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Afridonova ZE, Toptygina AP, Mikhaylov IS. Humoral and Cellular Immune Response to SARS-CoV-2 S and N Proteins. BIOCHEMISTRY. BIOKHIMIIA 2024; 89:872-882. [PMID: 38880648 DOI: 10.1134/s0006297924050080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 10/12/2023] [Accepted: 11/01/2023] [Indexed: 06/18/2024]
Abstract
The pandemic of a new coronavirus infection that has lasted for more than 3 years, is still accompanied by frequent mutations in the S protein of SARS-CoV-2 and emergence of new virus variants causing new disease outbreak. Of all coronaviral proteins, the S and N proteins are the most immunogenic. The aim of this study was to compare the features of the humoral and T-cell immune responses to the SARS-CoV-2 S and N proteins in people with different histories of interaction with this virus. The study included 27 individuals who had COVID-19 once, 23 people who were vaccinated twice with the Sputnik V vaccine and did not have COVID-19, 22 people who had COVID-19 and were vaccinated twice with Sputnik V 6-12 months after the disease, and 25 people who had COVID-19 twice. The level of antibodies was determined by the enzyme immunoassay, and the cellular immunity was assessed by the expression of CD107a on CD8high lymphocytes after recognition of SARS-CoV-2 antigens. It was shown that the humoral immune response to the N protein was formed mainly by short-lived plasma cells synthesizing IgG antibodies of all four subclasses with a gradual switch from IgG3 to IgG1. The response to the S protein was formed by short-lived plasma cells at the beginning of the response (IgG1 and IgG3 subclasses) and then by long-lived plasma cells (IgG1 subclass). The dynamics of antibody level synthesized by the short-lived plasma cells was described by the Fisher equation, while changes in the level of antibodies synthesized by the long-lived plasma cells were described by the Erlang equation. The level of antibodies in the groups with the hybrid immunity exceeded that in the group with the post-vaccination immunity; the highest antibody content was observed in the group with the breakthrough immunity. The cellular immunity to the S and N proteins differed depending on the mode of immune response induction (vaccination or disease). Importantly, the response of heterologous CD8+ T cell to the N proteins of other coronaviruses may be involved in the immune defense against SARS-CoV-2.
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Affiliation(s)
- Zulfiia E Afridonova
- G.N.Gabrichevsky Research Institute for Epidemiology and Microbiology, Moscow, 125212, Russia
| | - Anna P Toptygina
- G.N.Gabrichevsky Research Institute for Epidemiology and Microbiology, Moscow, 125212, Russia.
- Lomonosov Moscow State University, Moscow, 119991, Russia
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Colson P, Chaudet H, Delerce J, Pontarotti P, Levasseur A, Fantini J, La Scola B, Devaux C, Raoult D. Role of SARS-CoV-2 mutations in the evolution of the COVID-19 pandemic. J Infect 2024; 88:106150. [PMID: 38570164 DOI: 10.1016/j.jinf.2024.106150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 03/12/2024] [Accepted: 03/27/2024] [Indexed: 04/05/2024]
Abstract
OBJECTIVES The SARS-CoV-2 pandemic and large-scale genomic surveillance provided an exceptional opportunity to analyze mutations that appeared over three years in viral genomes. Here we studied mutations and their epidemic consequences for SARS-CoV-2 genomes from our center. METHODS We analyzed 61,397 SARS-CoV-2 genomes we sequenced from respiratory samples for genomic surveillance. Mutations frequencies were calculated using Nextclade, Microsoft Excel, and an in-house Python script. RESULTS A total of 22,225 nucleotide mutations were identified, 220 (1.0%) being each at the root of ≥836 genomes, classifying mutations as 'hyperfertile'. Two seeded the European pandemic: P323L in RNA polymerase, associated with an increased mutation rate, and D614G in spike that improved fitness. Most 'hyperfertile' mutations occurred in areas not predicted with increased virulence. Their mean number was 8±6 (0-22) per 1000 nucleotides per gene. They were 3.7-times more frequent in accessory than informational genes (13.8 versus 3.7/1000 nucleotides). Particularly, they were 4.1-times more frequent in ORF8 than in the RNA polymerase gene. Interestingly, stop codons were present in 97 positions, almost only in accessory genes, including ORF8 (21/100 codons). CONCLUSIONS most 'hyperfertile' mutations did not predict emergence of a new epidemic, and some were stop codons indicating the existence of so-named 'non-virulence' genes.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005 Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 Rue Saint-Pierre, 13005 Marseille, France
| | - Hervé Chaudet
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 Rue Saint-Pierre, 13005 Marseille, France; Aix-Marseille Université, Institut de Recherche pour le Développement (IRD), Vecteurs, Infections Tropicales et Méditerranéennes (VITROME), 27 Boulevard Jean Moulin, 13005 Marseille, France; French Armed Forces Center for Epidemiology and Public Health (CESPA), Camp de Sainte Marthe, Marseille, France
| | - Jérémy Delerce
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005 Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 Rue Saint-Pierre, 13005 Marseille, France
| | - Pierre Pontarotti
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Department of Biological Sciences, Centre National de la Recherche Scientifique (CNRS)-SNC5039, Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005 Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 Rue Saint-Pierre, 13005 Marseille, France
| | - Jacques Fantini
- "Aix-Marseille Université, INSERM UMR UA 16, Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005 Marseille, France; Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 Rue Saint-Pierre, 13005 Marseille, France
| | - Christian Devaux
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Department of Biological Sciences, Centre National de la Recherche Scientifique (CNRS)-SNC5039, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-21 Boulevard Jean Moulin, 13005 Marseille, France; Aix-Marseille Université, Microbes Evolution Phylogeny and Infections (MEPHI), 27 Boulevard Jean Moulin, 13005 Marseille, France.
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103
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Wang CX, Kohli R, Olaker VR, Terebuh P, Xu R, Kaelber DC, Davis PB. Risk for diagnosis or treatment of mood or anxiety disorders in adults after SARS-CoV-2 infection, 2020-2022. Mol Psychiatry 2024; 29:1350-1360. [PMID: 38238547 PMCID: PMC11189805 DOI: 10.1038/s41380-024-02414-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/05/2023] [Revised: 12/22/2023] [Accepted: 01/04/2024] [Indexed: 06/22/2024]
Abstract
COVID-19 is associated with increased risks for mood or anxiety disorders, but it remains uncertain how the association evolves over time or which patient groups are most affected. We conducted a retrospective cohort study using a nationwide database of electronic health records to determine the risk of depressive or anxiety disorder diagnoses after SARS-CoV-2 infection by 3-month blocks from January 2020 to April 2022. The study population comprised 822,756 patients (51.8% female; mean age 42.8 years) with COVID-19 and 2,034,353 patients with other respiratory tract infections (RTIs) (53.5% female, mean age 30.6 years). First time diagnoses of depressive or anxiety disorders 14 days to 3 months after infection, as well as new or new plus recurrent prescriptions of antidepressants or anxiolytics, were compared between propensity score matched cohorts using Kaplan-Meier survival analysis, including hazard ratio (HR) and 95% confidence interval (CI). Risk of a new diagnosis or prescription was also stratified by age, sex, and race to better characterize which groups were most affected. In the first three months of the pandemic, patients infected with SARS-CoV-2 had significantly increased risk of depression or anxiety disorder diagnosis (HR 1.65 [95% CI, 1.30-2.08]). October 2021 to January 2022 (HR, 1.12 [95% CI, 1.06-1.18]) and January to April 2022 (HR, 1.08 [95% CI, 1.01-1.14]). Similar temporal patterns were observed for antidepressant and anxiolytic prescriptions, when the control group was patients with bone fracture, when anxiety and depressive disorders were considered separately, when recurrent depressive disorder was tested, and when the test period was extended to 6 months. COVID-19 patients ≥65 years old demonstrated greatest absolute risk at the start of the pandemic (6.8%), which remained consistently higher throughout the study period (HR, 1.20 [95% CI, 1.13-1.27]), and overall, women with COVID-19 had greater risk than men (HR 1.35 [95% CI 1.30-1.40]).
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Affiliation(s)
- Christina X Wang
- Center for Artificial Intelligence in Drug Discovery, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Rhea Kohli
- Center for Artificial Intelligence in Drug Discovery, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Veronica R Olaker
- Center for Artificial Intelligence in Drug Discovery, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Pauline Terebuh
- Center for Community Health Integration, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - Rong Xu
- Center for Artificial Intelligence in Drug Discovery, Case Western Reserve University School of Medicine, Cleveland, OH, USA
| | - David C Kaelber
- The Center for Clinical Informatics Research and Education and the Departments of Internal Medicine, Pediatrics, and Population and Quantitative Health Sciences, Case Western Reserve University, The MetroHealth System, Cleveland, OH, USA
| | - Pamela B Davis
- Center for Community Health Integration, Case Western Reserve University School of Medicine, Cleveland, OH, USA.
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104
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Ogger PP, Martín MG, Jang S, Zhou J, Brown J, Sukhova K, Furnon W, Patel AH, Cowton V, Palmarini M, Barclay WS, Johansson C. SARS-CoV-2 strains bearing Omicron BA.1 spike replicate in C57BL/6 mice. Front Immunol 2024; 15:1383612. [PMID: 38742107 PMCID: PMC11089223 DOI: 10.3389/fimmu.2024.1383612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 04/08/2024] [Indexed: 05/16/2024] Open
Abstract
Introduction SARS-CoV-2, the cause of the COVID pandemic, is an RNA virus with a high propensity to mutate. Successive virus variants, including variants of concern (VOC), have emerged with increased transmission or immune escape. The original pandemic virus and early variants replicated poorly, if at all, in mice at least partly due to a mismatch between the receptor binding domain on the viral spike protein and the murine angiotensin converting enzyme 2 (ACE2). Omicron VOC emerged in late 2021 harboring > 50 new mutations, 35 of them in the spike protein. This variant resulted in a very large wave of infections, even in the face of prior immunity, albeit being inherently less severe than earlier variants. Reflecting the lower severity reported in humans, Omicron displayed attenuated infection in hamsters and also in the K18-hACE2 mouse model. K18-hACE2 mice express both the human ACE2 as well as the endogenous mouse ACE2. Methods Here we infected hACE2 knock-in mice that express only human ACE2 and no murine ACE2, or C57BL/6 wildtype mice with SARS-CoV-2 D614G (first-wave isolate), Delta or Omicron BA.1 variants and assessed infectivity and downstream innate immune responses. Results While replication of SARS-CoV-2 Omicron was lower in the lungs of hACE2 knock-in mice compared with SARS-CoV-2 D614G and VOC Delta, it replicated more efficiently than the earlier variants in C57BL/6 wildtype mice. This opens the opportunity to test the effect of host genetics on SARS-CoV-2 infections in wildtype mice. As a proof of principle, we tested Omicron infection in mice lacking expression of the interferon-alpha receptor-1 (IFNAR1). In these mice we found that loss of type I IFN receptor signaling resulted in higher viral loads in the lungs were detected. Finally, using a chimeric virus of first wave SARS-CoV-2 harboring the Omicron spike protein, we show that Omicron spike increase infection of C57BL/6 wildtype mice, but non-spike genes of Omicron confer attenuation of viral replication. Discussion Since this chimeric virus efficiently infected C57BL/6 wildtype mice, and replicated in their lungs, our findings illustrate a pathway for genetic mapping of virushost interactions during SARS-CoV-2 infection.
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Affiliation(s)
- Patricia P. Ogger
- Section of Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Minerva Garcia Martín
- Section of Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Soyeon Jang
- Section of Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
| | - Jie Zhou
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Jonathan Brown
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Ksenia Sukhova
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Wilhelm Furnon
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Arvind H. Patel
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Vanessa Cowton
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Massimo Palmarini
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | - Wendy S. Barclay
- Department of Infectious Disease, Imperial College London, London, United Kingdom
| | - Cecilia Johansson
- Section of Respiratory Infections, National Heart and Lung Institute, Imperial College London, London, United Kingdom
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105
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Guo H, Ha S, Botten JW, Xu K, Zhang N, An Z, Strohl WR, Shiver JW, Fu TM. SARS-CoV-2 Omicron: Viral Evolution, Immune Evasion, and Alternative Durable Therapeutic Strategies. Viruses 2024; 16:697. [PMID: 38793580 PMCID: PMC11125895 DOI: 10.3390/v16050697] [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: 04/10/2024] [Revised: 04/22/2024] [Accepted: 04/24/2024] [Indexed: 05/26/2024] Open
Abstract
Since the SARS-CoV-2 Omicron virus has gained dominance worldwide, its continual evolution with unpredictable mutations and patterns has revoked all authorized immunotherapeutics. Rapid viral evolution has also necessitated several rounds of vaccine updates in order to provide adequate immune protection. It remains imperative to understand how Omicron evolves into different subvariants and causes immune escape as this could help reevaluate the current intervention strategies mostly implemented in the clinics as emergency measures to counter the pandemic and, importantly, develop new solutions. Here, we provide a review focusing on the major events of Omicron viral evolution, including the features of spike mutation that lead to immune evasion against monoclonal antibody (mAb) therapy and vaccination, and suggest alternative durable options such as the ACE2-based experimental therapies superior to mAbs to address this unprecedented evolution of Omicron virus. In addition, this type of unique ACE2-based virus-trapping molecules can counter all zoonotic SARS coronaviruses, either from unknown animal hosts or from established wild-life reservoirs of SARS-CoV-2, and even seasonal alpha coronavirus NL63 that depends on human ACE2 for infection.
