science & Technology University, Beijing, 10029, PR China; School of Instrument Science and Opto-Electronics Engineering, Beijing Information Science and Technology University, Beijing, 100029, PR China
| | - Rui You
- Beijing Laboratory of Biomedical Detection Technology and Instrument, Beijing Information Science & Technology University, Beijing, 10029, PR China; School of Instrument Science and Opto-Electronics Engineering, Beijing Information Science and Technology University, Beijing, 100029, PR China.
| | - Xiaomeng Bian
- Beijing Laboratory of Biomedical Detection Technology and Instrument, Beijing Information Science & Technology University, Beijing, 10029, PR China; School of Instrument Science and Opto-Electronics Engineering, Beijing Information Science and Technology University, Beijing, 100029, PR China
| | - Peng Li
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instruments, Tsinghua University, Beijing, 100084, PR China; Key Laboratory of Smart Microsystem, Ministry of Education, Tsinghua University, Beijing, 100084, PR China; Beijing Advanced Innovation Center for Integrated Circuits, Beijing, 100084, PR China.
| | - Xiaoguang Zhao
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instruments, Tsinghua University, Beijing, 100084, PR China; Key Laboratory of Smart Microsystem, Ministry of Education, Tsinghua University, Beijing, 100084, PR China; Beijing Advanced Innovation Center for Integrated Circuits, Beijing, 100084, PR China.
| | - Zheng You
- State Key Laboratory of Precision Measurement Technology and Instruments, Department of Precision Instruments, Tsinghua University, Beijing, 100084, PR China; Key Laboratory of Smart Microsystem, Ministry of Education, Tsinghua University, Beijing, 100084, PR China; Beijing Advanced Innovation Center for Integrated Circuits, Beijing, 100084, PR China
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7
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Choga WT, Kurusa Gasenna GK, San JE, Ookame T, Gobe I, Chand M, Phafane B, Seru K, Matshosi P, Zuze B, Ndlovu N, Matsuru T, Maruapula D, Bareng OT, Macheke K, Kuate-Lere L, Tlale L, Lesetedi O, Tau M, Mbulawa MB, Smith-Lawrence P, Matshaba M, Shapiro R, Makhema J, Martin DP, de Oliveira T, Lessells RJ, Lockman S, Gaseitsiwe S, Moyo S. Rapid dynamic changes of FL.2 variant: A case report of COVID-19 breakthrough infection. Int J Infect Dis 2024; 138:91-96. [PMID: 37952911 PMCID: PMC10719116 DOI: 10.1016/j.ijid.2023.11.011] [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: 09/06/2023] [Revised: 10/23/2023] [Accepted: 11/07/2023] [Indexed: 11/14/2023] Open
Abstract
We investigated intra-host genetic evolution using two SARS-CoV-2 isolates from a fully vaccinated (primary schedule x2 doses of AstraZeneca plus a booster of Pfizer), >70-year-old woman with a history of lymphoma and hypertension who presented a SARS-CoV-2 infection for 3 weeks prior to death due to COVID-19. Two full genome sequences were determined from samples taken 13 days apart with both belonging to Pango lineage FL.2: the first detection of this Omicron sub-variant in Botswana. FL.2 is a sub-lineage of XBB.1.9.1. The repertoire of mutations and minority variants in the Spike protein differed between the two time points. Notably, we also observed deletions within the ORF1a and Membrane proteins; both regions are associated with high T-cell epitope density. The internal milieu of immune-suppressed individuals may accelerate SARS-CoV-2 evolution; hence, close monitoring is warranted.
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Affiliation(s)
- Wonderful T Choga
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; School of Allied Health Sciences, Faculty of Health Sciences, Gaborone, Botswana; Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | | | - James Emmanuel San
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory. Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | - Irene Gobe
- School of Allied Health Sciences, Faculty of Health Sciences, Gaborone, Botswana
| | - Mohammed Chand
- Diagnofirm Medical Laboratories, Plot 12583, Nyerere Drive MiddleStar, Gaborone, Botswana
| | - Badisa Phafane
- Diagnofirm Medical Laboratories, Plot 12583, Nyerere Drive MiddleStar, Gaborone, Botswana
| | - Kedumetse Seru
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | | | - Boitumelo Zuze
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | | | - Teko Matsuru
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | | | - Ontlametse T Bareng
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; School of Allied Health Sciences, Faculty of Health Sciences, Gaborone, Botswana
| | | | | | | | | | - Modiri Tau
- National Health laboratory, Gaborone, Botswana
| | | | | | - Mogomotsi Matshaba
- Botswana-Baylor Children's Clinical Centre of Excellence, Gaborone, Botswana; Department of Pediatrics, Baylor College of Medicine, Houston, USA
| | - Roger Shapiro
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, USA
| | - Joseph Makhema
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana
| | - Darren P Martin
- Institute of Infectious Diseases and Molecular Medicine, Division of Computational Biology, Department of Integrative Biomedical Sciences, University of Cape Town, South Africa
| | - Tulio de Oliveira
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory. Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa; Department of Global Health, University of Washington, Seattle, USA
| | - Richard J Lessells
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa; KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory. Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Shahin Lockman
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, USA
| | - Simani Gaseitsiwe
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, USA
| | - Sikhulile Moyo
- Botswana Harvard AIDS Institute Partnership, Gaborone, Botswana; Department of Immunology and Infectious Diseases, Harvard T.H. Chan School of Public Health, Boston, USA; School of Health Systems and Public Health, University of Pretoria, South Africa; Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa.
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8
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Gandhi RT, Castle AC, de Oliveira T, Lessells RJ. Case 40-2023: A 70-Year-Old Woman with Cough and Shortness of Breath. N Engl J Med 2023; 389:2468-2476. [PMID: 38157503 DOI: 10.1056/nejmcpc2300910] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/03/2024]
Affiliation(s)
- Rajesh T Gandhi
- From the Department of Medicine, Massachusetts General Hospital, and the Department of Medicine, Harvard Medical School - both in Boston (R.T.G., A.C.C.); and the Centre for Epidemic Response and Innovation, School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch (T.O.), and the KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban (T.O., R.J.L.) - both in South Africa
| | - Alison C Castle
- From the Department of Medicine, Massachusetts General Hospital, and the Department of Medicine, Harvard Medical School - both in Boston (R.T.G., A.C.C.); and the Centre for Epidemic Response and Innovation, School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch (T.O.), and the KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban (T.O., R.J.L.) - both in South Africa
| | - Tulio de Oliveira
- From the Department of Medicine, Massachusetts General Hospital, and the Department of Medicine, Harvard Medical School - both in Boston (R.T.G., A.C.C.); and the Centre for Epidemic Response and Innovation, School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch (T.O.), and the KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban (T.O., R.J.L.) - both in South Africa
| | - Richard J Lessells
- From the Department of Medicine, Massachusetts General Hospital, and the Department of Medicine, Harvard Medical School - both in Boston (R.T.G., A.C.C.); and the Centre for Epidemic Response and Innovation, School for Data Science and Computational Thinking, Stellenbosch University, Stellenbosch (T.O.), and the KwaZulu-Natal Research Innovation and Sequencing Platform, School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban (T.O., R.J.L.) - both in South Africa
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9
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Lustig G, Ganga Y, Rodel HE, Tegally H, Khairallah A, Jackson L, Cele S, Khan K, Jule Z, Reedoy K, Karim F, Bernstein M, Ndung’u T, Moosa MYS, Archary D, de Oliveira T, Lessells R, Neher RA, Abdool Karim SS, Sigal A. SARS-CoV-2 infection in immunosuppression evolves sub-lineages which independently accumulate neutralization escape mutations. Virus Evol 2023; 10:vead075. [PMID: 38361824 PMCID: PMC10868398 DOI: 10.1093/ve/vead075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2023] [Revised: 11/11/2023] [Accepted: 12/21/2023] [Indexed: 02/17/2024] Open
Abstract
One mechanism of variant formation may be evolution during long-term infection in immunosuppressed people. To understand the viral phenotypes evolved during such infection, we tested SARS-CoV-2 viruses evolved from an ancestral B.1 lineage infection lasting over 190 days post-diagnosis in an advanced HIV disease immunosuppressed individual. Sequence and phylogenetic analysis showed two evolving sub-lineages, with the second sub-lineage replacing the first sub-lineage in a seeming evolutionary sweep. Each sub-lineage independently evolved escape from neutralizing antibodies. The most evolved virus for the first sub-lineage (isolated day 34) and the second sub-lineage (isolated day 190) showed similar escape from ancestral SARS-CoV-2 and Delta-variant infection elicited neutralizing immunity despite having no spike mutations in common relative to the B.1 lineage. The day 190 isolate also evolved higher cell-cell fusion and faster viral replication and caused more cell death relative to virus isolated soon after diagnosis, though cell death was similar to day 34 first sub-lineage virus. These data show that SARS-CoV-2 strains in prolonged infection in a single individual can follow independent evolutionary trajectories which lead to neutralization escape and other changes in viral properties.
