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Mukherjee A, Lo M, Chandra P, Datta Chaudhuri R, De P, Dutta S, Chawla-Sarkar M. SARS-CoV-2 nucleocapsid protein promotes self-deacetylation by inducing HDAC6 to facilitate viral replication. Virol J 2024; 21:186. [PMID: 39135075 PMCID: PMC11321199 DOI: 10.1186/s12985-024-02460-5] [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: 01/03/2024] [Accepted: 08/05/2024] [Indexed: 08/15/2024] Open
Abstract
BACKGROUND The global outbreak of COVID-19 caused by the SARS-CoV-2 has led to millions of deaths. This unanticipated emergency has prompted virologists across the globe to delve deeper into the intricate dynamicity of the host-virus interface with an aim to identify antiviral targets and elucidate host and viral determinants of severe disease. AIM The present study was undertaken to analyse the role of histone deacetylase 6 (HDAC6) in regulating SARS-CoV-2 infection. RESULTS Gradual increase in HDAC6 expression was observed in different SARS-CoV-2-permissive cell lines following SARS-CoV-2 infection. The SARS-CoV-2 nucleocapsid protein (N protein) was identified as the primary viral factor responsible for upregulating HDAC6 expression. Downregulation of HDAC6 using shRNA or a specific inhibitor tubacin resulted in reduced viral replication suggesting proviral role of its deacetylase activity. Further investigations uncovered the interaction of HDAC6 with stress granule protein G3BP1 and N protein during infection. HDAC6-mediated deacetylation of SARS-CoV-2 N protein was found to be crucial for its association with G3BP1. CONCLUSION This study provides valuable insights into the molecular mechanisms underlying the disruption of cytoplasmic stress granules during SARS-CoV-2 infection and highlights the significance of HDAC6 in the process.
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Affiliation(s)
- Arpita Mukherjee
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal, 700010, India
| | - Mahadeb Lo
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal, 700010, India
| | - Pritam Chandra
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal, 700010, India
| | - Ratul Datta Chaudhuri
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal, 700010, India
| | - Papiya De
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal, 700010, India
| | - Shanta Dutta
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal, 700010, India
| | - Mamta Chawla-Sarkar
- Division of Virology, ICMR-National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal, 700010, India.
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Giacon N, Lo Cascio E, Pennacchietti V, De Maio F, Santarelli G, Sibilia D, Tiberio F, Sanguinetti M, Lattanzi W, Toto A, Arcovito A. PDZ2-conjugated-PLGA nanoparticles are tiny heroes in the battle against SARS-CoV-2. Sci Rep 2024; 14:13059. [PMID: 38844490 PMCID: PMC11156922 DOI: 10.1038/s41598-024-63239-w] [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: 03/22/2024] [Accepted: 05/27/2024] [Indexed: 06/09/2024] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 has highlighted the urgent need for innovative antiviral strategies to fight viral infections. Although a substantial part of the overall effort has been directed at the Spike protein to create an effective global vaccination strategy, other proteins have also been examined and identified as possible therapeutic targets. Among them, although initially underestimated, there is the SARS-CoV-2 E-protein, which turned out to be a key factor in viral pathogenesis due to its role in virus budding, assembly and spreading. The C-terminus of E-protein contains a PDZ-binding motif (PBM) that plays a key role in SARS-CoV-2 virulence as it is recognized and bound by the PDZ2 domain of the human tight junction protein ZO-1. The binding between the PDZ2 domain of ZO-1 and the C-terminal portion of SARS-CoV-2 E-protein has been extensively characterized. Our results prompted us to develop a possible adjuvant therapeutic strategy aimed at slowing down or inhibiting virus-mediated pathogenesis. Such innovation consists in the design and synthesis of externally PDZ2-ZO1 functionalized PLGA-based nanoparticles to be used as intracellular decoy. Contrary to conventional strategies, this innovative approach aims to capitalize on the E protein-PDZ2 interaction to prevent virus assembly and replication. In fact, the conjugation of the PDZ2 domain to polymeric nanoparticles increases the affinity toward the E protein effectively creating a "molecular sponge" able to sequester E proteins within the intracellular environment of infected cells. Our in vitro studies on selected cellular models, show that these nanodevices significantly reduce SARS-CoV-2-mediated virulence, emphasizing the importance of exploiting viral-host interactions for therapeutic benefit.
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Affiliation(s)
- Noah Giacon
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy
| | - Ettore Lo Cascio
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy
| | - Valeria Pennacchietti
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Sapienza Università di Roma, P.le A. Moro 5, 00185, Rome, Italy
| | - Flavio De Maio
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168, Rome, Italy
| | - Giulia Santarelli
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168, Rome, Italy
| | - Diego Sibilia
- Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy
| | - Federica Tiberio
- Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy
| | - Maurizio Sanguinetti
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168, Rome, Italy
| | - Wanda Lattanzi
- Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy
- Fondazione Policlinico Universitario "A. Gemelli", IRCCS, Largo A. Gemelli 8, 00168, Rome, Italy
| | - Angelo Toto
- Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Laboratory Affiliated to Istituto Pasteur Italia - Fondazione Cenci Bolognetti, Sapienza Università di Roma, P.le A. Moro 5, 00185, Rome, Italy.
| | - Alessandro Arcovito
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy.
- Dipartimento di Scienze della Vita e Sanità Pubblica, Università Cattolica del Sacro Cuore, Largo F. Vito 1, 00168, Rome, Italy.
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3
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Ceballos-Garzon A, Comtet-Marre S, Peyret P. Applying targeted gene hybridization capture to viruses with a focus to SARS-CoV-2. Virus Res 2024; 340:199293. [PMID: 38101578 PMCID: PMC10767490 DOI: 10.1016/j.virusres.2023.199293] [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: 04/03/2023] [Revised: 11/08/2023] [Accepted: 12/03/2023] [Indexed: 12/17/2023]
Abstract
Although next-generation sequencing technologies are advancing rapidly, many research topics often require selective sequencing of genomic regions of interest. In addition, sequencing low-titre viruses is challenging, especially for coronaviruses, which are the largest RNA viruses. Prior to sequencing, enrichment of viral particles can help to significantly increase target sequence information as well as avoid large sequencing efforts and, consequently, can increase sensitivity and reduce sequencing costs. Targeting nucleic acids using capture by hybridization is another efficient method that can be performed by applying complementary probes (DNA or RNA baits) to directly enrich genetic information of interest while removing background non-target material. In studies where sequence capture by hybridization has been applied to the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, most authors agree that this technique is useful to easily access sequence targets in complex samples. Furthermore, this approach allows for complete or near-complete sequencing of the viral genome, even in samples with low viral load or poor nucleic acid integrity. In addition, this strategy is highly efficient at discovering new variants by facilitating downstream investigations, such as phylogenetics, epidemiology, and evolution. Commercial kits, as well as in-house protocols, have been developed for enrichment of viral sequences. However, these kits have multiple variations in procedure, with differences in performance. This review compiles and describes studies in which hybridization capture has been applied to SARS-CoV-2 variant genomes.
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Affiliation(s)
| | | | - Pierre Peyret
- Université Clermont Auvergne, INRAE, MEDiS, 63000, Clermont-Ferrand, France.
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4
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Dos Santos Alves RP, Timis J, Miller R, Valentine K, Pinto PBA, Gonzalez A, Regla-Nava JA, Maule E, Nguyen MN, Shafee N, Landeras-Bueno S, Olmedillas E, Laffey B, Dobaczewska K, Mikulski Z, McArdle S, Leist SR, Kim K, Baric RS, Ollmann Saphire E, Elong Ngono A, Shresta S. Human coronavirus OC43-elicited CD4 + T cells protect against SARS-CoV-2 in HLA transgenic mice. Nat Commun 2024; 15:787. [PMID: 38278784 PMCID: PMC10817949 DOI: 10.1038/s41467-024-45043-2] [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: 08/18/2023] [Accepted: 01/10/2024] [Indexed: 01/28/2024] Open
Abstract
SARS-CoV-2-reactive T cells are detected in some healthy unexposed individuals. Human studies indicate these T cells could be elicited by the common cold coronavirus OC43. To directly test this assumption and define the role of OC43-elicited T cells that are cross-reactive with SARS-CoV-2, we develop a model of sequential infections with OC43 followed by SARS-CoV-2 in HLA-B*0702 and HLA-DRB1*0101 Ifnar1-/- transgenic mice. We find that OC43 infection can elicit polyfunctional CD8+ and CD4+ effector T cells that cross-react with SARS-CoV-2 peptides. Furthermore, pre-exposure to OC43 reduces subsequent SARS-CoV-2 infection and disease in the lung for a short-term in HLA-DRB1*0101 Ifnar1-/- transgenic mice, and a longer-term in HLA-B*0702 Ifnar1-/- transgenic mice. Depletion of CD4+ T cells in HLA-DRB1*0101 Ifnar1-/- transgenic mice with prior OC43 exposure results in increased viral burden in the lung but no change in virus-induced lung damage following infection with SARS-CoV-2 (versus CD4+ T cell-sufficient mice), demonstrating that the OC43-elicited SARS-CoV-2 cross-reactive T cell-mediated cross-protection against SARS-CoV-2 is partially dependent on CD4+ T cells. These findings contribute to our understanding of the origin of pre-existing SARS-CoV-2-reactive T cells and their effects on SARS-CoV-2 clinical outcomes, and also carry implications for development of broadly protective betacoronavirus vaccines.