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Affiliation(s)
- Hailong Guo
- IGM Biosciences, Mountain View, CA 94043, USA
| | - Sha Ha
- IGM Biosciences, Mountain View, CA 94043, USA
| | - Jason W. Botten
- Department of Medicine, Division of Pulmonary Disease and Critical Care Medicine, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT 05405, USA
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington, VT 05405, USA
| | - Kai Xu
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Ningyan Zhang
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
| | - Zhiqiang An
- Texas Therapeutics Institute, Brown Foundation Institute of Molecular Medicine, The University of Texas Health Science Center at Houston, Houston, TX 77030, USA
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106
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Suwanchaikasem P, Rattanapisit K, Strasser R, Phoolcharoen W. Quality control in SARS-CoV-2 RBD-Fc vaccine production using LC-MS to confirm strain selection and detect contaminations from other strains. Sci Rep 2024; 14:9629. [PMID: 38671013 PMCID: PMC11053075 DOI: 10.1038/s41598-024-59860-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
Coronavirus disease of 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is an ongoing outbreak, disrupting human life worldwide. Vaccine development was prioritized to obtain a biological substance for combating the viral pathogen and lessening disease severity. In vaccine production, biological origin and relevant materials must be carefully examined for potential contaminants in conformity with good manufacturing practice. Due to fast mutation, several SARS-CoV-2 variants and sublineages have been identified. Currently, most of COVID-19 vaccines are developed based on the protein sequence of the Wuhan wild type strain. New vaccines specific for emerging SARS-CoV-2 strains are continuously needed to tackle the incessant evolution of the virus. Therefore, in vaccine development and production, a reliable method to identify the nature of subunit vaccines is required to avoid cross-contamination. In this study, liquid chromatography-mass spectrometry using quadrupole-time of flight along with tryptic digestion was developed for distinguishing protein materials derived from different SARS-CoV-2 strains. After analyzing the recombinantly produced receptor-binding domain (RBD) of the SARS-CoV-2 spike protein, nine characteristic peptides were identified with acceptable limits of detection. They can be used together to distinguish 14 SARS-CoV-2 strains, except Kappa and Epsilon. Plant-produced RBD-Fc protein derived from Omicron strains can be easily distinguished from the others with 4-5 unique peptides. Eventually, a peptide key was developed based on the nine peptides, offering a prompt and precise flowchart to facilitate SARS-CoV-2 strain identification in COVID-19 vaccine manufacturing.
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Affiliation(s)
| | | | - Richard Strasser
- Department of Applied Genetics and Cell Biology, Institute of Plant Biotechnology and Cell Biology, University of Natural Resources and Life Sciences, 1180, Vienna, Austria
| | - Waranyoo Phoolcharoen
- Center of Excellence in Plant-Produced Pharmaceuticals, Chulalongkorn University, Bangkok, 10330, Thailand.
- Department of Pharmacognosy and Pharmaceutical Botany, Faculty of Pharmaceutical Sciences, Chulalongkorn University, Bangkok, 10330, Thailand.
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107
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Ye Q, Wang H, Xu F, Zhang S, Zhang S, Yang Z, Zhang L. Co-Mutations and Possible Variation Tendency of the Spike RBD and Membrane Protein in SARS-CoV-2 by Machine Learning. Int J Mol Sci 2024; 25:4662. [PMID: 38731879 PMCID: PMC11083383 DOI: 10.3390/ijms25094662] [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: 03/23/2024] [Revised: 04/18/2024] [Accepted: 04/23/2024] [Indexed: 05/13/2024] Open
Abstract
Since the onset of the coronavirus disease 2019 (COVID-19) pandemic, SARS-CoV-2 variants capable of breakthrough infections have attracted global attention. These variants have significant mutations in the receptor-binding domain (RBD) of the spike protein and the membrane (M) protein, which may imply an enhanced ability to evade immune responses. In this study, an examination of co-mutations within the spike RBD and their potential correlation with mutations in the M protein was conducted. The EVmutation method was utilized to analyze the distribution of the mutations to elucidate the relationship between the mutations in the spike RBD and the alterations in the M protein. Additionally, the Sequence-to-Sequence Transformer Model (S2STM) was employed to establish mapping between the amino acid sequences of the spike RBD and M proteins, offering a novel and efficient approach for streamlined sequence analysis and the exploration of their interrelationship. Certain mutations in the spike RBD, G339D-S373P-S375F and Q493R-Q498R-Y505, are associated with a heightened propensity for inducing mutations at specific sites within the M protein, especially sites 3 and 19/63. These results shed light on the concept of mutational synergy between the spike RBD and M proteins, illuminating a potential mechanism that could be driving the evolution of SARS-CoV-2.
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Affiliation(s)
- Qiushi Ye
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Q.Y.)
| | - He Wang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Q.Y.)
| | - Fanding Xu
- School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
| | - Sijia Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Q.Y.)
| | - Shengli Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Q.Y.)
| | - Zhiwei Yang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Q.Y.)
- School of Life Science and Technology, Xi’an Jiaotong University, Xi’an 710049, China
| | - Lei Zhang
- MOE Key Laboratory for Nonequilibrium Synthesis and Modulation of Condensed Matter, School of Physics, Xi’an Jiaotong University, Xi’an 710049, China; (Q.Y.)
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108
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Bukhari SNH, Elshiekh E, Abbas M. Physicochemical properties-based hybrid machine learning technique for the prediction of SARS-CoV-2 T-cell epitopes as vaccine targets. PeerJ Comput Sci 2024; 10:e1980. [PMID: 38686005 PMCID: PMC11057572 DOI: 10.7717/peerj-cs.1980] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 03/15/2024] [Indexed: 05/02/2024]
Abstract
Majority of the existing SARS-CoV-2 vaccines work by presenting the whole pathogen in the attenuated form to immune system to invoke an immune response. On the other hand, the concept of a peptide based vaccine (PBV) is based on the identification and chemical synthesis of only immunodominant peptides known as T-cell epitopes (TCEs) to induce a specific immune response against a particular pathogen. However PBVs have received less attention despite holding huge untapped potential for boosting vaccine safety and immunogenicity. To identify these TCEs for designing PBV, wet-lab experiments are difficult, expensive, and time-consuming. Machine learning (ML) techniques can accurately predict TCEs, saving time and cost for speedy vaccine development. This work proposes novel hybrid ML techniques based on the physicochemical properties of peptides to predict SARS-CoV-2 TCEs. The proposed hybrid ML technique was evaluated using various ML model evaluation metrics and demonstrated promising results. The hybrid technique of decision tree classifier with chi-squared feature weighting technique and forward search optimal feature searching algorithm has been identified as the best model with an accuracy of 98.19%. Furthermore, K-fold cross-validation (KFCV) was performed to ensure that the model is reliable and the results indicate that the hybrid random forest model performs consistently well in terms of accuracy with respect to other hybrid approaches. The predicted TCEs are highly likely to serve as promising vaccine targets, subject to evaluations both in-vivo and in-vitro. This development could potentially save countless lives globally, prevent future epidemic-scale outbreaks, and reduce the risk of mutation escape.
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Affiliation(s)
- Syed Nisar Hussain Bukhari
- National Institute of Electronics and Information Technology (NIELIT), Srinagar, Jammu and Kashmir, India
| | - E. Elshiekh
- Department of Radiological Sciences, College of Applied Medical Sciences, King Khalid University, Abha, Saudi Arabia
| | - Mohamed Abbas
- Electrical Engineering Department, College of Engineering, King Khalid University, Abha, Saudi Arabia
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109
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Visser LG. Identifying efficacious SARS-CoV-2 antivirals in a changing immune landscape. THE LANCET. INFECTIOUS DISEASES 2024:S1473-3099(24)00254-8. [PMID: 38677299 DOI: 10.1016/s1473-3099(24)00254-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 04/10/2024] [Indexed: 04/29/2024]
Affiliation(s)
- Leo G Visser
- Leiden University Center for Infectious Diseases, Leiden University Medical Center, 2333 ZA Leiden, Netherlands.
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110
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McGough L, Cobey S. A speed limit on serial strain replacement from original antigenic sin. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.04.574172. [PMID: 38260288 PMCID: PMC10802292 DOI: 10.1101/2024.01.04.574172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Many pathogens evolve to escape immunity, yet it remains difficult to predict whether immune pressure will lead to diversification, serial replacement of one variant by another, or more complex patterns. Pathogen strain dynamics are mediated by cross-protective immunity, whereby exposure to one strain partially protects against infection by antigenically diverged strains. There is growing evidence that this protection is influenced by early exposures, a phenomenon referred to as original antigenic sin (OAS) or imprinting. In this paper, we derive new constraints on the emergence of the pattern of successive strain replacements demonstrated by influenza, SARS-CoV-2, seasonal coronaviruses, and other pathogens. We find that OAS implies that the limited diversity found with successive strain replacement can only be maintained if R 0 is less than a threshold set by the characteristic antigenic distances for cross-protection and for the creation of new immune memory. This bound implies a "speed limit" on the evolution of new strains and a minimum variance of the distribution of infecting strains in antigenic space at any time. To carry out this analysis, we develop a theoretical model of pathogen evolution in antigenic space that implements OAS by decoupling the antigenic distances required for protection from infection and strain-specific memory creation. Our results demonstrate that OAS can play an integral role in the emergence of strain structure from host immune dynamics, preventing highly transmissible pathogens from maintaining serial strain replacement without diversification.
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Affiliation(s)
- Lauren McGough
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL
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111
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Padilla S, Ledesma C, García-Abellán J, García JA, Fernández-González M, de la Rica A, Galiana A, Gutiérrez F, Masiá M. Long COVID across SARS-CoV-2 variants, lineages, and sublineages. iScience 2024; 27:109536. [PMID: 38585665 PMCID: PMC10995878 DOI: 10.1016/j.isci.2024.109536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Revised: 02/09/2024] [Accepted: 03/17/2024] [Indexed: 04/09/2024] Open
Abstract
This prospective study aimed to determine the prevalence of long COVID in patients hospitalized for SARS-CoV-2 infection from March 2020 to July 2022 and assess the impact of different viral lineages. A total of 2,524 patients were followed up for 12 months, with persistent symptoms reported in 35.2% at one month, decreasing thereafter. Omicron variant patients initially showed higher symptom intensity, but this trend diminished over time. Certain viral lineages, notably Delta lineages AY.126 and AY.43, and Omicron sublineages BA.1.17, BA.2.56, and BA.5.1, consistently correlated with more severe symptoms. Overall, long COVID prevalence and severity were similar across SARS-CoV-2 variants. Specific lineages may influence post-COVID sequelae persistence and severity.
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Affiliation(s)
- Sergio Padilla
- Infectious Diseases Unit, Hospital General Universitario de Elche, Alicante, Spain
- Universidad Miguel Hernández de Elche, San Juan de Alicante, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Christian Ledesma
- Infectious Diseases Unit, Hospital General Universitario de Elche, Alicante, Spain
| | - Javier García-Abellán
- Infectious Diseases Unit, Hospital General Universitario de Elche, Alicante, Spain
- Universidad Miguel Hernández de Elche, San Juan de Alicante, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - José Alberto García
- Infectious Diseases Unit, Hospital General Universitario de Elche, Alicante, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Fernández-González
- Infectious Diseases Unit, Hospital General Universitario de Elche, Alicante, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Alba de la Rica
- Microbiology Service, Hospital General Universitario de Elche, Alicante, Spain
| | - Antonio Galiana
- Microbiology Service, Hospital General Universitario de Elche, Alicante, Spain
| | - Félix Gutiérrez
- Infectious Diseases Unit, Hospital General Universitario de Elche, Alicante, Spain
- Universidad Miguel Hernández de Elche, San Juan de Alicante, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Mar Masiá
- Infectious Diseases Unit, Hospital General Universitario de Elche, Alicante, Spain
- Universidad Miguel Hernández de Elche, San Juan de Alicante, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
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112
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Wu F, Jiang Y, Yang H, Ma L. Development of Detection Antibody Targeting the Linear Epitope in SARS-CoV-2 Nucleocapsid Protein with Ultra-High Sensitivity. Int J Mol Sci 2024; 25:4436. [PMID: 38674021 PMCID: PMC11050370 DOI: 10.3390/ijms25084436] [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: 03/12/2024] [Revised: 04/04/2024] [Accepted: 04/16/2024] [Indexed: 04/28/2024] Open
Abstract
The COVID-19 pandemic caused by SARS-CoV-2 highlighted the importance of reliable detection methods for disease control and surveillance. Optimizing detection antibodies by rational screening antigens would improve the sensitivity and specificity of antibody-based detection methods such as colloidal gold immunochromatography. In this study, we screened three peptide antigens with conserved sequences in the N protein of SARS-CoV-2 using bioinformatical and structural biological analyses. Antibodies that specifically recognize these peptides were prepared. The epitope of the peptide that had the highest binding affinity with its antibody was located on the surface of the N protein, which was favorable for antibody binding. Using the optimal antibody that can recognize this epitope, we developed colloidal gold immunochromatography, which can detect the N protein at 10 pg/mL. Importantly, this antibody could effectively recognize both the natural peptide antigen and mutated peptide antigen in the N protein, showing the feasibility of being applied in the large-scale population testing of SARS-CoV-2. Our study provides a platform with reference significance for the rational screening of detection antibodies with high sensitivity, specificity, and reliability for SARS-CoV-2 and other pathogens.