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Affiliation(s)
- Gila Lustig
- Centre for the AIDS Programme of Research in South Africa, 719 Umbilo Road, Durban 4001, South Africa
| | - Yashica Ganga
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
| | - Hylton E Rodel
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
- Division of Infection and Immunity, University College London, UCL Cruciform Building Gower Street, London WC1E 6BT, UK
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform, 719 Umbilo Road, Durban 4001, South Africa
- Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Francie Van Zijl Drive, Cape Town 7505, South Africa
| | - Afrah Khairallah
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
| | - Laurelle Jackson
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
| | - Sandile Cele
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
| | - Khadija Khan
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
| | - Zesuliwe Jule
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
| | - Kajal Reedoy
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
| | - Farina Karim
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
| | - Mallory Bernstein
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
| | - Thumbi Ndung’u
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
- Division of Infection and Immunity, University College London, UCL Cruciform Building Gower Street, London WC1E 6BT, UK
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
- HIV Pathogenesis Programme, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
- Ragon Institute of MGH, MIT and Harvard University, 400 Technology Square, Cambridge, MA 02139, USA
| | - Mahomed-Yunus S Moosa
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
| | - Derseree Archary
- Centre for the AIDS Programme of Research in South Africa, 719 Umbilo Road, Durban 4001, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform, 719 Umbilo Road, Durban 4001, South Africa
- Centre for Epidemic Response and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Francie Van Zijl Drive, Cape Town 7505, South Africa
- Department of Global Health, University of Washington, 3980 15th Avenue NE, Seattle, WA 98105, USA
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform, 719 Umbilo Road, Durban 4001, South Africa
| | - Richard A Neher
- SIB Swiss Institute of Bioinformatics, Quartier Sorge - Bâtiment Amphipôle, Lausanne 1015, Switzerland
- Biozentrum, University of Basel, Spitalstrasse 41 4056, Basel, Switzerland
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, 719 Umbilo Road, Durban 4001, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, 722 West 168th Street, New York, NY 10032, United States
| | - Alex Sigal
- Centre for the AIDS Programme of Research in South Africa, 719 Umbilo Road, Durban 4001, South Africa
- Africa Health Research Institute, 719 Umbilo Road, Durban 4001, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, 719 Umbilo Road, Durban 4001, South Africa
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10
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Swan CL, Dushimiyimana V, Ndishimye P, Buchanan R, Yourkowski A, Semafara S, Nsanzimana S, Francis ME, Thivierge B, Lew J, Facciuolo A, Gerdts V, Falzarano D, Sjaarda C, Kelvin DJ, Bitunguhari L, Kelvin AA. Third COVID-19 vaccine dose boosts antibody function in Rwandans with high HIV viral load. iScience 2023; 26:107959. [PMID: 37810226 PMCID: PMC10558770 DOI: 10.1016/j.isci.2023.107959] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 08/18/2023] [Accepted: 09/14/2023] [Indexed: 10/10/2023] Open
Abstract
SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) causing COVID-19 (coronavirus disease 2019) poses a greater health risk to immunocompromized individuals including people living with HIV (PLWH). However, most studies on PLWH have been conducted in higher-income countries. We investigated the post-vaccination antibody responses of PLWH in Rwanda by collecting peripheral blood from participants after receiving a second or third COVID-19 vaccine. Virus-binding antibodies as well as antibody neutralization ability against all major SARS-CoV-2 variants of concern were analyzed. We found that people with high HIV viral loads and two COVID-19 vaccine doses had lower levels of binding antibodies that were less virus neutralizing and less cross-reactive compared to control groups. A third vaccination increased neutralizing antibody titers. Our data suggest that people with high HIV viral loads require a third dose of vaccine to neutralize SARS-CoV-2 virus and new variants as they emerge.
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Affiliation(s)
- Cynthia L. Swan
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | | | - Pacifique Ndishimye
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
- African Institute for Mathematical Sciences, Kigali, Rwanda
| | - Rachelle Buchanan
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Anthony Yourkowski
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Sage Semafara
- Rwanda Network of the People living with HIV (RRP+), Kigali, Rwanda
| | | | - Magen E. Francis
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
| | - Brittany Thivierge
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Jocelyne Lew
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
| | - Antonio Facciuolo
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Volker Gerdts
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Darryl Falzarano
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | - Calvin Sjaarda
- Department of Pathology and Molecular Medicine, Queen’s University, Kingston, ON K7L 3N6, Canada
- Queen’s Genomics Lab at Ongwanada (Q-GLO), Ongwanada Resource Centre, Kingston, ON K7M 8A6, Canada
| | - David J. Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | | | - Alyson A. Kelvin
- Vaccine and Infectious Disease Organization VIDO, University of Saskatchewan, Saskatoon, SK S7N 5E3, Canada
- Department of Biochemistry, Microbiology, and Immunology, University of Saskatchewan, Saskatoon, SK S7N 5E5, Canada
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11
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Lassaunière R, Polacek C, Linnea Tingstedt J, Fomsgaard A. Preclinical evaluation of a SARS-CoV-2 variant B.1.351-based candidate DNA vaccine. Vaccine 2023; 41:6505-6513. [PMID: 37726179 DOI: 10.1016/j.vaccine.2023.09.021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 07/22/2023] [Accepted: 09/12/2023] [Indexed: 09/21/2023]
Abstract
The SARS-CoV-2 pandemic revealed the critical shortfalls of global vaccine availability for emergent pathogens and the need for exploring additional vaccine platforms with rapid update potential in response to new variants. Thus, it remains essential, for the present evolving SARS-CoV-2/Covid-19 and future pandemics, to continuously develop and characterize new and different vaccine platforms. Here, we describe an expression-optimized DNA vaccine candidate based on the SARS-CoV-2 spike protein of the Beta variant (B.1.351), pNTC-Spike.351, and, in animal models, compare its immunogenicity with a similar DNA vaccine encoding the ancestral index strain spike protein, pNTC-Spike. Both DNA vaccines induced neutralizing antibodies and a Th1 biased immune response. In contrast to the index-specific vaccine, the Beta-specific DNA vaccine induced antibodies in mice and rabbits that, even at low levels, efficiently neutralize the otherwise antibody resistant Beta variant. It similarly neutralized unrelated variants bearing the neutralization resistant E484K spike mutation. Intensive priming using two vaccinations with pNTC-Spike and a single booster immunization with the pNTC-Spike.351 induced a more robust neutralizing antibody response with comparable magnitude against different variants of concern. Thus, DNA vaccine technology with heterologous spike protein prime-boost should be explored further using the Beta derived pNTC-Spike.351 to broaden neutralizing antibody responses against emerging variants of concern.
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Affiliation(s)
- Ria Lassaunière
- Department of Virus and Microbiological Special Diagnostic, Statens Serum Institut, Copenhagen, Denmark
| | - Charlotta Polacek
- Department of Virus and Microbiological Special Diagnostic, Statens Serum Institut, Copenhagen, Denmark
| | - Jeanette Linnea Tingstedt
- Department of Virus and Microbiological Special Diagnostic, Statens Serum Institut, Copenhagen, Denmark
| | - Anders Fomsgaard
- Department of Virus and Microbiological Special Diagnostic, Statens Serum Institut, Copenhagen, Denmark; Infectious Disease Research Unit, Clinical Institute, University of Southern Denmark, Odense, Denmark.
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12
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Longo BM, Venuti F, Gaviraghi A, Lupia T, Ranzani FA, Pepe A, Ponzetta L, Vita D, Allice T, Gregorc V, Frascione PMM, De Rosa FG, Calcagno A, Bonora S. Sequential or Combination Treatments as Rescue Therapies in Immunocompromised Patients with Persistent SARS-CoV-2 Infection in the Omicron Era: A Case Series. Antibiotics (Basel) 2023; 12:1460. [PMID: 37760757 PMCID: PMC10525462 DOI: 10.3390/antibiotics12091460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 09/11/2023] [Accepted: 09/12/2023] [Indexed: 09/29/2023] Open
Abstract
Prolonged SARS-CoV-2 infections are widely described in immunosuppressed patients, but safe and effective treatment strategies are lacking. We aimed to outline our approach to treating persistent COVID-19 in patients with immunosuppression from different causes. In this case series, we retrospectively enrolled all immunosuppressed patients with persistent SARS-CoV-2 infections treated at our centers between March 2022 and February 2023. Patients received different sequential or combination regimens, including antivirals (remdesivir, nirmatrelvir/ritonavir, or molnupiravir) and/or monoclonal antibodies (mAbs) (tixagevimab/cilgavimab or sotrovimab). The main outcome was a complete virological response (negative SARS-CoV-2 RT-PCR on nasopharyngeal swabs) at the end of treatment. Fifteen patients were included as follows: eleven (11/15; 73%) with hematological disease and four (4/15; 27%) with recently diagnosed HIV/AIDS infection. Six patients (6/15; 40%) received a single antiviral course, four patients (4/15; 27%) received an antiviral and mAbs sequentially, and two patients (13%) received three lines of treatment (a sequence of three antivirals or two antivirals and mAbs). A combination of two antivirals or one antiviral plus mAbs was administered in three cases (3/15, 20%). One patient died while still positive for SARS-CoV-2, while fourteen (14/15; 93%) tested negative within 16 days after the end of treatment. The median time to negativization since the last treatment was 2.5 days. Both sequential and combination regimens used in this study demonstrated high efficacy and safety in the high-risk group of immunosuppressed patients.