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Affiliation(s)
| | - Julia Timis
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Robyn Miller
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Kristen Valentine
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | | | - Andrew Gonzalez
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Jose Angel Regla-Nava
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Microbiology and Pathology, University Center for Health Science (CUCS), University of Guadalajara, Guadalajara, 44340, Mexico
| | - Erin Maule
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Michael N Nguyen
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Norazizah Shafee
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Sara Landeras-Bueno
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Eduardo Olmedillas
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Brett Laffey
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Katarzyna Dobaczewska
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Zbigniew Mikulski
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Sara McArdle
- Microscopy and Histology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Sarah R Leist
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Kenneth Kim
- Histopathology Core Facility, La Jolla Institute for Immunology, La Jolla, CA, USA
| | - Ralph S Baric
- Department of Epidemiology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Erica Ollmann Saphire
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego (UCSD), La Jolla, CA, USA
| | - Annie Elong Ngono
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.
| | - Sujan Shresta
- Center for Infectious Disease and Vaccine Research, La Jolla Institute for Immunology, La Jolla, CA, USA.
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5
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Outteridge M, Nunn CM, Devine K, Patel B, McLean GR. Antivirals for Broader Coverage against Human Coronaviruses. Viruses 2024; 16:156. [PMID: 38275966 PMCID: PMC10820748 DOI: 10.3390/v16010156] [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: 12/08/2023] [Revised: 01/05/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
Coronaviruses (CoVs) are enveloped positive-sense single-stranded RNA viruses with a genome that is 27-31 kbases in length. Critical genes include the spike (S), envelope (E), membrane (M), nucleocapsid (N) and nine accessory open reading frames encoding for non-structural proteins (NSPs) that have multiple roles in the replication cycle and immune evasion (1). There are seven known human CoVs that most likely appeared after zoonotic transfer, the most recent being SARS-CoV-2, responsible for the COVID-19 pandemic. Antivirals that have been approved by the FDA for use against COVID-19 such as Paxlovid can target and successfully inhibit the main protease (MPro) activity of multiple human CoVs; however, alternative proteomes encoded by CoV genomes have a closer genetic similarity to each other, suggesting that antivirals could be developed now that target future CoVs. New zoonotic introductions of CoVs to humans are inevitable and unpredictable. Therefore, new antivirals are required to control not only the next human CoV outbreak but also the four common human CoVs (229E, OC43, NL63, HKU1) that circulate frequently and to contain sporadic outbreaks of the severe human CoVs (SARS-CoV, MERS and SARS-CoV-2). The current study found that emerging antiviral drugs, such as Paxlovid, could target other CoVs, but only SARS-CoV-2 is known to be targeted in vivo. Other drugs which have the potential to target other human CoVs are still within clinical trials and are not yet available for public use. Monoclonal antibody (mAb) treatment and vaccines for SARS-CoV-2 can reduce mortality and hospitalisation rates; however, they target the Spike protein whose sequence mutates frequently and drifts. Spike is also not applicable for targeting other HCoVs as these are not well-conserved sequences among human CoVs. Thus, there is a need for readily available treatments globally that target all seven human CoVs and improve the preparedness for inevitable future outbreaks. Here, we discuss antiviral research, contributing to the control of common and severe CoV replication and transmission, including the current SARS-CoV-2 outbreak. The aim was to identify common features of CoVs for antivirals, biologics and vaccines that could reduce the scientific, political, economic and public health strain caused by CoV outbreaks now and in the future.
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Affiliation(s)
- Mia Outteridge
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Christine M. Nunn
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Kevin Devine
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Bhaven Patel
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
| | - Gary R. McLean
- School of Human Sciences, London Metropolitan University, London N7 8DB, UK; (M.O.); (C.M.N.); (K.D.); (B.P.)
- National Heart and Lung Institute, Imperial College London, London W2 1PG, UK
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6
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Jia J, Garbarino E, Wang Y, Li J, Song M, Zhang X, Wang X, Li L, Chi J, Cui L, Tang H. Generation of SARS-CoV-2 spike receptor binding domain mutants and functional screening for immune evaders using a novel lentivirus-based system. J Med Virol 2024; 96:e29425. [PMID: 38258313 DOI: 10.1002/jmv.29425] [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: 08/17/2023] [Revised: 12/19/2023] [Accepted: 01/12/2024] [Indexed: 01/24/2024]
Abstract
The emergence of rapid and continuous mutations of severe acute respiratory syndrome 2 (SARS-CoV-2) spike glycoprotein that increased with the Omicron variant points out the necessity to anticipate such mutations for conceiving specific and adaptable therapies to avoid another pandemic. The crucial target for the antibody treatment and vaccine design is the receptor binding domain (RBD) of the SARS-CoV-2 spike. It is also the site where the virus has shown its high ability to mutate and consequently escape immune response. We developed a robust and simple method for generating a large number of functional SARS-CoV-2 spike RBD mutants by error-prone PCR and a novel nonreplicative lentivirus-based system. We prepared anti-RBD wild type (WT) polyclonal antibodies and used them to screen and select for mutant libraries that escape inhibition of virion entry into recipient cells expressing human angiotensin-converting enzyme 2 and transmembrane serine protease 2. We isolated, cloned, and sequenced six mutants totally bearing nine mutation sites. Eight mutations were found in successive WT variants, including Omicron and other recombinants, whereas one is novel. These results, together with the detailed functional analyses of two mutants provided the proof of concept for our approach.
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Affiliation(s)
- Junli Jia
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Emanuela Garbarino
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Yuhang Wang
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
- Department of Blood Transfusion, Children's Hospital of Nanjing Medical University, Nanjing, China
| | - Jiaming Li
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Minmin Song
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Xin Zhang
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Xinjie Wang
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
| | - Lingyun Li
- Department of Medical Genetics, Nanjing Medical University, Nanjing, China
| | - Jing Chi
- Department of Microbiological Laboratory, Baoan District Center for Disease Control and Prevention, Shenzhen, China
| | - Lunbiao Cui
- National Health Commission (NHC) Key Laboratory of Enteric Pathogenic Microbiology, Jiangsu Provincial Medical Key Laboratory of Pathogenic Microbiology in Emerging Major Infectious Diseases, Jiangsu Provincial Center for Disease Control and Prevention, Nanjing, China
| | - Huamin Tang
- Department of Immunology, National Vaccine Innovation Platform, School of Basic Medical Sciences, Nanjing Medical University, Nanjing, China
- The Laboratory Center for Basic Medical Sciences, Nanjing Medical University, Nanjing, China
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7
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Bergeron HC, Hansen MR, Tripp RA. Interferons-Implications in the Immune Response to Respiratory Viruses. Microorganisms 2023; 11:2179. [PMID: 37764023 PMCID: PMC10535750 DOI: 10.3390/microorganisms11092179] [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: 07/17/2023] [Revised: 08/15/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
Interferons (IFN) are an assemblage of signaling proteins made and released by various host cells in response to stimuli, including viruses. Respiratory syncytial virus (RSV), influenza virus, and SARS-CoV-2 are major causes of respiratory disease that induce or antagonize IFN responses depending on various factors. In this review, the role and function of type I, II, and III IFN responses to respiratory virus infections are considered. In addition, the role of the viral proteins in modifying anti-viral immunity is noted, as are the specific IFN responses that underly the correlates of immunity and protection from disease.
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Affiliation(s)
| | | | - Ralph A. Tripp
- Department of Infectious Diseases, University of Georgia College of Veterinary Medicine, Athens, GA 30605, USA; (H.C.B.); (M.R.H.)
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8
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López-Ayllón BD, de Lucas-Rius A, Mendoza-García L, García-García T, Fernández-Rodríguez R, Suárez-Cárdenas JM, Santos FM, Corrales F, Redondo N, Pedrucci F, Zaldívar-López S, Jiménez-Marín Á, Garrido JJ, Montoya M. SARS-CoV-2 accessory proteins involvement in inflammatory and profibrotic processes through IL11 signaling. Front Immunol 2023; 14:1220306. [PMID: 37545510 PMCID: PMC10399023 DOI: 10.3389/fimmu.2023.1220306] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 06/23/2023] [Indexed: 08/08/2023] Open
Abstract
SARS-CoV-2, the cause of the COVID-19 pandemic, possesses eleven accessory proteins encoded in its genome. Their roles during infection are still not completely understood. In this study, transcriptomics analysis revealed that both WNT5A and IL11 were significantly up-regulated in A549 cells expressing individual accessory proteins ORF6, ORF8, ORF9b or ORF9c from SARS-CoV-2 (Wuhan-Hu-1 isolate). IL11 is a member of the IL6 family of cytokines. IL11 signaling-related genes were also differentially expressed. Bioinformatics analysis disclosed that both WNT5A and IL11 were involved in pulmonary fibrosis idiopathic disease and functional assays confirmed their association with profibrotic cell responses. Subsequently, data comparison with lung cell lines infected with SARS-CoV-2 or lung biopsies from patients with COVID-19, evidenced altered profibrotic gene expression that matched those obtained in this study. Our results show ORF6, ORF8, ORF9b and ORF9c involvement in inflammatory and profibrotic responses. Thus, these accessory proteins could be targeted by new therapies against COVID-19 disease.