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Affiliation(s)
- Feng Wu
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (F.W.); (H.Y.)
- Shenzhen Institute of Drug Control, Shenzhen 518057, China
| | - Yike Jiang
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China;
| | - Hongtian Yang
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (F.W.); (H.Y.)
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China;
| | - Lan Ma
- Institute of Biopharmaceutical and Health Engineering, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China; (F.W.); (H.Y.)
- Institute of Biomedical Health Technology and Engineering, Shenzhen Bay Laboratory, Shenzhen 518132, China;
- State Key Laboratory of Chemical Oncogenomics, Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
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113
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Calderón LCL, Cabanne GS, Marcos A, Novo SG, Torres C, Perez AM, Pybus OG, König GA. Phylodynamic analysis of foot-and-mouth disease virus evolution in Mar Chiquita, Argentina. Arch Virol 2024; 169:101. [PMID: 38630189 DOI: 10.1007/s00705-024-06028-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 02/16/2024] [Indexed: 04/19/2024]
Abstract
Foot-and-mouth disease is a highly contagious disease affecting cloven-hoofed animals, resulting in considerable economic losses. Its causal agent is foot-and-mouth disease virus (FMDV), a picornavirus. Due to its error-prone replication and rapid evolution, the transmission and evolutionary dynamics of FMDV can be studied using genomic epidemiological approaches. To analyze FMDV evolution and identify possible transmission routes in an Argentinean region, field samples that tested positive for FMDV by PCR were obtained from 21 farms located in the Mar Chiquita district. Whole FMDV genome sequences were obtained by PCR amplification in seven fragments and sequencing using the Sanger technique. The genome sequences obtained from these samples were then analyzed using phylogenetic, phylogeographic, and evolutionary approaches. Three local transmission clusters were detected among the sampled viruses. The dataset was analyzed using Bayesian phylodynamic methods with appropriate coalescent and relaxed molecular clock models. The estimated mean viral evolutionary rate was 1.17 × 10- 2 substitutions/site/year. No significant differences in the rate of viral evolution were observed between farms with vaccinated animals and those with unvaccinated animals. The most recent common ancestor of the sampled sequences was dated to approximately one month before the first reported case in the outbreak. Virus transmission started in the south of the district and later dispersed to the west, and finally arrived in the east. Different transmission routes among the studied herds, such as non-replicating vectors and close contact contagion (i.e., aerosols), may be responsible for viral spread.
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Affiliation(s)
| | - Gustavo S Cabanne
- Museo Argentino de Ciencias Naturales "Bernardino Rivadavia"-CONICET, Buenos Aires, Argentina
| | - Andrea Marcos
- Coordinación general de Epidemiología y Análisis de Riesgo, SENASA, Buenos Aires, Argentina
| | - Sabrina Galdo Novo
- DGLYCT - Dirección de Laboratorio Animal, SENASA, Buenos Aires, Argentina
| | - Carolina Torres
- Instituto de Investigaciones en Bacteriología y Virología Molecular FFyB, UBA, Buenos Aires, Argentina
| | - Andrés M Perez
- Department of Veterinary Population Medicine, UMN, St Paul, USA
| | - Oliver G Pybus
- Department of Biology, University of Oxford, Oxford, UK
- Department of Pathobiology and Population Sciences, The Royal Veterinary College, London, United Kingdom
| | - Guido A König
- Instituto de Agrobiotecnología y Biología Molecular, INTA-CONICET, Buenos Aires, Argentina.
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114
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Reis AC, Pinto D, Monteiro S, Santos R, Martins JV, Sousa A, Páscoa R, Lourinho R, Cunha MV. Systematic SARS-CoV-2 S-gene sequencing in wastewater samples enables early lineage detection and uncovers rare mutations in Portugal. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 921:170961. [PMID: 38367735 DOI: 10.1016/j.scitotenv.2024.170961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2023] [Revised: 12/23/2023] [Accepted: 02/11/2024] [Indexed: 02/19/2024]
Abstract
As the COVID-19 pandemic reached its peak, many countries implemented genomic surveillance systems to track the evolution and transmission of SARS-CoV-2. Transition from the pandemic to the endemic phase prioritized alternative testing strategies to maintain effective epidemic surveillance at the population level, with less intensive sequencing efforts. One such promising approach was Wastewater-Based Surveillance (WBS), which offers non-invasive, cost-effective means for analysing virus trends at the sewershed level. From 2020 onwards, wastewater has been recognized as an instrumental source of information for public health, with national and international authorities exploring options to implement national wastewater surveillance systems and increasingly relying on WBS as early warning of potential pathogen outbreaks. In Portugal, several pioneer projects joined the academia, water utilities and Public Administration around WBS. To validate WBS as an effective genomic surveillance strategy, it is crucial to collect long term performance data. In this work, we present one year of systematic SARS-CoV-2 wastewater surveillance in Portugal, representing 35 % of the mainland population. We employed two complementary methods for lineage determination - allelic discrimination by RT-PCR and S-gene sequencing. This combination allowed us to monitor variant evolution in near-real-time and identify low-frequency mutations. Over the course of this year-long study, spanning from May 2022 to April 2023, we successfully tracked the dominant Omicron sub-lineages, their progression and evolution, which aligned with concurrent clinical surveillance data. Our results underscore the effectiveness of WBS as a tracking system for virus variants, with the ability to unveil mutations undetected via massive sequencing of clinical samples from Portugal, demonstrating the ability of WBS to uncover new mutations and detect rare genetic variants. Our findings emphasize that knowledge of the genetic diversity of SARS-CoV-2 at the population level can be extended far beyond via the combination of routine clinical genomic surveillance with wastewater sequencing and genotyping.
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Affiliation(s)
- Ana C Reis
- Centre for Ecology, Evolution and Environmental Changes (cE3c), CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Daniela Pinto
- Centre for Ecology, Evolution and Environmental Changes (cE3c), CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal
| | - Sílvia Monteiro
- Laboratório de Análises, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal; CERIS - Civil Engineering Research and Innovation for Sustainability, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal; DECN - Department of Nuclear Sciences and Engineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | - Ricardo Santos
- Laboratório de Análises, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal; CERIS - Civil Engineering Research and Innovation for Sustainability, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal; DECN - Department of Nuclear Sciences and Engineering, Instituto Superior Técnico, Universidade de Lisboa, Lisboa, Portugal
| | | | | | | | | | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), CHANGE - Global Change and Sustainability Institute, Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, Lisboa, Portugal.
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115
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Shi Y, Ma Y, Zheng Z, Qin Y, Du Z, Liu J. Development and validation of a predicting nomogram for in-hospital mortality of COVID-19 Omicron variant: A cohort study of 1324 cases in Beijing Anzhen Hospital. Heliyon 2024; 10:e28627. [PMID: 38590893 PMCID: PMC11000003 DOI: 10.1016/j.heliyon.2024.e28627] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2023] [Revised: 03/14/2024] [Accepted: 03/21/2024] [Indexed: 04/10/2024] Open
Abstract
Coronavirus disease 2019 (COVID-19) is continuously posing high global public health concerns due to its high morbidity and mortality. This study aimed to construct a convenient risk model for predicting in-hospital mortality of COVID-19 Omicron variant. A total of 1324 hospitalized patients with Omicron variant were enrolled from Beijing Anzhen Hospital. During hospitalization, the Omicron variant mortality rate was found to be 24.4%. Using the datasets of clinical demographics and laboratory tests, three machine learning algorithms, including best subset selection, stepwise selection, and least absolute shrinkage and selection operator regression analyses were employed to identify the potential predictors of in-hospital mortality. The results found that a panel of twenty-four clinical variables (including age, hyperlipemia, stroke, tumor, and several cardiovascular markers) identified by stepwise selection model exhibited significant performances in predicting the in-hospital mortality of COVID-19. The resultant nomogram showed good discrimination, highlighted by the areas under the curve values of 0.88 for 10 days, 0.81 for 20 days, and 0.82 for 30 days, respectively. Furthermore, decision curve analysis showed a significant reliability and precision for the established stepwise selection model. Collectively, this study developed an accurate and convenience risk model for predicting the in-hospital mortality of COVID-19 Omicron.
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Affiliation(s)
- Yuchen Shi
- Center for Coronary Artery Disease(CCAD), Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing, China
| | - Ying Ma
- The State Key Laboratory for Quality Ensurance and Sustainable Use of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, 100700, China
| | - Ze Zheng
- Center for Coronary Artery Disease(CCAD), Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing, China
| | - Yanwen Qin
- Center for Coronary Artery Disease(CCAD), Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing, China
| | - Zhiyong Du
- Center for Coronary Artery Disease(CCAD), Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing, China
| | - Jinghua Liu
- Center for Coronary Artery Disease(CCAD), Beijing Anzhen Hospital, Capital Medical University, Beijing Institute of Heart, Lung and Blood Vessel Diseases, Beijing, China
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116
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Sarkar A, Ghosh TA, Bandyopadhyay B, Maiti S, Panja AS. Prediction of Prospective Mutational Landscape of SARS-CoV-2 Spike ssRNA and Evolutionary Basis of Its Host Interaction. Mol Biotechnol 2024:10.1007/s12033-024-01146-1. [PMID: 38619800 DOI: 10.1007/s12033-024-01146-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 03/14/2024] [Indexed: 04/16/2024]
Abstract
Booster doses are crucial against severe COVID-19, as rapid virus mutations and variant emergence prolong the pandemic crisis. The virus's quick evolution, short generation-time, and adaptive changes impact virulence and evolvability, helping predictions about variant of concerns' (VOCs') landscapes. Here, in this study, we used a new computational algorithm, to predict the mutational pattern in SARS-CoV-2 ssRNA, proteomics, structural identification, mutation stability, and functional correlation, as well as immune escape mechanisms. Interestingly, the sequence diversity of SARS Coronavirus-2 has demonstrated a predominance of G- > A and C- > U substitutions. The best validation statistics are explored here in seven homologous models of the expected mutant SARS-CoV-2 spike ssRNA and employed for hACE2 and IgG interactions. The interactome profile of SARS-CoV-2 spike with hACE2 and IgG revealed a strong correlation between phylogeny and divergence time. The systematic adaptation of SARS-CoV-2 spike ssRNA influences infectivity and immune escape. Data suggest higher propensity of Adenine rich sequence promotes MHC system avoidance, preferred by A-rich codons. Phylogenetic data revealed the evolution of SARS-CoV-2 lineages' epidemiology. Our findings may unveil processes governing the genesis of immune-resistant variants, prompting a critical reassessment of the coronavirus mutation rate and exploration of hypotheses beyond mechanical aspects.
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Affiliation(s)
- Aniket Sarkar
- Post Graduate Department of Biotechnology, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Trijit Arka Ghosh
- Department of Computer Application, Burdwan Institute of Management and Computer Science, The University of Burdwan, Dewandighi, Burdwan, West Bengal, 713102, India
| | - Bidyut Bandyopadhyay
- Post Graduate Department of Biotechnology, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Smarajit Maiti
- Department of Medical Laboratory Technology, Haldia Institute of Health Sciences, ICARE Complex, Haldia, West Bengal, 721657, India
| | - Anindya Sundar Panja
- Post Graduate Department of Biotechnology, Molecular Informatics Laboratory, Oriental Institute of Science and Technology, Vidyasagar University, Midnapore, West Bengal, 721102, India.
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117
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Lina A, Keith H, Jenny H, Mariana M, Gregorio T, Laure WV, Paolo T. Facing SARS-CoV-2 emergence on the animal health perspective: The role of the World Organisation for Animal Health in preparedness and official reporting of disease occurrence. Zoonoses Public Health 2024. [PMID: 38584342 DOI: 10.1111/zph.13133] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Revised: 03/17/2024] [Accepted: 03/19/2024] [Indexed: 04/09/2024]
Abstract
AIMS Current data suggest that SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) emerged from an animal source. However, to date, there is insufficient scientific evidence to identify the source of SARS-CoV-2 or to explain the original route of transmission to humans. A wide range of mammalian species have been shown to be susceptible to the virus through experimental infection, and in natural environments when in contact with infected humans. The main objective of this work was to provide a summary of the official data shared by countries on SARS-CoV-2 in animals with the World Organisation for Animal Health (WOAH), to highlight the role of WOAH as an international organization in coordinating scientific information actions and to discuss the implications and impact of these activities. METHODS AND RESULTS Between January 2020 and December 2022, 36 countries in Europe, the Americas, Asia and Africa officially reported SARS-CoV-2 identification in 26 animal species. Affected countries were generally responsive in confirming the pathogen (median of 5 days after onset) and reporting to WOAH (median of 7 days after confirmation). CONCLUSIONS During the pandemic, WOAH, supported by its network of experts, played a crucial role in collecting, analysing and disseminating veterinary scientific information, acting as the reference organization on these issues, thus avoiding misinformation and disinformation. Future perspectives to avoid new emerging threats are discussed.
