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Nooruzzaman M, Johnson KEE, Rani R, Finkelsztein EJ, Caserta LC, Kodiyanplakkal RP, Wang W, Hsu J, Salpietro MT, Banakis S, Albert J, Westblade LF, Zanettini C, Marchionni L, Soave R, Ghedin E, Diel DG, Salvatore M. Emergence of transmissible SARS-CoV-2 variants with decreased sensitivity to antivirals in immunocompromised patients with persistent infections. Nat Commun 2024; 15:7999. [PMID: 39294134 PMCID: PMC11411086 DOI: 10.1038/s41467-024-51924-3] [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: 06/13/2024] [Accepted: 08/21/2024] [Indexed: 09/20/2024] Open
Abstract
We investigated the impact of antiviral treatment on the emergence of SARS-CoV-2 resistance during persistent infections in immunocompromised patients (n = 15). All patients received remdesivir and some also received nirmatrelvir-ritonavir (n = 3) or therapeutic monoclonal antibodies (n = 4). Sequence analysis showed that nine patients carried viruses with mutations in the nsp12 (RNA dependent RNA polymerase), while four had viruses with nsp5 (3C protease) mutations. Infectious SARS-CoV-2 with a double mutation in nsp5 (T169I) and nsp12 (V792I) was recovered from respiratory secretions 77 days after initial COVID-19 diagnosis from a patient sequentially treated with nirmatrelvir-ritonavir and remdesivir. In vitro characterization confirmed its decreased sensitivity to remdesivir and nirmatrelvir, which was overcome by combined antiviral treatment. Studies in golden Syrian hamsters demonstrated efficient transmission to contact animals. This study documents the isolation of SARS-CoV-2 carrying resistance mutations to both nirmatrelvir and remdesivir from a patient and demonstrates its transmissibility in vivo.
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Affiliation(s)
- Mohammed Nooruzzaman
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | | | - Ruchi Rani
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | | | - Leonardo C Caserta
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA
| | | | - Wei Wang
- Systems Genomics Section, NIH/NIAID/DIR/LPD, Bethesda, MD, USA
| | - Jingmei Hsu
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
- Transplantation and Cellular Therapy Program, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Maria T Salpietro
- Institutional Biorepository Core, Weill Cornell Medicine, New York, NY, USA
| | | | - Joshua Albert
- Systems Genomics Section, NIH/NIAID/DIR/LPD, Bethesda, MD, USA
| | - Lars F Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Claudio Zanettini
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Luigi Marchionni
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Rosemary Soave
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA
| | - Elodie Ghedin
- Systems Genomics Section, NIH/NIAID/DIR/LPD, Bethesda, MD, USA.
| | - Diego G Diel
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY, USA.
| | - Mirella Salvatore
- Department of Medicine, Weill Cornell Medicine, New York, NY, USA.
- Department of Population Health Science, Weill Cornell Medicine, New York, NY, USA.
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2
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Kinoshita S, Takemoto M, Asaoka M, Haraguchi Y, Adachi T, Iida S, Komatsu H. COVID-19 in patients receiving treatment at an outpatient chemotherapy unit. Jpn J Clin Oncol 2024:hyae129. [PMID: 39286869 DOI: 10.1093/jjco/hyae129] [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: 04/22/2024] [Accepted: 09/05/2024] [Indexed: 09/19/2024] Open
Abstract
During the COVID-19 pandemic period, many patients who required outpatient chemotherapy developed COVID-19, requiring chemotherapy interruption. However, there are no clear guidelines regarding the safe timing for restarting chemotherapy. We conducted a retrospective study to assess when such patients can safely recommence chemotherapy. Of the 40 patients included in this study, 34 restarted anticancer drug therapy after COVID-19 infection. Six patients, four with multiple myeloma, and one each with follicular lymphoma and glioma, remained SARS-CoV-2 antigen positive >20 days after COVID-19 onset. Multiple myeloma patients recorded significantly higher frequencies of SARS-CoV-2 antigen positivity >20 days after COVID-19 onset compared with solid tumor patients, with no significant differences in the frequency of SARS-CoV-2 positivity during 5-20 days from COVID-19 onset between them. According to our data, most solid tumor patients achieved SARS-CoV-2 antigen negativity after 20 days from COVID-19 onset. On the other hand, multiple myeloma patients might need serial antigen tests before restarting anticancer therapy in the outpatient chemotherapy setting.
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Affiliation(s)
- Shiori Kinoshita
- Department of Clinical Oncology, Nagoya City University, Nagoya, Japan
- Department of Hematology and Oncology, Nagoya City University, Nagoya, Japan
| | | | - Minami Asaoka
- Department of Clinical Oncology, Nagoya City University, Nagoya, Japan
- Department of Pharmacy, Nagoya City University, Nagoya, Japan
| | - Yoko Haraguchi
- Department of Nursing, Nagoya City University, Nagoya, Japan
| | - Tamami Adachi
- Department of Nursing, Nagoya City University, Nagoya, Japan
| | - Shinsuke Iida
- Department of Hematology and Oncology, Nagoya City University, Nagoya, Japan
| | - Hirokazu Komatsu
- Department of Clinical Oncology, Nagoya City University, Nagoya, Japan
- Department of Hematology and Oncology, Nagoya City University, Nagoya, Japan
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3
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Ferrare JT, Good BH. Evolution of evolvability in rapidly adapting populations. Nat Ecol Evol 2024:10.1038/s41559-024-02527-0. [PMID: 39261599 DOI: 10.1038/s41559-024-02527-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2023] [Accepted: 07/29/2024] [Indexed: 09/13/2024]
Abstract
Mutations can alter the short-term fitness of an organism, as well as the rates and benefits of future mutations. While numerous examples of these evolvability modifiers have been observed in rapidly adapting microbial populations, existing theory struggles to predict when they will be favoured by natural selection. Here we develop a mathematical framework for predicting the fates of genetic variants that modify the rates and benefits of future mutations in linked genomic regions. We derive analytical expressions showing how the fixation probabilities of these variants depend on the size of the population and the diversity of competing mutations. We find that competition between linked mutations can dramatically enhance selection for modifiers that increase the benefits of future mutations, even when they impose a strong direct cost on fitness. However, we also find that modest direct benefits can be sufficient to drive evolutionary dead ends to fixation. Our results suggest that subtle differences in evolvability could play an important role in shaping the long-term success of genetic variants in rapidly evolving microbial populations.
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Affiliation(s)
| | - Benjamin H Good
- Department of Applied Physics, Stanford University, Stanford, CA, USA.
- Department of Biology, Stanford University, Stanford, CA, USA.
- Chan Zuckerberg Biohub - San Francisco, San Francisco, CA, USA.
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4
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Wildenbeest JG, Lowe DM, Standing JF, Butler CC. Respiratory syncytial virus infections in adults: a narrative review. THE LANCET. RESPIRATORY MEDICINE 2024:S2213-2600(24)00255-8. [PMID: 39265602 DOI: 10.1016/s2213-2600(24)00255-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2024] [Revised: 08/05/2024] [Accepted: 08/06/2024] [Indexed: 09/14/2024]
Abstract
Respiratory syncytial virus (RSV), an RNA virus spread by droplet infection that affects all ages, is increasingly recognised as an important pathogen in adults, especially among older people living with comorbidities. Distinguishing RSV from other acute viral infections on clinical grounds alone, with sufficient precision to be clinically useful, is not possible. The reference standard diagnosis is by PCR: point-of-care tests perform less well with lower viral loads. Testing samples from a single respiratory tract site could result in underdetection. RSV is identified in 6-11% of outpatient respiratory tract infection (RTI) consultations in older adults (≥60 years, or ≥65 years, depending on the study) and accounts for 4-11% of adults (≥18 years) hospitalised with RTI, with 6-15% of those hospitalised admitted to intensive care, and 1-12% of all adults hospitalised with RSV respiratory tract infection dying. Community-based studies estimate the yearly incidence of RSV infection at around 3-7% in adults aged 60 years and older in high-income countries. Although RSV accounts for a similar disease burden as influenza in adults, those hospitalised with severe RSV disease are typically older (most ≥60 years) and have more comorbidities, more respiratory symptoms, and are frequently without fever. Long-term sequelae are common and include deterioration of underlying disease (typically heart failure and COPD). There are few evidence-based RSV-specific treatments currently available, with supportive care being the main modality. Two protein subunit vaccines for protection from severe RSV in adults aged 60 years and older were licensed in 2023, and a third-an mRNA-based vaccine-recently gained market approval in the USA. The phase 3 studies in these three vaccines showed good protection against severe disease. Data on real-world vaccine effectiveness in older adults, including subgroups at high risk for RSV-associated hospitalisation, are needed to establish the best use of these newly approved RSV vaccines. New diagnostics and therapeutics are being developed, which will also need rigorous evaluation within their target populations to ensure they are used only for those in whom there is evidence of improved outcomes. There is an urgent need to reconceptualise this illness from one that is serious in children, but far less important than influenza in older people, to thinking of RSV as also a major risk to health for older people that needs targeted prevention and treatment.
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Affiliation(s)
- Joanne G Wildenbeest
- Department of Paediatric Infectious Diseases and Immunology, Wilhelmina Children's Hospital, University Medical Centre Utrecht, Utrecht, Netherlands
| | - David M Lowe
- Institute of Immunity and Transplantation, University College London, London, UK; Department of Clinical Immunology, Royal Free London NHS Foundation Trust, London, UK
| | - Joseph F Standing
- Infection, Inflammation and Immunology, UCL Great Ormond Street Institute of Child Health, London, UK
| | - Christopher C Butler
- Nuffield Department of Primary Care Health Sciences, University of Oxford, Oxford, UK.
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5
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Ip JD, Chu WM, Chan WM, Chu AWH, Leung RCY, Peng Q, Tam AR, Chan BPC, Cai JP, Yuen KY, Kok KH, Shi Y, Hung IFN, To KKW. The significance of recurrent de novo amino acid substitutions that emerged during chronic SARS-CoV-2 infection: an observational study. EBioMedicine 2024; 107:105273. [PMID: 39146693 PMCID: PMC11379563 DOI: 10.1016/j.ebiom.2024.105273] [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: 01/25/2024] [Revised: 07/24/2024] [Accepted: 07/27/2024] [Indexed: 08/17/2024] Open
Abstract
BACKGROUND De novo amino acid substitutions (DNS) frequently emerge among immunocompromised patients with chronic SARS-CoV-2 infection. While previous studies have reported these DNS, their significance has not been systematically studied. METHODS We performed a review of DNS that emerged during chronic SARS-CoV-2 infection. We searched PubMed until June 2023 using the keywords "(SARS-CoV-2 or COVID-19) and (mutation or sequencing) and ((prolonged infection) or (chronic infection) or (long term))". We included patients with chronic SARS-CoV-2 infection who had SARS-CoV-2 sequencing performed for at least 3 time points over at least 60 days. We also included 4 additional SARS-CoV-2 patients with chronic infection of our hospital not reported previously. We determined recurrent DNS that has appeared in multiple patients and determined the significance of these mutations among epidemiologically-significant variants. FINDINGS A total of 34 cases were analyzed, including 30 that were published previously and 4 from our hospital. Twenty two DNS appeared in ≥3 patients, with 14 (64%) belonging to lineage-defining mutations (LDMs) of epidemiologically-significant variants and 10 (45%) emerging among chronically-infected patients before the appearance of the corresponding variant. Notably, nsp9-T35I substitution (Orf1a T4175I) emerged in all three patients with BA.2.2 infection in 2022 before the appearance of Variants of Interest that carry nsp9-T35I as LDM (EG.5 and BA.2.86/JN.1). Structural analysis suggests that nsp9-T35I substitution may affect nsp9-nsp12 interaction, which could be critical for the function of the replication and transcription complex. INTERPRETATION DNS that emerges recurrently in different chronically-infected patients may be used as a marker for potential epidemiologically-significant variants. FUNDING Theme-Based Research Scheme [T11/709/21-N] of the Research Grants Council (See acknowledgements for full list).
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Affiliation(s)
- Jonathan Daniel Ip
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Wing-Ming Chu
- Division of Infectious Diseases, Department of Medicine, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Wan-Mui Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Allen Wing-Ho Chu
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Rhoda Cheuk-Ying Leung
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Qi Peng
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Anthony Raymond Tam
- Division of Infectious Diseases, Department of Medicine, Queen Mary Hospital, Hong Kong Special Administrative Region, China
| | - Brian Pui-Chun Chan
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Jian-Piao Cai
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kwok-Yung Yuen
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Kin-Hang Kok
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China
| | - Yi Shi
- CAS Key Laboratory of Pathogen Microbiology and Immunology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, China
| | - Ivan Fan-Ngai Hung
- Division of Infectious Diseases, Department of Medicine, Queen Mary Hospital, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China; Infectious Diseases Division, Department of Medicine, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China
| | - Kelvin Kai-Wang To
- State Key Laboratory for Emerging Infectious Diseases, Carol Yu Centre for Infection, Department of Microbiology, School of Clinical Medicine, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong Special Administrative Region, China; Centre for Virology, Vaccinology and Therapeutics, Hong Kong Science and Technology Park, Hong Kong Special Administrative Region, China; Department of Microbiology, Queen Mary Hospital, Hong Kong Special Administrative Region, China; Department of Infectious Disease and Microbiology, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China.
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6
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Yazawa S, Fukuyama K, Kawakami R, Itamochi M, Higashi D, Tsuji N, Nakamura M, Oishi K, Kaya H, Tani H. Characteristics of virus and antibody response in an immunocompromised patient with persistent SARS-CoV-2 infection. J Infect Chemother 2024:S1341-321X(24)00241-1. [PMID: 39216594 DOI: 10.1016/j.jiac.2024.08.024] [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: 07/17/2024] [Revised: 08/19/2024] [Accepted: 08/27/2024] [Indexed: 09/04/2024]
Abstract
We have previously reported a clinical case in which a hospitalized patient with a history of hematopoietic stem cell transplantation for acute myeloid leukemia was persistently infected with SARS-CoV-2. This study investigated the neutralizing activity of patient sera against cultured viruses isolated at each time point. We also continued to decipher and analyze the whole-genome sequence of the virus. The results showed that the neutralizing activity against the cultured virus at each time point was higher in the sera collected in the late stage of infection. However, the cultured virus collected in the late stage of infection was less likely to be neutralized not only by the sera collected in the early stage of infection but also by the sera collected in the late stage. Moreover, the virus mutated in a manner that allowed it to escape neutralizing antibodies in a host vulnerable to prolonged infection, such as immunocompromised patients.
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Affiliation(s)
- Shunsuke Yazawa
- Department of Virology, Toyama Institute of Health, Toyama, Japan
| | - Kei Fukuyama
- Department of Virology, Toyama Institute of Health, Toyama, Japan
| | - Rie Kawakami
- Department of Virology, Toyama Institute of Health, Toyama, Japan
| | - Masae Itamochi
- Department of Virology, Toyama Institute of Health, Toyama, Japan
| | | | | | | | | | | | - Hideki Tani
- Department of Virology, Toyama Institute of Health, Toyama, Japan.
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7
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Ko SH, Radecki P, Belinky F, Bhiman JN, Meiring S, Kleynhans J, Amoako D, Guerra Canedo V, Lucas M, Kekana D, Martinson N, Lebina L, Everatt J, Tempia S, Bylund T, Rawi R, Kwong PD, Wolter N, von Gottberg A, Cohen C, Boritz EA. Rapid intra-host diversification and evolution of SARS-CoV-2 in advanced HIV infection. Nat Commun 2024; 15:7240. [PMID: 39174553 PMCID: PMC11341811 DOI: 10.1038/s41467-024-51539-8] [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: 12/14/2023] [Accepted: 08/12/2024] [Indexed: 08/24/2024] Open
Abstract
Previous studies have linked the evolution of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) genetic variants to persistent infections in people with immunocompromising conditions, but the processes responsible for these observations are incompletely understood. Here we use high-throughput, single-genome amplification and sequencing (HT-SGS) to sequence SARS-CoV-2 spike genes from people with HIV (PWH, n = 22) and people without HIV (PWOH, n = 25). In PWOH and PWH with CD4 T cell counts (i.e., CD4 counts) ≥ 200 cells/μL, we find that most SARS-CoV-2 genomes sampled in each person share one spike sequence. By contrast, in people with advanced HIV infection (i.e., CD4 counts < 200 cells/μL), HT-SGS reveals a median of 46 distinct linked groupings of spike mutations per person. Elevated intra-host spike diversity in people with advanced HIV infection is detected immediately after COVID-19 symptom onset, and early intra-host spike diversity predicts SARS-CoV-2 shedding duration among PWH. Analysis of longitudinal timepoints reveals rapid fluctuations in spike sequence populations, replacement of founder sequences by groups of new haplotypes, and positive selection at functionally important residues. These findings demonstrate remarkable intra-host genetic diversity of SARS-CoV-2 in advanced HIV infection and suggest that adaptive intra-host SARS-CoV-2 evolution in this setting may contribute to the emergence of new variants of concern.