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Affiliation(s)
- Bianca Maria Longo
- Unit of Infectious Diseases, Department of Medical Sciences, University of Turin, “Amedeo di Savoia” Hospital, ASL “Città di Torino”, 10060 Turin, Italy (F.V.); (D.V.); (F.G.D.R.)
| | - Francesco Venuti
- Unit of Infectious Diseases, Department of Medical Sciences, University of Turin, “Amedeo di Savoia” Hospital, ASL “Città di Torino”, 10060 Turin, Italy (F.V.); (D.V.); (F.G.D.R.)
| | - Alberto Gaviraghi
- Unit of Infectious Diseases, Department of Medical Sciences, University of Turin, “Amedeo di Savoia” Hospital, ASL “Città di Torino”, 10060 Turin, Italy (F.V.); (D.V.); (F.G.D.R.)
| | - Tommaso Lupia
- Unit of Infectious Diseases, Cardinal Massaia Hospital, 14100 Asti, Italy
| | - Fabio Antonino Ranzani
- Unit of Infectious Diseases, Department of Medical Sciences, University of Turin, “Amedeo di Savoia” Hospital, ASL “Città di Torino”, 10060 Turin, Italy (F.V.); (D.V.); (F.G.D.R.)
| | - Andrea Pepe
- Unit of Infectious Diseases, Department of Medical Sciences, University of Turin, “Amedeo di Savoia” Hospital, ASL “Città di Torino”, 10060 Turin, Italy (F.V.); (D.V.); (F.G.D.R.)
| | - Laura Ponzetta
- Unit of Infectious Diseases, Department of Medical Sciences, University of Turin, “Amedeo di Savoia” Hospital, ASL “Città di Torino”, 10060 Turin, Italy (F.V.); (D.V.); (F.G.D.R.)
| | - Davide Vita
- Unit of Infectious Diseases, Department of Medical Sciences, University of Turin, “Amedeo di Savoia” Hospital, ASL “Città di Torino”, 10060 Turin, Italy (F.V.); (D.V.); (F.G.D.R.)
| | - Tiziano Allice
- Microbiology and Molecular Biology Laboratory, “Amedeo di Savoia” Hospital, ASL “Città di Torino”, 10060 Turin, Italy;
| | - Vanesa Gregorc
- Unit of Oncology and Haematology, Candiolo Cancer Institute, FPO-IRCCS, 10060 Candiolo, Italy
| | | | - Francesco Giuseppe De Rosa
- Unit of Infectious Diseases, Department of Medical Sciences, University of Turin, “Amedeo di Savoia” Hospital, ASL “Città di Torino”, 10060 Turin, Italy (F.V.); (D.V.); (F.G.D.R.)
- Department of Medical Sciences, Infectious Diseases, University of Turin, 10126 Turin, Italy
| | - Andrea Calcagno
- Unit of Infectious Diseases, Department of Medical Sciences, University of Turin, “Amedeo di Savoia” Hospital, ASL “Città di Torino”, 10060 Turin, Italy (F.V.); (D.V.); (F.G.D.R.)
| | - Stefano Bonora
- Unit of Infectious Diseases, Department of Medical Sciences, University of Turin, “Amedeo di Savoia” Hospital, ASL “Città di Torino”, 10060 Turin, Italy (F.V.); (D.V.); (F.G.D.R.)
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13
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Richner J, Class J, Simons L, Lorenzo-Redondo R, Cooper L, Dangi T, Penaloza-MacMaster P, Ozer E, Rong L, Hultquist J. SARS-CoV-2 Bottlenecks and Tissue-Specific Adaptation in the Central Nervous System. RESEARCH SQUARE 2023:rs.3.rs-3220157. [PMID: 37790412 PMCID: PMC10543031 DOI: 10.21203/rs.3.rs-3220157/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Severe COVID-19 and post-acute sequelae of SARS-CoV-2 infection are associated with neurological complications that may be linked to direct infection of the central nervous system (CNS), but the selective pressures ruling neuroinvasion are poorly defined. Here, we assessed SARS-CoV-2 evolution in the lung versus CNS of infected mice. Higher levels of viral diversity were observed in the CNS than the lung after intranasal challenge with a high frequency of mutations in the Spike furin cleavage site (FCS). Deletion of the FCS significantly attenuated virulence after intranasal challenge, with lower viral titers and decreased morbidity compared to the wild-type virus. Intracranial inoculation of the FCS-deleted virus, however, was sufficient to restore virulence. After intracranial inoculation, both viruses established infection in the lung, but this required reversion of the FCS deletion. Cumulatively, these data suggest a critical role for the FCS in determining SARS-CoV-2 tropism and compartmentalization with possible implications for the treatment of neuroinvasive COVID-19.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Lijun Rong
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago
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14
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Motsoeneng BM, Manamela NP, Kaldine H, Kgagudi P, Hermanus T, Ayres F, Makhado Z, Moyo-Gwete T, van der Mescht MA, Abdullah F, Boswell MT, Ueckermann V, Rossouw TM, Madhi SA, Moore PL, Richardson SI. Despite delayed kinetics, people living with HIV achieve equivalent antibody function after SARS-CoV-2 infection or vaccination. Front Immunol 2023; 14:1231276. [PMID: 37600825 PMCID: PMC10435738 DOI: 10.3389/fimmu.2023.1231276] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/17/2023] [Indexed: 08/22/2023] Open
Abstract
The kinetics of Fc-mediated functions following SARS-CoV-2 infection or vaccination in people living with HIV (PLWH) are not known. We compared SARS-CoV-2 spike-specific Fc functions, binding, and neutralization in PLWH and people without HIV (PWOH) during acute infection (without prior vaccination) with either the D614G or Beta variants of SARS-CoV-2, or vaccination with ChAdOx1 nCoV-19. Antiretroviral treatment (ART)-naïve PLWH had significantly lower levels of IgG binding, neutralization, and antibody-dependent cellular phagocytosis (ADCP) compared with PLWH on ART. The magnitude of antibody-dependent cellular cytotoxicity (ADCC), complement deposition (ADCD), and cellular trogocytosis (ADCT) was differentially triggered by D614G and Beta. The kinetics of spike IgG-binding antibodies, ADCC, and ADCD were similar, irrespective of the infecting variant between PWOH and PLWH overall. However, compared with PWOH, PLWH infected with D614G had delayed neutralization and ADCP. Furthermore, Beta infection resulted in delayed ADCT, regardless of HIV status. Despite these delays, we observed improved coordination between binding and neutralizing responses and Fc functions in PLWH. In contrast to D614G infection, binding responses in PLWH following ChAdOx-1 nCoV-19 vaccination were delayed, while neutralization and ADCP had similar timing of onset, but lower magnitude, and ADCC was significantly higher than in PWOH. Overall, despite delayed and differential kinetics, PLWH on ART develop comparable responses to PWOH, supporting the prioritization of ART rollout and SARS-CoV-2 vaccination in PLWH.
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Affiliation(s)
- Boitumelo M. Motsoeneng
- South African Medical Research Council Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- HIV Virology Section, Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
| | - Nelia P. Manamela
- South African Medical Research Council Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- HIV Virology Section, Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
| | - Haajira Kaldine
- South African Medical Research Council Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- HIV Virology Section, Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
| | - Prudence Kgagudi
- South African Medical Research Council Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- HIV Virology Section, Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
| | - Tandile Hermanus
- South African Medical Research Council Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- HIV Virology Section, Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
| | - Frances Ayres
- South African Medical Research Council Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- HIV Virology Section, Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
| | - Zanele Makhado
- South African Medical Research Council Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- HIV Virology Section, Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
| | - Thandeka Moyo-Gwete
- South African Medical Research Council Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- HIV Virology Section, Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
| | - Mieke A. van der Mescht
- Department of Immunology, Faculty of Health Science, University of Pretoria, Pretoria, South Africa
| | - Fareed Abdullah
- Division for Infectious Diseases, Department of Internal Medicine, Steve Biko Academic Hospital and University of Pretoria, Pretoria, South Africa
- South African Medical Research Council Office of AIDS and TB Research, Pretoria, South Africa
| | - Michael T. Boswell
- Division for Infectious Diseases, Department of Internal Medicine, Steve Biko Academic Hospital and University of Pretoria, Pretoria, South Africa
| | - Veronica Ueckermann
- Division for Infectious Diseases, Department of Internal Medicine, Steve Biko Academic Hospital and University of Pretoria, Pretoria, South Africa
| | - Theresa M. Rossouw
- Department of Immunology, Faculty of Health Science, University of Pretoria, Pretoria, South Africa
| | - Shabir A. Madhi
- South African Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- African Leadership in Vaccinology Expertise, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- Infectious Diseases and Oncology Research Institute, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Penny L. Moore
- South African Medical Research Council Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- HIV Virology Section, Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- Centre for the AIDS Programme of Research in South Africa (CAPRISA), University of KwaZulu Natal, Durban, South Africa
| | - Simone I. Richardson
- South African Medical Research Council Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
- HIV Virology Section, Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
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15
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de Moor WRJ, Williamson AL, Schäfer G, Douglass N, Gers S, Sutherland AD, Blumenthal MJ, Margolin E, Shaw ML, Preiser W, Chapman R. LSDV-Vectored SARS-CoV-2 S and N Vaccine Protects against Severe Clinical Disease in Hamsters. Viruses 2023; 15:1409. [PMID: 37515096 PMCID: PMC10383203 DOI: 10.3390/v15071409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Revised: 06/17/2023] [Accepted: 06/18/2023] [Indexed: 07/30/2023] Open
Abstract
The SARS-CoV-2 pandemic demonstrated the need for potent and broad-spectrum vaccines. This study reports the development and testing of a lumpy skin disease virus (LSDV)-vectored vaccine against SARS-CoV-2, utilizing stabilized spike and conserved nucleocapsid proteins as antigens to develop robust immunogenicity. Construction of the vaccine (LSDV-SARS2-S,N) was confirmed by polymerase chain reaction (PCR) amplification and sequencing. In vitro characterization confirmed that cells infected with LSDV-SARS2-S,N expressed SARS-CoV-2 spike and nucleocapsid protein. In BALB/c mice, the vaccine elicited high magnitude IFN-γ ELISpot responses (spike: 2808 SFU/106 splenocytes) and neutralizing antibodies (ID50 = 6552). Testing in hamsters, which emulate human COVID-19 disease progression, showed the development of high titers of neutralizing antibodies against the Wuhan and Delta SARS-CoV-2 variants (Wuhan ID50 = 2905; Delta ID50 = 4648). Additionally, hamsters vaccinated with LSDV-SARS2-S,N displayed significantly less weight loss, lung damage, and reduced viral RNA copies following SARS-CoV-2 infection with the Delta variant as compared to controls, demonstrating protection against disease. These data demonstrate that LSDV-vectored vaccines display promise as an effective SARS-CoV-2 vaccine and as a potential vaccine platform for communicable diseases in humans and animals. Further efficacy testing and immune response analysis, particularly in non-human primates, are warranted.