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Affiliation(s)
- Awada Lina
- World Organisation for Animal Health (WOAH), Paris, France
| | - Hamilton Keith
- World Organisation for Animal Health (WOAH), Paris, France
| | | | | | | | | | - Tizzani Paolo
- World Organisation for Animal Health (WOAH), Paris, France
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118
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Bykonia EN, Kleymenov DA, Gushchin VA, Siniavin AE, Mazunina EP, Kozlova SR, Zolotar AN, Usachev EV, Kuznetsova NA, Shidlovskaya EV, Pochtovyi AA, Kustova DD, Ivanov IA, Dmitriev SE, Ivanov RA, Logunov DY, Gintsburg AL. Major Role of S-Glycoprotein in Providing Immunogenicity and Protective Immunity in mRNA Lipid Nanoparticle Vaccines Based on SARS-CoV-2 Structural Proteins. Vaccines (Basel) 2024; 12:379. [PMID: 38675761 PMCID: PMC11053793 DOI: 10.3390/vaccines12040379] [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: 02/07/2024] [Revised: 03/21/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
SARS-CoV-2 variants have evolved over time in recent years, demonstrating immune evasion of vaccine-induced neutralizing antibodies directed against the original S protein. Updated S-targeted vaccines provide a high level of protection against circulating variants of SARS-CoV-2, but this protection declines over time due to ongoing virus evolution. To achieve a broader protection, novel vaccine candidates involving additional antigens with low mutation rates are currently needed. Based on our recently studied mRNA lipid nanoparticle (mRNA-LNP) platform, we have generated mRNA-LNP encoding SARS-CoV-2 structural proteins M, N, S from different virus variants and studied their immunogenicity separately or in combination in vivo. As a result, all mRNA-LNP vaccine compositions encoding the S and N proteins induced excellent titers of RBD- and N-specific binding antibodies. The T cell responses were mainly specific CD4+ T cell lymphocytes producing IL-2 and TNF-alpha. mRNA-LNP encoding the M protein did not show a high immunogenicity. High neutralizing activity was detected in the sera of mice vaccinated with mRNA-LNP encoding S protein (alone or in combinations) against closely related strains, but was undetectable or significantly lower against an evolutionarily distant variant. Our data showed that the addition of mRNAs encoding S and M antigens to mRNA-N in the vaccine composition enhanced the immunogenicity of mRNA-N and induced a more robust immune response to the N protein. Based on our results, we suggested that the S protein plays a key role in enhancing the immune response to the N protein when they are both encoded in the mRNA-LNP vaccine.
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Affiliation(s)
- Evgeniia N. Bykonia
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
| | - Denis A. Kleymenov
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
| | - Vladimir A. Gushchin
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
- Department of Virology, Lomonosov Moscow State University, Moscow 119234, Russia
- Department of Medical Genetics, Federal State Autonomous Educational Institution of Higher Education I M Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow 119991, Russia
| | - Andrei E. Siniavin
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Elena P. Mazunina
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
| | - Sofia R. Kozlova
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
| | - Anastasia N. Zolotar
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
| | - Evgeny V. Usachev
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
| | - Nadezhda A. Kuznetsova
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
| | - Elena V. Shidlovskaya
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
| | - Andrei A. Pochtovyi
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
- Department of Virology, Lomonosov Moscow State University, Moscow 119234, Russia
- Department of Medical Genetics, Federal State Autonomous Educational Institution of Higher Education I M Sechenov First Moscow State Medical University of the Ministry of Health of the Russian Federation (Sechenov University), Moscow 119991, Russia
| | - Daria D. Kustova
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
- Department of Virology, Lomonosov Moscow State University, Moscow 119234, Russia
| | - Igor A. Ivanov
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
- Shemyakin-Ovchinnikov Institute of Bioorganic Chemistry of the Russian Academy of Sciences, Moscow 117997, Russia
| | - Sergey E. Dmitriev
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
- Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119234, Russia
- Faculty of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119991, Russia
| | - Roman A. Ivanov
- Translational Medicine Research Center, Sirius University of Science and Technology, Sochi 354340, Russia;
| | - Denis Y. Logunov
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
| | - Alexander L. Gintsburg
- Federal State Budget Institution “National Research Centre for Epidemiology and Microbiology Named after Honorary Academician N. F. Gamaleya” of the Ministry of Health of the Russian Federation, Moscow 123098, Russia; (D.A.K.); (A.E.S.); (E.P.M.); (S.R.K.); (A.N.Z.); (E.V.U.); (N.A.K.); (E.V.S.); (A.A.P.); (D.D.K.); (I.A.I.); (S.E.D.); (D.Y.L.); (A.L.G.)
- Infectiology Department, I. M. Sechenov First Moscow State Medical University, Moscow 119991, Russia
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Surie D, Yuengling KA, DeCuir J, Zhu Y, Lauring AS, Gaglani M, Ghamande S, Peltan ID, Brown SM, Ginde AA, Martinez A, Mohr NM, Gibbs KW, Hager DN, Ali H, Prekker ME, Gong MN, Mohamed A, Johnson NJ, Srinivasan V, Steingrub JS, Leis AM, Khan A, Hough CL, Bender WS, Duggal A, Bendall EE, Wilson JG, Qadir N, Chang SY, Mallow C, Kwon JH, Exline MC, Shapiro NI, Columbus C, Vaughn IA, Ramesh M, Mosier JM, Safdar B, Casey JD, Talbot HK, Rice TW, Halasa N, Chappell JD, Grijalva CG, Baughman A, Womack KN, Swan SA, Johnson CA, Lwin CT, Lewis NM, Ellington S, McMorrow ML, Martin ET, Self WH. Severity of Respiratory Syncytial Virus vs COVID-19 and Influenza Among Hospitalized US Adults. JAMA Netw Open 2024; 7:e244954. [PMID: 38573635 PMCID: PMC11192181 DOI: 10.1001/jamanetworkopen.2024.4954] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 02/06/2024] [Indexed: 04/05/2024] Open
Abstract
Importance On June 21, 2023, the Centers for Disease Control and Prevention recommended the first respiratory syncytial virus (RSV) vaccines for adults aged 60 years and older using shared clinical decision-making. Understanding the severity of RSV disease in adults can help guide this clinical decision-making. Objective To describe disease severity among adults hospitalized with RSV and compare it with the severity of COVID-19 and influenza disease by vaccination status. Design, Setting, and Participants In this cohort study, adults aged 18 years and older admitted to the hospital with acute respiratory illness and laboratory-confirmed RSV, SARS-CoV-2, or influenza infection were prospectively enrolled from 25 hospitals in 20 US states from February 1, 2022, to May 31, 2023. Clinical data during each patient's hospitalization were collected using standardized forms. Data were analyzed from August to October 2023. Exposures RSV, SARS-CoV-2, or influenza infection. Main Outcomes and Measures Using multivariable logistic regression, severity of RSV disease was compared with COVID-19 and influenza severity, by COVID-19 and influenza vaccination status, for a range of clinical outcomes, including the composite of invasive mechanical ventilation (IMV) and in-hospital death. Results Of 7998 adults (median [IQR] age, 67 [54-78] years; 4047 [50.6%] female) included, 484 (6.1%) were hospitalized with RSV, 6422 (80.3%) were hospitalized with COVID-19, and 1092 (13.7%) were hospitalized with influenza. Among patients with RSV, 58 (12.0%) experienced IMV or death, compared with 201 of 1422 unvaccinated patients with COVID-19 (14.1%) and 458 of 5000 vaccinated patients with COVID-19 (9.2%), as well as 72 of 699 unvaccinated patients with influenza (10.3%) and 20 of 393 vaccinated patients with influenza (5.1%). In adjusted analyses, the odds of IMV or in-hospital death were not significantly different among patients hospitalized with RSV and unvaccinated patients hospitalized with COVID-19 (adjusted odds ratio [aOR], 0.82; 95% CI, 0.59-1.13; P = .22) or influenza (aOR, 1.20; 95% CI, 0.82-1.76; P = .35); however, the odds of IMV or death were significantly higher among patients hospitalized with RSV compared with vaccinated patients hospitalized with COVID-19 (aOR, 1.38; 95% CI, 1.02-1.86; P = .03) or influenza disease (aOR, 2.81; 95% CI, 1.62-4.86; P < .001). Conclusions and Relevance Among adults hospitalized in this US cohort during the 16 months before the first RSV vaccine recommendations, RSV disease was less common but similar in severity compared with COVID-19 or influenza disease among unvaccinated patients and more severe than COVID-19 or influenza disease among vaccinated patients for the most serious outcomes of IMV or death.
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Affiliation(s)
- Diya Surie
- Coronavirus and Other Respiratory Viruses Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Katharine A. Yuengling
- Coronavirus and Other Respiratory Viruses Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Jennifer DeCuir
- Coronavirus and Other Respiratory Viruses Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Yuwei Zhu
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Adam S. Lauring
- Department of Internal Medicine, University of Michigan, Ann Arbor
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor
| | - Manjusha Gaglani
- Baylor Scott & White Health, Temple, Texas
- Texas A&M University College of Medicine, Temple
- Baylor College of Medicine, Temple, Texas
| | - Shekhar Ghamande
- Baylor Scott & White Health, Temple, Texas
- Texas A&M University College of Medicine, Temple
- Baylor College of Medicine, Temple, Texas
| | - Ithan D. Peltan
- Department of Medicine, Intermountain Medical Center, Murray, Utah and University of Utah, Salt Lake City
| | - Samuel M. Brown
- Department of Medicine, Intermountain Medical Center, Murray, Utah and University of Utah, Salt Lake City
| | - Adit A. Ginde
- Department of Emergency Medicine, University of Colorado School of Medicine, Aurora
| | - Amanda Martinez
- Department of Emergency Medicine, University of Colorado School of Medicine, Aurora
| | | | - Kevin W. Gibbs
- Department of Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - David N. Hager
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Harith Ali
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland
| | - Matthew E. Prekker
- Department of Emergency Medicine, Hennepin County Medical Center, Minneapolis, Minnesota
| | - Michelle N. Gong
- Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York
| | - Amira Mohamed
- Department of Medicine, Montefiore Medical Center, Albert Einstein College of Medicine, Bronx, New York
| | - Nicholas J. Johnson
- Department of Emergency Medicine, Division of Pulmonary, Critical Care and Sleep Medicine, University of Washington, Seattle
| | | | - Jay S. Steingrub
- Department of Medicine, Baystate Medical Center, Springfield, Massachusetts
| | - Aleda M. Leis
- School of Public Health, University of Michigan, Ann Arbor
| | - Akram Khan
- Department of Medicine, Oregon Health and Sciences University, Portland
| | | | | | - Abhijit Duggal
- Department of Medicine, Cleveland Clinic, Cleveland, Ohio
| | - Emily E. Bendall
- Department of Microbiology and Immunology, University of Michigan, Ann Arbor
| | - Jennifer G. Wilson
- Department of Emergency Medicine, Stanford University School of Medicine, Stanford, California
| | - Nida Qadir
- Department of Medicine, University of California, Los Angeles
| | - Steven Y. Chang
- Department of Medicine, University of California, Los Angeles
| | | | - Jennie H. Kwon
- Department of Medicine, Washington University in St Louis, St Louis, Missouri
| | | | - Nathan I. Shapiro
- Department of Emergency Medicine, Beth Israel Deaconess Medical Center, Boston, Massachusetts
| | - Cristie Columbus
- Baylor Scott &White Health, Dallas, Texas
- Texas A&M University College of Medicine, Dallas
| | - Ivana A. Vaughn
- Department of Public Health Sciences, Henry Ford Health, Detroit, Michigan
| | - Mayur Ramesh
- Division of Infectious Diseases, Henry Ford Health, Detroit, Michigan
| | | | - Basmah Safdar
- Yale University School of Medicine, New Haven, Connecticut
| | - Jonathan D. Casey
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - H. Keipp Talbot
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Todd W. Rice
- Department of Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Natasha Halasa
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - James D. Chappell
- Department of Pediatrics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Carlos G. Grijalva
- Department of Health Policy, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Adrienne Baughman
- Department of Emergency Medicine, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Kelsey N. Womack
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Sydney A. Swan
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Cassandra A. Johnson
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Cara T. Lwin
- Department of Biostatistics, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Nathaniel M. Lewis
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Sascha Ellington
- Influenza Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | - Meredith L. McMorrow
- Coronavirus and Other Respiratory Viruses Division, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia
| | | | - Wesley H. Self
- Vanderbilt Institute for Clinical and Translational Research, Vanderbilt University Medical Center, Nashville, Tennessee
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Satapathy P, Kumar P, Gupta JK, Rabaan AA, Al Kaabi NA, Mohanty D, Naveen P, Khatib MN, Gaidhane S, Zahiruddin QS, Neyazi A. The emergence and implications of SARS-CoV-2 omicron subvariant BA.2.86 on global health. Int J Surg 2024; 110:2498-2501. [PMID: 38215252 PMCID: PMC11020040 DOI: 10.1097/js9.0000000000001070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 12/24/2023] [Indexed: 01/14/2024]
Abstract
The SARS-CoV-2 subvariant BA.2.86 'Pirola', first identified in Denmark in August 2023, has manifested with a significantly mutated spike protein profile, suggesting a heightened ability to evade vaccine-induced and infection-induced antibodies. This article outlines the epidemiological spread, immune response implications, and global responses to BA.2.86. Preliminary observations indicate community transmissions of the subvariant, even among those previously infected or vaccinated. Notably, the BA.2.86 infection has shown a potential to amplify antibody responses. The variant's emergence has evoked memories of the Omicron variant's rise in late 2021, though global immunity levels might modulate the impact of BA.2.86 impact differently. Continuous genomic surveillance, coupled with integrated diagnostic and epidemiological strategies, proves crucial in early detection and management. The emergence of BA.2.86 reaffirms the unpredictable nature of the COVID-19 pandemic, emphasizing the need for ongoing research, adaptability, and global collaboration.