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Affiliation(s)
- Blanca D. López-Ayllón
- Molecular Biomedicine Department, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Ana de Lucas-Rius
- Molecular Biomedicine Department, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Laura Mendoza-García
- Molecular Biomedicine Department, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Tránsito García-García
- Department of Genetics, Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - Raúl Fernández-Rodríguez
- Department of Genetics, Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - José M. Suárez-Cárdenas
- Department of Genetics, Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - Fátima Milhano Santos
- Functional Proteomics Laboratory, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
| | - Fernando Corrales
- Functional Proteomics Laboratory, National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
| | - Natalia Redondo
- Molecular Biomedicine Department, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
- Unit of Infectious Diseases, University Hospital ‘12 de Octubre’, Institute for Health Research Hospital ‘12 de Octubre’ (imas12), Madrid, Spain
- Centre for Biomedical Research Network on Infectious Diseases (CIBERINFEC), Institute of Health Carlos III (ISCIII), Madrid, Spain
| | - Federica Pedrucci
- Molecular Biomedicine Department, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
| | - Sara Zaldívar-López
- Department of Genetics, Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - Ángeles Jiménez-Marín
- Department of Genetics, Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - Juan J. Garrido
- Department of Genetics, Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - María Montoya
- Molecular Biomedicine Department, Margarita Salas Center for Biological Research (CIB-CSIC), Madrid, Spain
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9
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Zhu JH, Tai CH, Ping CF, Chou PH, Tsai YL, Chung S, Bradner L, Pentella M, Gauger P, Zhang J. Evaluation of a Sample-to-Result POCKIT Central SARS-CoV-2 PCR System. Diagnostics (Basel) 2023; 13:2219. [PMID: 37443612 DOI: 10.3390/diagnostics13132219] [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: 04/25/2023] [Revised: 06/15/2023] [Accepted: 06/23/2023] [Indexed: 07/15/2023] Open
Abstract
The emergence of COVID-19 has caused unprecedented impacts on global public health and many other aspects. Meanwhile, many types of methods have been developed to detect the causative agent, SARS-CoV-2; this has greatly advanced the technologies in the diagnostic field. Here, we describe the development and validation of a sample-in-result-out POCKIT Central SARS-CoV-2 PCR system for detecting SARS-CoV-2 in comparison with a commercial reference real-time RT-PCR assay (TaqPath COVID-19 Combo Kit). Both assays were specific and did not cross-react with non-SARS-CoV-2 agents. Both assays were able to detect various SARS-CoV-2 strains including some variants. Based on testing serial dilutions of SARS-CoV-2 USA-WA1/2020 isolate, the limit of detection was 0.8 TCID50/mL (1.87 × 103 genomic copies/mL) for POCKIT Central SARS-CoV-2 PCR and 0.16 TCID50/mL (3.75 × 102 genomic copies/mL) for the reference PCR. Subsequently, 183 clinical samples were tested by both assays and the diagnostic sensitivity, specificity, and agreement of the POCKIT Central SARS-CoV-2 PCR were 91.7%, 100%, and 94.0%, respectively, when compared to the reference PCR. The compact sample-to-result POCKIT Central SARS-CoV-2 PCR system is a simplified and efficient point-of-care tool for SARS-CoV-2 detection. In addition, this platform can be readily adapted to detect other human and animal viruses.
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Affiliation(s)
- Jin-Hui Zhu
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Chia-Hsing Tai
- GeneReach Biotechnology Corporation, Taichung 407, Taiwan
| | - Chia-Fong Ping
- GeneReach Biotechnology Corporation, Taichung 407, Taiwan
| | - Pin-Hsing Chou
- GeneReach Biotechnology Corporation, Taichung 407, Taiwan
| | - Yun-Long Tsai
- GeneReach Biotechnology Corporation, Taichung 407, Taiwan
| | - Simon Chung
- GeneReach Biotechnology Corporation, Taichung 407, Taiwan
| | - Laura Bradner
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Michael Pentella
- State Hygienic Laboratory, University of Iowa, Coralville, IA 52241, USA
| | - Phillip Gauger
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
| | - Jianqiang Zhang
- Department of Veterinary Diagnostic and Production Animal Medicine, College of Veterinary Medicine, Iowa State University, Ames, IA 50011, USA
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10
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Donia A, Furqan Shahid M, Hassan SU, Shahid R, Ahmad A, Javed A, Nawaz M, Yaqub T, Bokhari H. Integration of RT-LAMP and Microfluidic Technology for Detection of SARS-CoV-2 in Wastewater as an Advanced Point-of-Care Platform. FOOD AND ENVIRONMENTAL VIROLOGY 2022; 14:364-373. [PMID: 35508752 PMCID: PMC9067896 DOI: 10.1007/s12560-022-09522-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 04/04/2022] [Indexed: 05/21/2023]
Abstract
Development of lab-on-a-chip (LOC) system based on integration of reverse transcription loop-mediated isothermal amplification (RT-LAMP) and microfluidic technology is expected to speed up SARS-CoV-2 diagnostics allowing early intervention. In the current work, reverse transcriptase quantitative polymerase chain reaction (RT-qPCR) and RT-LAMP assays were performed on extracted RNA of seven wastewater samples from COVID-19 hotspots. RT‑LAMP assay was also performed on wastewater samples without RNA extraction. Current detection of SARS-CoV-2 is mainly by RT-qPCR of ORF (ORF1ab) and N genes so we targeted both to find the best target gene for SARS-CoV-2 detection. We also performed RT-LAMP with/without RNA extraction inside microfluidic device to target both genes. Positivity rates of RT-qPCR and RT-LAMP performed on extracted RNA were 100.0% (7/7) and 85.7% (6/7), respectively. RT-qPCR results revealed that all 7 wastewater samples were positive for N gene (Ct range 37-39), and negative for ORF1ab, suggesting that N gene could be the best target gene for SARS-CoV-2 detection. RT-LAMP of N and ORF (ORF1a) genes performed on wastewater samples without RNA extraction indicated that all 7 samples remains pink (negative). The color remains pink in all microchannels except microchannels which subjected to RT-LAMP for targeting N region after RNA extraction (yellow color) in 6 out of 7 samples. This study shows that SARS-CoV-2 was successfully detected from wastewater samples using RT-LAMP in microfluidic chips. This study brings the novelty involving the use of wastewater samples for detection of SARS-CoV-2 without previous virus concentration and with/without RNA extraction.
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Affiliation(s)
- Ahmed Donia
- Department of Biosciences, Faculty of Science, COMSATS University Islamabad, Islamabad, Pakistan
| | - Muhammad Furqan Shahid
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Sammer-ul Hassan
- Department of Mechanical Engineering, University of Hong Kong, Pok Fu Lam, Hong Kong, Hong Kong
| | - Ramla Shahid
- Department of Biosciences, Faculty of Science, COMSATS University Islamabad, Islamabad, Pakistan
| | | | - Aneela Javed
- Healthcare Biotechnology, Atta-ur-Rahman School of Applied Biosciences, National University of Science and Technology, Islamabad, Pakistan
| | - Muhammad Nawaz
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Tahir Yaqub
- Institute of Microbiology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Habib Bokhari
- Department of Biosciences, Faculty of Science, COMSATS University Islamabad, Islamabad, Pakistan
- Kohsar University Murree, Murree, Pakistan
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11
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García-García T, Fernández-Rodríguez R, Redondo N, de Lucas-Rius A, Zaldívar-López S, López-Ayllón BD, Suárez-Cárdenas JM, Jiménez-Marín Á, Montoya M, Garrido JJ. Impairment of antiviral immune response and disruption of cellular functions by SARS-CoV-2 ORF7a and ORF7b. iScience 2022; 25:105444. [PMID: 36310646 PMCID: PMC9597514 DOI: 10.1016/j.isci.2022.105444] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2022] [Revised: 09/20/2022] [Accepted: 10/21/2022] [Indexed: 11/09/2022] Open
Abstract
SARS-CoV-2, the causative agent of the present COVID-19 pandemic, possesses eleven accessory proteins encoded in its genome, and some have been implicated in facilitating infection and pathogenesis through their interaction with cellular components. Among these proteins, accessory protein ORF7a and ORF7b functions are poorly understood. In this study, A549 cells were transduced to express ORF7a and ORF7b, respectively, to explore more in depth the role of each accessory protein in the pathological manifestation leading to COVID-19. Bioinformatic analysis and integration of transcriptome results identified defined canonical pathways and functional groupings revealing that after expression of ORF7a or ORF7b, the lung cells are potentially altered to create conditions more favorable for SARS-CoV-2, by inhibiting the IFN-I response, increasing proinflammatory cytokines release, and altering cell metabolic activity and adhesion. Based on these results, it is plausible to suggest that ORF7a or ORF7b could be used as biomarkers of progression in this pandemic.