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Affiliation(s)
- Warren R J de Moor
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town 7925, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Anna-Lise Williamson
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town 7925, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | - Georgia Schäfer
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- International Centre for Genetic Engineering and Biotechnology, Observatory, Cape Town 7925, South Africa
- Wellcome Trust Centre for Infectious Disease Research in Africa, University of Cape Town, Cape Town 7925, South Africa
| | - Nicola Douglass
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town 7925, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
| | | | - Andrew D Sutherland
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University Tygerberg Campus, Cape Town 7505, South Africa
| | - Melissa J Blumenthal
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- International Centre for Genetic Engineering and Biotechnology, Observatory, Cape Town 7925, South Africa
| | - Emmanuel Margolin
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
- Wellcome Trust Centre for Infectious Disease Research in Africa, University of Cape Town, Cape Town 7925, South Africa
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town 7701, South Africa
| | - Megan L Shaw
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University Tygerberg Campus, Cape Town 7505, South Africa
- Department of Medical Biosciences, Faculty of Natural Sciences, University of the Western Cape, Bellville, Cape Town 7535, South Africa
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University Tygerberg Campus, Cape Town 7505, South Africa
| | - Rosamund Chapman
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Observatory, Cape Town 7925, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town 7925, South Africa
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16
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Perumal R, Shunmugam L, Naidoo K, Wilkins D, Garzino-Demo A, Brechot C, Vahlne A, Nikolich J. Biological mechanisms underpinning the development of long COVID. iScience 2023; 26:106935. [PMID: 37265584 PMCID: PMC10193768 DOI: 10.1016/j.isci.2023.106935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023] Open
Abstract
As COVID-19 evolves from a pandemic to an endemic disease, the already staggering number of people that have been or will be infected with SARS-CoV-2 is only destined to increase, and the majority of humanity will be infected. It is well understood that COVID-19, like many other viral infections, leaves a significant fraction of the infected with prolonged consequences. Continued high number of SARS-CoV-2 infections, viral evolution with escape from post-infection and vaccinal immunity, and reinfections heighten the potential impact of Long COVID. Hence, the impact of COVID-19 on human health will be seen for years to come until more effective vaccines and pharmaceutical treatments become available. To that effect, it is imperative that the mechanisms underlying the clinical manifestations of Long COVID be elucidated. In this article, we provide an in-depth analysis of the evidence on several potential mechanisms of Long COVID and discuss their relevance to its pathogenesis.
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Affiliation(s)
- Rubeshan Perumal
- South African Medical Research Council (SAMRC)-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4001, South Africa
- Department of Pulmonology and Critical Care, Division of Internal Medicine, School of Clinical Medicine, Nelson R Mandela School of Medicine, University of KwaZulu-Natal, Durban 4001, South Africa
- Department of Immunobiology and the University of Arizona Center on Aging, University of Arizona College of Medicine-Tucson, Tucson, AZ 85724, USA
| | - Letitia Shunmugam
- South African Medical Research Council (SAMRC)-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4001, South Africa
| | - Kogieleum Naidoo
- South African Medical Research Council (SAMRC)-CAPRISA HIV-TB Pathogenesis and Treatment Research Unit, Centre for the AIDS Programme of Research in South Africa (CAPRISA), Durban 4001, South Africa
| | - Dave Wilkins
- The Global Virus Network, Baltimore, MD 21201, USA
| | - Alfredo Garzino-Demo
- The Global Virus Network, Baltimore, MD 21201, USA
- Department of Molecular Medicine, University of Padova, Padova 1- 35129, Italy
| | - Christian Brechot
- The Global Virus Network, Baltimore, MD 21201, USA
- Infectious Disease and International Health, University of South Florida, Tampa, FL 33620, USA
| | - Anders Vahlne
- The Global Virus Network, Baltimore, MD 21201, USA
- Division of Clinical Microbiology, Karolinska Institute, Stockholm 17165, Sweden
| | - Janko Nikolich
- The Global Virus Network, Baltimore, MD 21201, USA
- The Aegis Consortium for Pandemic-Free Future, University of Arizona Health Sciences, University of Arizona College of Medicine-Tucson, Tucson, AZ 85724, USA
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17
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Wang Q, Zhang QR, Zhang Y, Chen T. [Repeatedly re-detectable positive for SARS-CoV-2 by RT-PCR in the immunosuppressive therapy of a patient: a case report and literature review]. ZHONGHUA XUE YE XUE ZA ZHI = ZHONGHUA XUEYEXUE ZAZHI 2023; 44:520-522. [PMID: 37550213 PMCID: PMC10450550 DOI: 10.3760/cma.j.issn.0253-2727.2023.06.016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Indexed: 08/09/2023]
Affiliation(s)
- Q Wang
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Q R Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - Y Zhang
- Department of Infectious Diseases, Huashan Hospital, Fudan University, Shanghai 200040, China
| | - T Chen
- Department of Hematology, Huashan Hospital, Fudan University, Shanghai 200040, China
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18
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Kassanjee R, Davies M, Ngwenya O, Osei‐Yeboah R, Jacobs T, Morden E, Timmerman V, Britz S, Mendelson M, Taljaard J, Riou J, Boulle A, Tiffin N, Zinyakatira N. COVID-19 among adults living with HIV: correlates of mortality among public sector healthcare users in Western Cape, South Africa. J Int AIDS Soc 2023; 26:e26104. [PMID: 37339333 PMCID: PMC10281639 DOI: 10.1002/jia2.26104] [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: 10/20/2022] [Accepted: 05/02/2023] [Indexed: 06/22/2023] Open
Abstract
INTRODUCTION While a large proportion of people with HIV (PWH) have experienced SARS-CoV-2 infections, there is uncertainty about the role of HIV disease severity on COVID-19 outcomes, especially in lower-income settings. We studied the association of mortality with characteristics of HIV severity and management, and vaccination, among adult PWH. METHODS We analysed observational cohort data on all PWH aged ≥15 years experiencing a diagnosed SARS-CoV-2 infection (until March 2022), who accessed public sector healthcare in the Western Cape province of South Africa. Logistic regression was used to study the association of mortality with evidence of antiretroviral therapy (ART) collection, time since first HIV evidence, CD4 cell count, viral load (among those with evidence of ART collection) and COVID-19 vaccination, adjusting for demographic characteristics, comorbidities, admission pressure, location and time period. RESULTS Mortality occurred in 5.7% (95% CI: 5.3,6.0) of 17,831 first-diagnosed infections. Higher mortality was associated with lower recent CD4, no evidence of ART collection, high or unknown recent viral load and recent first HIV evidence, differentially by age. Vaccination was protective. The burden of comorbidities was high, and tuberculosis (especially more recent episodes of tuberculosis), chronic kidney disease, diabetes and hypertension were associated with higher mortality, more strongly in younger adults. CONCLUSIONS Mortality was strongly associated with suboptimal HIV control, and the prevalence of these risk factors increased in later COVID-19 waves. It remains a public health priority to ensure PWH are on suppressive ART and vaccinated, and manage any disruptions in care that occurred during the pandemic. The diagnosis and management of comorbidities, including for tuberculosis, should be optimized.