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Affiliation(s)
- Prakasini Satapathy
- Center for Global Health Research, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences, Saveetha University, Chennai, Tamil Nadu
- School of Pharmacy, Graphic Era Hill University
- School of Applied and Life Sciences, Uttaranchal University, Dehradun, Uttarakhand
| | - Pawan Kumar
- Global Center for Evidence Synthesis, Chandigarh
- EvidenceSynthesis Lab, Kolkata, West Bengal
| | - Jeetendra K. Gupta
- Institute of Pharmaceutical Research, GLA University, Mathura, Uttar Pradesh
| | - Ali A. Rabaan
- Molecular Diagnostic Laboratory, Johns Hopkins Aramco Healthcare, Dhahran
- College of Medicine, Alfaisal University, Riyadh
- Department of Public Health and Nutrition, The University of Haripur, Haripur, Pakistan
| | - Nawal A. Al Kaabi
- College of Medicine and Health Science, Khalifa University
- Sheikh Khalifa Medical City, Abu Dhabi Health Services Company (SEHA), Abu Dhabi, United Arab Emirates
| | | | | | | | - Shilpa Gaidhane
- One Health Centre (COHERD), Jawaharlal Nehru Medical College, Datta Meghe Institute of Higher Education, Wardha, Maharashtra, India
| | | | - Ahmad Neyazi
- Afghanistan Center for Epidemiological Studies
- Academic Affairs, Herat Regional Hospital, Herat, Afghanistan
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Qiu Y, Mo C, Chen L, Ye W, Chen G, Zhu T. Alterations in microbiota of patients with COVID-19: implications for therapeutic interventions. MedComm (Beijing) 2024; 5:e513. [PMID: 38495122 PMCID: PMC10943180 DOI: 10.1002/mco2.513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 02/20/2024] [Accepted: 02/21/2024] [Indexed: 03/19/2024] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) recently caused a global pandemic, resulting in more than 702 million people being infected and over 6.9 million deaths. Patients with coronavirus disease (COVID-19) may suffer from diarrhea, sleep disorders, depression, and even cognitive impairment, which is associated with long COVID during recovery. However, there remains no consensus on effective treatment methods. Studies have found that patients with COVID-19 have alterations in microbiota and their metabolites, particularly in the gut, which may be involved in the regulation of immune responses. Consumption of probiotics may alleviate the discomfort caused by inflammation and oxidative stress. However, the pathophysiological process underlying the alleviation of COVID-19-related symptoms and complications by targeting the microbiota remains unclear. In the current study, we summarize the latest research and evidence on the COVID-19 pandemic, together with symptoms of SARS-CoV-2 and vaccine use, with a focus on the relationship between microbiota alterations and COVID-19-related symptoms and vaccine use. This work provides evidence that probiotic-based interventions may improve COVID-19 symptoms by regulating gut microbiota and systemic immunity. Probiotics may also be used as adjuvants to improve vaccine efficacy.
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Affiliation(s)
- Yong Qiu
- Department of AnesthesiologyNational Clinical Research Center for Geriatrics and The Research Units of West China (2018RU012)West China HospitalSichuan UniversityChengduChina
- Laboratory of Anesthesia and Critical Care MedicineNational‐Local Joint Engineering Research Center of Translational Medicine of AnesthesiologyWest China HospitalSichuan UniversityChengduChina
| | - Chunheng Mo
- Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOEState Key Laboratory of BiotherapyWest China Second University HospitalSichuan UniversityChengduChina
| | - Lu Chen
- Department of AnesthesiologyNational Clinical Research Center for Geriatrics and The Research Units of West China (2018RU012)West China HospitalSichuan UniversityChengduChina
- Laboratory of Anesthesia and Critical Care MedicineNational‐Local Joint Engineering Research Center of Translational Medicine of AnesthesiologyWest China HospitalSichuan UniversityChengduChina
| | - Wanlin Ye
- Department of AnesthesiologyNational Clinical Research Center for Geriatrics and The Research Units of West China (2018RU012)West China HospitalSichuan UniversityChengduChina
- Laboratory of Anesthesia and Critical Care MedicineNational‐Local Joint Engineering Research Center of Translational Medicine of AnesthesiologyWest China HospitalSichuan UniversityChengduChina
| | - Guo Chen
- Department of AnesthesiologyNational Clinical Research Center for Geriatrics and The Research Units of West China (2018RU012)West China HospitalSichuan UniversityChengduChina
- Laboratory of Anesthesia and Critical Care MedicineNational‐Local Joint Engineering Research Center of Translational Medicine of AnesthesiologyWest China HospitalSichuan UniversityChengduChina
| | - Tao Zhu
- Department of AnesthesiologyNational Clinical Research Center for Geriatrics and The Research Units of West China (2018RU012)West China HospitalSichuan UniversityChengduChina
- Laboratory of Anesthesia and Critical Care MedicineNational‐Local Joint Engineering Research Center of Translational Medicine of AnesthesiologyWest China HospitalSichuan UniversityChengduChina
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Ameratunga R, Woon ST, Leung E, Lea E, Chan L, Mehrtens J, Longhurst HJ, Steele R, Lehnert K, Lindsay K. The autoimmune rheumatological presentation of Common Variable Immunodeficiency Disorders with an overview of genetic testing. Semin Arthritis Rheum 2024; 65:152387. [PMID: 38330740 DOI: 10.1016/j.semarthrit.2024.152387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Revised: 01/06/2024] [Accepted: 01/16/2024] [Indexed: 02/10/2024]
Abstract
Primary immunodeficiency Disorders (PIDS) are rare, mostly monogenetic conditions which can present to a number of specialties. Although infections predominate in most PIDs, some individuals can manifest autoimmune or inflammatory sequelae as their initial clinical presentation. Identifying patients with PIDs can be challenging, as some can present later in life. This is often seen in patients with Common Variable Immunodeficiency Disorders (CVID), where symptoms can begin in the sixth or even seventh decades of life. Some patients with PIDs including CVID can initially present to rheumatologists with autoimmune musculoskeletal manifestations. It is imperative for these patients to be identified promptly as immunosuppression could lead to life-threatening opportunistic infections in these immunocompromised individuals. These risks could be mitigated by prior treatment with subcutaneous or intravenous (SCIG/IVIG) immunoglobulin replacement or prophylactic antibiotics. Importantly, many of these disorders have an underlying genetic defect. Individualized treatments may be available for the specific mutation, which may obviate or mitigate the need for hazardous broad-spectrum immunosuppression. Identification of the genetic defect has profound implications not only for the patient but also for affected family members, who may be at risk of symptomatic disease following an environmental trigger such as a viral infection. Finally, there may be clinical clues to the underlying PID, such as recurrent infections, the early presentation of severe or multiple autoimmune disorders, as well as a relevant family history. Early referral to a clinical immunologist will facilitate appropriate diagnostic evaluation and institution of treatment such as SCIG/IVIG immunoglobulin replacement. This review comprises three sections; an overview of PIDs, focusing on CVID, secondly genetic testing of PIDs and finally the clinical presentation of these disorders to rheumatologists.
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Affiliation(s)
- Rohan Ameratunga
- Department of Clinical immunology, Auckland Hospital, Park Rd, Grafton 1010, Auckland, New Zealand; Department of Virology and Immunology, Auckland Hospital, Park Rd, Grafton 1010, Auckland, New Zealand; Department of Molecular Medicine and Pathology, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland, New Zealand.
| | - See-Tarn Woon
- Department of Virology and Immunology, Auckland Hospital, Park Rd, Grafton 1010, Auckland, New Zealand; Department of Molecular Medicine and Pathology, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland, New Zealand
| | - Euphemia Leung
- Maurice Wilkins Centre, School of Biological Sciences, University of Auckland, Symonds St, Auckland, New Zealand; Auckland Cancer Society Research Centre, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland, Auckland, New Zealand
| | - Edward Lea
- Department of Clinical immunology, Auckland Hospital, Park Rd, Grafton 1010, Auckland, New Zealand
| | - Lydia Chan
- Department of Clinical immunology, Auckland Hospital, Park Rd, Grafton 1010, Auckland, New Zealand
| | - James Mehrtens
- Department of Clinical immunology, Auckland Hospital, Park Rd, Grafton 1010, Auckland, New Zealand
| | - Hilary J Longhurst
- Department of Clinical immunology, Auckland Hospital, Park Rd, Grafton 1010, Auckland, New Zealand; Department of Virology and Immunology, Auckland Hospital, Park Rd, Grafton 1010, Auckland, New Zealand; Department of Medicine, School of Medicine, Faculty of Medical and Health Sciences, University of Auckland, New Zealand
| | - Richard Steele
- Department of Clinical immunology, Auckland Hospital, Park Rd, Grafton 1010, Auckland, New Zealand; Department of Respiratory Medicine, Wellington Hospital, Wellington, New Zealand
| | - Klaus Lehnert
- Maurice Wilkins Centre, School of Biological Sciences, University of Auckland, Symonds St, Auckland, New Zealand; Applied Translational Genetics, School of Biological Sciences, University of Auckland, Auckland, New Zealand
| | - Karen Lindsay
- Department of Clinical immunology, Auckland Hospital, Park Rd, Grafton 1010, Auckland, New Zealand
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Lee K, Na Y, Kim M, Lee D, Choi J, Kim G, Kim M. Ursodeoxycholic acid may protect from severe acute respiratory syndrome coronavirus 2 Omicron variant by reducing angiotensin-converting enzyme 2. Pharmacol Res Perspect 2024; 12:e1194. [PMID: 38573021 PMCID: PMC10993777 DOI: 10.1002/prp2.1194] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/22/2024] [Accepted: 03/09/2024] [Indexed: 04/05/2024] Open
Abstract
The SARS-CoV-2 caused COVID-19 pandemic has posed a global health hazard. While some vaccines have been developed, protection against viral infection is not perfect because of the urgent approval process and the emergence of mutant SARS-CoV-2 variants. Here, we employed UDCA as an FXR antagonist to regulate ACE2 expression, which is one of the key pathways activated by SARS-CoV-2 Delta variant infection. UDCA is a well-known reagent of liver health supplements and the only clinically approved bile acid. In this paper, we investigated the protective efficacy of UDCA on Omicron variation, since it has previously been verified for protection against Delta variant. When co-housing with an Omicron variant-infected hamster group resulted in spontaneous airborne transmission, the UDCA pre-supplied group was protected from weight loss relative to the non-treated group at 4 days post-infection by more than 5%-10%. Furthermore, UDCA-treated groups had a 3-fold decrease in ACE2 expression in nasal cavities, as well as reduced viral expressing genes in the respiratory tract. Here, the data show that the UDCA serves an alternative option for preventive drug, providing SARS-CoV-2 protection against not only Delta but also Omicron variant. Our results of this study will help to propose drug-repositioning of UDCA from liver health supplement to preventive drug of SARS-CoV-2 infection.