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Affiliation(s)
- Sung Hee Ko
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Pierce Radecki
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Frida Belinky
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Jinal N Bhiman
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- SAMRC Antibody Immunity Research Unit, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Susan Meiring
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Jackie Kleynhans
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Daniel Amoako
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- Department of Integrative Biology and Bioinformatics, College of Biological Sciences, University of Guelph, Ontario, Canada
| | - Vanessa Guerra Canedo
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Margaret Lucas
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Dikeledi Kekana
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Neil Martinson
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
- Johns Hopkins University, Center for TB Research, Baltimore, MD, USA
| | - Limakatso Lebina
- Perinatal HIV Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Josie Everatt
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Stefano Tempia
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Tatsiana Bylund
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Reda Rawi
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Peter D Kwong
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Nicole Wolter
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Anne von Gottberg
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Pathology, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Cheryl Cohen
- National Institute for Communicable Diseases, a division of the National Health Laboratory Service, Johannesburg, South Africa
- School of Public Health, Faculty of Health Sciences, University of the Witwatersrand, Johannesburg, South Africa
| | - Eli A Boritz
- Vaccine Research Center, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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8
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Choudhary MC, Deo R, Evering TH, Chew KW, Giganti MJ, Moser C, Ritz J, Regan J, Flynn JP, Crain CR, Wohl DA, Currier JS, Eron JJ, Margolis D, Zhu Q, Zhon L, Ya L, Greninger AL, Hughes MD, Smith D, Daar ES, Li JZ. Characterization of Treatment Resistance and Viral Kinetics in the Setting of Single-Active Versus Dual-Active Monoclonal Antibodies Against Severe Acute Respiratory Syndrome Coronavirus 2. J Infect Dis 2024; 230:394-402. [PMID: 38716969 PMCID: PMC11326811 DOI: 10.1093/infdis/jiae192] [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: 03/15/2024] [Accepted: 04/11/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Monoclonal antibodies (mAbs) represent a crucial antiviral strategy for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, but it is unclear whether combination mAbs offer a benefit over single-active mAb treatment. Amubarvimab and romlusevimab significantly reduced the risk of hospitalizations or death in the ACTIV-2/A5401 trial. Certain SARS-CoV-2 variants are intrinsically resistant against romlusevimab, leading to only single-active mAb therapy with amubarvimab in these variants. We evaluated virologic outcomes in individuals treated with single- versus dual-active mAbs. METHODS Participants were nonhospitalized adults at higher risk of clinical progression randomized to amubarvimab plus romlusevimab or placebo. Quantitative SARS-CoV-2 RNA levels and targeted S-gene next-generation sequencing was performed on anterior nasal samples. We compared viral load kinetics and resistance emergence between individuals treated with effective single- versus dual-active mAbs depending on the infecting variant. RESULTS Study participants receiving single- or dual-active mAbs had similar demographics, baseline nasal viral load, symptom score, and symptom duration. Compared with single-active mAb treatment, treatment with dual-active mAbs led to faster viral load decline at study days 3 (P < .001) and 7 (P < .01). Treatment-emergent resistance mutations were more likely to be detected after amubarvimab plus romlusevimab treatment than with placebo (2.6% vs 0%; P < .001) and were more frequently detected in the setting of single-active compared with dual-active mAb treatment (7.3% vs 1.1%; P < .01). Single-active and dual-active mAb treatment resulted in similar decrease in rates of hospitalizations or death. CONCLUSIONS Compared with single-active mAb therapy, dual-active mAbs led to similar clinical outcomes but significantly faster viral load decline and a lower risk of emergent resistance.
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Affiliation(s)
- Manish C Choudhary
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Rinki Deo
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Teresa H Evering
- Department of Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Kara W Chew
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Mark J Giganti
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Carlee Moser
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Justin Ritz
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - James Regan
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - James P Flynn
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Charles R Crain
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - David Alain Wohl
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | - Judith S Currier
- Department of Medicine, David Geffen School of Medicine at UCLA, Los Angeles, California, USA
| | - Joseph J Eron
- Department of Medicine, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, USA
| | | | - Qing Zhu
- Brii Biosciences, Durham, North Carolina, USA
| | - Lijie Zhon
- Brii Biosciences, Durham, North Carolina, USA
| | - Li Ya
- Brii Biosciences, Durham, North Carolina, USA
| | - Alexander L Greninger
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, Washington, USA
| | - Michael D Hughes
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, Massachusetts, USA
| | - Davey Smith
- Department of Medicine, University of California, San Diego, La Jolla, California, USA
| | - Eric S Daar
- Department of Medicine, Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Jonathan Z Li
- Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA
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9
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Jenkins F, Mapulanga T, Thapa G, da Costa KAS, Temperton NJ. Conference Report: LPMHealthcare Emerging Viruses 2023 (EVOX23): Pandemics-Learning from the Past and Present to Prepare for the Future. Pathogens 2024; 13:679. [PMID: 39204279 PMCID: PMC11357271 DOI: 10.3390/pathogens13080679] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2024] [Revised: 08/06/2024] [Accepted: 08/08/2024] [Indexed: 09/03/2024] Open
Abstract
The emergence of SARS-CoV-2 has meant that pandemic preparedness has become a major focus of the global scientific community. Gathered in the historic St Edmund Hall college in Oxford, the one-day LPMHealthcare conference on emerging viruses (6 September 2023) sought to review and learn from past pandemics-the current SARS-CoV-2 pandemic and the Mpox outbreak-and then look towards potential future pandemics. This includes an emphasis on monitoring the "traditional" reservoirs of viruses with zoonotic potential, as well as possible new sources of spillover events, e.g., bats, which we are coming into closer contact with due to climate change and the impacts of human activities on habitats. Continued vigilance and investment into creative scientific solutions is required for issues including the long-term physical and psychological effects of COVID-19, i.e., long COVID. The evaluation of current systems, including environmental monitoring, communication (with the public, regulatory authorities, and governments), and training; assessment of the effectiveness of the technologies/assays we have in place currently; and lobbying of the government and the public to work with scientists are all required in order to build trust moving forward. Overall, the SARS-CoV-2 pandemic has shown how many sectors can work together to achieve a global impact in times of crisis.
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Affiliation(s)
| | - Tobias Mapulanga
- Medway School of Pharmacy, The Universities of Kent and Greenwich at Medway, Chatham ME4 4BF, UK; (T.M.); (G.T.)
| | - Gauri Thapa
- Medway School of Pharmacy, The Universities of Kent and Greenwich at Medway, Chatham ME4 4BF, UK; (T.M.); (G.T.)
| | - Kelly A. S. da Costa
- Medway School of Pharmacy, The Universities of Kent and Greenwich at Medway, Chatham ME4 4BF, UK; (T.M.); (G.T.)
| | - Nigel J. Temperton
- Medway School of Pharmacy, The Universities of Kent and Greenwich at Medway, Chatham ME4 4BF, UK; (T.M.); (G.T.)
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10
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Gai X, Sun X, Liu B, Yan W, Sheng Z, Zhou Q, Sun Y. Efficacy of Combination of Antiviral Therapy With Neutralizing Monoclonal Antibodies for Recurrent Persistent SARS-CoV-2 Pneumonia in Patients With Lymphoma. BIOMED RESEARCH INTERNATIONAL 2024; 2024:8182887. [PMID: 39140001 PMCID: PMC11321881 DOI: 10.1155/2024/8182887] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 05/18/2024] [Accepted: 06/25/2024] [Indexed: 08/15/2024]
Abstract
Despite the potential of neutralizing antibodies in the management of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2), clinical research on its efficacy in Chinese patients remains limited. This study is aimed at investigating the therapeutic effect of combination of antiviral therapy with neutralizing monoclonal antibodies for recurrent persistent SARS-CoV-2 pneumonia in patients with lymphoma complicated by B cell depletion. A prospective study was conducted on Chinese patients who were treated with antiviral nirmatrelvir/ritonavir therapy and the neutralizing antibody tixagevimab-cilgavimab (tix-cil). The primary outcome was the rate of recurrent SARS-CoV-2 infection. Five patients with lymphoma experienced recurrent SARS-CoV-2 pneumonia and received tix-cil treatment. All patients had a history of CD20 monoclonal antibody use within the year preceding SARS-CoV-2 infection, and two patients also had a history of Bruton's tyrosine kinase (BTK) inhibitor use. These patients had notably low lymphocyte counts and exhibited near depletion of B cells. All five patients tested negative for serum SARS-CoV-2 IgG and IgM antibodies. None of the patients developed reinfection with SARS-CoV-2 pneumonia after antiviral and tix-cil treatment during the 6-month follow-up period. In conclusion, the administration of antiviral and SARS-CoV-2-neutralizing antibodies showed encouraging therapeutic efficacy against SARS-CoV-2 pneumonia in patients with lymphoma complicated by B cell depletion, along with the potential preventive effect of neutralizing antibodies for up to 6 months.
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Affiliation(s)
- Xiaoyan Gai
- Department of Pulmonary and Critical Care Medicine Peking University Third Hospital, Beijing 100083, China
| | - Xiaoyan Sun
- Department of Pulmonary and Critical Care Medicine Peking University Third Hospital, Beijing 100083, China
| | - Beibei Liu
- Department of Pulmonary and Critical Care Medicine Peking University Third Hospital, Beijing 100083, China
| | - Wei Yan
- Department of Pulmonary and Critical Care Medicine Peking University Third Hospital, Beijing 100083, China
| | - Zikang Sheng
- Department of Pulmonary and Critical Care Medicine Peking University Third Hospital, Beijing 100083, China
| | - Qingtao Zhou
- Department of Pulmonary and Critical Care Medicine Peking University Third Hospital, Beijing 100083, China
| | - Yongchang Sun
- Department of Pulmonary and Critical Care Medicine Peking University Third Hospital, Beijing 100083, China
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11
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Focosi D, Spezia PG, Maggi F. Subsequent Waves of Convergent Evolution in SARS-CoV-2 Genes and Proteins. Vaccines (Basel) 2024; 12:887. [PMID: 39204013 PMCID: PMC11358953 DOI: 10.3390/vaccines12080887] [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: 07/20/2024] [Revised: 08/02/2024] [Accepted: 08/03/2024] [Indexed: 09/03/2024] Open
Abstract
Beginning in 2022, following widespread infection and vaccination among the global population, the SARS-CoV-2 virus mainly evolved to evade immunity derived from vaccines and past infections. This review covers the convergent evolution of structural, nonstructural, and accessory proteins in SARS-CoV-2, with a specific look at common mutations found in long-lasting infections that hint at the virus potentially reverting to an enteric sarbecovirus type.
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Affiliation(s)
- Daniele Focosi
- North-Western Tuscany Blood Bank, Pisa University Hospital, 56124 Pisa, Italy;
| | - Pietro Giorgio Spezia
- Laboratory of Virology and Laboratory of Biosecurity, National Institute of Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy;
| | - Fabrizio Maggi
- Laboratory of Virology and Laboratory of Biosecurity, National Institute of Infectious Diseases Lazzaro Spallanzani—IRCCS, 00149 Rome, Italy;
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12
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Manuelpillai B, Zendt M, Chang-Rabley E, Ricotta EE. Stuck in pandemic uncertainty: a review of the persistent effects of COVID-19 infection in immune-deficient people. Clin Microbiol Infect 2024; 30:1007-1011. [PMID: 38552795 PMCID: PMC11254561 DOI: 10.1016/j.cmi.2024.03.027] [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: 01/17/2024] [Revised: 03/04/2024] [Accepted: 03/23/2024] [Indexed: 04/15/2024]
Abstract
BACKGROUND People who are immune-deficient/disordered (IDP) are underrepresented in COVID-19 studies. Specifically, there is limited research on post-SARS-CoV-2 infection outcomes, including viral persistence and long-term sequelae in these populations. OBJECTIVES This review aimed to examine the published literature on the occurrence of persistent SARS-CoV-2 positivity, relapse, reinfections, variant coinfection, and post-acute sequelae of COVID-19 in IDP. Although the available literature largely centred on those with secondary immunodeficiencies, studies on people with inborn errors of immunity are also included. SOURCES PubMed was searched using medical subject headings terms to identify relevant articles from the last 4 years. Articles on primary and secondary immunodeficiencies were chosen, and a special emphasis was placed on including articles that studied people with inborn errors of immunity. The absence of extensive cohort studies including these individuals has limited most articles in this review to case reports, whereas the articles focusing on secondary immunodeficiencies include larger cohort, case-control, and cross-sectional studies. Articles focusing solely on HIV/AIDS were excluded. CONTENT Scientific literature suggests that IDP of any age are more likely to experience persistent SARS-CoV-2 infections. Although adult IDP exhibits a higher rate of post-acute sequelae of COVID-19, milder COVID-19 infections in children may reduce their risk of experiencing post-acute sequelae of COVID-19. Reinfections and coinfections may occur at a slightly higher rate in IDP than in the general population. IMPLICATIONS Although IDP experience increased viral persistence and inter-host evolution, it is unlikely that enough evidence can be generated at the population-level to support or refute the hypothesis that infections in IDP are significantly more likely to result in variants of concern than infections in the general population. Additional research on the relationship between viral persistence and the rate of long-term sequelae in IDP could inform the understanding of the immune response to SARS-CoV-2 in IDP and the general population.
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Affiliation(s)
- Bevin Manuelpillai
- Rollins School of Public Health, Emory University, Atlanta, GA, USA; Epidemiology and Data Management Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mackenzie Zendt
- Epidemiology and Data Management Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Emma Chang-Rabley
- Epidemiology and Data Management Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Emily E Ricotta
- Epidemiology and Data Management Unit, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
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13
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Izadi A, Nordenfelt P. Protective non-neutralizing SARS-CoV-2 monoclonal antibodies. Trends Immunol 2024; 45:609-624. [PMID: 39034185 DOI: 10.1016/j.it.2024.06.003] [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: 06/17/2024] [Revised: 06/24/2024] [Accepted: 06/24/2024] [Indexed: 07/23/2024]
Abstract
Recent studies show an important role for non-neutralizing anti-spike antibodies, including monoclonal antibodies (mAbs), in robustly protecting against SARS-CoV-2 infection. These mAbs use Fc-mediated functions such as complement activation, phagocytosis, and cellular cytotoxicity. There is an untapped potential for using non-neutralizing mAbs in durable antibody treatments; because of their available conserved epitopes, they may not be as sensitive to virus mutations as neutralizing mAbs. Here, we discuss evidence of non-neutralizing mAb-mediated protection against SARS-CoV-2 infection. We explore how non-neutralizing mAb Fc-mediated functions can be enhanced via novel antibody-engineering techniques. Important questions remain to be answered regarding the characteristics of protective non-neutralizing mAbs, including the models and assays used for study, the risks of ensuing detrimental inflammation, as well as the durability and mechanisms of protection.
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Affiliation(s)
- Arman Izadi
- Department of Clinical Sciences Lund, Division of Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden; Karolinska University Hospital, Stockholm, Sweden
| | - Pontus Nordenfelt
- Department of Clinical Sciences Lund, Division of Infection Medicine, Faculty of Medicine, Lund University, Lund, Sweden; Department of Laboratory Medicine, Clinical Microbiology, Skåne University Hospital Lund, Lund University, Lund, Sweden.