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Affiliation(s)
- Tránsito García-García
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - Raúl Fernández-Rodríguez
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - Natalia Redondo
- Molecular Biomedicine Department, Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid 28040, Spain
| | - Ana de Lucas-Rius
- Molecular Biomedicine Department, Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid 28040, Spain
| | - Sara Zaldívar-López
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - Blanca Dies López-Ayllón
- Molecular Biomedicine Department, Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid 28040, Spain
| | - José M. Suárez-Cárdenas
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - Ángeles Jiménez-Marín
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
| | - María Montoya
- Molecular Biomedicine Department, Centro de Investigaciones Biológicas Margarita Salas (CIB), CSIC, Madrid 28040, Spain
- Corresponding author
| | - Juan J. Garrido
- Immunogenomics and Molecular Pathogenesis Group, UIC Zoonoses and Emergent Diseases ENZOEM, Department of Genetics, University of Córdoba, Córdoba, Spain
- Maimónides Biomedical Research Institute of Córdoba (IMIBIC), GA-14 Research Group, Córdoba, Spain
- Corresponding author
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12
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Mannsverk S, Bergholm J, Palanisamy N, Ellström P, Kaden R, Lindh J, Lennerstrand J. SARS-CoV-2 variants of concern and spike protein mutational dynamics in a Swedish cohort during 2021, studied by Nanopore sequencing. Virol J 2022; 19:164. [PMID: 36258215 DOI: 10.1186/s12985-022-01896-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Revised: 09/08/2022] [Accepted: 10/05/2022] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Since the beginning of the COVID-19 pandemic, new variants of significance to public health have emerged. Consequently, early detection of new mutations and variants through whole-genome sequencing remains crucial to assist health officials in employing appropriate public health measures. METHODS We utilized the ARTIC Network SARS-CoV-2 tiled amplicon approach and Nanopore sequencing to sequence 4,674 COVID-19 positive patient samples from Uppsala County, Sweden, between week 15 and 52 in 2021. Using this data, we mapped the circulating variants of concern (VOC) in the county over time and analysed the Spike (S) protein mutational dynamics in the Delta variant throughout 2021. RESULTS The distribution of the SARS-CoV-2 VOC matched the national VOC distribution in Sweden, in 2021. In the S protein of the Delta variant, we detected mutations attributable to variants under monitoring and variants of interest (e.g., E484Q, Q613H, Q677H, A222V and Y145H) and future VOC (e.g., T95I and Y144 deletion, which are signature mutations in the Omicron variant). We also frequently detected some less well-described S protein mutations in our Delta sequences, that might play a role in shaping future emerging variants. These include A262S, Q675K, I850L, Q1201H, V1228L and M1237I. Lastly, we observed that some of the Delta variant's signature mutations were underrepresented in our study due to artifacts of the used bioinformatics tools, approach and sequencing method. We therefore discuss some pitfalls and considerations when sequencing SARS-CoV-2 genomes. CONCLUSION Our results suggest that genomic surveillance in a small, representative cohort can be used to make predictions about the circulating variants nationally. Moreover, we show that detection of transient mutations in currently circulating variants can give valuable clues to signature mutations of future VOC. Here we suggest six such mutations, that we detected frequently in the Delta variant during 2021. Lastly, we report multiple systematic errors that occurred when following the ARTIC Network SARS-CoV-2 tiled amplicon approach using the V3 primers and Nanopore sequencing, which led to the masking of some of the important signature mutations in the Delta sequences.
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Affiliation(s)
- Steinar Mannsverk
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene, Uppsala University, 751 85, Uppsala, Sweden.,Department of Cell and Molecular Biology, Uppsala University, 752 37, Uppsala, Sweden
| | - Julia Bergholm
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene, Uppsala University, 751 85, Uppsala, Sweden
| | | | - Patrik Ellström
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene, Uppsala University, 751 85, Uppsala, Sweden
| | - René Kaden
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene, Uppsala University, 751 85, Uppsala, Sweden
| | - Johan Lindh
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene, Uppsala University, 751 85, Uppsala, Sweden
| | - Johan Lennerstrand
- Department of Medical Sciences, Section for Clinical Microbiology and Hospital Hygiene, Uppsala University, 751 85, Uppsala, Sweden.
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13
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Ballmann R, Hotop SK, Bertoglio F, Steinke S, Heine PA, Chaudhry MZ, Jahn D, Pucker B, Baldanti F, Piralla A, Schubert M, Čičin-Šain L, Brönstrup M, Hust M, Dübel S. ORFeome Phage Display Reveals a Major Immunogenic Epitope on the S2 Subdomain of SARS-CoV-2 Spike Protein. Viruses 2022; 14:1326. [PMID: 35746797 PMCID: PMC9229677 DOI: 10.3390/v14061326] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 02/01/2023] Open
Abstract
The development of antibody therapies against SARS-CoV-2 remains a challenging task during the ongoing COVID-19 pandemic. All approved therapeutic antibodies are directed against the receptor binding domain (RBD) of the spike, and therefore lose neutralization efficacy against emerging SARS-CoV-2 variants, which frequently mutate in the RBD region. Previously, phage display has been used to identify epitopes of antibody responses against several diseases. Such epitopes have been applied to design vaccines or neutralize antibodies. Here, we constructed an ORFeome phage display library for the SARS-CoV-2 genome. Open reading frames (ORFs) representing the SARS-CoV-2 genome were displayed on the surface of phage particles in order to identify enriched immunogenic epitopes from COVID-19 patients. Library quality was assessed by both NGS and epitope mapping of a monoclonal antibody with a known binding site. The most prominent epitope captured represented parts of the fusion peptide (FP) of the spike. It is associated with the cell entry mechanism of SARS-CoV-2 into the host cell; the serine protease TMPRSS2 cleaves the spike within this sequence. Blocking this mechanism could be a potential target for non-RBD binding therapeutic anti-SARS-CoV-2 antibodies. As mutations within the FP amino acid sequence have been rather rare among SARS-CoV-2 variants so far, this may provide an advantage in the fight against future virus variants.
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Affiliation(s)
- Rico Ballmann
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
| | - Sven-Kevin Hotop
- Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany; (S.-K.H.); (M.Z.C.); (L.Č.-Š.); (M.B.)
| | - Federico Bertoglio
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
| | - Stephan Steinke
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
| | - Philip Alexander Heine
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
| | - M. Zeeshan Chaudhry
- Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany; (S.-K.H.); (M.Z.C.); (L.Č.-Š.); (M.B.)
| | - Dieter Jahn
- Institut für Mikrobiologie, Technische Universität Braunschweig, Spielmannstr. 7, 38106 Braunschweig, Germany;
| | - Boas Pucker
- Institute of Plant Biology, Technische Universität Braunschweig, Humboldtstr 1, 38106 Braunschweig, Germany;
| | - Fausto Baldanti
- Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, 27100 Pavia, Italy;
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS Fondazione Policlinico, 27100 Pavia, Italy;
| | - Antonio Piralla
- Molecular Virology Unit, Microbiology and Virology Department, IRCCS Fondazione Policlinico, 27100 Pavia, Italy;
| | - Maren Schubert
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
| | - Luka Čičin-Šain
- Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany; (S.-K.H.); (M.Z.C.); (L.Č.-Š.); (M.B.)
| | - Mark Brönstrup
- Helmholtz Centre for Infection Research, Inhoffenstr. 7, 38124 Braunschweig, Germany; (S.-K.H.); (M.Z.C.); (L.Č.-Š.); (M.B.)
| | - Michael Hust
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
| | - Stefan Dübel
- Institut für Biochemie, Biotechnologie und Bioinformatik, Abteilung Biotechnologie, Technische Universität Braunschweig, Spielmannstr 7, 38106 Braunschweig, Germany; (F.B.); (S.S.); (P.A.H.); (M.S.)