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Affiliation(s)
- Kyungmin Lee
- Pharmaceutical Technology CenterDaewoong Pharmaceutical Co., LtdYongin‐siGyeonggi‐doRepublic of Korea
- College of Pharmacy, Pusan National UniversityBusanRepublic of Korea
| | - Yujeong Na
- Pharmaceutical Technology CenterDaewoong Pharmaceutical Co., LtdYongin‐siGyeonggi‐doRepublic of Korea
| | - Minjin Kim
- Drug Discovery CenterDaewoong Pharmaceutical Co., LtdYongin‐siGyeonggi‐doRepublic of Korea
| | - Dongjin Lee
- Pharmaceutical Technology CenterDaewoong Pharmaceutical Co., LtdYongin‐siGyeonggi‐doRepublic of Korea
| | - Jongseo Choi
- Pharmaceutical Technology CenterDaewoong Pharmaceutical Co., LtdYongin‐siGyeonggi‐doRepublic of Korea
| | - Gwanyoung Kim
- Pharmaceutical Technology CenterDaewoong Pharmaceutical Co., LtdYongin‐siGyeonggi‐doRepublic of Korea
| | - Min‐Soo Kim
- College of Pharmacy, Pusan National UniversityBusanRepublic of Korea
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Majumdar R, Taye B, Bjornberg C, Giljork M, Lynch D, Farah F, Abdullah I, Osiecki K, Yousaf I, Luckstein A, Turri W, Sampathkumar P, Moyer AM, Kipp BR, Cattaneo R, Sussman CR, Navaratnarajah CK. From pandemic to endemic: Divergence of COVID-19 positive-tests and hospitalization numbers from SARS-CoV-2 RNA levels in wastewater of Rochester, Minnesota. Heliyon 2024; 10:e27974. [PMID: 38515669 PMCID: PMC10955309 DOI: 10.1016/j.heliyon.2024.e27974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 03/06/2024] [Accepted: 03/08/2024] [Indexed: 03/23/2024] Open
Abstract
Traditionally, public health surveillance relied on individual-level data but recently wastewater-based epidemiology (WBE) for the detection of infectious diseases including COVID-19 became a valuable tool in the public health arsenal. Here, we use WBE to follow the course of the COVID-19 pandemic in Rochester, Minnesota (population 121,395 at the 2020 census), from February 2021 to December 2022. We monitored the impact of SARS-CoV-2 infections on public health by comparing three sets of data: quantitative measurements of viral RNA in wastewater as an unbiased reporter of virus level in the community, positive results of viral RNA or antigen tests from nasal swabs reflecting community reporting, and hospitalization data. From February 2021 to August 2022 viral RNA levels in wastewater were closely correlated with the oscillating course of COVID-19 case and hospitalization numbers. However, from September 2022 cases remained low and hospitalization numbers dropped, whereas viral RNA levels in wastewater continued to oscillate. The low reported cases may reflect virulence reduction combined with abated inclination to report, and the divergence of virus levels in wastewater from reported cases may reflect COVID-19 shifting from pandemic to endemic. WBE, which also detects asymptomatic infections, can provide an early warning of impending cases, and offers crucial insights during pandemic waves and in the transition to the endemic phase.
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Affiliation(s)
| | - Biruhalem Taye
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | | | | | | | | | | | - Iris Yousaf
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | | | | | - Priya Sampathkumar
- Division of Infectious Diseases, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
| | - Ann M. Moyer
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Benjamin R. Kipp
- Advanced Diagnostics Laboratory, Mayo Clinic, Rochester, MN, USA
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN, USA
| | - Roberto Cattaneo
- Department of Molecular Medicine, Mayo Clinic, Rochester, MN, USA
| | - Caroline R. Sussman
- Division of Nephrology and Hypertension, Department of Internal Medicine, Mayo Clinic, Rochester, MN, USA
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125
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Ahmad Wadi AFA, Onomura D, Funamori H, Khatun MM, Okada S, Iizasa H, Yoshiyama H. Effects of Strain Differences, Humidity Changes, and Saliva Contamination on the Inactivation of SARS-CoV-2 by Ion Irradiation. Viruses 2024; 16:520. [PMID: 38675863 PMCID: PMC11055001 DOI: 10.3390/v16040520] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 03/22/2024] [Accepted: 03/26/2024] [Indexed: 04/28/2024] Open
Abstract
One of the methods to inactivate viruses is to denature viral proteins using released ions. However, there have been no reports detailing the effects of changes in humidity or contamination with body fluids on the inactivation of viruses. This study investigated the effects of humidity changes and saliva contamination on the efficacy of SARS-CoV-2 inactivation with ions using multiple viral strains. Virus solutions with different infectious titers were dropped onto a circular nitrocellulose membrane and irradiated with ions from 10 cm above the membrane. After the irradiation of ions for 60, 90, and 120 min, changes in viral infectious titers were measured. The effect of ions on virus inactivation under different humidity conditions was also examined using virus solutions containing 90% mixtures of saliva collected from 10 people. A decrease in viral infectivity was observed over time for all strains, but ion irradiation further accelerated the decrease in viral infectivity. Ion irradiation can inactivate all viral strains, but at 80% humidity, the effect did not appear until 90 min after irradiation. The presence of saliva protected the virus from drying and maintained infectiousness for a longer period compared with no saliva. In particular, the Omicron strain retained its infectivity titer longer than the other strains. Ion irradiation demonstrated a consistent reduction in the number of infectious viruses when compared to the control across varying levels of humidity and irradiation periods. This underscores the notable effectiveness of irradiation, even when the reduction effect is as modest as 50%, thereby emphasizing its crucial role in mitigating the rapid dissemination of SARS-CoV-2.
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Affiliation(s)
- Afifah Fatimah Azzahra Ahmad Wadi
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo 693-8504, Shimane, Japan; (A.F.A.A.W.); (M.M.K.); (S.O.); (H.I.)
- Faculty of Medicine, University of Muslim Indonesia, Makassar 9023, South Sulawesi, Indonesia
| | - Daichi Onomura
- Division of Virology, Department of Infection and Immunity, Faculty of Medicine, Jichi Medical University, Shimotsuke 329-0498, Tochigi, Japan;
| | | | - Mst Mahmuda Khatun
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo 693-8504, Shimane, Japan; (A.F.A.A.W.); (M.M.K.); (S.O.); (H.I.)
| | - Shunpei Okada
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo 693-8504, Shimane, Japan; (A.F.A.A.W.); (M.M.K.); (S.O.); (H.I.)
| | - Hisashi Iizasa
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo 693-8504, Shimane, Japan; (A.F.A.A.W.); (M.M.K.); (S.O.); (H.I.)
| | - Hironori Yoshiyama
- Department of Microbiology, Faculty of Medicine, Shimane University, 89-1 Enya, Izumo 693-8504, Shimane, Japan; (A.F.A.A.W.); (M.M.K.); (S.O.); (H.I.)
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126
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Kibria MK, Ali MA, Yaseen M, Khan IA, Bhat MA, Islam MA, Mahumud RA, Mollah MNH. Discovery of Bacterial Key Genes from 16S rRNA-Seq Profiles That Are Associated with the Complications of SARS-CoV-2 Infections and Provide Therapeutic Indications. Pharmaceuticals (Basel) 2024; 17:432. [PMID: 38675393 PMCID: PMC11053588 DOI: 10.3390/ph17040432] [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: 02/26/2024] [Revised: 03/18/2024] [Accepted: 03/21/2024] [Indexed: 04/28/2024] Open
Abstract
SARS-CoV-2 infections, commonly referred to as COVID-19, remain a critical risk to both human life and global economies. Particularly, COVID-19 patients with weak immunity may suffer from different complications due to the bacterial co-infections/super-infections/secondary infections. Therefore, different variants of alternative antibacterial therapeutic agents are required to inhibit those infection-causing drug-resistant pathogenic bacteria. This study attempted to explore these bacterial pathogens and their inhibitors by using integrated statistical and bioinformatics approaches. By analyzing bacterial 16S rRNA sequence profiles, at first, we detected five bacterial genera and taxa (Bacteroides, Parabacteroides, Prevotella Clostridium, Atopobium, and Peptostreptococcus) based on differentially abundant bacteria between SARS-CoV-2 infection and control samples that are significantly enriched in 23 metabolic pathways. A total of 183 bacterial genes were found in the enriched pathways. Then, the top-ranked 10 bacterial genes (accB, ftsB, glyQ, hldD, lpxC, lptD, mlaA, ppsA, ppc, and tamB) were selected as the pathogenic bacterial key genes (bKGs) by their protein-protein interaction (PPI) network analysis. Then, we detected bKG-guided top-ranked eight drug molecules (Bemcentinib, Ledipasvir, Velpatasvir, Tirilazad, Acetyldigitoxin, Entreatinib, Digitoxin, and Elbasvir) by molecular docking. Finally, the binding stability of the top-ranked three drug molecules (Bemcentinib, Ledipasvir, and Velpatasvir) against three receptors (hldD, mlaA, and lptD) was investigated by computing their binding free energies with molecular dynamic (MD) simulation-based MM-PBSA techniques, respectively, and was found to be stable. Therefore, the findings of this study could be useful resources for developing a proper treatment plan against bacterial co-/super-/secondary-infection in SARS-CoV-2 infections.
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Affiliation(s)
- Md. Kaderi Kibria
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
- Department of Statistics, Hajee Mohammad Danesh Science and Technology University, Dinajpur 5200, Bangladesh
| | - Md. Ahad Ali
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
- Department of Chemistry, University of Rajshahi, Rajshahi 6205, Bangladesh
| | - Muhammad Yaseen
- Institute of Chemical Sciences, University of Swat, Main Campus, Charbagh 19130, Pakistan;
| | - Imran Ahmad Khan
- Department of Chemistry, Government College University, Faisalabad 38000, Pakistan;
| | - Mashooq Ahmad Bhat
- Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11421, Saudi Arabia;
| | - Md. Ariful Islam
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
| | - Rashidul Alam Mahumud
- NHMRC Clinical Trials Centre, Faculty of Medicine and Health, The University of Sydney, Camperdown, NSW 2006, Australia;
| | - Md. Nurul Haque Mollah
- Bioinformatics Laboratory, Department of Statistics, University of Rajshahi, Rajshahi 6205, Bangladesh; (M.K.K.); (M.A.A.); (M.A.I.)
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127
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Rizzi M, Avellis V, Messina A, Germano C, Tavella E, Dodaro V, Vitale R, Revelli A, Zola P, Picone S, Paolillo PM, Mondì V, Masturzo B, Manzoni P, Sainaghi PP. Vitamin D Supplementation in Neonatal and Infant MIS-C Following COVID-19 Infection. Int J Mol Sci 2024; 25:3712. [PMID: 38612523 PMCID: PMC11011671 DOI: 10.3390/ijms25073712] [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: 12/13/2023] [Revised: 03/20/2024] [Accepted: 03/22/2024] [Indexed: 04/14/2024] Open
Abstract
To date, the SARS-CoV-2 pandemic still represents a great clinical challenge worldwide, and effective anti-COVID-19 drugs are limited. For this reason, nutritional supplements have been investigated as adjuvant therapeutic approaches in disease management. Among such supplements, vitamin D has gained great interest, due to its immunomodulatory and anti-inflammatory actions both in adult and pediatric populations. Even if there is conflicting evidence about its prevention and/or mitigation effectiveness in SARS-CoV-2 infection, several studies demonstrated a strict correlation between hypovitaminosis D and disease severity in acute COVID-19 and MIS-C (multisystem inflammatory syndrome in children). This narrative review offers a resume of the state of the art about vitamin D's role in immunity and its clinical use in the context of the current pandemic, specially focusing on pediatric manifestations and MIS-C. It seems biologically reasonable that interventions aimed at normalizing circulating vitamin D levels could be beneficial. To help clinicians in establishing the correct prophylaxis and/or supportive therapy with vitamin D, well-designed and adequately statistically powered clinical trials involving both adult and pediatric populations are needed. Moreover, this review will also discuss the few other nutraceuticals evaluated in this context.
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Affiliation(s)
- Manuela Rizzi
- Department of Health Sciences (DiSS), Università del Piemonte Orientale (UPO), 28100 Novara, Italy
- IRCAD (Interdisciplinary Research Center of Autoimmune Diseases), Università del Piemonte Orientale (UPO), 28100 Novara, Italy
| | - Vincenzo Avellis
- School of Medicine, University of Turin, 10124 Turin, Italy
- Sant’Anna Hospital, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy (B.M.)
| | - Alessandro Messina
- School of Medicine, University of Turin, 10124 Turin, Italy
- Sant’Anna Hospital, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy (B.M.)
| | - Chiara Germano
- Sant’Anna Hospital, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy (B.M.)
- Department of Maternal, Neonatal and Infant Medicine, University Hospital “Degli Infermi”, 13875 Ponderano, Italy
| | - Elena Tavella
- School of Medicine, University of Turin, 10124 Turin, Italy
- Sant’Anna Hospital, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy (B.M.)
| | - Valentina Dodaro
- Sant’Anna Hospital, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy (B.M.)
| | - Raffaele Vitale
- School of Medicine, University of Turin, 10124 Turin, Italy
- Sant’Anna Hospital, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy (B.M.)
| | - Alberto Revelli
- School of Medicine, University of Turin, 10124 Turin, Italy
- Sant’Anna Hospital, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy (B.M.)
| | - Paolo Zola
- School of Medicine, University of Turin, 10124 Turin, Italy
- Sant’Anna Hospital, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy (B.M.)
| | - Simonetta Picone
- Neonatology and Neonatal Intensive Care Unit, Policlinico Casilino, 00169 Rome, Italy
| | - Pier Michele Paolillo
- Neonatology and Neonatal Intensive Care Unit, Policlinico Casilino, 00169 Rome, Italy
| | - Vito Mondì
- Neonatology and Neonatal Intensive Care Unit, Policlinico Casilino, 00169 Rome, Italy
| | - Bianca Masturzo
- Sant’Anna Hospital, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy (B.M.)