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14
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Meijer SE, Paran Y, Belkin A, Ben-Ami R, Maor Y, Nesher L, Hussein K, Rahav G, Brosh-Nissimov T. Persistent COVID-19 in immunocompromised patients-Israeli society of infectious diseases consensus statement on diagnosis and management. Clin Microbiol Infect 2024; 30:1012-1017. [PMID: 38642895 DOI: 10.1016/j.cmi.2024.04.009] [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: 01/05/2024] [Revised: 04/05/2024] [Accepted: 04/15/2024] [Indexed: 04/22/2024]
Abstract
BACKGROUND Immunocompromised patients with impaired humoral immunity are at risk for persistent COVID-19 (pCOVID), a protracted symptomatic disease with active viral replication. OBJECTIVES To establish a national consensus statement on the diagnosis, treatment, management, isolation, and prevention of pCOVID in adults. SOURCES We base our suggestions on the available literature, our own experience, and clinical reasoning. CONTENT Literature on the treatment of pCOVID is scarce and consists of few case reports and case series. The available studies provide low-quality evidence for monoclonal antibodies, convalescent plasma, antiviral drugs, and immunomodulators. Different combination therapies are described. Continuous viral replication and antiviral treatment may lead to the development of mutations that confer resistance to therapy. IMPLICATIONS To reduce the risk of resistance and improve outcomes, we suggest treating pCOVID with a combination of antibody-based therapy and two antiviral drugs for duration of 5-10 days. Immunomodulatory therapy can be added in patients with an inflammatory clinical picture. In cases of treatment failure or relapse, prolonged antiviral treatment can be considered. For the prevention of pCOVID, we suggest active and passive vaccination and early initiation of treatment for acute COVID-19. Additional research on pCOVID treatment is urgently needed.
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Affiliation(s)
- Suzy E Meijer
- Infectious Disease Unit, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Yael Paran
- Infectious Disease Unit, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ana Belkin
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Sheba Medical Center, Tel Hashomer, Israel
| | - Ronen Ben-Ami
- Infectious Disease Unit, Tel Aviv Sourasky Medical Center, Tel Aviv, Israel; Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yasmin Maor
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Infectious Disease Unit, Edith Wolfson Medical Center, Holon, Israel
| | - Lior Nesher
- Infectious Disease Institute, Soroka University Medical Center, Beer Sheba, Israel; Faculty of Health Sciences, Ben Gurion University in the Negev, Beer Sheba, Israel
| | | | - Galia Rahav
- Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel; Sheba Medical Center, Tel Hashomer, Israel
| | - Tal Brosh-Nissimov
- Infectious Diseases Unit, Samson Assuta Ashdod University Hospital, Ashdod, Israel; Faculty of Health Sciences, Ben Gurion University in the Negev, Beer Sheba, Israel
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15
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Bonetti Franceschi V, Volz E. Phylogenetic signatures reveal multilevel selection and fitness costs in SARS-CoV-2. Wellcome Open Res 2024; 9:85. [PMID: 39132669 PMCID: PMC11316176 DOI: 10.12688/wellcomeopenres.20704.2] [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] [Accepted: 07/16/2024] [Indexed: 08/13/2024] Open
Abstract
Background Large-scale sequencing of SARS-CoV-2 has enabled the study of viral evolution during the COVID-19 pandemic. Some viral mutations may be advantageous to viral replication within hosts but detrimental to transmission, thus carrying a transient fitness advantage. By affecting the number of descendants, persistence times and growth rates of associated clades, these mutations generate localised imbalance in phylogenies. Quantifying these features in closely-related clades with and without recurring mutations can elucidate the tradeoffs between within-host replication and between-host transmission. Methods We implemented a novel phylogenetic clustering algorithm ( mlscluster, https://github.com/mrc-ide/mlscluster) to systematically explore time-scaled phylogenies for mutations under transient/multilevel selection. We applied this method to a SARS-CoV-2 time-calibrated phylogeny with >1.2 million sequences from England, and characterised these recurrent mutations that may influence transmission fitness across PANGO-lineages and genomic regions using Poisson regressions and summary statistics. Results We found no major differences across two epidemic stages (before and after Omicron), PANGO-lineages, and genomic regions. However, spike, nucleocapsid, and ORF3a were proportionally more enriched for transmission fitness polymorphisms (TFP)-homoplasies than other proteins. We provide a catalog of SARS-CoV-2 sites under multilevel selection, which can guide experimental investigations within and beyond the spike protein. Conclusions This study provides empirical evidence for the existence of important tradeoffs between within-host replication and between-host transmission shaping the fitness landscape of SARS-CoV-2. This method may be used as a fast and scalable means to shortlist large sequence databases for sites under putative multilevel selection which may warrant subsequent confirmatory analyses and experimental confirmation.
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Affiliation(s)
- Vinicius Bonetti Franceschi
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, England, W2 1PG, UK
| | - Erik Volz
- Department of Infectious Disease Epidemiology, School of Public Health, Imperial College London, London, England, W2 1PG, UK
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16
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Goldswain H, Penrice-Randal R, Donovan-Banfield I, Duffy CW, Dong X, Randle N, Ryan Y, Rzeszutek AM, Pilgrim J, Keyser E, Weller SA, Hutley EJ, Hartley C, Prince T, Darby AC, Aye Maung N, Nwume H, Hiscox JA, Emmett SR. SARS-CoV-2 population dynamics in immunocompetent individuals in a closed transmission chain shows genomic diversity over the course of infection. Genome Med 2024; 16:89. [PMID: 39014481 PMCID: PMC11251137 DOI: 10.1186/s13073-024-01360-1] [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: 09/23/2023] [Accepted: 07/04/2024] [Indexed: 07/18/2024] Open
Abstract
BACKGROUND SARS-CoV-2 remains rapidly evolving, and many biologically important genomic substitutions/indels have characterised novel SARS-CoV-2 lineages, which have emerged during successive global waves of the pandemic. Worldwide genomic sequencing has been able to monitor these waves, track transmission clusters, and examine viral evolution in real time to help inform healthcare policy. One school of thought is that an apparent greater than average divergence in an emerging lineage from contemporary variants may require persistent infection, for example in an immunocompromised host. Due to the nature of the COVID-19 pandemic and sampling, there were few studies that examined the evolutionary trajectory of SARS-CoV-2 in healthy individuals. METHODS We investigated viral evolutionary trends and participant symptomatology within a cluster of 16 SARS-CoV-2 infected, immunocompetent individuals with no co-morbidities in a closed transmission chain. Longitudinal nasopharyngeal swab sampling allowed characterisation of SARS-CoV-2 intra-host variation over time at both the dominant and minor genomic variant levels through Nimagen-Illumina sequencing. RESULTS A change in viral lineage assignment was observed in individual infections; however, there was only one indel and no evidence of recombination over the period of an acute infection. Minor and dominant genomic modifications varied between participants, with some minor genomic modifications increasing in abundance to become the dominant viral sequence during infection. CONCLUSIONS Data from this cohort of SARS-CoV-2-infected participants demonstrated that long-term persistent infection in an immunocompromised host was not necessarily a prerequisite for generating a greater than average frequency of amino acid substitutions. Amino acid substitutions at both the dominant and minor genomic sequence level were observed in immunocompetent individuals during infection showing that viral lineage changes can occur generating viral diversity.
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Affiliation(s)
- Hannah Goldswain
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Rebekah Penrice-Randal
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - I'ah Donovan-Banfield
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Craig W Duffy
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Xiaofeng Dong
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Nadine Randle
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Yan Ryan
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | | | - Jack Pilgrim
- Centre for Genomic Research, University of Liverpool, Liverpool, L69 3BX, UK
| | - Emma Keyser
- Defence Science Technology Laboratory, Porton Down, Salisbury, SP4 0JQ, UK
| | - Simon A Weller
- Defence Science Technology Laboratory, Porton Down, Salisbury, SP4 0JQ, UK
| | - Emma J Hutley
- Centre for Defence Pathology, Royal Centre for Defence Medicine, OCT Centre, Birmingham, B15 2WB, UK
| | - Catherine Hartley
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Tessa Prince
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Alistair C Darby
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK
| | - Niall Aye Maung
- British Army, Hunter House, St Omer Barracks, Aldershot, Hampshire, GU11 2BG, UK
| | - Henry Nwume
- Defence Science Technology Laboratory, Porton Down, Salisbury, SP4 0JQ, UK
| | - Julian A Hiscox
- Institute for Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, L3 5RF, UK.
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Connexis North Tower, 1 Fusionopolis Way, Singapore, #20-10138632, Singapore.
| | - Stevan R Emmett
- Defence Science Technology Laboratory, Porton Down, Salisbury, SP4 0JQ, UK.
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17
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Fonager J, Nytofte NJS, Schouw CH, Poulsen CB, Wiese L, Fomsgaard A, Bennedbæk M, Rasmussen M, Nielsen XC. Emergence and fixation of SARS-CoV-2 minority variants in a chronically infected patient receiving therapy in Denmark. APMIS 2024. [PMID: 38961316 DOI: 10.1111/apm.13454] [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: 02/07/2024] [Accepted: 06/24/2024] [Indexed: 07/05/2024]
Abstract
SARS-CoV-2 variants of concern (VOC), such as Delta and Omicron have harbored mutations, which increased viral infectivity or ability to evade neutralizing antibodies. Immunocompromised patients might be a source of some of these emerging variants. In this study, we sequenced 17 consecutive samples from an immunocompromised patient with a long-term SARS-CoV-2 infection with the pre-VOC era lineage B.1.177.35. We here describe the emergence of 73 nonsynonymous minority variants in this patient and show that 10 of these mutations became dominant in the viral population during the treatment period. Four of these were seen throughout the infection period and had a very low global prevalence, although three of them were also observed later in the Alpha, Delta, and Omicron lineages. We also found that two adjacent nsp12 variants (M785I and S786P) belonged to different quasi-species and competed during the early stages of infection and remdesivir administration. This emphasizes the importance of ongoing genome surveillance of SARS-CoV-2 among immunocpromised patients.
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Affiliation(s)
- Jannik Fonager
- Virus Research and Development Laboratory, Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Nikolaj Julian Skrøder Nytofte
- Department of Medicine, Zealand University Hospital, Køge, Denmark
- Centre for Thrombosis and Anticoagulation, NSR Hospitals, Næstved, Denmark
| | | | | | - Lothar Wiese
- Department of Infectious Diseases, Zealand University Hospital, Roskilde, Denmark
| | - Anders Fomsgaard
- Virus Research and Development Laboratory, Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Marc Bennedbæk
- Virus Research and Development Laboratory, Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
| | - Morten Rasmussen
- Virus Research and Development Laboratory, Department of Virus and Microbiological Special Diagnostics, Statens Serum Institut, Copenhagen, Denmark
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18
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Machkovech HM, Hahn AM, Garonzik Wang J, Grubaugh ND, Halfmann PJ, Johnson MC, Lemieux JE, O'Connor DH, Piantadosi A, Wei W, Friedrich TC. Persistent SARS-CoV-2 infection: significance and implications. THE LANCET. INFECTIOUS DISEASES 2024; 24:e453-e462. [PMID: 38340735 DOI: 10.1016/s1473-3099(23)00815-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/06/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 02/12/2024]
Abstract
SARS-CoV-2 causes persistent infections in a subset of individuals, which is a major clinical and public health problem that should be prioritised for further investigation for several reasons. First, persistent SARS-CoV-2 infection often goes unrecognised, and therefore might affect a substantial number of people, particularly immunocompromised individuals. Second, the formation of tissue reservoirs (including in non-respiratory tissues) might underlie the pathophysiology of the persistent SARS-CoV-2 infection and require new strategies for diagnosis and treatment. Finally, persistent SARS-CoV-2 replication, particularly in the setting of suboptimal immune responses, is a possible source of new, divergent virus variants that escape pre-existing immunity on the individual and population levels. Defining optimal diagnostic and treatment strategies for patients with persistent virus replication and monitoring viral evolution are therefore urgent medical and public health priorities.
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Affiliation(s)
- Heather M Machkovech
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Anne M Hahn
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA
| | | | - Nathan D Grubaugh
- Department of Epidemiology of Microbial Diseases, School of Public Health, Yale University, New Haven, CT, USA
| | - Peter J Halfmann
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Marc C Johnson
- Department of Molecular Microbiology and Immunology, University of Missouri-School of Medicine, Columbia, MO, USA
| | - Jacob E Lemieux
- Department of Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - David H O'Connor
- Department of Pathology and Laboratory Medicine, School of Medicine and Public Health, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Anne Piantadosi
- Department of Pathology and Laboratory Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - Wanting Wei
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA
| | - Thomas C Friedrich
- Department of Pathobiological Sciences, University of Wisconsin-Madison, Madison, WI, USA.
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19
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Kavikondala S, Haeussler K, Wang X, Spellman A, Bausch-Jurken MT, Sharma P, Amiri M, Krivelyova A, Vats S, Nassim M, Kumar N, Van de Velde N. Immunogenicity of mRNA-1273 and BNT162b2 in Immunocompromised Patients: Systematic Review and Meta-analysis Using GRADE. Infect Dis Ther 2024; 13:1419-1438. [PMID: 38802704 PMCID: PMC11219657 DOI: 10.1007/s40121-024-00987-2] [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: 03/14/2024] [Accepted: 04/30/2024] [Indexed: 05/29/2024] Open
Abstract
INTRODUCTION Immunocompromised (IC) patients mount poor immune responses to vaccination. Higher-dose coronavirus disease 2019 (COVID-19) vaccines may offer increased immunogenicity. METHODS A pairwise meta-analysis of 98 studies reporting comparisons of mRNA-1273 (50 or 100 mcg/dose) and BNT162b2 (30 mcg/dose) in IC adults was performed. Outcomes were seroconversion, total and neutralizing antibody titers, and cellular immune responses. RESULTS mRNA-1273 was associated with a significantly higher seroconversion likelihood [relative risk, 1.11 (95% CI, 1.08, 1.14); P < 0.0001; I2 = 66.8%] and higher total antibody titers [relative increase, 50.45% (95% CI, 34.63%, 66.28%); P < 0.0001; I2 = 89.5%] versus BNT162b2. mRNA-1273 elicited higher but statistically nonsignificant relative increases in neutralizing antibody titers and cellular immune responses versus BNT162b2. CONCLUSION Higher-dose mRNA-1273 had increased immunogenicity versus BNT162b2 in IC patients.
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20
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De Grazia S, Pollicino F, Giannettino C, Errera CM, Veronese N, Giammanco GM, Cacioppo F, Sanfilippo GL, Barbagallo M. Factors Associated with Prolonged SARS-CoV-2 Viral Positivity in an Italian Cohort of Hospitalized Patients. Diseases 2024; 12:138. [PMID: 39057109 PMCID: PMC11275323 DOI: 10.3390/diseases12070138] [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: 05/28/2024] [Revised: 06/24/2024] [Accepted: 06/26/2024] [Indexed: 07/28/2024] Open
Abstract
Clinical or microbiological factors potentially associated with prolonged COVID-19 PCR positivity are still poorly underexplored, but they could be of importance for public-health and clinical reasons. The objective of our analysis is to explore demographic, clinical, and microbiological factors potentially associated with a prolonged positivity to SARS-CoV-2 among 222 hospitalized patients. Prolonged detection positivity for SARS-CoV-2 RNA in swap samples, defined as positivity more than 21 days, was the outcome of interest. The 56 cases with a prolonged positivity to SARS-CoV-2 were matched for age and sex with 156 controls. The cases reported a significantly higher presence of diabetes mellitus, autoimmune diseases, chronic kidney diseases, and acute coronary syndrome. Moreover, the viral load was significantly higher in a period of prolonged positivity compared to a normal period. In the multivariable analysis, the presence of autoimmune diseases and chronic kidney disease were significantly associated with an increased risk of prolonged positivity as well as medium viral load or high viral load, i.e., low Ct value ≤ 30 indicating high viral load. The results of this study confirmed that in a large population of hospitalized patients with COVID-19 manifestations, the prolonged positivity of SARS-CoV-2 detection with nasopharyngeal swab was mainly related to autoimmune diseases, chronic kidney disease, and to baseline viral load.
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Affiliation(s)
| | | | | | | | - Nicola Veronese
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy; (S.D.G.); (F.P.); (C.G.); (C.M.E.); (G.M.G.); (F.C.); (G.L.S.); (M.B.)
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21
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Nooruzzaman M, Johnson KEE, Rani R, Finkelsztein EJ, Caserta LC, Kodiyanplakkal RP, Wang W, Hsu J, Salpietro MT, Banakis S, Albert J, Westblade L, Zanettini C, Marchionni L, Soave R, Ghedin E, Diel DG, Salvatore M. Emergence of transmissible SARS-CoV-2 variants with decreased sensitivity to antivirals in immunocompromised patients with persistent infections. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.06.14.24308523. [PMID: 38946967 PMCID: PMC11213110 DOI: 10.1101/2024.06.14.24308523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/02/2024]
Abstract
We investigated the impact of antiviral treatment on the emergence of SARS-CoV-2 resistance during persistent infections in immunocompromised patients (n=15). All patients received remdesivir and some also received nirmatrelvir-ritonavir or monoclonal antibodies. Sequence analysis showed that nine patients carried viruses with mutations in the nsp12 (RNA dependent RNA polymerase), while four had viruses with nsp5 (3C protease) mutations. Infectious SARS-CoV-2 with a double mutation in nsp5 (T169I) and nsp12 (V792I) was recovered from respiratory secretions 77 days after initial COVID-19 diagnosis from a patient treated with remdesivir and nirmatrelvir-ritonavir. In vitro characterization confirmed its decreased sensitivity to remdesivir and nirmatrelvir, which was overcome by combined antiviral treatment. Studies in golden Syrian hamsters demonstrated efficient transmission to contact animals. This study documents the isolation of SARS-CoV-2 carrying resistance mutations to both nirmatrelvir and remdesivir from a patient and demonstrates its transmissibility in vivo.