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Affiliation(s)
- Reshma Kassanjee
- School of Public HealthUniversity of Cape TownCape TownSouth Africa
| | - Mary‐Ann Davies
- School of Public HealthUniversity of Cape TownCape TownSouth Africa
- Department of HealthWestern Cape GovernmentCape TownSouth Africa
| | - Olina Ngwenya
- Wellcome Centre for Infectious Disease Research in AfricaInstitute of Infectious Diseases and Molecular MedicineUniversity of Cape TownCape TownSouth Africa
| | - Richard Osei‐Yeboah
- Division of Computational BiologyIntegrative Biomedical Sciences DepartmentFaculty of Health SciencesUniversity of Cape TownCape TownSouth Africa
| | - Theuns Jacobs
- Department of HealthWestern Cape GovernmentCape TownSouth Africa
| | - Erna Morden
- School of Public HealthUniversity of Cape TownCape TownSouth Africa
- Department of HealthWestern Cape GovernmentCape TownSouth Africa
| | - Venessa Timmerman
- School of Public HealthUniversity of Cape TownCape TownSouth Africa
- Department of HealthWestern Cape GovernmentCape TownSouth Africa
| | - Stefan Britz
- Department of Statistical SciencesUniversity of Cape TownCape TownSouth Africa
| | - Marc Mendelson
- Division of Infectious Diseases and HIV MedicineDepartment of MedicineGroote Schuur HospitalUniversity of Cape TownCape TownSouth Africa
| | - Jantjie Taljaard
- Division of Infectious DiseasesDepartment of MedicineTygerberg HospitalStellenbosch UniversityCape TownSouth Africa
| | - Julien Riou
- Institute of Social and Preventive MedicineUniversity of BernBernSwitzerland
| | - Andrew Boulle
- School of Public HealthUniversity of Cape TownCape TownSouth Africa
- Department of HealthWestern Cape GovernmentCape TownSouth Africa
| | - Nicki Tiffin
- South African National Bioinformatics InstituteUniversity of the Western CapeCape TownSouth Africa
| | - Nesbert Zinyakatira
- School of Public HealthUniversity of Cape TownCape TownSouth Africa
- Department of HealthWestern Cape GovernmentCape TownSouth Africa
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19
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Yi Y, Han X, Cui X, Wang P, Wang X, Liu H, Wang Y, Zhu N, Li Y, Lin Y, Li X. Safety and Immunogenicity of the Inactivated COVID-19 Vaccine Booster in People Living with HIV in China. Vaccines (Basel) 2023; 11:1019. [PMID: 37376408 DOI: 10.3390/vaccines11061019] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 05/18/2023] [Accepted: 05/20/2023] [Indexed: 06/29/2023] Open
Abstract
Current knowledge regarding the long-term humoral response of people infected with human immunodeficiency virus to the third dose of inactivated coronavirus disease (COVID-19) vaccine is incomplete. As a result, concerns remain about the safety and efficacy of the vaccination. To improve our understanding of the safety and immunogenicity of the COVID-19 inactivated vaccine booster in people living with HIV (PLWH), a prospective study was conducted on participants who had not yet received a third dose of the COVID-19 inactivated vaccine, had no history of SARS-CoV-2 infection, and had received a second dose of the vaccine more than six months prior. The primary safety outcomes included the incidence of adverse reactions, changes in CD4+ T-cell count, viral load, blood routine examination, liver and kidney function examination, blood sugar, and blood lipid examination. The pseudovirus-neutralizing antibody responses to the D614G variant, Delta variant, and Omicron variants BA.5 and BF.7 were evaluated before vaccination, 14 days, 28 days, 3 months, and 6 months after vaccination to evaluate the immune response of PLWH to the injection of inactivated vaccine booster and the safety of the vaccine. In conclusion, COVID-19 vaccine booster shots were effective in PLWH, resulting in an increase in the number of CD4+ T-cells, neutralizing antibodies that lasted up to six months, and higher levels of neutralizing antibodies lasting approximately 3 months. However, the vaccine protection against the two variants of BA.5 and BF.7 was significantly lower than that of D614G and Delta.
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Affiliation(s)
- Yunyun Yi
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Xiaoxu Han
- Beijing Key Laboratory for HIV/AIDS Research, Clinical and Research, Center for Infectious Diseases, Beijing Youan Hospital, Capital Medical University, Beijing 100069, China
| | - Xinyu Cui
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Peng Wang
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Xin Wang
- Center of Integrative Medicine, Peking University Ditan Teaching Hospital, Beijing 100015, China
| | - Hui Liu
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Yuqi Wang
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Na Zhu
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Yanyan Li
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
| | - Yingying Lin
- Center of Integrative Medicine, Peking University Ditan Teaching Hospital, Beijing 100015, China
| | - Xin Li
- Center of Integrative Medicine, Beijing Ditan Hospital, Capital Medical University, Beijing 100015, China
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20
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Maponga TG, Jeffries M, Tegally H, Sutherland A, Wilkinson E, Lessells RJ, Msomi N, van Zyl G, de Oliveira T, Preiser W. Reply to Molldrem. Clin Infect Dis 2023; 76:1702-1703. [PMID: 36718545 DOI: 10.1093/cid/ciad049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 01/24/2023] [Indexed: 02/01/2023] Open
Affiliation(s)
- Tongai G Maponga
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Montenique Jeffries
- Department of Medicine, Stellenbosch University and Tygerberg Academic Hospital, Cape Town, South Africa
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Andrew Sutherland
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
| | - Eduan Wilkinson
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
| | - Richard J Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Nokukhanya Msomi
- Discipline of Virology, School of Laboratory Medicine and Medical Sciences and National Health Laboratory Service (NHLS), University of KwaZulu-Natal, Durban, South Africa
| | - Gert van Zyl
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- National Health Laboratory Service, Tygerberg Business Unit, Cape Town, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform (KRISP), School of Laboratory Medicine & Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Department of Global Health, University of Washington, Seattle, Washington, USA
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University, Cape Town, South Africa
- National Health Laboratory Service, Tygerberg Business Unit, Cape Town, South Africa
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21
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Molldrem S. Research on the Development of Severe Acute Respiratory Syndrome Coronavirus 2 Variants of Concern in People With Advanced Human Immunodeficiency Virus Disease Should Highlight Structural Conditions and Avoid Harmful Stereotypes. Clin Infect Dis 2023; 76:1701-1702. [PMID: 36718523 DOI: 10.1093/cid/ciad048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2022] [Accepted: 01/24/2023] [Indexed: 02/01/2023] Open
Affiliation(s)
- Stephen Molldrem
- Department of Bioethics and Health Humanities, School of Public and Population Health, The University of Texas Medical Branch at Galveston, Galveston, Texas, USA
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22
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Riddell AC, Cutino-Moguel T. The origins of new SARS-COV-2 variants in immunocompromised individuals. Curr Opin HIV AIDS 2023; 18:148-156. [PMID: 36977190 DOI: 10.1097/coh.0000000000000794] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023]
Abstract
PURPOSE OF REVIEW To explore the origins of new severe acute respiratory coronavirus 2 (SARS-CoV-2) variants in immunocompromised individuals and whether the emergence of novel mutations in these individuals is responsible for the development of variants of concern (VOC). RECENT FINDINGS Next generation sequencing of samples from chronically infected immunocompromised patients has enabled identification of VOC- defining mutations in individuals prior to the emergence of these variants worldwide. Whether these individuals are the source of variant generation is uncertain. Vaccine effectiveness in immunocompromised individuals and with respect to VOCs is also discussed. SUMMARY Current evidence on chronic SARS-CoV-2 infection in immunocompromised populations is reviewed including the relevance of this to the generation of novel variants. Continued viral replication in the absence of an effective immune response at an individual level or high levels of viral infection at the population level are likely to have contributed to the appearance of the main VOC.
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Affiliation(s)
- Anna C Riddell
- Department of Virology, Division of Infection, Barts Health NHS Trust, London, UK
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23
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Margolin E, Schäfer G, Allen JD, Gers S, Woodward J, Sutherland AD, Blumenthal M, Meyers A, Shaw ML, Preiser W, Strasser R, Crispin M, Williamson AL, Rybicki EP, Chapman R. A plant-produced SARS-CoV-2 spike protein elicits heterologous immunity in hamsters. FRONTIERS IN PLANT SCIENCE 2023; 14:1146234. [PMID: 36959936 PMCID: PMC10028082 DOI: 10.3389/fpls.2023.1146234] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2023] [Accepted: 02/17/2023] [Indexed: 06/16/2023]
Abstract
Molecular farming of vaccines has been heralded as a cheap, safe and scalable production platform. In reality, however, differences in the plant biosynthetic machinery, compared to mammalian cells, can complicate the production of viral glycoproteins. Remodelling the secretory pathway presents an opportunity to support key post-translational modifications, and to tailor aspects of glycosylation and glycosylation-directed folding. In this study, we applied an integrated host and glyco-engineering approach, NXS/T Generation™, to produce a SARS-CoV-2 prefusion spike trimer in Nicotiana benthamiana as a model antigen from an emerging virus. The size exclusion-purified protein exhibited a characteristic prefusion structure when viewed by transmission electron microscopy, and this was indistinguishable from the equivalent mammalian cell-produced antigen. The plant-produced protein was decorated with under-processed oligomannose N-glycans and exhibited a site occupancy that was comparable to the equivalent protein produced in mammalian cell culture. Complex-type glycans were almost entirely absent from the plant-derived material, which contrasted against the predominantly mature, complex glycans that were observed on the mammalian cell culture-derived protein. The plant-derived antigen elicited neutralizing antibodies against both the matched Wuhan and heterologous Delta SARS-CoV-2 variants in immunized hamsters, although titres were lower than those induced by the comparator mammalian antigen. Animals vaccinated with the plant-derived antigen exhibited reduced viral loads following challenge, as well as significant protection from SARS-CoV-2 disease as evidenced by reduced lung pathology, lower viral loads and protection from weight loss. Nonetheless, animals immunized with the mammalian cell-culture-derived protein were better protected in this challenge model suggesting that more faithfully reproducing the native glycoprotein structure and associated glycosylation of the antigen may be desirable.