- Department of Maternal, Neonatal and Infant Medicine, University Hospital “Degli Infermi”, 13875 Ponderano, Italy
| | - Paolo Manzoni
- Sant’Anna Hospital, Department of Surgical Sciences, University of Turin, 10126 Turin, Italy (B.M.)
- Department of Maternal, Neonatal and Infant Medicine, University Hospital “Degli Infermi”, 13875 Ponderano, Italy
| | - Pier Paolo Sainaghi
- IRCAD (Interdisciplinary Research Center of Autoimmune Diseases), Università del Piemonte Orientale (UPO), 28100 Novara, Italy
- Department of Translational Medicine (DiMeT), Università del Piemonte Orientale (UPO), 28100 Novara, Italy
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128
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Scarpa F, Branda F, Petrosillo N, Ciccozzi M. On the SARS-CoV-2 Variants. Infect Dis Rep 2024; 16:289-297. [PMID: 38667750 PMCID: PMC11050187 DOI: 10.3390/idr16020024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Revised: 03/09/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
The evolutionary dynamics of viruses, particularly exemplified by SARS-CoV-2 during the ongoing COVID-19 pandemic, underscore the intricate interplay between genetics, host adaptation, and viral spread. This paper delves into the genetic evolution of SARS-CoV-2, emphasizing the implications of viral variants on global health. Initially emerging from the Wuhan-Hu-1 lineage, SARS-CoV-2 rapidly diversified into numerous variants, each characterized by distinct mutations in the spike protein and other genomic regions. Notable variants such as B.1.1.7 (α), B.1.351 (β), P.1 (γ), B.1.617.2 (δ), and the Omicron variant have garnered significant attention due to their heightened transmissibility and immune evasion capabilities. In particular, the Omicron variant has presented a myriad of subvariants, raising concerns about its potential impact on public health. Despite the emergence of numerous variants, the vast majority have exhibited limited expansion capabilities and have not posed significant threats akin to early pandemic strains. Continued genomic surveillance is imperative to identify emerging variants of concern promptly. While genetic adaptation is intrinsic to viral evolution, effective public health responses must be grounded in empirical evidence to navigate the evolving landscape of the pandemic with resilience and precision.
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Affiliation(s)
- Fabio Scarpa
- Department of Biomedical Sciences, University of Sassari, Viale San Pietro 43b, 07100 Sassari, Italy
| | - Francesco Branda
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, 00128 Rome, Italy; (F.B.); (M.C.)
| | - Nicola Petrosillo
- Infection Prevention Control/Infectious Disease Service, Fondazione Policlinico Universitario Campus Bio-Medico, 00127 Rome, Italy
| | - Massimo Ciccozzi
- Unit of Medical Statistics and Molecular Epidemiology, Università Campus Bio-Medico di Roma, 00128 Rome, Italy; (F.B.); (M.C.)
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129
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Nonaka CKV, de Jesus Ribeiro AM, Rocha GV, da Hora HS, Junior AAF, Lima FDM, Bastos IN, Teles SAS, Weber TGL, Costa VF, Costa-Ferro ZS, Rocha CAG, Sardi SI, Soares G, Mendes AVA, Souza BSDF. Assessing the Clinical Impact of the SARS-CoV-2 Gamma Variant on Intensive Care Unit Admissions: Insights from a Reference Hospital in Northeastern Brazil. Viruses 2024; 16:467. [PMID: 38543835 PMCID: PMC10974300 DOI: 10.3390/v16030467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 02/26/2024] [Accepted: 02/27/2024] [Indexed: 05/23/2024] Open
Abstract
The global challenge posed by the prolonged COVID-19 pandemic underscores the critical need for ongoing genomic surveillance to identify emerging variants and formulate effective public health strategies. This retrospective observational study, conducted in a reference hospital in Northeast Brazil and comprising 2116 cases, employed PCR genotyping together with epidemiological data to elucidate the impact of the Gamma variant during its emergence, revealing distinct patterns in hospitalization rates, severity of illness, and outcomes. The study emphasizes the challenges posed by the variant, particularly an increased tendency for ICU admissions and respiratory support, especially among adults aged 18 to 59 without comorbidities. Laboratory analyses further demonstrate elevated inflammatory, coagulation, and hepatic markers in the Gamma variant cohort, suggesting a more severe systemic response. Despite limitations, including a retrospective approach and single-institution data, the study underscores the importance of ongoing genomic surveillance. Overall, this research contributes valuable insights into the impact of the Gamma variant on COVID-19 dynamics, advocating for continued research and surveillance to inform effective public health strategies regarding evolving viral variants.
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Affiliation(s)
- Carolina Kymie Vasques Nonaka
- D’Or Institute for Research and Education (IDOR), Salvador 41253-190, BA, Brazil; (C.K.V.N.); (G.V.R.); (Z.S.C.-F.); (C.A.G.R.)
- São Rafael Hospital, Salvador 41253-190, BA, Brazil; (S.A.S.T.); (T.G.L.W.); (V.F.C.); (A.V.A.M.)
| | | | - Gisele Vieira Rocha
- D’Or Institute for Research and Education (IDOR), Salvador 41253-190, BA, Brazil; (C.K.V.N.); (G.V.R.); (Z.S.C.-F.); (C.A.G.R.)
- Gonçalo Moniz Institute, FIOCRUZ, Salvador 40296-710, BA, Brazil
| | - Helena Souza da Hora
- Institute of Health Sciences, Federal University of Bahia, Salvador 40231-300, BA, Brazil; (A.M.d.J.R.); (G.S.)
| | | | | | - Iasmin Nogueira Bastos
- Faculty of Medicine and Dentistry, Federal University of Bahia, Salvador 40110-100, BA, Brazil;
| | - Samara Alves Sa Teles
- São Rafael Hospital, Salvador 41253-190, BA, Brazil; (S.A.S.T.); (T.G.L.W.); (V.F.C.); (A.V.A.M.)
| | | | - Vanessa Ferreira Costa
- São Rafael Hospital, Salvador 41253-190, BA, Brazil; (S.A.S.T.); (T.G.L.W.); (V.F.C.); (A.V.A.M.)
| | - Zaquer Suzana Costa-Ferro
- D’Or Institute for Research and Education (IDOR), Salvador 41253-190, BA, Brazil; (C.K.V.N.); (G.V.R.); (Z.S.C.-F.); (C.A.G.R.)
| | - Clarissa Araújo Gurgel Rocha
- D’Or Institute for Research and Education (IDOR), Salvador 41253-190, BA, Brazil; (C.K.V.N.); (G.V.R.); (Z.S.C.-F.); (C.A.G.R.)
- Gonçalo Moniz Institute, FIOCRUZ, Salvador 40296-710, BA, Brazil
- Faculty of Medicine and Dentistry, Federal University of Bahia, Salvador 40110-100, BA, Brazil;
| | - Silvia Inês Sardi
- Institute of Health Sciences, Federal University of Bahia, Salvador 40231-300, BA, Brazil; (A.M.d.J.R.); (G.S.)
| | - Gúbio Soares
- Institute of Health Sciences, Federal University of Bahia, Salvador 40231-300, BA, Brazil; (A.M.d.J.R.); (G.S.)
| | | | - Bruno Solano de Freitas Souza
- D’Or Institute for Research and Education (IDOR), Salvador 41253-190, BA, Brazil; (C.K.V.N.); (G.V.R.); (Z.S.C.-F.); (C.A.G.R.)
- São Rafael Hospital, Salvador 41253-190, BA, Brazil; (S.A.S.T.); (T.G.L.W.); (V.F.C.); (A.V.A.M.)
- Gonçalo Moniz Institute, FIOCRUZ, Salvador 40296-710, BA, Brazil
- Instituto Gonçalo Moniz, Fundação Oswaldo Cruz, Rua Waldemar Falcão, 121, Salvador 40296-710, BA, Brazil
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130
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Arevalo-Romero JA, Chingaté-López SM, Camacho BA, Alméciga-Díaz CJ, Ramirez-Segura CA. Next-generation treatments: Immunotherapy and advanced therapies for COVID-19. Heliyon 2024; 10:e26423. [PMID: 38434363 PMCID: PMC10907543 DOI: 10.1016/j.heliyon.2024.e26423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Revised: 02/12/2024] [Accepted: 02/13/2024] [Indexed: 03/05/2024] Open
Abstract
The COVID-19 pandemic, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), emerged in 2019 following prior outbreaks of coronaviruses like SARS and MERS in recent decades, underscoring their high potential of infectivity in humans. Insights from previous outbreaks of SARS and MERS have played a significant role in developing effective strategies to mitigate the global impact of SARS-CoV-2. As of January 7, 2024, there have been 774,075,242 confirmed cases of COVID-19 worldwide. To date, 13.59 billion vaccine doses have been administered, and there have been 7,012,986 documented fatalities (https://www.who.int/) Despite significant progress in addressing the COVID-19 pandemic, the rapid evolution of SARS-CoV-2 challenges human defenses, presenting ongoing global challenges. The emergence of new SARS-CoV-2 lineages, shaped by mutation and recombination processes, has led to successive waves of infections. This scenario reveals the need for next-generation vaccines as a crucial requirement for ensuring ongoing protection against SARS-CoV-2. This demand calls for formulations that trigger a robust adaptive immune response without leading the acute inflammation linked with the infection. Key mutations detected in the Spike protein, a critical target for neutralizing antibodies and vaccine design -specifically within the Receptor Binding Domain region of Omicron variant lineages (B.1.1.529), currently dominant worldwide, have intensified concerns due to their association with immunity evasion from prior vaccinations and infections. As the world deals with this evolving threat, the narrative extends to the realm of emerging variants, each displaying new mutations with implications that remain largely misunderstood. Notably, the JN.1 Omicron lineage is gaining global prevalence, and early findings suggest it stands among the immune-evading variants, a characteristic attributed to its mutation L455S. Moreover, the detrimental consequences of the novel emergence of SARS-CoV-2 lineages bear a particularly critical impact on immunocompromised individuals and older adults. Immunocompromised individuals face challenges such as suboptimal responses to COVID-19 vaccines, rendering them more susceptible to severe disease. Similarly, older adults have an increased risk of severe disease and the presence of comorbid conditions, find themselves at a heightened vulnerability to develop COVID-19 disease. Thus, recognizing these intricate factors is crucial for effectively tailoring public health strategies to protect these vulnerable populations. In this context, this review aims to describe, analyze, and discuss the current progress of the next-generation treatments encompassing immunotherapeutic approaches and advanced therapies emerging as complements that will offer solutions to counter the disadvantages of the existing options. Preliminary outcomes show that these strategies target the virus and address the immunomodulatory responses associated with COVID-19. Furthermore, the capacity to promote tissue repair has been demonstrated, which can be particularly noteworthy for immunocompromised individuals who stand as vulnerable actors in the global landscape of coronavirus infections. The emerging next-generation treatments possess broader potential, offering protection against a wide range of variants and enhancing the ability to counter the impact of the constant evolution of the virus. Furthermore, advanced therapies are projected as potential treatment alternatives for managing Chronic Post-COVID-19 syndromeand addressing its associated long-term complications.