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Affiliation(s)
- Mohammed Nooruzzaman
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University
| | | | - Ruchi Rani
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University
| | | | - Leonardo C Caserta
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University
| | | | - Wei Wang
- Systems Genomics Section, NIH/NIAID/DIR/LPD
| | - Jingmei Hsu
- Department of Medicine, Weill Cornell Medicine
| | | | | | | | - Lars Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine
| | - Claudio Zanettini
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine
| | - Luigi Marchionni
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine
| | | | | | - Diego G Diel
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University
| | - Mirella Salvatore
- Department of Medicine, Weill Cornell Medicine
- Department of Population Health Science, Weill Cornell Medicine
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22
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Huygens S, GeurtsvanKessel C, Gharbharan A, Bogers S, Worp N, Boter M, Bax HI, Kampschreur LM, Hassing RJ, Fiets RB, Levenga H, Afonso PM, Koopmans M, Rijnders BJA, Oude Munnink BB. Clinical and Virological Outcome of Monoclonal Antibody Therapies Across SARS-CoV-2 Variants in 245 Immunocompromised Patients: A Multicenter Prospective Cohort Study. Clin Infect Dis 2024; 78:1514-1521. [PMID: 38445721 PMCID: PMC11175671 DOI: 10.1093/cid/ciae026] [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: 09/22/2023] [Indexed: 03/07/2024] Open
Abstract
BACKGROUND Immunocompromised patients (ICPs) have an increased risk for a severe and prolonged COVID-19. SARS-CoV-2 monoclonal antibodies (mAbs) were extensively used in these patients, but data from randomized trials that focus on ICPs are lacking. We evaluated the clinical and virological outcome of COVID-19 in ICPs treated with mAbs across SARS-CoV-2 variants. METHODS In this multicenter prospective cohort study, we enrolled B-cell- and/or T-cell-deficient patients treated with casirivimab/imdevimab, sotrovimab, or tixagevimab/cilgavimab. SARS-CoV-2 RNA was quantified and sequenced weekly, and time to viral clearance, viral genome mutations, hospitalization, and death rates were registered. RESULTS Two hundred and forty five patients infected with the Delta (50%) or Omicron BA.1, 2, or 5 (50%) variant were enrolled. Sixty-seven percent were vaccinated; 78 treated as outpatients, of whom 2 required hospital admission, but both survived. Of the 159 patients hospitalized at time of treatment, 43 (27%) required mechanical ventilation or died. The median time to viral clearance was 14 days (interquartile range, 7-22); however, it took >30 days in 15%. Resistance-associated spike mutations emerged in 9 patients in whom the median time to viral clearance was 63 days (95% confidence interval, 57-69; P < .001). Spike mutations were observed in 1 of 42 (2.4%) patients after treatment with 2 active mAbs, in 5 of 34 (14.7%) treated with actual monotherapy (sotrovimab), and 3 of 20 (12%) treated with functional monotherapy (ie, tixagevimab/cilgavimab against tixagevimab-resistant variant). CONCLUSIONS Despite treatment with mAbs, morbidity and mortality of COVID-19 in ICPs remained substantial. Combination antiviral therapy should be further explored and may be preferred in severely ICPs.
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Affiliation(s)
- Sammy Huygens
- Department of Internal Medicine, Section of Infectious Diseases and Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Corine GeurtsvanKessel
- Department of Viroscience, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Arvind Gharbharan
- Department of Internal Medicine, Section of Infectious Diseases and Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Susanne Bogers
- Department of Viroscience, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Nathalie Worp
- Department of Viroscience, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Marjan Boter
- Department of Viroscience, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Hannelore I Bax
- Department of Internal Medicine, Section of Infectious Diseases and Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Linda M Kampschreur
- Department of Internal Medicine, Medical Center Leeuwarden, Leeuwarden, The Netherlands
| | - Robert-Jan Hassing
- Department of Internal Medicine, Rijnstate Hospital, Arnhem, The Netherlands
| | - Roel B Fiets
- Department of Internal Medicine, Amphia Hospital, Breda, The Netherlands
| | - Henriette Levenga
- Department of Internal Medicine, Groene Hart Gouda, Gouda, The Netherlands
| | - Pedro Miranda Afonso
- Department of Biostatistics, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
- Department of Epidemiology, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Marion Koopmans
- Department of Viroscience, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Bart J A Rijnders
- Department of Internal Medicine, Section of Infectious Diseases and Department of Medical Microbiology and Infectious Diseases, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
| | - Bas B Oude Munnink
- Department of Viroscience, Erasmus MC, University Medical Center, Rotterdam, The Netherlands
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23
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Zhang Y, Zhou Y, Chen J, Wu J, Wang X, Zhang Y, Wang S, Cui P, Xu Y, Li Y, Shen Z, Xu T, Zhang Q, Cai J, Zhang H, Wang P, Ai J, Jiang N, Qiu C, Zhang W. Vaccination Shapes Within-Host SARS-CoV-2 Diversity of Omicron BA.2.2 Breakthrough Infection. J Infect Dis 2024; 229:1711-1721. [PMID: 38149984 DOI: 10.1093/infdis/jiad572] [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: 07/18/2023] [Accepted: 12/19/2023] [Indexed: 12/28/2023] Open
Abstract
BACKGROUND Low-frequency intrahost single-nucleotide variants of SARS-CoV-2 have been recognized as predictive indicators of selection. However, the impact of vaccination on the intrahost evolution of SARS-CoV-2 remains uncertain at present. METHODS We investigated the genetic variation of SARS-CoV-2 in individuals who were unvaccinated, partially vaccinated, or fully vaccinated during Shanghai's Omicron BA.2.2 wave. We substantiated the connection between particular amino acid substitutions and immune-mediated selection through a pseudovirus neutralization assay or by cross-verification with the human leukocyte antigen-associated T-cell epitopes. RESULTS In contrast to those with immunologic naivety or partial vaccination, participants who were fully vaccinated had intrahost variant spectra characterized by reduced diversity. Nevertheless, the distribution of mutations in the fully vaccinated group was enriched in the spike protein. The distribution of intrahost single-nucleotide variants in individuals who were immunocompetent did not demonstrate notable signs of positive selection, in contrast to the observed adaptation in 2 participants who were immunocompromised who had an extended period of viral shedding. CONCLUSIONS In SARS-CoV-2 infections, vaccine-induced immunity was associated with decreased diversity of within-host variant spectra, with milder inflammatory pathophysiology. The enrichment of mutations in the spike protein gene indicates selection pressure exerted by vaccination on the evolution of SARS-CoV-2.
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Affiliation(s)
- Yi Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yang Zhou
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Sci-Tech Inno Center for Infection & Immunity, Shanghai, China
| | - Jiazhen Chen
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Sci-Tech Inno Center for Infection & Immunity, Shanghai, China
| | - Jing Wu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Sci-Tech Inno Center for Infection & Immunity, Shanghai, China
| | - Xun Wang
- School of Life Sciences, Fudan University, Shanghai, China
| | - Yumeng Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Sci-Tech Inno Center for Infection & Immunity, Shanghai, China
| | - Shiyong Wang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Peng Cui
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Sci-Tech Inno Center for Infection & Immunity, Shanghai, China
| | - Yuanyuan Xu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Yang Li
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Zhongliang Shen
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Tao Xu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Sci-Tech Inno Center for Infection & Immunity, Shanghai, China
| | - Qiran Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Jianpeng Cai
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Haocheng Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Pengfei Wang
- School of Life Sciences, Fudan University, Shanghai, China
| | - Jingwen Ai
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Sci-Tech Inno Center for Infection & Immunity, Shanghai, China
| | - Ning Jiang
- Shanghai Sci-Tech Inno Center for Infection & Immunity, Shanghai, China
- School of Life Sciences, Fudan University, Shanghai, China
| | - Chao Qiu
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Sci-Tech Inno Center for Infection & Immunity, Shanghai, China
| | - Wenhong Zhang
- Department of Infectious Diseases, Shanghai Key Laboratory of Infectious Diseases and Biosafety Emergency Response, National Medical Center for Infectious Diseases, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
- Shanghai Sci-Tech Inno Center for Infection & Immunity, Shanghai, China
- School of Life Sciences, Fudan University, Shanghai, China
- National Clinical Research Center for Aging and Medicine, Huashan Hospital, Fudan University, Shanghai, China
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24
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Kinsella PM, Moso MA, Morrissey CO, Dendle C, Guy S, Bond K, Sasadeusz J, Slavin MA. Antiviral therapies for the management of persistent coronavirus disease 2019 in immunocompromised hosts: A narrative review. Transpl Infect Dis 2024; 26:e14301. [PMID: 38809102 DOI: 10.1111/tid.14301] [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: 12/10/2023] [Revised: 04/11/2024] [Accepted: 05/08/2024] [Indexed: 05/30/2024]
Abstract
Antiviral agents with activity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) have played a critical role in disease management; however, little is known regarding the efficacy of these medications in the treatment of SARS-CoV-2 infection in immunocompromised patients, particularly in the management of persistent SARS-CoV-2 positivity. This narrative review discusses the management of persistent coronavirus disease 2019 in immunocompromised hosts, with a focus on antiviral therapies. We identified 84 cases from the literature describing a variety of approaches, including prolonged antiviral therapy (n = 11), combination antivirals (n = 13), and mixed therapy with antiviral and antibody treatments (n = 60). A high proportion had an underlying haematologic malignancy (n = 67, 80%), and were in receipt of anti-CD20 agents (n = 51, 60%). Success was reported in 70 cases (83%) which varied according to the therapy type. Combination therapies with antivirals may be an effective approach for individuals with persistent SARS-CoV-2 positivity, particularly those that incorporate treatments aimed at increasing neutralizing antibody levels. Any novel approaches taken to this difficult management dilemma should be mindful of the emergence of antiviral resistance.
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Affiliation(s)
- Paul M Kinsella
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, Australia
- Department of Infectious Diseases, University of Melbourne at the Doherty Institute of Infection and Immunity, Melbourne, Australia
| | - Michael A Moso
- Department of Infectious Diseases, University of Melbourne at the Doherty Institute of Infection and Immunity, Melbourne, Australia
- Victorian Infectious Diseases Service, Royal Melbourne Hospital at the Doherty Institute of Infection and Immunity, Melbourne, Australia
| | | | - Claire Dendle
- Monash Infectious Diseases, Monash Health, Melbourne, Australia
- School of Clinical Sciences, Monash University, Melbourne, Australia
| | - Stephen Guy
- Department of Infectious Diseases, Eastern Health, Melbourne, Australia
- Eastern Health Clinical School, Monash University, Melbourne, Australia
| | - Katherine Bond
- Department of Microbiology, Royal Melbourne Hospital, Melbourne, Australia
- Victorian Infectious Diseases Reference Laboratory (VIDRL) at the Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Microbiology and Immunology, University of Melbourne at the Doherty Institute of Infection and Immunity, Melbourne, Australia
| | - Joseph Sasadeusz
- Department of Infectious Diseases, University of Melbourne at the Doherty Institute of Infection and Immunity, Melbourne, Australia
- Victorian Infectious Diseases Service, Royal Melbourne Hospital at the Doherty Institute of Infection and Immunity, Melbourne, Australia
| | - Monica A Slavin
- Department of Infectious Diseases, Peter MacCallum Cancer Centre, Melbourne, Australia
- Victorian Infectious Diseases Service, Royal Melbourne Hospital at the Doherty Institute of Infection and Immunity, Melbourne, Australia
- Sir Peter MacCallum Department of Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
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25
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Pavia G, Quirino A, Marascio N, Veneziano C, Longhini F, Bruni A, Garofalo E, Pantanella M, Manno M, Gigliotti S, Giancotti A, Barreca GS, Branda F, Torti C, Rotundo S, Lionello R, La Gamba V, Berardelli L, Gullì SP, Trecarichi EM, Russo A, Palmieri C, De Marco C, Viglietto G, Casu M, Sanna D, Ciccozzi M, Scarpa F, Matera G. Persistence of SARS-CoV-2 infection and viral intra- and inter-host evolution in COVID-19 hospitalized patients. J Med Virol 2024; 96:e29708. [PMID: 38804179 DOI: 10.1002/jmv.29708] [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: 01/10/2024] [Revised: 05/11/2024] [Accepted: 05/14/2024] [Indexed: 05/29/2024]
Abstract
Severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) persistence in COVID-19 patients could play a key role in the emergence of variants of concern. The rapid intra-host evolution of SARS-CoV-2 may result in an increased transmissibility, immune and therapeutic escape which could be a direct consequence of COVID-19 epidemic currents. In this context, a longitudinal retrospective study on eight consecutive COVID-19 patients with persistent SARS-CoV-2 infection, from January 2022 to March 2023, was conducted. To characterize the intra- and inter-host viral evolution, whole genome sequencing and phylogenetic analysis were performed on nasopharyngeal samples collected at different time points. Phylogenetic reconstruction revealed an accelerated SARS-CoV-2 intra-host evolution and emergence of antigenically divergent variants. The Bayesian inference and principal coordinate analysis analysis showed a host-based genomic structuring among antigenically divergent variants, that might reflect the positive effect of containment practices, within the critical hospital area. All longitudinal antigenically divergent isolates shared a wide range of amino acidic (aa) changes, particularly in the Spike (S) glycoprotein, that increased viral transmissibility (K417N, S477N, N501Y and Q498R), enhanced infectivity (R346T, S373P, R408S, T478K, Q498R, Y505H, D614G, H655Y, N679K and P681H), caused host immune escape (S371L, S375F, T376A, K417N, and K444T/R) and displayed partial or complete resistance to treatments (G339D, R346K/T, S371F/L, S375F, T376A, D405N, N440K, G446S, N460K, E484A, F486V, Q493R, G496S and Q498R). These results suggest that multiple novel variants which emerge in the patient during persistent infection, might spread to another individual and continue to evolve. A pro-active genomic surveillance of persistent SARS-CoV-2 infected patients is recommended to identify genetically divergent lineages before their diffusion.