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14
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McLean G, Kamil J, Lee B, Moore P, Schulz TF, Muik A, Sahin U, Türeci Ö, Pather S. The Impact of Evolving SARS-CoV-2 Mutations and Variants on COVID-19 Vaccines. mBio 2022; 13:e0297921. [PMID: 35352979 PMCID: PMC9040821 DOI: 10.1128/mbio.02979-21] [Citation(s) in RCA: 109] [Impact Index Per Article: 54.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2022] [Indexed: 12/26/2022] Open
Abstract
The emergence of several new variants of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in recent months has raised concerns around the potential impact on ongoing vaccination programs. Data from clinical trials and real-world evidence suggest that current vaccines remain highly effective against the alpha variant (B.1.1.7), while some vaccines have reduced efficacy and effectiveness against symptomatic disease caused by the beta variant (B.1.351) and the delta variant (B.1.617.2); however, effectiveness against severe disease and hospitalization caused by delta remains high. Although data on the effectiveness of the primary regimen against omicron (B.1.1.529) are limited, booster programs using mRNA vaccines have been shown to restore protection against infection and symptomatic disease (regardless of the vaccine used for the primary regimen) and maintain high effectiveness against hospitalization. However, effectiveness against infection and symptomatic disease wanes with time after the booster dose. Studies have demonstrated reductions of varying magnitude in neutralizing activity of vaccine-elicited antibodies against a range of SARS-CoV-2 variants, with the omicron variant in particular exhibiting partial immune escape. However, evidence suggests that T-cell responses are preserved across vaccine platforms, regardless of variant of concern. Nevertheless, various mitigation strategies are under investigation to address the potential for reduced efficacy or effectiveness against current and future SARS-CoV-2 variants, including modification of vaccines for certain variants (including omicron), multivalent vaccine formulations, and different delivery mechanisms.
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Affiliation(s)
- Gary McLean
- School of Human Sciences, London Metropolitan University and National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Jeremy Kamil
- Louisiana State University Health, Shreveport, Louisiana, USA
| | - Benhur Lee
- Icahn School of Medicine at Mount Sinai, New York, New York, USA
| | - Penny Moore
- Centre for HIV and STIs, National Institute for Communicable Diseases of the National Health Laboratory Services, Johannesburg, South Africa
- MRC Antibody Immunity Research Unit, School of Pathology, The University of the Witwatersrand, Johannesburg, South Africa
| | - Thomas F. Schulz
- Institute of Virology, Hannover Medical School, Hannover, Germany
- Cluster of Excellence 2155 RESIST, Hannover, Germany
- German Centre for Infection Research, Hannover-Braunschweig Site, Germany
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15
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Barua A, Grot N, Plawski A. The basis of mink susceptibility to SARS-CoV-2 infection. J Appl Genet 2022; 63:543-555. [PMID: 35396646 PMCID: PMC8993591 DOI: 10.1007/s13353-022-00689-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 12/29/2021] [Accepted: 12/30/2021] [Indexed: 02/07/2023]
Abstract
Of all known airborne diseases in the twenty-first century, coronavirus disease 19 (COVID-19) has the highest infection and death rate. Over the past few decades, animal origin viral diseases, notably those of bats-linked, have increased many folds in humans with cross-species transmissions noted and the ongoing COVID-19 pandemic has emphasized the importance of understanding the evolution of natural hosts in response to viral pathogens. Cross-species transmissions are possible due to the possession of the angiotensin-converting enzyme 2 (ACE2) receptor in animals. ACE2 recognition by SARS-CoV-2 is a critical determinant of the host range, interspecies transmission, and viral pathogenesis. Thus, the phenomenon of breaking the cross-species barrier is mainly associated with mutations in the receptor-binding domain (RBD) of the spike (S) protein that interacts with ACE2. In this review, we raise the issue of cross-species transmission based on sequence alignment of S protein. Based on previous reports and our observations, we can conclude that the occurrence of one of two mutations D614G or Y453F is sufficient for infection of minks by SARS-CoV-2 from humans. Unfortunately, D614G is observed in the world’s most common line of virus B.1.1.7 and the latest SARS-CoV-2 variants B.1.617.1, B.1.617.2, and B.1.617.3 too.
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Affiliation(s)
- Avishak Barua
- Department of Biochemistry and Biotechnology, Poznań University of Life Sciences, Dojazd 11, 60-631, Poznań, Poland
| | - Natalia Grot
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479, Poznań, Poland
| | - Andrzej Plawski
- Institute of Human Genetics, Polish Academy of Sciences, Strzeszyńska 32, 60-479, Poznań, Poland. .,Department of General and Endocrine Surgery and Gastroenterological Oncology, Poznań University of Medical Sciences, Przybyszewskiego 49, 60-355, Poznań, Poland.
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16
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Antoine D, Mohammadi M, Vitt M, Dickie JM, Jyoti SS, Tilbury MA, Johnson PA, Wawrousek KE, Wall JG. Rapid, Point-of-Care scFv-SERS Assay for Femtogram Level Detection of SARS-CoV-2. ACS Sens 2022; 7:866-873. [PMID: 35271769 PMCID: PMC8961876 DOI: 10.1021/acssensors.1c02664] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 03/02/2022] [Indexed: 12/19/2022]
Abstract
Rapid, sensitive, on-site identification of SARS-CoV-2 infections is an important tool in the control and management of COVID-19. We have developed a surface-enhanced Raman scattering (SERS) immunoassay for highly sensitive detection of SARS-CoV-2. Single-chain Fv (scFv) recombinant antibody fragments that bind the SARS-CoV-2 spike protein were isolated by biopanning a human scFv library. ScFvs were conjugated to magnetic nanoparticles and SERS nanotags, followed by immunocomplex formation and detection of the SARS-CoV-2 spike protein with a limit of detection of 257 fg/mL in 30 min in viral transport medium. The assay also detected B.1.1.7 ("alpha"), B.1.351 ("beta"), and B.1.617.2 ("delta") spike proteins, while no cross-reactivity was observed with the common human coronavirus HKU1 spike protein. Inactivated whole SARS-CoV-2 virus was detected at 4.1 × 104 genomes/mL, which was 10-100-fold lower than virus loads typical of infectious individuals. The assay exhibited higher sensitivity for SARS-CoV-2 than commercial lateral flow assays, was compatible with viral transport media and saliva, enabled rapid pivoting to detect new virus variants, and facilitated highly sensitive, point-of-care diagnosis of COVID-19 in clinical and public health settings.
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Affiliation(s)
- Delphine Antoine
- Microbiology,
College of Science and Engineering, and SFI Centre for Medical Devices
(CÚRAM), National University of Ireland,
Galway (NUI Galway), Galway H91 TK33, Ireland
| | - Moein Mohammadi
- Chemical
Engineering, University of Wyoming, Laramie, Wyoming 82072, United States
| | - Madison Vitt
- Chemical
Engineering, University of Wyoming, Laramie, Wyoming 82072, United States
| | - Julia Marie Dickie
- Chemical
Engineering, University of Wyoming, Laramie, Wyoming 82072, United States
| | | | - Maura A. Tilbury
- Microbiology,
College of Science and Engineering, and SFI Centre for Medical Devices
(CÚRAM), National University of Ireland,
Galway (NUI Galway), Galway H91 TK33, Ireland
| | - Patrick A. Johnson
- Chemical
Engineering, University of Wyoming, Laramie, Wyoming 82072, United States
| | - Karen E. Wawrousek
- Chemical
Engineering, University of Wyoming, Laramie, Wyoming 82072, United States
| | - J. Gerard Wall
- Microbiology,
College of Science and Engineering, and SFI Centre for Medical Devices
(CÚRAM), National University of Ireland,
Galway (NUI Galway), Galway H91 TK33, Ireland
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17
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De Pace V, Bruzzone B, Orsi A, Ricucci V, Domnich A, Guarona G, Randazzo N, Stefanelli F, Battolla E, Dusi PA, Lillo F, Icardi G. Comparative Analysis of Five Multiplex RT-PCR Assays in the Screening of SARS-CoV-2 Variants. Microorganisms 2022; 10:306. [PMID: 35208761 PMCID: PMC8876857 DOI: 10.3390/microorganisms10020306] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/18/2022] [Accepted: 01/26/2022] [Indexed: 11/16/2022] Open
Abstract
The rapid and presumptive detection of SARS-CoV-2 variants may be performed using multiplex RT-PCR assays. The aim of this study was to evaluate the diagnostic performance of five qualitative RT-PCR tests as compared with next-generation sequencing (NGS). We retrospectively examined a multi-variant panel (n = 72) of SARS-CoV-2-positive nasopharyngeal swabs categorized as variants of concern (Alpha, Beta, Gamma and Delta), variants under monitoring (Iota and Kappa) and wild-type strains circulating in Liguria (Italy) from January to August 2021. First, NGS libraries of study samples were prepared and mapped to the reference genome. Then, specimens were screened for the detection of L452R, W152C, K417T, K417N, E484Q, E484K and N501Y mutations using the SARS-CoV-2 Variants II Assay Allplex, UltraGene Assay SARS-CoV-2 452R & 484K & 484Q Mutations V1, COVID-19 Ultra Variant Catcher, SARS-CoV-2 Extended ELITe MGB and Simplexa SARS-CoV-2 Variants Direct. The overall accuracy of these assays ranged from 96.9% to 100%. Specificity and sensitivity were 100% and 96-100%, respectively. We highly recommend the use of these assays as second-level tests in the routine workflow of SARS-CoV-2 laboratory diagnostics, as they are accurate, user friendly, low cost, may identify specific mutations in about 2-3 h and, therefore, optimize the surveillance of SARS-CoV-2 variants.