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Affiliation(s)
- Emmanuel Margolin
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Wellcome Trust Centre for Infectious Disease Research in Africa, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Georgia Schäfer
- Wellcome Trust Centre for Infectious Disease Research in Africa, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- International Centre for Genetic Engineering and Biotechnology, Observatory, Cape Town, Cape Town, South Africa
| | - Joel D Allen
- School of Biological Sciences and Institute of Life Sciences, University of Southampton, Southampton, United Kingdom
| | | | - Jeremy Woodward
- Electron Microscope Unit, University of Cape Town, Cape Town, South Africa
| | - Andrew D Sutherland
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University Tygerberg Campus, Cape Town, South Africa
| | - Melissa Blumenthal
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- International Centre for Genetic Engineering and Biotechnology, Observatory, Cape Town, Cape Town, South Africa
| | - Ann Meyers
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Megan L Shaw
- Department of Medical Biosciences, University of the Western Cape, Cape Town, South Africa
| | - Wolfgang Preiser
- Division of Medical Virology, Faculty of Medicine and Health Sciences, Stellenbosch University Tygerberg Campus, Cape Town, South Africa
| | - Richard Strasser
- Department of Applied Genetics and Cell Biology, University of Natural Resources and Life Sciences, Vienna, Austria
| | - Max Crispin
- School of Biological Sciences and Institute of Life Sciences, University of Southampton, Southampton, United Kingdom
| | - Anna-Lise Williamson
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Edward P Rybicki
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Biopharming Research Unit, Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa
| | - Ros Chapman
- Division of Medical Virology, Department of Pathology, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
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24
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Thornhill J, Orkin C, Cevik M. Estimating the global impact of coronavirus disease 2019 on people living with HIV. Curr Opin Infect Dis 2023; 36:20-25. [PMID: 36729763 DOI: 10.1097/qco.0000000000000898] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
PURPOSE OF REVIEW The COVID-19 pandemic and public health response have directly and indirectly affected broader health outcomes, especially for those with existing chronic conditions, including HIV. We examine our current understanding of the global impact of COVID-19 on people with HIV (PWH). RECENT FINDINGS The interaction between COVID-19 and HIV is complex, making it challenging to estimate its true impact on PWH. Evidence to date does not suggest that HIV confers a higher risk of acquiring SARS-CoV-2. However, once acquired, HIV increases the risk of severe COVID-19 and mortality, particularly in immunosuppressed viraemic individuals and in the context of traditional COVID-19 risk factors, including disparities in social determinants of health. In addition, COVID-19 vaccines may be less effective in the context of HIV infection with additional doses needed. The consequences of disruption of access to essential prevention and treatment services because of the pandemic are becoming evident and will likely adversely affect outcomes, risking decades of progress. SUMMARY Given the increased mortality risk and reduced vaccine effectiveness seen in PWH, specific prevention and support measures are needed, including prioritization of vaccination and boosters, funding to mitigate the impact of pandemic and enabling integrated healthcare delivery during pandemics will be critical.
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Affiliation(s)
- John Thornhill
- Department of Infection and Immunity, Blizzard Institute, Queen Mary University of London
| | - Chloe Orkin
- Department of Infection and Immunity, Blizzard Institute, Queen Mary University of London
- Royal London Hospital, Barts Health NHS Trust, London
| | - Muge Cevik
- Division of Infection and Global Health Research, School of Medicine, University of St Andrews, St Andrews
- NHS Lothian Infection Service, Regional Infectious Diseases Unit, Western General Hospital, Edinburgh, UK
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25
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Venturas JP. HIV and COVID-19 Disease. Semin Respir Crit Care Med 2023; 44:35-49. [PMID: 36646084 DOI: 10.1055/s-0042-1758852] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Despite effective antiretroviral therapy (ART), HIV infected individuals throughout the world remain at significant risk of respiratory infections and non-communicable disease. Severe disease from SARS-CoV-2 is associated with a hyperinflammatory phenotype which manifests in the lungs as pneumonia and in some cases can lead to acute respiratory failure. Progression to severe COVID-19 is associated with comorbid disease such as obesity, diabetes mellitus and cardiovascular disease, however data concerning the associated risks of HIV coinfection are still conflicting, with large population studies demonstrating poorer outcomes, whilst smaller, case-controlled studies showing better outcomes. Furthermore, underlying immunopathological processes within the lungs and elsewhere, including interactions with other opportunistic infections (OI), remain largely undefined. Nonetheless, new and repurposed anti-viral therapies and vaccines which have been developed are safe to use in this population, and anti-inflammatory agents are recommended with the caveat that the coexistence of opportunistic infections is considered and excluded. Finally, HIV infected patients remain reliant on good ART adherence practices to maintain HIV viral suppression, and some of these practices were disrupted during the COVID-19 pandemic, putting these patients at further risk for acute and long-term adverse outcomes.
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Affiliation(s)
- Jacqui P Venturas
- Department of Internal Medicine and Pulmonology, Charlotte Maxeke Johannesburg Academic Hospital and Universtity of the Witwatersrand, Johannesburg, South Africa
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26
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Kang S, Kim JY, Park H, Lim SY, Kim J, Chang E, Bae S, Jung J, Kim MJ, Chong YP, Lee S, Choi S, Kim YS, Park M, Kim S. Comparison of secondary attack rate and viable virus shedding between patients with SARS-CoV-2 Delta and Omicron variants: A prospective cohort study. J Med Virol 2023; 95:e28369. [PMID: 36458559 PMCID: PMC9877691 DOI: 10.1002/jmv.28369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 11/12/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022]
Abstract
There are limited data comparing the transmission rates and kinetics of viable virus shedding of the Omicron variant to those of the Delta variant. We compared these rates in hospitalized patients infected with Delta and Omicron variants. We prospectively enrolled adult patients with COVID-19 admitted to a tertiary care hospital in South Korea between September 2021 and May 2022. Secondary attack rates were calculated by epidemiologic investigation, and daily saliva samples were collected to evaluate viral shedding kinetics. Genomic and subgenomic SARS-CoV-2 RNA was measured by PCR, and virus culture was performed from daily saliva samples. A total of 88 patients with COVID-19 who agreed to daily sampling and were interviewed, were included. Of the 88 patients, 48 (59%) were infected with Delta, and 34 (41%) with Omicron; a further 5 patients gave undetectable or inconclusive RNA PCR results and 1 was suspected of being coinfected with both variants. Omicron group had a higher secondary attack rate (31% [38/124] vs. 7% [34/456], p < 0.001). Survival analysis revealed that shorter viable virus shedding period was observed in Omicron variant compared with Delta variant (median 4, IQR [1-7], vs. 8.5 days, IQR [5-12 days], p < 0.001). Multivariable analysis revealed that moderate-to-critical disease severity (HR: 1.96), and immunocompromised status (HR: 2.17) were independent predictors of prolonged viral shedding, whereas completion of initial vaccine series or first booster-vaccinated status (HR: 0.49), and Omicron infection (HR: 0.44) were independently associated with shorter viable virus shedding. Patients with Omicron infections had higher transmission rates but shorter periods of transmissible virus shedding than those with Delta infections.
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Affiliation(s)
- Sung‐Woon Kang
- Department of Infectious Diseases, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Ji Yeun Kim
- Department of Infectious Diseases, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Heedo Park
- Department of Biomedical Sciences, BK21 Graduate ProgramKorea University College of MedicineSeoulRepublic of Korea
- Department of Microbiology, Institute for Viral Diseases, Vaccine Innovation Center, College of MedicineKorea UniversitySeoulSouth Korea
| | - So Yun Lim
- Department of Infectious Diseases, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Jeonghun Kim
- Department of Biomedical Sciences, BK21 Graduate ProgramKorea University College of MedicineSeoulRepublic of Korea
- Department of Microbiology, Institute for Viral Diseases, Vaccine Innovation Center, College of MedicineKorea UniversitySeoulSouth Korea
| | - Euijin Chang
- Department of Infectious Diseases, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Seongman Bae
- Department of Infectious Diseases, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Jiwon Jung
- Department of Infectious Diseases, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Min Jae Kim
- Department of Infectious Diseases, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Yong Pil Chong
- Department of Infectious Diseases, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Sang‐Oh Lee
- Department of Infectious Diseases, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Sang‐Ho Choi
- Department of Infectious Diseases, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Yang Soo Kim
- Department of Infectious Diseases, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
| | - Man‐Seong Park
- Department of Biomedical Sciences, BK21 Graduate ProgramKorea University College of MedicineSeoulRepublic of Korea
- Department of Microbiology, Institute for Viral Diseases, Vaccine Innovation Center, College of MedicineKorea UniversitySeoulSouth Korea
| | - Sung‐Han Kim
- Department of Infectious Diseases, Asan Medical CenterUniversity of Ulsan College of MedicineSeoulRepublic of Korea
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Lustig G, Ganga Y, Rodel H, Tegally H, Jackson L, Cele S, Khan K, Jule Z, Reedoy K, Karim F, Bernstein M, Moosa MYS, Archary D, de Oliveira T, Lessells R, Abdool Karim SS, Sigal A. SARS-CoV-2 evolves increased infection elicited cell death and fusion in an immunosuppressed individual. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.11.23.22282673. [PMID: 36451879 PMCID: PMC9709797 DOI: 10.1101/2022.11.23.22282673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 06/17/2023]
Abstract
The milder clinical manifestations of Omicron infection relative to pre-Omicron SARS CoV-2 raises the possibility that extensive evolution results in reduced pathogenicity. To test this hypothesis, we quantified induction of cell fusion and cell death in SARS CoV-2 evolved from ancestral virus during long-term infection. Both cell fusion and death were reduced in Omicron BA.1 infection relative to ancestral virus. Evolved virus was isolated at different times during a 6-month infection in an immunosuppressed individual with advanced HIV disease. The virus isolated 16 days post-reported symptom onset induced fusogenicity and cell death at levels similar to BA.1. However, fusogenicity was increased in virus isolated at 6 months post-symptoms to levels intermediate between BA.1 and ancestral SARS-CoV-2. Similarly, infected cell death showed a graded increase from earlier to later isolates. These results may indicate that, at least by the cellular measures used here, evolution in long-term infection does not necessarily attenuate the virus.