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Affiliation(s)
- Grazia Pavia
- Unit of Clinical Microbiology, Department of Health Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Angela Quirino
- Unit of Clinical Microbiology, Department of Health Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Nadia Marascio
- Unit of Clinical Microbiology, Department of Health Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Claudia Veneziano
- Department of Experimental and Clinical Medicine, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
- Interdepartmental Center of Services (CIS), Molecular Genomics and Pathology, "Magna Græcia" University of Catanzaro, Catanzaro, Italy
| | - Federico Longhini
- Unit of Anesthesia and Intensive Care, Department of Medical and Surgical Sciences, "Magna Graecia" University, Catanzaro, Italy
| | - Andrea Bruni
- Unit of Anesthesia and Intensive Care, Department of Medical and Surgical Sciences, "Magna Graecia" University, Catanzaro, Italy
| | - Eugenio Garofalo
- Unit of Anesthesia and Intensive Care, Department of Medical and Surgical Sciences, "Magna Graecia" University, Catanzaro, Italy
| | - Marta Pantanella
- Unit of Clinical Microbiology, Department of Health Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Michele Manno
- Unit of Clinical Microbiology, Department of Health Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Simona Gigliotti
- Unit of Clinical Microbiology, Department of Health Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Aida Giancotti
- Unit of Clinical Microbiology, Department of Health Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Giorgio Settimo Barreca
- Unit of Clinical Microbiology, Department of Health Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Francesco Branda
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, Rome, Italy
| | - Carlo Torti
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli" IRCCS, Rome, Italy
- Dipartimento di Sicurezza e Bioetica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Salvatore Rotundo
- Unit of Infectious and Tropical Disease, Department of Medical and Surgical Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Rosaria Lionello
- Unit of Infectious and Tropical Disease, Department of Medical and Surgical Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Valentina La Gamba
- Unit of Infectious and Tropical Disease, Department of Medical and Surgical Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Lavinia Berardelli
- Unit of Infectious and Tropical Disease, Department of Medical and Surgical Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Sara Palma Gullì
- Unit of Infectious and Tropical Disease, Department of Medical and Surgical Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Enrico Maria Trecarichi
- Unit of Infectious and Tropical Disease, Department of Medical and Surgical Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Alessandro Russo
- Unit of Infectious and Tropical Disease, Department of Medical and Surgical Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
| | - Camillo Palmieri
- Department of Experimental and Clinical Medicine, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
| | - Carmela De Marco
- Department of Experimental and Clinical Medicine, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
- Interdepartmental Center of Services (CIS), Molecular Genomics and Pathology, "Magna Græcia" University of Catanzaro, Catanzaro, Italy
| | - Giuseppe Viglietto
- Department of Experimental and Clinical Medicine, "Magna Graecia" University of Catanzaro, Catanzaro, Italy
- Interdepartmental Center of Services (CIS), Molecular Genomics and Pathology, "Magna Græcia" University of Catanzaro, Catanzaro, Italy
| | - Marco Casu
- Department of Veterinary Medicine, University of Sassari, Sassari, Italy
| | - Daria Sanna
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, Rome, Italy
| | - Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, Sassari, Italy
| | - Giovanni Matera
- Unit of Clinical Microbiology, Department of Health Sciences, "Magna Græcia" University Hospital, Catanzaro, Italy
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26
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Xue S, Han Y, Wu F, Wang Q. Mutations in the SARS-CoV-2 spike receptor binding domain and their delicate balance between ACE2 affinity and antibody evasion. Protein Cell 2024; 15:403-418. [PMID: 38442025 PMCID: PMC11131022 DOI: 10.1093/procel/pwae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/05/2024] [Indexed: 03/07/2024] Open
Abstract
Intensive selection pressure constrains the evolutionary trajectory of SARS-CoV-2 genomes and results in various novel variants with distinct mutation profiles. Point mutations, particularly those within the receptor binding domain (RBD) of SARS-CoV-2 spike (S) protein, lead to the functional alteration in both receptor engagement and monoclonal antibody (mAb) recognition. Here, we review the data of the RBD point mutations possessed by major SARS-CoV-2 variants and discuss their individual effects on ACE2 affinity and immune evasion. Many single amino acid substitutions within RBD epitopes crucial for the antibody evasion capacity may conversely weaken ACE2 binding affinity. However, this weakened effect could be largely compensated by specific epistatic mutations, such as N501Y, thus maintaining the overall ACE2 affinity for the spike protein of all major variants. The predominant direction of SARS-CoV-2 evolution lies neither in promoting ACE2 affinity nor evading mAb neutralization but in maintaining a delicate balance between these two dimensions. Together, this review interprets how RBD mutations efficiently resist antibody neutralization and meanwhile how the affinity between ACE2 and spike protein is maintained, emphasizing the significance of comprehensive assessment of spike mutations.
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Affiliation(s)
- Song Xue
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Yuru Han
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Fan Wu
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
| | - Qiao Wang
- Key Laboratory of Medical Molecular Virology (MOE/NHC/CAMS), Shanghai Institute of Infectious Disease and Biosecurity, Shanghai Frontiers Science Center of Pathogenic Microorganisms and Infection, School of Basic Medical Sciences, Shanghai Medical College, Fudan University, Shanghai 200032, China
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27
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Liu C, Zhou D, Dijokaite-Guraliuc A, Supasa P, Duyvesteyn HME, Ginn HM, Selvaraj M, Mentzer AJ, Das R, de Silva TI, Ritter TG, Plowright M, Newman TAH, Stafford L, Kronsteiner B, Temperton N, Lui Y, Fellermeyer M, Goulder P, Klenerman P, Dunachie SJ, Barton MI, Kutuzov MA, Dushek O, Fry EE, Mongkolsapaya J, Ren J, Stuart DI, Screaton GR. A structure-function analysis shows SARS-CoV-2 BA.2.86 balances antibody escape and ACE2 affinity. Cell Rep Med 2024; 5:101553. [PMID: 38723626 PMCID: PMC11148769 DOI: 10.1016/j.xcrm.2024.101553] [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: 10/06/2023] [Revised: 01/10/2024] [Accepted: 04/11/2024] [Indexed: 05/24/2024]
Abstract
BA.2.86, a recently described sublineage of SARS-CoV-2 Omicron, contains many mutations in the spike gene. It appears to have originated from BA.2 and is distinct from the XBB variants responsible for many infections in 2023. The global spread and plethora of mutations in BA.2.86 has caused concern that it may possess greater immune-evasive potential, leading to a new wave of infection. Here, we examine the ability of BA.2.86 to evade the antibody response to infection using a panel of vaccinated or naturally infected sera and find that it shows marginally less immune evasion than XBB.1.5. We locate BA.2.86 in the antigenic landscape of recent variants and look at its ability to escape panels of potent monoclonal antibodies generated against contemporary SARS-CoV-2 infections. We demonstrate, and provide a structural explanation for, increased affinity of BA.2.86 to ACE2, which may increase transmissibility.
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Affiliation(s)
- Chang Liu
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Daming Zhou
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK
| | | | - Piyada Supasa
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Helen M E Duyvesteyn
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK
| | - Helen M Ginn
- Centre for Free Electron Laser Science, Hamburg, Germany
| | - Muneeswaran Selvaraj
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Alexander J Mentzer
- Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Raksha Das
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK
| | - Thushan I de Silva
- Division of Clinical Medicine, School of Medicine and Population Health, University of Sheffield, Sheffield, UK; Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | - Thomas G Ritter
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Megan Plowright
- Sheffield Teaching Hospitals NHS Foundation Trust, Sheffield, UK
| | | | - Lizzie Stafford
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Barbara Kronsteiner
- NDM Centre for Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK
| | - Nigel Temperton
- Viral Pseudotype Unit, Medway School of Pharmacy, University of Kent and University of Greenwich Chatham Maritime, Kent ME4 4TB, UK
| | - Yuan Lui
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Martin Fellermeyer
- Radcliffe Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, UK
| | - Philip Goulder
- Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK; Department of Paediatrics, University of Oxford, Oxford, UK
| | - Paul Klenerman
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK; Translational Gastroenterology Unit, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Susanna J Dunachie
- NIHR Oxford Biomedical Research Centre, Oxford University Hospitals NHS Foundation Trust, Oxford, UK; NDM Centre for Global Health Research, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Peter Medawar Building for Pathogen Research, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand
| | - Michael I Barton
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Mikhail A Kutuzov
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Omer Dushek
- Diamond Light Source Ltd, Harwell Science & Innovation Campus, Didcot, UK
| | - Elizabeth E Fry
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK.
| | - Juthathip Mongkolsapaya
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK; Mahidol-Oxford Tropical Medicine Research Unit, Mahidol University, Bangkok, Thailand.
| | - Jingshan Ren
- Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK.
| | - David I Stuart
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Division of Structural Biology, Nuffield Department of Medicine, University of Oxford, Centre for Human Genetics, Oxford, UK; Sir William Dunn School of Pathology, Oxford, UK.
| | - Gavin R Screaton
- Chinese Academy of Medical Science (CAMS) Oxford Institute (COI), University of Oxford, Oxford, UK; Centre for Human Genetics, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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28
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Yu Y, Zhang M, Huang L, Chen Y, Wu X, Li T, Li Y, Wang Y, Huang W. COVID-19 Serum Drives Spike-Mediated SARS-CoV-2 Variation. Viruses 2024; 16:763. [PMID: 38793644 PMCID: PMC11126028 DOI: 10.3390/v16050763] [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: 03/29/2024] [Revised: 04/26/2024] [Accepted: 05/09/2024] [Indexed: 05/26/2024] Open
Abstract
Neutralizing antibodies targeting the spike (S) protein of SARS-CoV-2, elicited either by natural infection or vaccination, are crucial for protection against the virus. Nonetheless, the emergence of viral escape mutants presents ongoing challenges by contributing to breakthrough infections. To define the evolution trajectory of SARS-CoV-2 within the immune population, we co-incubated replication-competent rVSV/SARS-CoV-2/GFP chimeric viruses with sera from COVID-19 convalescents. Our findings revealed that the E484D mutation contributes to increased viral resistant against both convalescent and vaccinated sera, while the L1265R/H1271Y double mutation enhanced viral infectivity in 293T-hACE2 and Vero cells. These findings suggest that under the selective pressure of polyclonal antibodies, SARS-CoV-2 has the potential to accumulate mutations that facilitate either immune evasion or greater infectivity, facilitating its adaption to neutralizing antibody responses. Although the mutations identified in this study currently exhibit low prevalence in the circulating SARS-CoV-2 populations, the continuous and meticulous surveillance of viral mutations remains crucial. Moreover, there is an urgent necessity to develop next-generation antibody therapeutics and vaccines that target diverse, less mutation-prone antigenic sites to ensure more comprehensive and durable immune protection against SARS-CoV-2.
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Affiliation(s)
- Yuanling Yu
- Changping Laboratory, Beijing 102206, China; (Y.Y.); (L.H.)
| | - Mengyi Zhang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing 102629, China; (M.Z.)
- National Institutes for Food and Drug Control, Chinese Academy of Medical Science & Peking Union Medical College, No. 9 Dongdan Santiao, Dongcheng District, Beijing 100730, China
| | - Lan Huang
- Changping Laboratory, Beijing 102206, China; (Y.Y.); (L.H.)
| | - Yanhong Chen
- Changping Laboratory, Beijing 102206, China; (Y.Y.); (L.H.)
| | - Xi Wu
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing 102629, China; (M.Z.)
- State Key Laboratory of Drug Regulatory Science, National Institutes for Food and Drug Control (NIFDC), Beijing 102629, China
| | - Tao Li
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing 102629, China; (M.Z.)
| | - Yanbo Li
- Beijing Yunling Biotechnology Co., Ltd., Beijing 100176, China
| | - Youchun Wang
- Changping Laboratory, Beijing 102206, China; (Y.Y.); (L.H.)
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming 650118, China
| | - Weijin Huang
- Division of HIV/AIDS and Sex-Transmitted Virus Vaccines, Institute for Biological Product Control, National Institutes for Food and Drug Control (NIFDC), Beijing 102629, China; (M.Z.)
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29
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Ose NJ, Campitelli P, Modi T, Kazan IC, Kumar S, Ozkan SB. Some mechanistic underpinnings of molecular adaptations of SARS-COV-2 spike protein by integrating candidate adaptive polymorphisms with protein dynamics. eLife 2024; 12:RP92063. [PMID: 38713502 PMCID: PMC11076047 DOI: 10.7554/elife.92063] [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] [Indexed: 05/08/2024] Open
Abstract
We integrate evolutionary predictions based on the neutral theory of molecular evolution with protein dynamics to generate mechanistic insight into the molecular adaptations of the SARS-COV-2 spike (S) protein. With this approach, we first identified candidate adaptive polymorphisms (CAPs) of the SARS-CoV-2 S protein and assessed the impact of these CAPs through dynamics analysis. Not only have we found that CAPs frequently overlap with well-known functional sites, but also, using several different dynamics-based metrics, we reveal the critical allosteric interplay between SARS-CoV-2 CAPs and the S protein binding sites with the human ACE2 (hACE2) protein. CAPs interact far differently with the hACE2 binding site residues in the open conformation of the S protein compared to the closed form. In particular, the CAP sites control the dynamics of binding residues in the open state, suggesting an allosteric control of hACE2 binding. We also explored the characteristic mutations of different SARS-CoV-2 strains to find dynamic hallmarks and potential effects of future mutations. Our analyses reveal that Delta strain-specific variants have non-additive (i.e., epistatic) interactions with CAP sites, whereas the less pathogenic Omicron strains have mostly additive mutations. Finally, our dynamics-based analysis suggests that the novel mutations observed in the Omicron strain epistatically interact with the CAP sites to help escape antibody binding.
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Affiliation(s)
- Nicholas James Ose
- Department of Physics and Center for Biological Physics, Arizona State UniversityTempeUnited States
| | - Paul Campitelli
- Department of Physics and Center for Biological Physics, Arizona State UniversityTempeUnited States
| | - Tushar Modi
- Department of Physics and Center for Biological Physics, Arizona State UniversityTempeUnited States
| | - I Can Kazan
- Department of Physics and Center for Biological Physics, Arizona State UniversityTempeUnited States
| | - Sudhir Kumar
- Institute for Genomics and Evolutionary Medicine, Temple UniversityPhiladelphiaUnited States
- Department of Biology, Temple UniversityPhiladelphiaUnited States
- Center for Genomic Medicine Research, King Abdulaziz UniversityJeddahSaudi Arabia
| | - Sefika Banu Ozkan
- Department of Physics and Center for Biological Physics, Arizona State UniversityTempeUnited States
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30
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Feng S, Reid GE, Clark NM, Harrington A, Uprichard SL, Baker SC. Evidence of SARS-CoV-2 convergent evolution in immunosuppressed patients treated with antiviral therapies. Virol J 2024; 21:105. [PMID: 38715113 PMCID: PMC11075269 DOI: 10.1186/s12985-024-02378-y] [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: 02/05/2024] [Accepted: 04/29/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND The factors contributing to the accelerated convergent evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) are not fully understood. Unraveling the contribution of viral replication in immunocompromised patients is important for the early detection of novel mutations and developing approaches to limit COVID-19. METHODS We deep sequenced SARS-CoV-2 RNA from 192 patients (64% hospitalized, 39% immunosuppressed) and compared the viral genetic diversity within the patient groups of different immunity and hospitalization status. Serial sampling of 14 patients was evaluated for viral evolution in response to antiviral treatments. RESULTS We identified hospitalized and immunosuppressed patients with significantly higher levels of viral genetic diversity and variability. Further evaluation of serial samples revealed accumulated mutations associated with escape from neutralizing antibodies in a subset of the immunosuppressed patients treated with antiviral therapies. Interestingly, the accumulated viral mutations that arose in this early Omicron wave, which were not common in the patient viral lineages, represent convergent mutations that are prevalent in the later Omicron sublineages, including the XBB, BA.2.86.1 and its descendent JN sublineages. CONCLUSIONS Our results illustrate the importance of identifying convergent mutations generated during antiviral therapy in immunosuppressed patients, as they may contribute to the future evolutionary landscape of SARS-CoV-2. Our study also provides evidence of a correlation between SARS-CoV-2 convergent mutations and specific antiviral treatments. Evaluating high-confidence genomes from distinct waves in the pandemic with detailed patient metadata allows for discerning of convergent mutations that contribute to the ongoing evolution of SARS-CoV-2.
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Affiliation(s)
- Shuchen Feng
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Gail E Reid
- Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Nina M Clark
- Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Amanda Harrington
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Department of Pathology and Laboratory Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Susan L Uprichard
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Department of Medicine, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA
| | - Susan C Baker
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA.
- Infectious Disease and Immunology Research Institute, Stritch School of Medicine, Loyola University Chicago, Maywood, IL, 60153, USA.
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31
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Igari H, Sakao S, Ishige T, Saito K, Murata S, Yahaba M, Taniguchi T, Suganami A, Matsushita K, Tamura Y, Suzuki T, Ido E. Dynamic diversity of SARS-CoV-2 genetic mutations in a lung transplantation patient with persistent COVID-19. Nat Commun 2024; 15:3604. [PMID: 38684722 PMCID: PMC11058237 DOI: 10.1038/s41467-024-47941-x] [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: 05/29/2023] [Accepted: 04/15/2024] [Indexed: 05/02/2024] Open
Abstract
Numerous SARS-CoV-2 variant strains with altered characteristics have emerged since the onset of the COVID-19 pandemic. Remdesivir (RDV), a ribonucleotide analogue inhibitor of viral RNA polymerase, has become a valuable therapeutic agent. However, immunosuppressed hosts may respond inadequately to RDV and develop chronic persistent infections. A patient with respiratory failure caused by interstitial pneumonia, who had undergone transplantation of the left lung, developed COVID-19 caused by Omicron BA.5 strain with persistent chronic viral shedding, showing viral fusogenicity. Genome-wide sequencing analyses revealed the occurrence of several viral mutations after RDV treatment, followed by dynamic changes in the viral populations. The C799F mutation in nsp12 was found to play a pivotal role in conferring RDV resistance, preventing RDV-triphosphate from entering the active site of RNA-dependent RNA polymerase. The occurrence of diverse mutations is a characteristic of SARS-CoV-2, which mutates frequently. Herein, we describe the clinical case of an immunosuppressed host in whom inadequate treatment resulted in highly diverse SARS-CoV-2 mutations that threatened the patient's health due to the development of drug-resistant variants.