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Affiliation(s)
- Vanessa De Pace
- Hygiene Unit, Ospedale Policlinico San Martino—IRCCS, 16132 Genoa, Italy; (B.B.); (V.R.); (A.D.); (N.R.); (F.S.)
| | - Bianca Bruzzone
- Hygiene Unit, Ospedale Policlinico San Martino—IRCCS, 16132 Genoa, Italy; (B.B.); (V.R.); (A.D.); (N.R.); (F.S.)
| | - Andrea Orsi
- Department of Health Sciences (DISSAL), University of Genoa, 16132 Genoa, Italy; (A.O.); (G.G.); (G.I.)
| | - Valentina Ricucci
- Hygiene Unit, Ospedale Policlinico San Martino—IRCCS, 16132 Genoa, Italy; (B.B.); (V.R.); (A.D.); (N.R.); (F.S.)
| | - Alexander Domnich
- Hygiene Unit, Ospedale Policlinico San Martino—IRCCS, 16132 Genoa, Italy; (B.B.); (V.R.); (A.D.); (N.R.); (F.S.)
| | - Giulia Guarona
- Department of Health Sciences (DISSAL), University of Genoa, 16132 Genoa, Italy; (A.O.); (G.G.); (G.I.)
| | - Nadia Randazzo
- Hygiene Unit, Ospedale Policlinico San Martino—IRCCS, 16132 Genoa, Italy; (B.B.); (V.R.); (A.D.); (N.R.); (F.S.)
| | - Federica Stefanelli
- Hygiene Unit, Ospedale Policlinico San Martino—IRCCS, 16132 Genoa, Italy; (B.B.); (V.R.); (A.D.); (N.R.); (F.S.)
| | - Enrico Battolla
- Division of Clinical Pathology, Azienda Sanitaria Locale n°5, 19121 La Spezia, Italy;
| | - Pier Andrea Dusi
- Microbiology Department, Sanremo Hospital, 18038 Imperia, Italy;
| | - Flavia Lillo
- Laboratory of Clinical Pathology, ASL2 Savonese, 17100 Savona, Italy;
| | - Giancarlo Icardi
- Department of Health Sciences (DISSAL), University of Genoa, 16132 Genoa, Italy; (A.O.); (G.G.); (G.I.)
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18
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Muñoz M, Patiño LH, Ballesteros N, Castañeda S, Luna N, Delgado L, Hernandez-Pereira C, Shaban MV, Muñoz SA, Paniz-Mondolfi A, Ramírez JD. Striking lineage diversity of severe acute respiratory syndrome coronavirus 2 from non-human sources. One Health 2021; 14:100363. [PMID: 34931174 PMCID: PMC8673956 DOI: 10.1016/j.onehlt.2021.100363] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2021] [Revised: 12/13/2021] [Accepted: 12/14/2021] [Indexed: 12/18/2022] Open
Abstract
Due to the necessity to control human-to-human spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the overwhelming majority of the generated data on this virus was solely related to the genomic characteristics of strains infecting humans; conversely, this work aimed to recover and analyze the diversity of viral genomes from non-human sources. From a set of 3595 publicly available SARS-CoV-2 genome sequences, 128 lineages were identified in non-human hosts, the majority represented by the variants of concern Delta (n = 1105, 30.7%) and Alpha (n = 466, 12.9%), followed by B.1.1.298 lineage (n = 458, 12.7%). Environment, Neovison vison, Odocoileus virginianus and Felis catus were the non-human sources with the highest number of lineages (14, 12 and 10, respectively). Phylogenomic analyses showed viral clusters from environmental sources, N. vison, O. virginianus, Panthera tigris, and Panthera leo. These clusters were collectively related to human viruses as well as all other non-human sources that were heterogeneously distributed in the phylogenetic tree. Further, the genetic details of viral genomes from bats and pangolins were independently investigated owing to their high divergence, revealing five distinct clusters. Cluster 4 exclusively included bat-sourced genomes and the SARS-CoV-2 reference strain Wuhan-01. In summary, this study identified new genetic landmarks of SARS-CoV-2 evolution. We propose potential interspecies transmission routes of SARS-CoV-2 between animals and humans, which should be considered in order to establish better pathogen surveillance and containment strategies.
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Affiliation(s)
- Marina Muñoz
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Luz Helena Patiño
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Nathalia Ballesteros
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Sergio Castañeda
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Nicolás Luna
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia
| | - Lourdes Delgado
- Instituto de Investigaciones Biomédicas IDB/Incubadora Venezolana de la Ciencia, Barquisimeto, Venezuela
| | - Carlos Hernandez-Pereira
- Instituto de Investigaciones Biomédicas IDB/Incubadora Venezolana de la Ciencia, Barquisimeto, Venezuela
| | - Maryia V Shaban
- Instituto de Investigaciones Biomédicas IDB/Incubadora Venezolana de la Ciencia, Barquisimeto, Venezuela
| | - Shirly Alexandra Muñoz
- Centro de Tecnología en Salud (CETESA), Innovaseq SAS, Bogotá, Colombia.,Unidad de Salud de Ibagué (USI) E.S.E., Ibagué, Colombia
| | - Alberto Paniz-Mondolfi
- Instituto de Investigaciones Biomédicas IDB/Incubadora Venezolana de la Ciencia, Barquisimeto, Venezuela.,Microbiology Division, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
| | - Juan David Ramírez
- Centro de Investigaciones en Microbiología y Biotecnología-UR (CIMBIUR), Facultad de Ciencias Naturales, Universidad del Rosario, Bogotá, Colombia.,Microbiology Division, Department of Pathology, Molecular and Cell-Based Medicine, Icahn School of Medicine at Mount Sinai, New York, USA
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19
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Ozger ZB, Cihan P. A novel ensemble fuzzy classification model in SARS-CoV-2 B-cell epitope identification for development of protein-based vaccine. Appl Soft Comput 2021; 116:108280. [PMID: 34931117 PMCID: PMC8673934 DOI: 10.1016/j.asoc.2021.108280] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 11/25/2021] [Accepted: 12/03/2021] [Indexed: 12/23/2022]
Abstract
B-cell epitope prediction research has received growing interest since the development of the first method. B-cell epitope identification with the aid of an accurate prediction method is one of the most important steps in epitope-based vaccine development, immunodiagnostic testing, antibody production, disease diagnosis, and treatment. Nevertheless, using experimental methods in epitope mapping is very time-consuming, costly, and labor-intensive. Therefore, although successful predictions with in silico methods are very important in epitope prediction, there are limited studies in this area. The aim of this study is to propose a new approach for successfully predicting B-cell epitopes for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). In this study, the SARS-CoV B-cell epitope prediction performances of different fuzzy learning classification models genetic cooperative competitive learning (GCCL), fuzzy genetics-based machine learning (GBML), Chi’s method (CHI), Ishibuchi’s method with weight factor (W), structural learning algorithm on vague environment (SLAVE) and the state-of-the-art ensemble fuzzy classification model were compared. The obtained results showed that the proposed ensemble approach has the lowest error in SARS-CoV B-cell epitope estimation compared to the base fuzzy learners (average error rates; ensemble fuzzy=8.33, GCCL=30.42, GBML=23.82, CHI=29.17, W=46.25, and SLAVE=20.42). SARS-CoV and SARS-CoV-2 have high genome similarities. Therefore, the most successful method determined for SARS-CoV B-cell epitope prediction was used in SARS-CoV-2 cell epitope prediction. Finally, the eventual B-cell epitope prediction results obtained for SARS-CoV-2 with the ensemble fuzzy classification model were compared with the epitope sequences predicted by the BepiPred server and immunoinformatics studies in the literature for the same protein sequences according to VaxiJen 2.0 scores. We hope that the developed epitope prediction method will help design effective vaccines and drugs against future outbreaks of the coronavirus family, especially SARS-CoV-2 and its possible mutations.
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Affiliation(s)
- Zeynep Banu Ozger
- Department of Computer Engineering, Sutcu Imam University, 46040, Kahramanmaras, Turkey
| | - Pınar Cihan
- Department of Computer Engineering, Tekirdag Namik Kemal University, 59860, Corlu, Tekirdag, Turkey
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20
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Halley JM, Vokou D, Pappas G, Sainis I. SARS-CoV-2 mutational cascades and the risk of hyper-exponential growth. Microb Pathog 2021; 161:105237. [PMID: 34653544 PMCID: PMC8507571 DOI: 10.1016/j.micpath.2021.105237] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 10/05/2021] [Accepted: 10/06/2021] [Indexed: 11/30/2022]
Abstract
The emergence of novel SARS-CoV-2 variants of concern (VOC), in late 2020, with selective transmission advantage and partial immunity escape potential, has been driving further evolution in the pandemic. The timing of mutational evolution and its limits are thus of paramount importance in preparedness planning. Here, we present a model predicting the pattern of epidemic growth including the emergence of variants through mutation. It is based on the SEIR (Susceptible, Exposed, Infected, Removed) model, but its equations are modified according to the transmission parameters of novel variants. Since more transmissible strains will drive a further increase in the number of cases, they will also lead to further novel mutations. As one cannot predict whether there is a viral mutational evolutionary limit, we model a cascade that could lead to hyper-exponential growth (HEG) involving the emergence of even more transmissible mutants that could overwhelm any systematic response. Our results are consistent with the timing, since the beginning of the pandemic, of the concurrent and independent emergence of the VOCs. The current dominance of the Delta variant and the need for additional public health measures indicates some of the risks of a possible HEG. We examine conditions that favor the expected appearance of similar variants, thus enabling better preparedness and more targeted research.