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Affiliation(s)
- Gila Lustig
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Yashica Ganga
- Africa Health Research Institute, Durban, South Africa
| | - Hylton Rodel
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Division of Infection and Immunity, University College London, London, UK
| | - Houriiyah Tegally
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | | | - Sandile Cele
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Khadija Khan
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | - Zesuliwe Jule
- Africa Health Research Institute, Durban, South Africa
| | - Kajal Reedoy
- Africa Health Research Institute, Durban, South Africa
| | - Farina Karim
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
| | | | - Mahomed-Yunus S Moosa
- Department of Infectious Diseases, Nelson R. Mandela School of Clinical Medicine, University of KwaZulu-Natal, Durban, South Africa
| | - Derseree Archary
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
| | - Tulio de Oliveira
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
- Centre for Epidemic Response and Innovation (CERI), School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa
- Department of Global Health, University of Washington, Seattle, USA
| | - Richard Lessells
- KwaZulu-Natal Research Innovation and Sequencing Platform, Durban, South Africa
| | - Salim S Abdool Karim
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Department of Epidemiology, Mailman School of Public Health, Columbia University, New York, NY, United States
| | - Alex Sigal
- Centre for the AIDS Programme of Research in South Africa, Durban, South Africa
- Africa Health Research Institute, Durban, South Africa
- School of Laboratory Medicine and Medical Sciences, University of KwaZulu-Natal, Durban, South Africa
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28
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Kassanjee R, Davies MA, Ngwenya O, Osei-Yeboah R, Jacobs T, Morden E, Timmerman V, Britz S, Mendelson M, Taljaard J, Riou J, Boulle A, Tiffin N, Zinyakatira N. COVID-19 among adults living with HIV: Correlates of mortality in a general population in a resource-limited setting. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.10.17.22281085. [PMID: 36299434 PMCID: PMC9603837 DOI: 10.1101/2022.10.17.22281085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Introduction While a large proportion of people with HIV (PWH) have experienced SARS-CoV-2 infections, there is uncertainty about the role of HIV disease severity on COVID-19 outcomes, especially in lower income settings. We studied the association between mortality and characteristics of HIV severity and management, and vaccination, among adult PWH. Methods We analysed observational cohort data on all PWH aged ≥15 years experiencing a diagnosed SARS-CoV-2 infection (until March 2022), who accessed public sector healthcare in the Western Cape province of South Africa. Logistic regression was used to study the association of mortality with CD4 cell count, viral load, evidence of ART, time since first HIV evidence, and vaccination, adjusting for demographic characteristics, comorbidities, admission pressure, location and time period. Results Mortality occurred in 5.7% (95% CI: 5.3,6.0) of 17 831 first diagnosed infections. Higher mortality was associated with lower recent CD4, no evidence of ART collection, high or unknown recent viral load (among those with ART evidence), and recent first HIV evidence, differentially by age. Vaccination was protective. The burden of comorbidities was high, and tuberculosis, chronic kidney disease, diabetes and hypertension were associated with higher mortality, more strongly in younger adults. Conclusions Mortality was strongly associated with suboptimal HIV control, and prevalence of these risk factors increased in later COVID-19 waves. It remains a public health priority to ensure PWH are on suppressive ART and vaccinated, and manage any disruptions in care that occurred during the pandemic. The diagnosis and management of comorbidities, including for tuberculosis, should be optimised.
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Affiliation(s)
- Reshma Kassanjee
- School of Public Health, University of Cape Town, Cape Town, South Africa
| | - Mary-Ann Davies
- School of Public Health, University of Cape Town, Cape Town, South Africa
- Western Cape Government: Health and Wellness, Cape Town, South Africa
| | - Olina Ngwenya
- Wellcome Centre for Infectious Disease Research in Africa, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Cape Town, South Africa
| | - Richard Osei-Yeboah
- Division of Computational Biology, Integrative Biomedical Sciences Department, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
| | - Theuns Jacobs
- School of Public Health, University of Cape Town, Cape Town, South Africa
- Western Cape Government: Health and Wellness, Cape Town, South Africa
| | - Erna Morden
- School of Public Health, University of Cape Town, Cape Town, South Africa
- Western Cape Government: Health and Wellness, Cape Town, South Africa
| | - Venessa Timmerman
- Western Cape Government: Health and Wellness, Cape Town, South Africa
| | - Stefan Britz
- Department of Statistical Sciences, University of Cape Town, Cape Town, South Africa
| | - Marc Mendelson
- Division of Infectious Diseases and HIV Medicine, Department of Medicine, Groote Schuur Hospital, University of Cape Town, South Africa
| | - Jantjie Taljaard
- Division of Infectious Diseases, Department of Medicine, Tygerberg Hospital, Stellenbosch University, South Africa
| | - Julien Riou
- Institute of Social and Preventive Medicine, University of Bern, Bern, Switzerland
| | - Andrew Boulle
- School of Public Health, University of Cape Town, Cape Town, South Africa
- Western Cape Government: Health and Wellness, Cape Town, South Africa
| | - Nicki Tiffin
- Western Cape Government: Health and Wellness, Cape Town, South Africa
- University of the Western Cape, Cape Town, South Africa
| | - Nesbert Zinyakatira
- School of Public Health, University of Cape Town, Cape Town, South Africa
- Western Cape Government: Health and Wellness, Cape Town, South Africa
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29
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Hensley KS, Jongkees MJ, Geers D, GeurtsvanKessel CH, Mueller YM, Dalm VASH, Papageorgiou G, Steggink H, Gorska A, Bogers S, den Hollander JG, Bierman WFW, Gelinck LBS, Schippers EF, Ammerlaan HSM, van der Valk M, van Vonderen MGA, Delsing CE, Gisolf EH, Bruns AHW, Lauw FN, Berrevoets MAH, Sigaloff KCE, Soetekouw R, Branger J, de Mast Q, Lammers AJJ, Lowe SH, de Vries RD, Katsikis PD, Rijnders BJA, Brinkman K, Roukens AHE, Rokx C. Immunogenicity and reactogenicity of SARS-CoV-2 vaccines in people living with HIV in the Netherlands: A nationwide prospective cohort study. PLoS Med 2022; 19:e1003979. [PMID: 36301821 PMCID: PMC9612532 DOI: 10.1371/journal.pmed.1003979] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 09/20/2022] [Indexed: 11/07/2022] Open
Abstract
BACKGROUND Vaccines can be less immunogenic in people living with HIV (PLWH), but for SARS-CoV-2 vaccinations this is unknown. In this study we set out to investigate, for the vaccines currently approved in the Netherlands, the immunogenicity and reactogenicity of SARS-CoV-2 vaccinations in PLWH. METHODS AND FINDINGS We conducted a prospective cohort study to examine the immunogenicity of BNT162b2, mRNA-1273, ChAdOx1-S, and Ad26.COV2.S vaccines in adult PLWH without prior COVID-19, and compared to HIV-negative controls. The primary endpoint was the anti-spike SARS-CoV-2 IgG response after mRNA vaccination. Secondary endpoints included the serological response after vector vaccination, anti-SARS-CoV-2 T-cell response, and reactogenicity. Between 14 February and 7 September 2021, 1,154 PLWH (median age 53 [IQR 44-60] years, 85.5% male) and 440 controls (median age 43 [IQR 33-53] years, 28.6% male) were included in the final analysis. Of the PLWH, 884 received BNT162b2, 100 received mRNA-1273, 150 received ChAdOx1-S, and 20 received Ad26.COV2.S. In the group of PLWH, 99% were on antiretroviral therapy, 97.7% were virally suppressed, and the median CD4+ T-cell count was 710 cells/μL (IQR 520-913). Of the controls, 247 received mRNA-1273, 94 received BNT162b2, 26 received ChAdOx1-S, and 73 received Ad26.COV2.S. After mRNA vaccination, geometric mean antibody concentration was 1,418 BAU/mL in PLWH (95% CI 1322-1523), and after adjustment for age, sex, and vaccine type, HIV status remained associated with a decreased response (0.607, 95% CI 0.508-0.725, p < 0.001). All controls receiving an mRNA vaccine had an adequate response, defined as >300 BAU/mL, whilst in PLWH this response rate was 93.6%. In PLWH vaccinated with mRNA-based vaccines, higher antibody responses were predicted by CD4+ T-cell count 250-500 cells/μL (2.845, 95% CI 1.876-4.314, p < 0.001) or >500 cells/μL (2.936, 95% CI 1.961-4.394, p < 0.001), whilst a viral load > 50 copies/mL was associated with a reduced response (0.454, 95% CI 0.286-0.720, p = 0.001). Increased IFN-γ, CD4+ T-cell, and CD8+ T-cell responses were observed after stimulation with SARS-CoV-2 spike peptides in ELISpot and activation-induced marker assays, comparable to controls. Reactogenicity was generally mild, without vaccine-related serious adverse events. Due to the control of vaccine provision by the Dutch National Institute for Public Health and the Environment, there were some differences between vaccine groups in the age, sex, and CD4+ T-cell counts of recipients. CONCLUSIONS After vaccination with BNT162b2 or mRNA-1273, anti-spike SARS-CoV-2 antibody levels were reduced in PLWH compared to HIV-negative controls. To reach and maintain the same serological responses as HIV-negative controls, additional vaccinations are probably required. TRIAL REGISTRATION The trial was registered in the Netherlands Trial Register (NL9214). https://www.trialregister.nl/trial/9214.