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Affiliation(s)
- Hidetoshi Igari
- Department of Infectious Diseases, Chiba University Hospital, Chiba, Chiba, Japan.
- Future Mucosal Vaccine Research and Development Center, Chiba University Hospital, Chiba, Chiba, Japan.
- COVID-19 Vaccine Center, Chiba University Hospital, Chiba, Chiba, Japan.
- Research Institute of Disaster Medicine, Chiba University, Chiba, Chiba, Japan.
| | - Seiichiro Sakao
- Department of Respiratory Medicine, Chiba University Hospital, Chiba, Chiba, Japan
- Department of Pulmonary Medicine, School of Medicine, International University of Health and Welfare, Narita, Chiba, Japan
| | - Takayuki Ishige
- Division of Laboratory Medicine, Chiba University Hospital, Chiba, Chiba, Japan.
| | - Kengo Saito
- Department of Molecular Virology, Graduate School of Medicine, Chiba University, Chiba, Chiba, Japan
| | - Shota Murata
- Division of Laboratory Medicine, Chiba University Hospital, Chiba, Chiba, Japan
| | - Misuzu Yahaba
- Department of Infectious Diseases, Chiba University Hospital, Chiba, Chiba, Japan
| | - Toshibumi Taniguchi
- Department of Infectious Diseases, Chiba University Hospital, Chiba, Chiba, Japan
- Research Institute of Disaster Medicine, Chiba University, Chiba, Chiba, Japan
| | - Akiko Suganami
- Department of Bioinformatics, Graduate School of Medicine, Chiba University, Chiba, Chiba, Japan
| | - Kazuyuki Matsushita
- Division of Laboratory Medicine, Chiba University Hospital, Chiba, Chiba, Japan
| | - Yutaka Tamura
- Department of Bioinformatics, Graduate School of Medicine, Chiba University, Chiba, Chiba, Japan
| | - Takuji Suzuki
- Future Mucosal Vaccine Research and Development Center, Chiba University Hospital, Chiba, Chiba, Japan
- Department of Respiratory Medicine, Chiba University Hospital, Chiba, Chiba, Japan
- Synergy Institute for Futuristic Mucosal Vaccine Research and Development, Chiba University, Chiba, Chiba, Japan
| | - Eiji Ido
- Department of Infectious Diseases, Chiba University Hospital, Chiba, Chiba, Japan.
- Department of Molecular Virology, Graduate School of Medicine, Chiba University, Chiba, Chiba, Japan.
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32
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Iketani S, Ho DD. SARS-CoV-2 resistance to monoclonal antibodies and small-molecule drugs. Cell Chem Biol 2024; 31:632-657. [PMID: 38640902 PMCID: PMC11084874 DOI: 10.1016/j.chembiol.2024.03.008] [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: 09/07/2023] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/21/2024]
Abstract
Over four years have passed since the beginning of the COVID-19 pandemic. The scientific response has been rapid and effective, with many therapeutic monoclonal antibodies and small molecules developed for clinical use. However, given the ability for viruses to become resistant to antivirals, it is perhaps no surprise that the field has identified resistance to nearly all of these compounds. Here, we provide a comprehensive review of the resistance profile for each of these therapeutics. We hope that this resource provides an atlas for mutations to be aware of for each agent, particularly as a springboard for considerations for the next generation of antivirals. Finally, we discuss the outlook and thoughts for moving forward in how we continue to manage this, and the next, pandemic.
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Affiliation(s)
- Sho Iketani
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA
| | - David D Ho
- Aaron Diamond AIDS Research Center, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Division of Infectious Diseases, Department of Medicine, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA; Department of Microbiology and Immunology, Columbia University Vagelos College of Physicians and Surgeons, New York, NY, USA.
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33
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Sarkar A, Ghosh TA, Bandyopadhyay B, Maiti S, Panja AS. Prediction of Prospective Mutational Landscape of SARS-CoV-2 Spike ssRNA and Evolutionary Basis of Its Host Interaction. Mol Biotechnol 2024:10.1007/s12033-024-01146-1. [PMID: 38619800 DOI: 10.1007/s12033-024-01146-1] [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: 01/23/2024] [Accepted: 03/14/2024] [Indexed: 04/16/2024]
Abstract
Booster doses are crucial against severe COVID-19, as rapid virus mutations and variant emergence prolong the pandemic crisis. The virus's quick evolution, short generation-time, and adaptive changes impact virulence and evolvability, helping predictions about variant of concerns' (VOCs') landscapes. Here, in this study, we used a new computational algorithm, to predict the mutational pattern in SARS-CoV-2 ssRNA, proteomics, structural identification, mutation stability, and functional correlation, as well as immune escape mechanisms. Interestingly, the sequence diversity of SARS Coronavirus-2 has demonstrated a predominance of G- > A and C- > U substitutions. The best validation statistics are explored here in seven homologous models of the expected mutant SARS-CoV-2 spike ssRNA and employed for hACE2 and IgG interactions. The interactome profile of SARS-CoV-2 spike with hACE2 and IgG revealed a strong correlation between phylogeny and divergence time. The systematic adaptation of SARS-CoV-2 spike ssRNA influences infectivity and immune escape. Data suggest higher propensity of Adenine rich sequence promotes MHC system avoidance, preferred by A-rich codons. Phylogenetic data revealed the evolution of SARS-CoV-2 lineages' epidemiology. Our findings may unveil processes governing the genesis of immune-resistant variants, prompting a critical reassessment of the coronavirus mutation rate and exploration of hypotheses beyond mechanical aspects.
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Affiliation(s)
- Aniket Sarkar
- Post Graduate Department of Biotechnology, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Trijit Arka Ghosh
- Department of Computer Application, Burdwan Institute of Management and Computer Science, The University of Burdwan, Dewandighi, Burdwan, West Bengal, 713102, India
| | - Bidyut Bandyopadhyay
- Post Graduate Department of Biotechnology, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Smarajit Maiti
- Department of Medical Laboratory Technology, Haldia Institute of Health Sciences, ICARE Complex, Haldia, West Bengal, 721657, India
| | - Anindya Sundar Panja
- Post Graduate Department of Biotechnology, Molecular Informatics Laboratory, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, West Bengal, 721102, India.
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34
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Guilbaud R, Franco Yusti AM, Leducq V, Zafilaza K, Bridier-Nahmias A, Todesco E, Soulie C, Fauchois A, Le Hingrat Q, Kramer L, Goulenok T, Salpin M, Daugas E, Dorent R, Ottaviani S, Zalcman G, Ghosn J, Choquet S, Cacoub P, Amoura Z, Barroux B, Pourcher V, Spano JP, Louet M, Marcelin AG, Calvez V, Charpentier C, Descamps D, Marot S, Ferré VM, Coppée R. Higher Levels of SARS-CoV-2 Genetic Variation in Immunocompromised Patients: A Retrospective Case-Control Study. J Infect Dis 2024; 229:1041-1049. [PMID: 37956413 DOI: 10.1093/infdis/jiad499] [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: 07/19/2023] [Revised: 10/30/2023] [Accepted: 11/10/2023] [Indexed: 11/15/2023] Open
Abstract
BACKGROUND A severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection lasts longer in immunocompromised hosts than in immunocompetent patients. Prolonged infection is associated with a higher probability of selection for novel SARS-CoV-2 mutations, particularly in the spike protein, a critical target for vaccines and therapeutics. METHODS From December 2020 to September 2022, respiratory samples from 444 immunocompromised patients and 234 health care workers positive for SARS-CoV-2, diagnosed at 2 hospitals in Paris, France, were analyzed using whole-genome sequencing using Nanopore technology. Custom scripts were developed to assess the SARS-CoV-2 genetic diversity between the 2 groups and within the host. RESULTS Most infections were SARS-CoV-2 Delta or Omicron lineages. Viral genetic diversity was significantly higher in infections of immunocompromised patients than those of controls. Minor mutations were identified in viruses sequenced from immunocompromised individuals, which became signature mutations for newer SARS-CoV-2 variants as the epidemic progressed. Two patients were coinfected with Delta and Omicron variants. The follow-up of immunocompromised patients revealed that the SARS-CoV-2 genome evolution differed in the upper and lower respiratory tracts. CONCLUSIONS This study found that SARS-CoV-2 infection in immunocompromised patients is associated with higher genetic diversity, which could lead to the emergence of new SARS-CoV-2 variants with possible immune evasion or different virulence characteristics.
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Affiliation(s)
- Romane Guilbaud
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Anna-Maria Franco Yusti
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Valentin Leducq
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Karen Zafilaza
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Antoine Bridier-Nahmias
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Eve Todesco
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Cathia Soulie
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Antoine Fauchois
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Quentin Le Hingrat
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Laura Kramer
- Service de Pharmacie, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Tiphaine Goulenok
- Service de Médecine Interne, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Mathilde Salpin
- Service de Pneumologie, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Eric Daugas
- Service de Néphrologie, Université Paris Cité, Inserm U1149, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Richard Dorent
- Service de Cardiologie, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Sébastien Ottaviani
- Service de Rhumatologie, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Gérard Zalcman
- Service d'Oncologie Thoracique, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Jade Ghosn
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
- Service de Maladies Infectieuses, Assistance Publique-Hôpitaux de Paris, Hôpital Bichat-Claude-Bernard, Paris, France
| | - Sylvain Choquet
- Service d'Hématologie Clinique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Patrice Cacoub
- Service de Médecine Interne et Immunologie Clinique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Zahir Amoura
- Service de Médecine Interne 2, Centre National de Référence des Histiocytoses, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Benoit Barroux
- Service d'Urologie et de Transplantation Rénale, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Valérie Pourcher
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
- Service de Maladies Infectieuses et Tropicales, Assistance Publique-Hôpitaux de Paris, Hôpitaux Universitaires Pitié-Salpêtrière, Paris, France
| | - Jean-Philippe Spano
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
- Service d'Oncologie Médicale, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Martine Louet
- Service de Santé au Travail, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Anne-Geneviève Marcelin
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Vincent Calvez
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Charlotte Charpentier
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Diane Descamps
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Stéphane Marot
- Service de Virologie, Sorbonne Université, Inserm, Institut Pierre Louis d'Epidémiologie et de Santé Publique, Assistance Publique-Hôpitaux de Paris, Hôpital Pitié-Salpêtrière, Paris, France
| | - Valentine Marie Ferré
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
| | - Romain Coppée
- Infection, Antimicrobials, Modelling, Evolution, Université Paris Cité and Sorbonne Paris Nord, Inserm, Paris, France
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Tan TJC, Verma AK, Odle A, Lei R, Meyerholz DK, Matreyek KA, Perlman S, Wong LYR, Wu NC. Evidence of antigenic drift in the fusion machinery core of SARS-CoV-2 spike. Proc Natl Acad Sci U S A 2024; 121:e2317222121. [PMID: 38557175 PMCID: PMC11009667 DOI: 10.1073/pnas.2317222121] [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: 10/04/2023] [Accepted: 02/23/2024] [Indexed: 04/04/2024] Open
Abstract
Antigenic drift of SARS-CoV-2 is typically defined by mutations in the N-terminal domain and receptor binding domain of spike protein. In contrast, whether antigenic drift occurs in the S2 domain remains largely elusive. Here, we perform a deep mutational scanning experiment to identify S2 mutations that affect binding of SARS-CoV-2 spike to three S2 apex public antibodies. Our results indicate that spatially diverse mutations, including D950N and Q954H, which are observed in Delta and Omicron variants, respectively, weaken the binding of spike to these antibodies. Although S2 apex antibodies are known to be nonneutralizing, we show that they confer protection in vivo through Fc-mediated effector functions. Overall, this study indicates that the S2 domain of SARS-CoV-2 spike can undergo antigenic drift, which represents a potential challenge for the development of more universal coronavirus vaccines.
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Affiliation(s)
- Timothy J. C. Tan
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL61801
| | - Abhishek K. Verma
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA52242
| | - Abby Odle
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA52242
| | - Ruipeng Lei
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL61801
| | | | - Kenneth A. Matreyek
- Department of Pathology, Case Western Reserve University School of Medicine, Cleveland, OH44106
| | - Stanley Perlman
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA52242
- Department of Pediatrics, University of Iowa, Iowa City, IA52242
| | - Lok-Yin Roy Wong
- Department of Microbiology and Immunology, University of Iowa, Iowa City, IA52242
- Center for Virus-Host-Innate Immunity, Rutgers New Jersey Medical School, Newark, NJ07103
- Department of Microbiology, Biochemistry and Molecular Genetics, Rutgers New Jersey Medical School, Newark, NJ07103
| | - Nicholas C. Wu
- Center for Biophysics and Quantitative Biology, University of Illinois Urbana-Champaign, Urbana, IL61801
- Department of Biochemistry, University of Illinois Urbana-Champaign, Urbana, IL61801
- Carl R. Woese Institute for Genomic Biology, University of Illinois Urbana-Champaign, Urbana, IL61801
- Carle Illinois College of Medicine, University of Illinois Urbana-Champaign, Urbana, IL61801
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Qian J, Zhang S, Wang F, Li J, Zhang J. What makes SARS-CoV-2 unique? Focusing on the spike protein. Cell Biol Int 2024; 48:404-430. [PMID: 38263600 DOI: 10.1002/cbin.12130] [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: 10/09/2023] [Revised: 12/25/2023] [Accepted: 01/02/2024] [Indexed: 01/25/2024]
Abstract
Severe acute respiratory syndrome-related coronavirus 2 (SARS-CoV-2) seriously threatens public health and safety. Genetic variants determine the expression of SARS-CoV-2 structural proteins, which are associated with enhanced transmissibility, enhanced virulence, and immune escape. Vaccination is encouraged as a public health intervention, and different types of vaccines are used worldwide. However, new variants continue to emerge, especially the Omicron complex, and the neutralizing antibody responses are diminished significantly. In this review, we outlined the uniqueness of SARS-CoV-2 from three perspectives. First, we described the detailed structure of the spike (S) protein, which is highly susceptible to mutations and contributes to the distinct infection cycle of the virus. Second, we systematically summarized the immunoglobulin G epitopes of SARS-CoV-2 and highlighted the central role of the nonconserved regions of the S protein in adaptive immune escape. Third, we provided an overview of the vaccines targeting the S protein and discussed the impact of the nonconserved regions on vaccine effectiveness. The characterization and identification of the structure and genomic organization of SARS-CoV-2 will help elucidate its mechanisms of viral mutation and infection and provide a basis for the selection of optimal treatments. The leaps in advancements regarding improved diagnosis, targeted vaccines and therapeutic remedies provide sound evidence showing that scientific understanding, research, and technology evolved at the pace of the pandemic.
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Affiliation(s)
- Jingbo Qian
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Shichang Zhang
- Department of Clinical Laboratory Medicine, Shenzhen Hospital of Southern Medical University, Shenzhen, China
| | - Fang Wang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, Beijing, China
- National Center for Clinical Laboratories, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
- Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, China
| | - Jiexin Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
- Branch of National Clinical Research Center for Laboratory Medicine, Nanjing, China
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Lim T, Rajoriya S, Kim B, Natasha A, Im H, Shim HS, Yoo J, Kim JW, Lee EW, Shin HJ, Kim SH, Kim WK. In vitro broad-spectrum antiviral activity of MIT-001, a mitochondria-targeted reactive oxygen species scavenger, against severe acute respiratory syndrome coronavirus 2 and multiple zoonotic viruses. Virus Res 2024; 342:199325. [PMID: 38309472 PMCID: PMC10851010 DOI: 10.1016/j.virusres.2024.199325] [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: 09/06/2023] [Revised: 12/31/2023] [Accepted: 01/17/2024] [Indexed: 02/05/2024]
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 becomes a serious threat to global health and requires the development of effective antiviral therapies. Current therapies that target viral proteins have limited efficacy with side effects. In this study, we investigated the antiviral activity of MIT-001, a small molecule reactive oxygen species (ROS) scavenger targeting mitochondria, against SARS-CoV-2 and other zoonotic viruses in vitro. The antiviral activity of MIT-001 was quantified by RT-qPCR and plaque assay. We also evaluated the functional analysis of MIT-001 by JC-1 staining to measure mitochondrial depolarization, total RNA sequencing to investigate gene expression changes, and immunoblot to quantify protein expression levels. The results showed that MIT-001 effectively inhibited the replication of B.1.617.2 and BA.1 strains, Zika virus, Seoul virus, and Vaccinia virus. Treatment with MIT-001 restored the expression of heme oxygenase-1 (HMOX1) and NAD(P)H: quinone oxidoreductase 1 (NqO1) genes, anti-oxidant enzymes reduced by SARS-CoV-2, to normal levels. The presence of MIT-001 also alleviated mitochondrial depolarization caused by SARS-CoV-2 infection. These findings highlight the potential of MIT-001 as a broad-spectrum antiviral compound that targets for zoonotic RNA and DNA viruses, providing a promising therapeutic approach to combat viral infection.