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Affiliation(s)
- John M Halley
- Laboratory of Ecology, Department of Biological Applications and Technology, Faculty of Health Sciences, University of Ioannina, 45110, Ioannina, Greece.
| | - Despoina Vokou
- Department of Ecology, School of Biology, Aristotle University of Thessaloniki, 54124, Thessaloniki, Greece
| | - Georgios Pappas
- Institute of Continuing Medical Education of Ioannina, Ioannina, Greece
| | - Ioannis Sainis
- Medical School, Faculty of Health Sciences, University of Ioannina, 45110, Ioannina, Greece
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21
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Lennerstrand J, Palanisamy N. Global Prevalence of Adaptive and Prolonged Infections' Mutations in the Receptor-Binding Domain of the SARS-CoV-2 Spike Protein. Viruses 2021; 13:1974. [PMID: 34696404 PMCID: PMC8538289 DOI: 10.3390/v13101974] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Revised: 09/23/2021] [Accepted: 09/27/2021] [Indexed: 12/15/2022] Open
Abstract
Several vaccines with varying efficacies have been developed and are currently administered globally to minimize the spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Despite having an RNA-dependent RNA polymerase with a proofreading activity, new variants of SARS-CoV-2 are on the rise periodically. Some of the mutations in these variants, especially mutations on the spike protein, aid the virus in transmission, infectivity and host immune evasion. Further, these mutations also reduce the effectiveness of some of the current vaccines and monoclonal antibodies (mAbs). In the present study, using the available 984,769 SARS-CoV-2 nucleotide sequences on the NCBI database from the end of 2019 till 28 July 2021, we have estimated the global prevalence of so-called 'adaptive mutations' and 'mutations identified in the prolonged infections', in the receptor-binding domain (RBD) of the spike (S) protein. Irrespective of the geographical region, in the case of the adaptive mutations, N501Y (48.38%) was found to be the dominant mutation followed by L452R (17.52%), T478K (14.31%), E484K (4.69%), S477N (3.29%), K417T (1.64%), N439K (0.7%) and S494P (0.7%). Other mutations were found to be less prevalent (less than 0.7%). Since the last two months, there has been a massive increase of L452R and T478K mutations (delta variant) in certain areas. In the case of prolonged infections' mutations (long-term SARS-CoV-2 infections), V483A (0.009%) was found to be dominant followed by Q493R (0.009%), while other mutations were found in less than 0.007% of the studied sequences. The data obtained in this study will aid in the development of better infection control policies, thereby curbing the spread of this virus.
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Affiliation(s)
- Johan Lennerstrand
- Department of Medical Sciences, Section of Clinical Microbiology, Uppsala University, 751 85 Uppsala, Sweden;
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22
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CoVrimer: A tool for aligning SARS-CoV-2 primer sequences and selection of conserved/degenerate primers. Genomics 2021; 113:3174-3184. [PMID: 34293476 PMCID: PMC8289724 DOI: 10.1016/j.ygeno.2021.07.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2021] [Revised: 05/30/2021] [Accepted: 07/17/2021] [Indexed: 01/17/2023]
Abstract
As mutations in SARS-CoV-2 virus accumulate rapidly, novel primers that amplify this virus sensitively and specifically are in demand. We have developed a webserver named CoVrimer by which users can search for and align existing or newly designed conserved/degenerate primer pair sequences against the viral genome and assess the mutation load of both primers and amplicons. CoVrimer uses mutation data obtained from an online platform established by NGDC-CNCB (12 May 2021) to identify genomic regions, either conserved or with low levels of mutations, from which potential primer pairs are designed and provided to the user for filtering based on generalized and SARS-CoV-2 specific parameters. Alignments of primers and probes can be visualized with respect to the reference genome, indicating variant details and the level of conservation. Consequently, CoVrimer is likely to help researchers with the challenges posed by viral evolution and is freely available at http://konulabapps.bilkent.edu.tr:3838/CoVrimer/.
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23
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Assadi F. Fighting an Invisible Enemy: Beginning a New Chapter in the COVID-19 Era. Int J Prev Med 2021; 12:82. [PMID: 34447524 PMCID: PMC8356973 DOI: 10.4103/ijpvm.ijpvm_22_21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2021] [Accepted: 02/01/2021] [Indexed: 11/20/2022] Open
Affiliation(s)
- F Assadi
- Department of Pediatrics, Division of Nephrology, Rush University Medical Center, Chicago, Illinois, USA
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24
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Cohen KW, Linderman SL, Moodie Z, Czartoski J, Lai L, Mantus G, Norwood C, Nyhoff LE, Edara VV, Floyd K, De Rosa SC, Ahmed H, Whaley R, Patel SN, Prigmore B, Lemos MP, Davis CW, Furth S, O’Keefe JB, Gharpure MP, Gunisetty S, Stephens K, Antia R, Zarnitsyna VI, Stephens DS, Edupuganti S, Rouphael N, Anderson EJ, Mehta AK, Wrammert J, Suthar MS, Ahmed R, McElrath MJ. Longitudinal analysis shows durable and broad immune memory after SARS-CoV-2 infection with persisting antibody responses and memory B and T cells. Cell Rep Med 2021; 2:100354. [PMID: 34250512 PMCID: PMC8253687 DOI: 10.1016/j.xcrm.2021.100354] [Citation(s) in RCA: 246] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2021] [Revised: 05/27/2021] [Accepted: 06/24/2021] [Indexed: 01/10/2023]
Abstract
Ending the COVID-19 pandemic will require long-lived immunity to SARS-CoV-2. Here, we evaluate 254 COVID-19 patients longitudinally up to 8 months and find durable broad-based immune responses. SARS-CoV-2 spike binding and neutralizing antibodies exhibit a bi-phasic decay with an extended half-life of >200 days suggesting the generation of longer-lived plasma cells. SARS-CoV-2 infection also boosts antibody titers to SARS-CoV-1 and common betacoronaviruses. In addition, spike-specific IgG+ memory B cells persist, which bodes well for a rapid antibody response upon virus re-exposure or vaccination. Virus-specific CD4+ and CD8+ T cells are polyfunctional and maintained with an estimated half-life of 200 days. Interestingly, CD4+ T cell responses equally target several SARS-CoV-2 proteins, whereas the CD8+ T cell responses preferentially target the nucleoprotein, highlighting the potential importance of including the nucleoprotein in future vaccines. Taken together, these results suggest that broad and effective immunity may persist long-term in recovered COVID-19 patients.
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Affiliation(s)
- Kristen W. Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Susanne L. Linderman
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Zoe Moodie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Julie Czartoski
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Lilin Lai
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA
- Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Grace Mantus
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Carson Norwood
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Lindsay E. Nyhoff
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA
| | - Venkata Viswanadh Edara
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA
- Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Katharine Floyd
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA
- Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Stephen C. De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Departments of Laboratory Medicine and Medicine, University of Washington, Seattle, WA 98195, USA
| | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Rachael Whaley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Shivan N. Patel
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Brittany Prigmore
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Maria P. Lemos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Carl W. Davis
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Sarah Furth
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - James B. O’Keefe
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Mohini P. Gharpure
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Sivaram Gunisetty
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Kathy Stephens
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA
| | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Veronika I. Zarnitsyna
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - David S. Stephens
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Srilatha Edupuganti
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
- Hope Clinic of Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30330, USA
| | - Nadine Rouphael
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
- Hope Clinic of Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30330, USA
| | - Evan J. Anderson
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA
| | - Aneesh K. Mehta
- Department of Medicine, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Jens Wrammert
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA
| | - Mehul S. Suthar
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA
- Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Rafi Ahmed
- Emory Vaccine Center, Emory University, Atlanta, GA 30322, USA
- Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
- Departments of Laboratory Medicine and Medicine, University of Washington, Seattle, WA 98195, USA
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25
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Redondo N, Zaldívar-López S, Garrido JJ, Montoya M. SARS-CoV-2 Accessory Proteins in Viral Pathogenesis: Knowns and Unknowns. Front Immunol 2021; 12:708264. [PMID: 34305949 PMCID: PMC8293742 DOI: 10.3389/fimmu.2021.708264] [Citation(s) in RCA: 172] [Impact Index Per Article: 57.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2021] [Accepted: 06/22/2021] [Indexed: 12/23/2022] Open
Abstract
There are still many unanswered questions concerning viral SARS-CoV-2 pathogenesis in COVID-19. Accessory proteins in SARS-CoV-2 consist of eleven viral proteins whose roles during infection are still not completely understood. Here, a review on the current knowledge of SARS-CoV-2 accessory proteins is summarized updating new research that could be critical in understanding SARS-CoV-2 interaction with the host. Some accessory proteins such as ORF3b, ORF6, ORF7a and ORF8 have been shown to be important IFN-I antagonists inducing an impairment in the host immune response. In addition, ORF3a is involved in apoptosis whereas others like ORF9b and ORF9c interact with cellular organelles leading to suppression of the antiviral response in infected cells. However, possible roles of ORF7b and ORF10 are still awaiting to be described. Also, ORF3d has been reassigned. Relevant information on the knowns and the unknowns in these proteins is analyzed, which could be crucial for further understanding of SARS-CoV-2 pathogenesis and to design strategies counteracting their actions evading immune responses in COVID-19.