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Affiliation(s)
- Kathryn S. Hensley
- Department of Internal Medicine, Section Infectious Diseases, and Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Marlou J. Jongkees
- Department of Internal Medicine, Section Infectious Diseases, and Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Daryl Geers
- Department of Viroscience, Erasmus University Medical Centre, Rotterdam, Netherlands
| | | | - Yvonne M. Mueller
- Department of Immunology, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Virgil A. S. H. Dalm
- Department of Immunology, Erasmus University Medical Centre, Rotterdam, Netherlands
- Department of Internal Medicine, Division of Allergy & Clinical Immunology, Erasmus University Medical Centre, Rotterdam, Netherlands
| | | | - Hanka Steggink
- Department of Internal Medicine and Infectious Diseases, OLVG Hospital, Amsterdam, Netherlands
| | - Alicja Gorska
- Department of Internal Medicine, Section Infectious Diseases, and Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Susanne Bogers
- Department of Viroscience, Erasmus University Medical Centre, Rotterdam, Netherlands
| | | | - Wouter F. W. Bierman
- Department of Internal Medicine, Section Infectious Diseases, University of Groningen, Groningen, Netherlands
| | - Luc B. S. Gelinck
- Department of Internal Medicine and Infectious Diseases, Haaglanden Medical Centre, The Hague, Netherlands
| | - Emile F. Schippers
- Department of Internal Medicine, Haga Teaching Hospital, The Hague, Netherlands
- Department of Infectious Diseases, Leiden University Medical Centre, Leiden Netherlands
| | | | - Marc van der Valk
- Department of Internal Medicine and Infectious Diseases, DC Klinieken, Amsterdam, Netherlands
- Department of Infectious Diseases, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Centre, University of Amsterdam, Amsterdam, Netherlands
| | | | - Corine E. Delsing
- Department of Internal Medicine and Infectious Diseases, Medisch Spectrum Twente, Enschede, Netherlands
| | - Elisabeth H. Gisolf
- Department of Internal Medicine and Infectious Diseases, Rijnstate Hospital, Arnhem, Netherlands
| | - Anke H. W. Bruns
- Department of Internal Medicine and Infectious Diseases, University Medical Centre Utrecht, Utrecht, Netherlands
| | - Fanny N. Lauw
- Department of Internal Medicine and Infectious Diseases, Medical Centre Jan van Goyen, Amsterdam, Netherlands
| | | | - Kim C. E. Sigaloff
- Department of Internal Medicine, Division of Infectious Diseases, Amsterdam Institute for Infection and Immunity, Amsterdam University Medical Centre, Vrije Universiteit Amsterdam, Amsterdam, Netherlands
| | - Robert Soetekouw
- Department of Internal Medicine and Infectious Diseases, Spaarne Gasthuis, Haarlem, Netherlands
| | - Judith Branger
- Department of Internal Medicine, Flevo Hospital, Almere, Netherlands
| | - Quirijn de Mast
- Department of Internal Medicine, Radboud Centre for Infectious Diseases, Radboud University Medical Centre, Nijmegen, Netherlands
| | - Adriana J. J. Lammers
- Department of Internal Medicine and Infectious Diseases, Isala Hospital, Zwolle, Netherlands
| | - Selwyn H. Lowe
- Department of Internal Medicine and Infectious Diseases, Maastricht University Medical Centre, Maastricht, Netherlands
| | - Rory D. de Vries
- Department of Viroscience, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Peter D. Katsikis
- Department of Immunology, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Bart J. A. Rijnders
- Department of Internal Medicine, Section Infectious Diseases, and Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre, Rotterdam, Netherlands
| | - Kees Brinkman
- Department of Internal Medicine and Infectious Diseases, OLVG Hospital, Amsterdam, Netherlands
| | - Anna H. E. Roukens
- Department of Infectious Diseases, Leiden University Medical Centre, Leiden Netherlands
| | - Casper Rokx
- Department of Internal Medicine, Section Infectious Diseases, and Department of Medical Microbiology and Infectious Diseases, Erasmus University Medical Centre, Rotterdam, Netherlands
- * E-mail:
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30
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Peters JL, Fall A, Langerman SD, El Asmar M, Nakazawa M, Mustapha A, Tobian AAR, Mostafa HH, Blankson JN. Prolonged Severe Acute Respiratory Syndrome Coronavirus 2 Delta Variant Shedding in a Patient With AIDS: Case Report and Review of the Literature. Open Forum Infect Dis 2022; 9:ofac479. [PMID: 36193230 PMCID: PMC9494428 DOI: 10.1093/ofid/ofac479] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Accepted: 09/14/2022] [Indexed: 11/15/2022] Open
Abstract
We describe the case of a patient with AIDS who had persistent infection with a severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Delta variant for >80 days. The variant contained mutations that were not present in other Delta viruses in our hospital. Prolonged infection in immunosuppressed individuals may lead to evolution of SARS-CoV-2 lineages.
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Affiliation(s)
- Jillian L Peters
- Department of Medicine, Johns Hopkins Medicine , Baltimore, Maryland , USA
| | - Amary Fall
- Department of Pathology, Johns Hopkins Medicine , Baltimore, Maryland , USA
| | - Steven D Langerman
- Department of Medicine, Johns Hopkins Medicine , Baltimore, Maryland , USA
| | | | - Mari Nakazawa
- Department of Medicine, Johns Hopkins Medicine , Baltimore, Maryland , USA
| | - Aishat Mustapha
- Department of Medicine, Johns Hopkins Medicine , Baltimore, Maryland , USA
| | - Aaron A R Tobian
- Department of Pathology, Johns Hopkins Medicine , Baltimore, Maryland , USA
| | - Heba H Mostafa
- Department of Pathology, Johns Hopkins Medicine , Baltimore, Maryland , USA
| | - Joel N Blankson
- Department of Medicine, Johns Hopkins Medicine , Baltimore, Maryland , USA
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31
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Chaguza C, Hahn AM, Petrone ME, Zhou S, Ferguson D, Breban MI, Pham K, Peña-Hernández MA, Castaldi C, Hill V, Schulz W, Swanstrom RI, Roberts SC, Grubaugh ND. Accelerated SARS-CoV-2 intrahost evolution leading to distinct genotypes during chronic infection. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2022:2022.06.29.22276868. [PMID: 35794895 PMCID: PMC9258298 DOI: 10.1101/2022.06.29.22276868] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
The chronic infection hypothesis for novel SARS-CoV-2 variant emergence is increasingly gaining credence following the appearance of Omicron. Here we investigate intrahost evolution and genetic diversity of lineage B.1.517 during a SARS-CoV-2 chronic infection lasting for 471 days (and still ongoing) with consistently recovered infectious virus and high viral loads. During the infection, we found an accelerated virus evolutionary rate translating to 35 nucleotide substitutions per year, approximately two-fold higher than the global SARS-CoV-2 evolutionary rate. This intrahost evolution led to the emergence and persistence of at least three genetically distinct genotypes suggesting the establishment of spatially structured viral populations continually reseeding different genotypes into the nasopharynx. Finally, using unique molecular indexes for accurate intrahost viral sequencing, we tracked the temporal dynamics of genetic diversity to identify advantageous mutations and highlight hallmark changes for chronic infection. Our findings demonstrate that untreated chronic infections accelerate SARS-CoV-2 evolution, ultimately providing opportunity for the emergence of genetically divergent and potentially highly transmissible variants as seen with Delta and Omicron.
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Affiliation(s)
- Chrispin Chaguza
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Correspondence: (C.C.) and (N.D.G.)
| | - Anne M. Hahn
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mary E. Petrone
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Shuntai Zhou
- Department of Microbiology and Immunology, University of North Carolina, Chapel Hill, NC, USA
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | - David Ferguson
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
| | - Mallery I. Breban
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Kien Pham
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | - Mario A. Peña-Hernández
- Department of Biological and Biomedical Sciences, Yale School of Medicine, New Haven, Connecticut, USA
| | | | - Verity Hill
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
| | | | - Wade Schulz
- Department of Laboratory Medicine, Yale School of Medicine, New Haven, CT, USA
- Center for Outcomes Research and Evaluation, Yale New Haven Hospital, New Haven, CT, USA
| | - Ronald I. Swanstrom
- Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
- Department of Biochemistry and Biophysics, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina, USA
| | | | - Nathan D. Grubaugh
- Department of Epidemiology of Microbial Diseases, Yale School of Public Health, New Haven, CT, USA
- Department of Ecology and Evolutionary Biology, Yale University, New Haven, CT, USA
- Correspondence: (C.C.) and (N.D.G.)
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