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Affiliation(s)
- Taehun Lim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Shivani Rajoriya
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Bohyeon Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Augustine Natasha
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea
| | - Hyeonjoo Im
- Laboratory of Regenerative Medicine For Neurodegenerative Disease, Stand Up Therapeutics, Hannamdaero 98, Seoul 04418, Republic of Korea
| | - Hyun Soo Shim
- Laboratory of Regenerative Medicine For Neurodegenerative Disease, Stand Up Therapeutics, Hannamdaero 98, Seoul 04418, Republic of Korea
| | - Junsang Yoo
- Laboratory of Regenerative Medicine For Neurodegenerative Disease, Stand Up Therapeutics, Hannamdaero 98, Seoul 04418, Republic of Korea
| | - Jong Woo Kim
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Functional Genomics, University of Science and Technology (UST), Daejeon 34141, Republic of Korea
| | - Eun-Woo Lee
- Metabolic Regulation Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon 34141, Republic of Korea; Department of Functional Genomics, University of Science and Technology (UST), Daejeon 34141, Republic of Korea; School of pharmacy, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Hye Jin Shin
- College of Medicine, Chungnam National University, Daejeon, Republic of Korea
| | - Soon Ha Kim
- Mitoimmune Therapeutics Inc., Gangnam-gu, Seoul 06253, Republic of Korea
| | - Won-Keun Kim
- Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Republic of Korea; Institute of Medical Science, College of Medicine, Hallym University, Chuncheon, Republic of Korea.
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Feuth E, Nieminen V, Palomäki A, Ranti J, Sucksdorff M, Finnilä T, Oksi J, Vuorinen T, Feuth T. Prolonged viral pneumonia and high mortality in COVID-19 patients on anti-CD20 monoclonal antibody therapy. Eur J Clin Microbiol Infect Dis 2024; 43:723-734. [PMID: 38358552 DOI: 10.1007/s10096-024-04776-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2023] [Accepted: 02/05/2024] [Indexed: 02/16/2024]
Abstract
PURPOSE In clinical practice, we observed an apparent overrepresentation of COVID-19 patients on anti-CD20 monoclonal antibody therapy. The aim of this study was to characterize the clinical picture of COVID-19 in these patients. METHODS All adult patients from Turku University Hospital, Turku, Finland, with COVID-19 diagnosis and/or positive SARS-CoV-2 PCR test result up to March 2023, and with anti-CD20 therapy within 12 months before COVID-19 were included. Data was retrospectively obtained from electronic patient records. RESULTS Ninety-eight patients were identified. 44/93 patients (47.3%) were hospitalized due to COVID-19. Patients with demyelinating disorder (n = 20) were youngest (median age 36.5 years, interquartile range 33-45 years), had less comorbidities, and were least likely to be hospitalized (2/20; 10.0%) or die (n = 0). COVID-19 mortality was 13.3% in the whole group, with age and male sex as independent risk factors. Persistent symptoms were documented in 33/94 patients (35.1%) alive by day 30, in 21/89 patients (23.6%) after 60 days, and in 15/85 after 90 days (17.6%), mostly in patients with haematological malignancy or connective tissue disease. Prolonged symptoms after 60 days predisposed to persistent radiological findings (odds ratio 64.0; 95% confidence interval 6.3-711; p < 0.0001) and persistently positive PCR (odds ratio 45.5, 95% confidence interval 4.0-535; p < 0.0001). Several patients displayed rapid response to late antiviral therapy. CONCLUSION Anti-CD20 monoclonal antibody therapy is associated with high COVID-19 mortality and with a phenotype consistent with prolonged viral pneumonia. Our study provides rationale for retesting of immunocompromised patients with prolonged COVID-19 symptoms and considering antiviral therapy.
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Affiliation(s)
- Eeva Feuth
- Department of Infectious Diseases, Turku University Hospital and University of Turku, Turku, Finland
| | - Valtteri Nieminen
- Department of Pulmonary Diseases and Clinical Allergology, Turku University Hospital and University of Turku, Turku, Finland
| | - Antti Palomäki
- Centre for Rheumatology and Clinical Immunology, and Department of Medicine, Turku University Hospital and University of Turku, Turku, Finland
| | - Juha Ranti
- Department of Haematology, Turku University Hospital, Turku, Finland
| | - Marcus Sucksdorff
- Turku PET Centre, and Division of Clinical Neurosciences, Turku University Hospital and University of Turku, Turku, Finland
| | - Taru Finnilä
- Department of Hospital Hygiene & Infection Control, Turku University Hospital, Turku, Finland
| | - Jarmo Oksi
- Department of Infectious Diseases, Turku University Hospital and University of Turku, Turku, Finland
| | - Tytti Vuorinen
- Department of Clinical Microbiology, Turku University Hospital and Institute of Biomedicine, University of Turku, Turku, Finland
| | - Thijs Feuth
- Department of Pulmonary Diseases and Clinical Allergology, Turku University Hospital and University of Turku, Turku, Finland.
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Rogozin IB, Saura A, Poliakov E, Bykova A, Roche-Lima A, Pavlov YI, Yurchenko V. Properties and Mechanisms of Deletions, Insertions, and Substitutions in the Evolutionary History of SARS-CoV-2. Int J Mol Sci 2024; 25:3696. [PMID: 38612505 PMCID: PMC11011937 DOI: 10.3390/ijms25073696] [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: 02/25/2024] [Revised: 03/22/2024] [Accepted: 03/23/2024] [Indexed: 04/14/2024] Open
Abstract
SARS-CoV-2 has accumulated many mutations since its emergence in late 2019. Nucleotide substitutions leading to amino acid replacements constitute the primary material for natural selection. Insertions, deletions, and substitutions appear to be critical for coronavirus's macro- and microevolution. Understanding the molecular mechanisms of mutations in the mutational hotspots (positions, loci with recurrent mutations, and nucleotide context) is important for disentangling roles of mutagenesis and selection. In the SARS-CoV-2 genome, deletions and insertions are frequently associated with repetitive sequences, whereas C>U substitutions are often surrounded by nucleotides resembling the APOBEC mutable motifs. We describe various approaches to mutation spectra analyses, including the context features of RNAs that are likely to be involved in the generation of recurrent mutations. We also discuss the interplay between mutations and natural selection as a complex evolutionary trend. The substantial variability and complexity of pipelines for the reconstruction of mutations and the huge number of genomic sequences are major problems for the analyses of mutations in the SARS-CoV-2 genome. As a solution, we advocate for the development of a centralized database of predicted mutations, which needs to be updated on a regular basis.
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Affiliation(s)
- Igor B. Rogozin
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Andreu Saura
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Eugenia Poliakov
- National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Anastassia Bykova
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
| | - Abiel Roche-Lima
- Center for Collaborative Research in Health Disparities—RCMI Program, Medical Sciences Campus, University of Puerto Rico, San Juan 00936, Puerto Rico
| | - Youri I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Vyacheslav Yurchenko
- Life Science Research Centre, Faculty of Science, University of Ostrava, 710 00 Ostrava, Czech Republic
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Hoang KL, Read TD, King KC. Incomplete immunity in a natural animal-microbiota interaction selects for higher pathogen virulence. Curr Biol 2024; 34:1357-1363.e3. [PMID: 38430909 PMCID: PMC10962313 DOI: 10.1016/j.cub.2024.02.015] [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: 10/09/2023] [Revised: 12/18/2023] [Accepted: 02/07/2024] [Indexed: 03/05/2024]
Abstract
Incomplete immunity in recovered hosts is predicted to favor more virulent pathogens upon re-infection in the population.1 The microbiota colonizing animals can generate a similarly long-lasting, partial immune response, allowing for infection but dampened disease severity.2 We tracked the evolutionary trajectories of a widespread pathogen (Pseudomonas aeruginosa), experimentally passaged through populations of nematodes immune-primed by a natural microbiota member (P. berkeleyensis). This bacterium can induce genes regulated by a mitogen-activated protein kinase (MAPK) signaling pathway effective at conferring protection against pathogen-induced death despite infection.3 Across host populations, this incomplete immunity selected for pathogens more than twice as likely to kill as those evolved in non-primed (i.e., naive) or immune-compromised (mutants with a knockout of the MAPK ortholog) control populations. Despite the higher virulence, pathogen molecular evolution in immune-primed hosts was slow and constrained. In comparison, evolving pathogens in immune-compromised hosts were characterized by substantial genomic differentiation and attenuated virulence. These findings directly attribute the incomplete host immunity induced from microbiota as a significant force shaping the virulence and evolutionary dynamics of novel infectious diseases.
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Affiliation(s)
- Kim L Hoang
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK; Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA 30322, USA.
| | - Timothy D Read
- Division of Infectious Diseases, Emory University School of Medicine, 1760 Haygood Drive, Atlanta, GA 30322, USA
| | - Kayla C King
- Department of Biology, University of Oxford, 11a Mansfield Road, Oxford OX1 3SZ, UK; Department of Zoology, University of British Columbia, 6270 University Boulevard, Vancouver, BC V6T 1Z4, Canada; Department of Microbiology & Immunology, University of British Columbia, 1365 - 2350 Health Sciences Mall, Vancouver, BC V6T 1Z3, Canada.
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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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Azzeri A, Mohamed NA, Wan Rosli SH, Abdul Samat MN, Rashid ZZ, Mohamad Jamali MA, Md Zoqratt MZH, Mohammad Nasir MA, Ranjit Singh HK, Azmi L. Unravelling the link between SARS-CoV-2 mutation frequencies, patient comorbidities, and structural dynamics. PLoS One 2024; 19:e0291892. [PMID: 38483913 PMCID: PMC10939192 DOI: 10.1371/journal.pone.0291892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Accepted: 02/23/2024] [Indexed: 03/17/2024] Open
Abstract
Genomic surveillance is crucial for tracking emergence and spread of novel variants of pathogens, such as SARS-CoV-2, to inform public health interventions and to enforce control measures. However, in some settings especially in low- and middle- income counties, where sequencing platforms are limited, only certain patients get to be selected for sequencing surveillance. Here, we show that patients with multiple comorbidities potentially harbour SARS-CoV-2 with higher mutation rates and thus deserve more attention for genomic surveillance. The relationship between the patient comorbidities, and type of amino acid mutations was assessed. Correlation analysis showed that there was a significant tendency for mutations to occur within the ORF1a region for patients with higher number of comorbidities. Frequency analysis of the amino acid substitution within ORF1a showed that nsp3 P822L of the PLpro protease was one of the highest occurring mutations. Using molecular dynamics, we simulated that the P822L mutation in PLpro represents a system with lower Root Mean Square Deviation (RMSD) fluctuations, and consistent Radius of gyration (Rg), Solvent Accessible Surface Area (SASA) values-indicate a much stabler protein than the wildtype. The outcome of this study will help determine the relationship between the clinical status of a patient and the mutations of the infecting SARS-CoV-2 virus.
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Affiliation(s)
- Amirah Azzeri
- Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, Nilai, Negeri Sembilan, Malaysia
| | - Nurul Azmawati Mohamed
- Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, Nilai, Negeri Sembilan, Malaysia
| | - Saarah Huurieyah Wan Rosli
- Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, Nilai, Negeri Sembilan, Malaysia
| | - Muttaqillah Najihan Abdul Samat
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur, Malaysia
| | - Zetti Zainol Rashid
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Universiti Kebangsaan Malaysia, Cheras, Kuala Lumpur, Malaysia
| | | | - Muhammad Zarul Hanifah Md Zoqratt
- Fast Genomics Solutions, Subang Jaya, Selangor Darul Ehsan, Malaysia
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Muhammad Azamuddeen Mohammad Nasir
- Fast Genomics Solutions, Subang Jaya, Selangor Darul Ehsan, Malaysia
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Harpreet Kaur Ranjit Singh
- Fast Genomics Solutions, Subang Jaya, Selangor Darul Ehsan, Malaysia
- School of Science, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Liyana Azmi
- Faculty of Medicine and Health Sciences, Universiti Sains Islam Malaysia, Nilai, Negeri Sembilan, Malaysia
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Lin C, Li M, Lin Y, Zhang Y, Xu H, Chen B, Yan X, Xu Y. Impact of plasma Epstein-Barr virus DNA in posttreatment nasopharyngeal carcinoma patients after SARS-CoV-2 infection. Infect Agent Cancer 2024; 19:8. [PMID: 38486290 PMCID: PMC10938826 DOI: 10.1186/s13027-024-00570-x] [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: 01/19/2024] [Accepted: 03/01/2024] [Indexed: 03/18/2024] Open
Abstract
BACKGROUND Nasopharyngeal carcinoma (NPC) is prevalent in southern China. EBV DNA is the most useful biomarker in NPC. However, the value of EBV DNA in posttreatment NPC patients infected with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) remains unclear. METHODS Sixty-four eligible NPC patients were enrolled between December 2022 and February 2023. Patients who met the following criteria were included: had non-metastatic NPC, completed radical treatment, were first firstly infected with SARS-CoV-2 and their EBV DNA changed from undetectable to detectable. RESULTS At the end of follow-up, 81.25% (52/64) of patients were confirmed not to relapse with undetectable EBV DNA (no-relapse). In addition, 18.75% (12/64) of patients experienced relapse with consistent detection of EBV DNA (yes-relapse). For all 64 patients, the average time from diagnosis of coronavirus disease 2019 (COVID-19) to detection of detectable EBV DNA was 35.41 days (2 to 139 days). For 52 no-relapse patients, the average time from EBV DNA changing from detectable to undetectable was 63.12 days (6 to 147 days). The levels of EBV DNA were greater in yes-relapse patients than that in no-relapse patients, and the average of EBV DNA levels were 1216 copies/ml and 53.18 copies/ml, respectively. Using 62.3 copies/mL as the threshold, the area under the curve for EBV DNA was 0.88 for distinguishing yes-relapse patients from no-relapse patients. The sensitivity and specificity were 81.97% (95% CI 0.71-0.95) and 86.67% (95% CI 0.70-0.95), respectively. CONCLUSION For NPC patients infected with SARS-CoV-2, EBV DNA alone is insufficient for monitoring relapse after radical therapy. Long-term follow-up and underlying mechanistic investigations of EBV DNA changes are urgently needed.
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Affiliation(s)
- Cheng Lin
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian Province, China
- Interdisciplinary College of Medicine and Engineering, Fuzhou University, Fuzhou, Fujian, China
| | - Meifang Li
- Department of Medical Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian Province, China
| | - Yingying Lin
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian Province, China
| | - Yu Zhang
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian Province, China
| | - Hanchuan Xu
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian Province, China
| | - Bijuan Chen
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian Province, China
| | - Xia Yan
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian Province, China
| | - Yun Xu
- Department of Radiation Oncology, Clinical Oncology School of Fujian Medical University, Fujian Cancer Hospital, Fuzhou, Fujian Province, China.
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Manuto L, Bado M, Cola M, Vanzo E, Antonello M, Mazzotti G, Pacenti M, Cordioli G, Sasset L, Cattelan AM, Toppo S, Lavezzo E. Immune System Deficiencies Do Not Alter SARS-CoV-2 Evolutionary Rate but Favour the Emergence of Mutations by Extending Viral Persistence. Viruses 2024; 16:447. [PMID: 38543811 PMCID: PMC10974344 DOI: 10.3390/v16030447] [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: 02/19/2024] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 05/23/2024] Open
Abstract
During the COVID-19 pandemic, immunosuppressed patients showed prolonged SARS-CoV-2 infections, with several studies reporting the accumulation of mutations in the viral genome. The weakened immune system present in these individuals, along with the effect of antiviral therapies, are thought to create a favourable environment for intra-host viral evolution and have been linked to the emergence of new viral variants which strongly challenged containment measures and some therapeutic treatments. To assess whether impaired immunity could lead to the increased instability of viral genomes, longitudinal nasopharyngeal swabs were collected from eight immunocompromised patients and fourteen non-immunocompromised subjects, all undergoing SARS-CoV-2 infection. Intra-host viral evolution was compared between the two groups through deep sequencing, exploiting a probe-based enrichment method to minimise the possibility of artefactual mutations commonly generated in amplicon-based methods, which heavily rely on PCR amplification. Although, as expected, immunocompromised patients experienced significantly longer infections, the acquisition of novel intra-host viral mutations was similar between the two groups. Moreover, a thorough analysis of viral quasispecies showed that the variability of viral populations in the two groups is comparable not only at the consensus level, but also when considering low-frequency mutations. This study suggests that a compromised immune system alone does not affect SARS-CoV-2 within-host genomic variability.