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Affiliation(s)
- Natalia Redondo
- Molecular Biomedicine Department, Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain
| | - Sara Zaldívar-López
- Animal Breeding and Genomics Group, Department of Genetics, Faculty of Veterinary Medicine, University of Córdoba, Córdoba, Spain
- Immunogenomics and Molecular Pathogenesis GA14 Group, Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
| | - Juan J. Garrido
- Animal Breeding and Genomics Group, Department of Genetics, Faculty of Veterinary Medicine, University of Córdoba, Córdoba, Spain
- Immunogenomics and Molecular Pathogenesis GA14 Group, Maimónides Biomedical Research Institute of Córdoba (IMIBIC), Córdoba, Spain
| | - Maria Montoya
- Molecular Biomedicine Department, Centro de Investigaciones Biológicas Margarita Salas (CIB-CSIC), Madrid, Spain
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26
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Cohen KW, Linderman SL, Moodie Z, Czartoski J, Lai L, Mantus G, Norwood C, Nyhoff LE, Edara VV, Floyd K, De Rosa SC, Ahmed H, Whaley R, Patel SN, Prigmore B, Lemos MP, Davis CW, Furth S, O’Keefe J, Gharpure MP, Gunisetty S, Stephens KA, Antia R, Zarnitsyna VI, Stephens DS, Edupuganti S, Rouphael N, Anderson EJ, Mehta AK, Wrammert J, Suthar MS, Ahmed R, McElrath MJ. Longitudinal analysis shows durable and broad immune memory after SARS-CoV-2 infection with persisting antibody responses and memory B and T cells. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2021:2021.04.19.21255739. [PMID: 33948610 PMCID: PMC8095229 DOI: 10.1101/2021.04.19.21255739] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Ending the COVID-19 pandemic will require long-lived immunity to SARS-CoV-2. Here, we evaluate 254 COVID-19 patients longitudinally up to eight months and find durable broad-based immune responses. SARS-CoV-2 spike binding and neutralizing antibodies exhibit a bi-phasic decay with an extended half-life of >200 days suggesting the generation of longer-lived plasma cells. SARS-CoV-2 infection also boosts antibody titers to SARS-CoV-1 and common betacoronaviruses. In addition, spike-specific IgG+ memory B cells persist, which bodes well for a rapid antibody response upon virus re-exposure or vaccination. Virus-specific CD4+ and CD8+ T cells are polyfunctional and maintained with an estimated half-life of 200 days. Interestingly, CD4+ T cell responses equally target several SARS-CoV-2 proteins, whereas the CD8+ T cell responses preferentially target the nucleoprotein, highlighting the potential importance of including the nucleoprotein in future vaccines. Taken together, these results suggest that broad and effective immunity may persist long-term in recovered COVID-19 patients.
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Affiliation(s)
- Kristen W. Cohen
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Susanne L. Linderman
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Zoe Moodie
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Julie Czartoski
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Lilin Lai
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA,Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Grace Mantus
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA
| | - Carson Norwood
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA
| | - Lindsay E. Nyhoff
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA,Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Venkata Viswanadh Edara
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA,Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Katharine Floyd
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA,Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Stephen C. De Rosa
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA,Departments of Laboratory Medicine and Medicine, University of Washington, Seattle, WA 98195, USA
| | - Hasan Ahmed
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Rachael Whaley
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Shivan N. Patel
- Department of Medicine, Division of Infectious Diseases, Hope Clinic of Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Brittany Prigmore
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Maria P. Lemos
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - Carl W. Davis
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Sarah Furth
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA
| | - James O’Keefe
- Emory University School of Medicine, Department of Medicine, Atlanta, GA 30322, USA
| | - Mohini P. Gharpure
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - Sivaram Gunisetty
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | | | - Rustom Antia
- Department of Biology, Emory University, Atlanta, GA 30322, USA
| | - Veronika I. Zarnitsyna
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA,Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - David S. Stephens
- Emory University School of Medicine, Department of Medicine, Atlanta, GA 30322, USA
| | - Srilatha Edupuganti
- Department of Medicine, Division of Infectious Diseases, Hope Clinic of Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Nadine Rouphael
- Department of Medicine, Division of Infectious Diseases, Hope Clinic of Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA 30329, USA
| | - Evan J. Anderson
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA,Emory University School of Medicine, Department of Medicine, Atlanta, GA 30322, USA
| | - Aneesh K. Mehta
- Emory University School of Medicine, Department of Medicine, Atlanta, GA 30322, USA
| | - Jens Wrammert
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA
| | - Mehul S. Suthar
- Center for Childhood Infections and Vaccines of Children’s Healthcare of Atlanta, Emory University Department of Pediatrics Department of Medicine, Atlanta, GA 30322, USA,Yerkes National Primate Research Center, Atlanta, GA 30329, USA
| | - Rafi Ahmed
- Emory Vaccine Center and Department of Microbiology and Immunology, Emory University, Atlanta, GA 30322, USA
| | - M. Juliana McElrath
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA, 98109, USA,Departments of Laboratory Medicine and Medicine, University of Washington, Seattle, WA 98195, USA
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27
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Fayad N, Abi Habib W, Kandeil A, El-Shesheny R, Kamel MN, Mourad Y, Mokhbat J, Kayali G, Goldstein J, Abdallah J. SARS-CoV-2 Variants in Lebanon: Evolution and Current Situation. BIOLOGY 2021; 10:531. [PMID: 34198622 PMCID: PMC8232177 DOI: 10.3390/biology10060531] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 05/30/2021] [Accepted: 06/08/2021] [Indexed: 12/18/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has seen a worldwide spread since its emergence in 2019, including to Lebanon, where 534,968 confirmed cases (8% of the population) and 7569 deaths have been reported as of 14 May 2021. With the genome sequencing of strains from various countries, several classification systems were established via genome comparison. For instance, the GISAID clades classification highlights key mutations in the encoded proteins that could potentially affect the virus' infectivity and transmission rates. In this study, 58 genomes of Lebanese SARS-CoV-2 strains were analyzed, 28 of which were sequenced for this study, and 30 retrieved from the GISAID and GenBank databases. We aimed to classify these strains, establish their phylogenetic relationships, and extract the mutations causing amino acid substitutions within, particularly, the structural proteins. The sequenced Lebanese SARS-COV-2 strains were classified into four GISAID clades and 11 Pango lineages. Moreover, 21 uncommon mutations in the structural proteins were found in the newly sequenced strains, underlining interesting combinations of mutations in the spike proteins. Hence, this study constitutes an observation and description of the current SARS-CoV-2 genetic and clade situation in Lebanon according to the available sequenced strains.
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Affiliation(s)
- Nancy Fayad
- School of Pharmacy, Lebanese American University, P.O. Box 36, Byblos, Lebanon; (N.F.); (W.A.H.)
| | - Walid Abi Habib
- School of Pharmacy, Lebanese American University, P.O. Box 36, Byblos, Lebanon; (N.F.); (W.A.H.)
| | - Ahmed Kandeil
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; (A.K.); (R.E.-S.); (M.N.K.)
| | - Rabeh El-Shesheny
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; (A.K.); (R.E.-S.); (M.N.K.)
- St. Jude Children’s Research Hospital, 262 Danny Thomas Place, Memphis, TN 38105, USA
| | - Mina Nabil Kamel
- Center of Scientific Excellence for Influenza Viruses, National Research Centre, Giza 12622, Egypt; (A.K.); (R.E.-S.); (M.N.K.)
| | - Youmna Mourad
- Al Hadi Laboratory and IVF Center, P.O. Box 44, Beirut, Lebanon;
| | - Jacques Mokhbat
- School of Medicine, Lebanese American University, P.O. Box 36, Byblos, Lebanon;
| | - Ghazi Kayali
- Human Link, Dubai 971, United Arab Emirates;
- Department of Epidemiology, Human Genetics, and Environmental Sciences, University of Texas, Houston, TX 77030, USA
| | - Jimi Goldstein
- Human Link, Dubai 971, United Arab Emirates;
- School of Engineering and Technology, University of Hertfordshire, Hatfield, Hertfordshire AL10 9AB, UK
| | - Jad Abdallah
- School of Pharmacy, Lebanese American University, P.O. Box 36, Byblos, Lebanon; (N.F.); (W.A.H.)
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