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Affiliation(s)
- Laura Manuto
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
| | - Martina Bado
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
| | - Marco Cola
- Department of Medicine, DIMED, University of Padova, 35128 Padova, Italy;
| | - Elena Vanzo
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
| | - Maria Antonello
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
| | - Giorgia Mazzotti
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
| | - Monia Pacenti
- Unit of Microbiology and Virology, University Hospital of Padova, 35128 Padova, Italy;
| | - Giampaolo Cordioli
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
| | - Lolita Sasset
- Unit of Infectious Diseases, University Hospital of Padova, 35128 Padova, Italy;
| | - Anna Maria Cattelan
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
- Unit of Infectious Diseases, University Hospital of Padova, 35128 Padova, Italy;
| | - Stefano Toppo
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
| | - Enrico Lavezzo
- Department of Molecular Medicine, DMM, University of Padova, 35121 Padova, Italy; (L.M.); (M.B.); (E.V.); (M.A.); (G.M.); (G.C.); (A.M.C.)
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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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Raglow Z, Surie D, Chappell JD, Zhu Y, Martin ET, Kwon JH, Frosch AE, Mohamed A, Gilbert J, Bendall EE, Bahr A, Halasa N, Talbot HK, Grijalva CG, Baughman A, Womack KN, Johnson C, Swan SA, Koumans E, McMorrow ML, Harcourt JL, Atherton LJ, Burroughs A, Thornburg NJ, Self WH, Lauring AS. SARS-CoV-2 shedding and evolution in patients who were immunocompromised during the omicron period: a multicentre, prospective analysis. THE LANCET. MICROBE 2024; 5:e235-e246. [PMID: 38286131 DOI: 10.1016/s2666-5247(23)00336-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 01/31/2024]
Abstract
BACKGROUND Prolonged SARS-CoV-2 infections in people who are immunocompromised might predict or source the emergence of highly mutated variants. The types of immunosuppression placing patients at highest risk for prolonged infection have not been systematically investigated. We aimed to assess risk factors for prolonged SARS-CoV-2 infection and associated intrahost evolution. METHODS In this multicentre, prospective analysis, participants were enrolled at five US medical centres. Eligible patients were aged 18 years or older, were SARS-CoV-2-positive in the previous 14 days, and had a moderately or severely immunocompromising condition or treatment. Nasal specimens were tested by real-time RT-PCR every 2-4 weeks until negative in consecutive specimens. Positive specimens underwent viral culture and whole genome sequencing. A Cox proportional hazards model was used to assess factors associated with duration of infection. FINDINGS From April 11, 2022, to Oct 1, 2022, 156 patients began the enrolment process, of whom 150 were enrolled and included in the analyses. Participants had B-cell malignancy or anti-B-cell therapy (n=18), solid organ transplantation or haematopoietic stem-cell transplantation (HSCT; n=59), AIDS (n=5), non-B-cell malignancy (n=23), and autoimmune or autoinflammatory conditions (n=45). 38 (25%) participants were real-time RT-PCR-positive and 12 (8%) were culture-positive 21 days or longer after initial SARS-CoV-2 detection or illness onset. Compared with the group with autoimmune or autoinflammatory conditions, patients with B-cell dysfunction (adjusted hazard ratio 0·32 [95% CI 0·15-0·64]), solid organ transplantation or HSCT (0·60 [0·38-0·94]), and AIDS (0·28 [0·08-1·00]) had longer duration of infection, defined as time to last positive real-time RT-PCR test. There was no significant difference in the non-B-cell malignancy group (0·58 [0·31-1·09]). Consensus de novo spike mutations were identified in five individuals who were real-time RT-PCR-positive longer than 56 days; 14 (61%) of 23 were in the receptor-binding domain. Mutations shared by multiple individuals were rare (<5%) in global circulation. INTERPRETATION In this cohort, prolonged replication-competent omicron SARS-CoV-2 infections were uncommon. Within-host evolutionary rates were similar across patients, but individuals with infections lasting longer than 56 days accumulated spike mutations, which were distinct from those seen globally. Populations at high risk should be targeted for repeated testing and treatment and monitored for the emergence of antiviral resistance. FUNDING US Centers for Disease Control and Prevention.
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Affiliation(s)
- Zoe Raglow
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Diya Surie
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - James D Chappell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Yuwei Zhu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Emily T Martin
- School of Public Health, University of Michigan, Ann Arbor, MI, USA
| | - Jennie H Kwon
- Department of Medicine, Washington University, St Louis, MO, USA
| | - Anne E Frosch
- Department of Medicine, Hennepin County Medical Center, Minneapolis, MN, USA
| | - Amira Mohamed
- Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, NY, USA
| | - Julie Gilbert
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Emily E Bendall
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA
| | - Auden Bahr
- Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Natasha Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - H Keipp Talbot
- Department of Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Department of Health Policy, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Carlos G Grijalva
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Adrienne Baughman
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Kelsey N Womack
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Cassandra Johnson
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Sydney A Swan
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Emilia Koumans
- Division of STD Prevention, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Meredith L McMorrow
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jennifer L Harcourt
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Lydia J Atherton
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Ashley Burroughs
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Natalie J Thornburg
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Wesley H Self
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, TN, USA; Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Adam S Lauring
- Department of Internal Medicine, University of Michigan, Ann Arbor, MI, USA; Department of Microbiology and Immunology, University of Michigan, Ann Arbor, MI, USA.
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Wilson C, Thomson EC. Resilience to emerging infectious diseases and the importance of scientific innovation. Future Healthc J 2024; 11:100023. [PMID: 38646044 PMCID: PMC11025050 DOI: 10.1016/j.fhj.2024.100023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/23/2024]
Abstract
This opinion piece emphasies the critical role of translational research in enhancing the UK's resilience against future pandemics. The COVID-19 pandemic demonstrated the lifesaving potential of scientific innovation, including genomic tracking of SARS-CoV-2, vaccine development, data linkage, modelling, and new treatments. These advances, achieved through collaborations between academic institutions, industry, government, public health bodies, and the NHS, occurred at an unprecedented pace. However, the UK's pandemic preparedness planning, as reflected in the 2016 Exercise Cygnus report, notably lacked provision for scientific innovation. This oversight highlights the necessity of integrating innovation and research into future preparedness strategies, not as a luxury but as a vital component of the healthcare infrastructure. The COVID-19 pandemic has underlined the importance of surge capacity for diagnostic labs, vaccine development and deployment strategies, real-time research embedded within the NHS, efficient data sharing, clear public communication, and the use of genomic tools for outbreak surveillance and monitoring pathogen response. Despite world-leading aspects of some of the UK's research response, the need to build much of the infrastructure in real-time led to avoidable delays. A proactive approach in incorporating research and innovation into the NHS's operational framework will be needed to ensure swift, evidence-based responses to future pandemics.
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Affiliation(s)
| | - Emma C. Thomson
- NHS Greater Glasgow & Clyde (NHS GG&C), Glasgow, United Kingdom
- MRC-University of Glasgow Centre for Virus Research (CVR), Glasgow, United Kingdom
- London School of Hygiene and Tropical Medicine (LSHTM), London, United Kingdom
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Olorunfemi AB, Suliman SA, Tran TT, Ayorinde B, Fowora MA, Iwalokun BA, Olowe OA, Opaleye OO, Osman M, Salako BL, Adegbola R, Thomas BN, Pallerla SR, Velavan TP, Ojurongbe O. Whole genome sequencing and phylogenetic analysis of SARS-CoV-2 strains isolated during the COVID-19 pandemic in Nigeria. IJID REGIONS 2024; 10:174-178. [PMID: 38322246 PMCID: PMC10845906 DOI: 10.1016/j.ijregi.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Revised: 01/09/2024] [Accepted: 01/10/2024] [Indexed: 02/08/2024]
Abstract
Objectives The emergence and spread of SARS-CoV-2 have stimulated ongoing research into the virus transmission dynamics, circulating variants, and potential mutations. This study was conducted to understand the genomic dynamics of the epidemic in Nigeria. Design Whole genome sequencing was conducted on SARS-CoV-2 samples collected during the first and second outbreaks using the Oxford Nanopore MinION sequencing platform. Phylogenetic analysis was conducted, and genomes were grouped into different pangolin lineages. Results The study revealed four circulating SARS-CoV-2 variants. The Alpha (B.1.1.7) variant was the most prevalent (32.7%), followed by Beta (B.1 B.1.1, L.3, and B.1.1.318) (30.8%), Eta (B.1.525) (28.9%), and Delta (B.1.617, AY.1, AY.109, and AY.36) (7.7%). Phylogenetic analysis revealed three clusters with four Nextstrain clades (20I, 20B, 21D, and 21J). The Alpha lineages (B.1.1.7) clustered with references from Italy. The Beta lineages (Clade 20B) (B.11, B.11318, and L3) and sub-lineage B.11 were distinct. Sub-lineage B.11318 is clustered with references from the USA, whereas sub-lineage L3 is clustered with references from Russia, the Philippines, Australia, and Japan. The 21D and 21J, belonging to two Pango lineages, Eta (B.1525) and Delta (B.1.617 and AY.109), showed high genetic similarity. Conclusion The phylogenetic relatedness of the lineages suggests multiple virus introduction, which could be a source of more virulent, locally adapted variants.
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Affiliation(s)
- Adedolapo B. Olorunfemi
- Center for Emerging and Re-emerging Infectious Diseases, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | | | - Tung T. Tran
- Vietnamese-German Center for Medical Research (VG-CARE), Hanoi, Vietnam
| | - Babatunde Ayorinde
- Molecular Biology & Biotechnology Department, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
- Central Research Laboratory, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Muinah A. Fowora
- Molecular Biology & Biotechnology Department, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
- Central Research Laboratory, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Bamidele A. Iwalokun
- Molecular Biology & Biotechnology Department, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
- Central Research Laboratory, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Olugbenga A. Olowe
- Center for Emerging and Re-emerging Infectious Diseases, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Oluyinka O. Opaleye
- Center for Emerging and Re-emerging Infectious Diseases, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
| | - Mohamed Osman
- Institute of Endemic Diseases, University of Khartoum, Sudan
- York Biomedical Research Institute, Department of Biology, University of York, Wentworth Way, York YO10 5DD, UK
| | - Babatunde L. Salako
- Molecular Biology & Biotechnology Department, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
- Central Research Laboratory, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Richard Adegbola
- Molecular Biology & Biotechnology Department, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
- Central Research Laboratory, Nigerian Institute of Medical Research (NIMR), Yaba, Lagos, Nigeria
| | - Bolaji N. Thomas
- Department of Biomedical Sciences, College of Health Sciences and Technology, Rochester Institute of Technology, Rochester, NY 14623, USA
| | - Srinivas Reddy Pallerla
- Institute for Medical Virology, University Hospital Frankfurt, Goethe University Frankfurt, Frankfurt, Germany
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Universität Tübingen, Germany
| | - Thirumalaisamy P. Velavan
- Vietnamese-German Center for Medical Research (VG-CARE), Hanoi, Vietnam
- Institute of Tropical Medicine, Universitätsklinikum Tübingen, Universität Tübingen, Germany
| | - Olusola Ojurongbe
- Center for Emerging and Re-emerging Infectious Diseases, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
- Department of Medical Microbiology and Parasitology, Ladoke Akintola University of Technology, Ogbomoso, Nigeria
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Meijer SE, Halutz O, Adler A, Levytskyi K, Tau L, Dekel M, Cohen-Poradosu R, Katchman E, Shasha D, Ablin J, Choshen G, Jacob G, Wasserman A, Ingbir M, Cohen YC, Perry C, Ram R, Herishanu Y, Bar On Y, van Thijn E, Rutsinsky N, Harari S, Stern A, Ben-Ami R, Paran Y. Dual anti-viral treatment for persistent COVID-19 in immunocompromised hemato-oncological patients is associated with a favorable prognosis and minor side effects. J Infect Chemother 2024; 30:271-275. [PMID: 37944697 DOI: 10.1016/j.jiac.2023.10.022] [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: 02/22/2023] [Revised: 10/11/2023] [Accepted: 10/28/2023] [Indexed: 11/12/2023]
Abstract
In hemato-oncological patients, COVID-19 can present as a persistent infection with ongoing symptoms and viral replication over a prolonged period of time. Data are scarce on the preferred treatment options for these patients. We describe our experience with a five-day course of dual anti-viral treatment with remdesivir and nirmatrelvir/ritonavir for hemato-oncological immunocompromised patients with persistent COVID-19. Fifteen patients with a history of lymphoma, CLL, and MM were included. Eight were male, median age was 74. All patients had an immediate clinical and virological response. In 73 % of patients, PCR for SARS-CoV-2 became negative at the end of treatment and the rest had an increase in PCR cycle threshold (CT) values, with a median increase of 6 cycles. After a follow-up of three months, 60 % of patients remained in full clinical and virological remission. None required invasive mechanical ventilation or died. The side effects we observed, neutropenia, lactatemia and elevated transaminases, were mild and almost all transient in nature. We conclude that dual anti-viral treatment appears to be a valid treatment option for persistent COVID-19.
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Affiliation(s)
- Suzy E Meijer
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel.
| | - Ora Halutz
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Amos Adler
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Katya Levytskyi
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Luba Tau
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Michal Dekel
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Evgene Katchman
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - David Shasha
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Jacob Ablin
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | | | - Giris Jacob
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Asaf Wasserman
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Merav Ingbir
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yael C Cohen
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Chava Perry
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Ron Ram
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yair Herishanu
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yael Bar On
- Shaare Zedek Medical Center, Jerusalem, Israel
| | | | - Natalie Rutsinsky
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Sheri Harari
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Adi Stern
- The Shmunis School of Biomedicine and Cancer Research, George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - Ronen Ben-Ami
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Yael Paran
- Sourasky Medical Center and Sackler School of Medicine, Tel Aviv University, Tel Aviv, Israel
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Bohmwald K, Diethelm-Varela B, Rodríguez-Guilarte L, Rivera T, Riedel CA, González PA, Kalergis AM. Pathophysiological, immunological, and inflammatory features of long COVID. Front Immunol 2024; 15:1341600. [PMID: 38482000 PMCID: PMC10932978 DOI: 10.3389/fimmu.2024.1341600] [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: 11/20/2023] [Accepted: 02/09/2024] [Indexed: 04/12/2024] Open
Abstract
The COVID-19 pandemic continues to cause severe global disruption, resulting in significant excess mortality, overwhelming healthcare systems, and imposing substantial social and economic burdens on nations. While most of the attention and therapeutic efforts have concentrated on the acute phase of the disease, a notable proportion of survivors experience persistent symptoms post-infection clearance. This diverse set of symptoms, loosely categorized as long COVID, presents a potential additional public health crisis. It is estimated that 1 in 5 COVID-19 survivors exhibit clinical manifestations consistent with long COVID. Despite this prevalence, the mechanisms and pathophysiology of long COVID remain poorly understood. Alarmingly, evidence suggests that a significant proportion of cases within this clinical condition develop debilitating or disabling symptoms. Hence, urgent priority should be given to further studies on this condition to equip global public health systems for its management. This review provides an overview of available information on this emerging clinical condition, focusing on the affected individuals' epidemiology, pathophysiological mechanisms, and immunological and inflammatory profiles.
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Affiliation(s)
- Karen Bohmwald
- Millennium Institute on Immunology and Immunotherapy. Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Instituto de Ciencias Biomédicas, Facultad de Ciencias de la Salud, Universidad Autónoma de Chile, Santiago, Chile
| | - Benjamín Diethelm-Varela
- Millennium Institute on Immunology and Immunotherapy. Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Linmar Rodríguez-Guilarte
- Millennium Institute on Immunology and Immunotherapy. Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Thomas Rivera
- Millennium Institute on Immunology and Immunotherapy. Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Claudia A. Riedel
- Millennium Institute on Immunology and Immunotherapy, Departamento de Ciencias Biológicas, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Pablo A. González
- Millennium Institute on Immunology and Immunotherapy. Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Alexis M. Kalergis
- Millennium Institute on Immunology and Immunotherapy. Facultad de Ciencias Biológicas, Pontificia Universidad Católica de Chile, Santiago, Chile
- Departamento de Endocrinología, Facultad de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
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