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Affiliation(s)
- Jenny Andrea Arevalo-Romero
- Laboratorio de Investigación en Ingeniería Celular y Molecular, Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud, IDCBIS, 111611, Bogotá, DC, Colombia
- Instituto de Errores Innatos del Metabolismo, Facultad de Ciencias, Pontificia Universidad Javeriana, 110231, Bogotá, D.C., Colombia
| | - Sandra M. Chingaté-López
- Laboratorio de Investigación en Ingeniería Celular y Molecular, Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud, IDCBIS, 111611, Bogotá, DC, Colombia
| | - Bernardo Armando Camacho
- Laboratorio de Investigación en Ingeniería Celular y Molecular, Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud, IDCBIS, 111611, Bogotá, DC, Colombia
| | - Carlos Javier Alméciga-Díaz
- Instituto de Errores Innatos del Metabolismo, Facultad de Ciencias, Pontificia Universidad Javeriana, 110231, Bogotá, D.C., Colombia
| | - Cesar A. Ramirez-Segura
- Laboratorio de Investigación en Ingeniería Celular y Molecular, Instituto Distrital de Ciencia, Biotecnología e Innovación en Salud, IDCBIS, 111611, Bogotá, DC, Colombia
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131
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Priyadarsinee L, Jamir E, Nagamani S, Mahanta HJ, Kumar N, John L, Sarma H, Kumar A, Gaur AS, Sahoo R, Vaikundamani S, Murugan NA, Priyakumar UD, Raghava GPS, Bharatam PV, Parthasarathi R, Subramanian V, Sastry GM, Sastry GN. Molecular Property Diagnostic Suite for COVID-19 (MPDS COVID-19): an open-source disease-specific drug discovery portal. GIGABYTE 2024; 2024:gigabyte114. [PMID: 38525218 PMCID: PMC10958779 DOI: 10.46471/gigabyte.114] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 03/11/2024] [Indexed: 03/26/2024] Open
Abstract
Molecular Property Diagnostic Suite (MPDS) was conceived and developed as an open-source disease-specific web portal based on Galaxy. MPDSCOVID-19 was developed for COVID-19 as a one-stop solution for drug discovery research. Galaxy platforms enable the creation of customized workflows connecting various modules in the web server. The architecture of MPDSCOVID-19 effectively employs Galaxy v22.04 features, which are ported on CentOS 7.8 and Python 3.7. MPDSCOVID-19 provides significant updates and the addition of several new tools updated after six years. Tools developed by our group in Perl/Python and open-source tools are collated and integrated into MPDSCOVID-19 using XML scripts. Our MPDS suite aims to facilitate transparent and open innovation. This approach significantly helps bring inclusiveness in the community while promoting free access and participation in software development. Availability & Implementation The MPDSCOVID-19 portal can be accessed at https://mpds.neist.res.in:8085/.
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Affiliation(s)
- Lipsa Priyadarsinee
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Esther Jamir
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
| | - Selvaraman Nagamani
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Hridoy Jyoti Mahanta
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Nandan Kumar
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
| | - Lijo John
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
| | - Himakshi Sarma
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
| | - Asheesh Kumar
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
| | - Anamika Singh Gaur
- CSIR-Indian Institute of Toxicology Research, Lucknow, 226001, Uttar Pradesh, India
| | - Rosaleen Sahoo
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - S. Vaikundamani
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
| | - N. Arul Murugan
- Indraprastha Institute of Information Technology, Delhi, 110020, India
| | - U. Deva Priyakumar
- International Institute of Information Technology, Gachibowli, Hyderabad, 500032, India
| | - G. P. S. Raghava
- Indraprastha Institute of Information Technology, Delhi, 110020, India
| | - Prasad V. Bharatam
- National Institute of Pharmaceutical Education and Research, S.A.S. Nagar (Mohali), 160062, India
| | - Ramakrishnan Parthasarathi
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- CSIR-Indian Institute of Toxicology Research, Lucknow, 226001, Uttar Pradesh, India
| | - V. Subramanian
- Department of Chemistry, Indian Institute of Technology, Chennai, 600036, India
| | - G. Madhavi Sastry
- Schrödinger Inc., Octave, Salarpuria Sattva Knowledge City, 1st Floor, Unit 3A, Hyderabad, 500081, India
| | - G. Narahari Sastry
- CSIR–North East Institute of Science and Technology, Jorhat, 785006, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
- Indian Institute of Technology (IIT) Hyderabad, Kandi, Sangareddy, Telangana, 502284, India
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Marques AD, Graham-Wooten J, Fitzgerald AS, Sobel Leonard A, Cook EJ, Everett JK, Rodino KG, Moncla LH, Kelly BJ, Collman RG, Bushman FD. SARS-CoV-2 evolution during prolonged infection in immunocompromised patients. mBio 2024; 15:e0011024. [PMID: 38364100 PMCID: PMC10936176 DOI: 10.1128/mbio.00110-24] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 01/25/2024] [Indexed: 02/18/2024] Open
Abstract
Prolonged infection with severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in immunocompromised patients provides an opportunity for viral evolution, potentially leading to the generation of new pathogenic variants. To investigate the pathways of viral evolution, we carried out a study on five patients experiencing prolonged SARS-CoV-2 infection (quantitative polymerase chain reaction-positive for 79-203 days) who were immunocompromised due to treatment for lymphoma or solid organ transplantation. For each timepoint analyzed, we generated at least two independent viral genome sequences to assess the heterogeneity and control for sequencing error. Four of the five patients likely had prolonged infection; the fifth apparently experienced a reinfection. The rates of accumulation of substitutions in the viral genome per day were higher in hospitalized patients with prolonged infection than those estimated for the community background. The spike coding region accumulated a significantly greater number of unique mutations than other viral coding regions, and the mutation density was higher. Two patients were treated with monoclonal antibodies (bebtelovimab and sotrovimab); by the next sampled timepoint, each virus population showed substitutions associated with monoclonal antibody resistance as the dominant forms (spike K444N and spike E340D). All patients received remdesivir, but remdesivir-resistant substitutions were not detected. These data thus help elucidate the trends of emergence, evolution, and selection of mutational variants within long-term infected immunocompromised individuals. IMPORTANCE SARS-CoV-2 is responsible for a global pandemic, driven in part by the emergence of new viral variants. Where do these new variants come from? One model is that long-term viral persistence in infected individuals allows for viral evolution in response to host pressures, resulting in viruses more likely to replicate efficiently in humans. In this study, we characterize replication in several hospitalized and long-term infected individuals, documenting efficient pathways of viral evolution.
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Affiliation(s)
- Andrew D. Marques
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Jevon Graham-Wooten
- Division of Pulmonary, Allergy, and Critical Care, Philadelphia, Pennsylvania, USA
| | | | - Ashley Sobel Leonard
- Division of Infectious Diseases, Children’s Hospital of Philadelphia, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Emma J. Cook
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - John K. Everett
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Kyle G. Rodino
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Louise H. Moncla
- Department of Pathobiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Brendan J. Kelly
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Ronald G. Collman
- Division of Pulmonary, Allergy, and Critical Care, Philadelphia, Pennsylvania, USA
| | - Frederic D. Bushman
- Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
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Kern AL, Pink I, Bonifacius A, Kaireit T, Speth M, Behrendt L, Klimeš F, Voskrebenzev A, Hohlfeld JM, Hoeper MM, Welte T, Wacker F, Eiz-Vesper B, Vogel-Claussen J. Alveolar membrane and capillary function in COVID-19 convalescents: insights from chest MRI. Eur Radiol 2024:10.1007/s00330-024-10669-9. [PMID: 38460013 DOI: 10.1007/s00330-024-10669-9] [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: 10/24/2023] [Revised: 01/22/2024] [Accepted: 02/10/2024] [Indexed: 03/11/2024]
Abstract
OBJECTIVES To investigate potential presence and resolution of longer-term pulmonary diffusion limitation and microvascular perfusion impairment in COVID-19 convalescents. MATERIALS AND METHODS This prospective, longitudinal study was carried out between May 2020 and April 2023. COVID-19 convalescents repeatedly and age/sex-matched healthy controls once underwent MRI including hyperpolarized 129Xe MRI. Blood samples were obtained in COVID-19 convalescents for immunophenotyping. Ratios of 129Xe in red blood cells (RBC), tissue/plasma (TP), and gas phase (GP) as well as lung surface-volume ratio were quantified and correlations with CD4+/CD8+ T cell frequencies were assessed using Pearson's correlation coefficient. Signed-rank tests were used for longitudinal and U tests for group comparisons. RESULTS Thirty-five participants were recruited. Twenty-three COVID-19 convalescents (age 52.1 ± 19.4 years, 13 men) underwent baseline MRI 12.6 ± 4.2 weeks after symptom onset. Fourteen COVID-19 convalescents underwent follow-up MRI and 12 were included for longitudinal comparison (baseline MRI at 11.5 ± 2.7 weeks and follow-up 38.0 ± 5.5 weeks). Twelve matched controls were included for comparison. In COVID-19 convalescents, RBC-TP was increased at follow-up (p = 0.04). Baseline RBC-TP was lower in patients treated on intensive care unit (p = 0.03) and in patients with severe/critical disease (p = 0.006). RBC-TP correlated with CD4+/CD8+ T cell frequencies (R = 0.61/ - 0.60) at baseline. RBC-TP was not significantly different compared to matched controls at follow-up (p = 0.25). CONCLUSION Impaired microvascular pulmonary perfusion and alveolar membrane function persisted 12 weeks after symptom onset and resolved within 38 weeks after COVID-19 symptom onset. CLINICAL RELEVANCE STATEMENT 129Xe MRI shows improvement of microvascular pulmonary perfusion and alveolar membrane function between 11.5 ± 2.7 weeks and 38.0 ± 5.5 weeks after symptom onset in patients after COVID-19, returning to normal in subjects without significant prior disease. KEY POINTS • The study aims to investigate long-term effects of COVID-19 on lung function, in particular gas uptake efficiency, and on the cardiovascular system. • In COVID-19 convalescents, the ratio of 129Xe in red blood cells/tissue plasma increased longitudinally (p = 0.04), but was not different from matched controls at follow-up (p = 0.25). • Microvascular pulmonary perfusion and alveolar membrane function are impaired 11.5 weeks after symptom onset in patients after COVID-19, returning to normal in subjects without significant prior disease at 38.0 weeks.
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Affiliation(s)
- Agilo Luitger Kern
- Institute for Diagnostic and Interventional Radiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Carl-Neuberg-Str. 1, 30625, Hannover, Germany.
- Medizinische Hochschule Hannover, Carl-Neuberg-Straße 1, Hannover, 30625, Germany.
| | - Isabell Pink
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Department of Respiratory Medicine and Infectious Diseases, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Agnes Bonifacius
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover/Brunswick, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Till Kaireit
- Institute for Diagnostic and Interventional Radiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Milan Speth
- Institute for Diagnostic and Interventional Radiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Lea Behrendt
- Institute for Diagnostic and Interventional Radiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Filip Klimeš
- Institute for Diagnostic and Interventional Radiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Andreas Voskrebenzev
- Institute for Diagnostic and Interventional Radiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Jens M Hohlfeld
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Medizinische Hochschule Hannover, Carl-Neuberg-Straße 1, Hannover, 30625, Germany
- Department of Clinical Airway Research, Fraunhofer Institute for Toxicology and Experimental Medicine, Nikolai-Fuchs-Str. 1, 30625, Hannover, Germany
| | - Marius M Hoeper
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Department of Respiratory Medicine and Infectious Diseases, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Tobias Welte
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Department of Respiratory Medicine and Infectious Diseases, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Frank Wacker
- Institute for Diagnostic and Interventional Radiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Carl-Neuberg-Str. 1, 30625, Hannover, Germany
| | - Britta Eiz-Vesper
- Institute of Transfusion Medicine and Transplant Engineering, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- German Center for Infection Research (DZIF), Partner Site Hannover/Brunswick, Inhoffenstr. 7, 38124, Braunschweig, Germany
| | - Jens Vogel-Claussen
- Institute for Diagnostic and Interventional Radiology, Hannover Medical School, Carl-Neuberg-Str. 1, 30625, Hannover, Germany
- Biomedical Research in Endstage and Obstructive Lung Disease Hannover (BREATH), German Center for Lung Research (DZL), Carl-Neuberg-Str. 1, 30625, Hannover, Germany
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Generalova LV, Laryushkin DP, Leneva IA, Ivanina AV, Trunova GV, Dolinnyi SV, Generalov EA. Evaluation of the Polysaccharide "Immeran" Activity in Syrian hamsters' Model of SARS-CoV-2. Viruses 2024; 16:423. [PMID: 38543788 PMCID: PMC10976179 DOI: 10.3390/v16030423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 03/04/2024] [Accepted: 03/07/2024] [Indexed: 05/23/2024] Open
Abstract
COVID-19 is a highly contagious respiratory disease with a high number of lethal cases in humans, which causes the need to search for new therapeutic agents. Polysaccharides could be one of the prospective types of molecules with a large variety of biological activities, especially antiviral. The aim of this work was to study the specific antiviral activity of the drug "Immeran" on a model of a new coronavirus infection SARS-CoV-2 in hamsters. Based on the second experiment, intraperitoneal treatment with the drug according to a treatment regimen in doses of 500 and 1000 μg/kg (administration after an hour, then once a day every other day, a total of 3 administrations) was effective, reliably suppressing the replication of the virus in the lungs and, at a dose of 1000 μg/kg, prevented weight loss in animals. In all cases, the treatment stimulated the formation of virus-neutralizing antibodies to the SARS-CoV-2 virus, which suggests that the drug possesses adjuvant properties.
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Affiliation(s)
- Liubov Viktorovna Generalova
- Faculty of Medicine, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia; (L.V.G.); (S.V.D.)
| | - Denis Pavlovich Laryushkin
- Federal Research Center “Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences”, Institute of Cell Biophysics of the Russian Academy of Sciences, 142290 Pushchino, Russia;
| | - Irina Anatolievna Leneva
- Mechnikov Research Institute of Vaccines and Sera, Department of Virology, 105064 Moscow, Russia; (I.A.L.); (A.V.I.)
| | - Anna Valerievna Ivanina
- Mechnikov Research Institute of Vaccines and Sera, Department of Virology, 105064 Moscow, Russia; (I.A.L.); (A.V.I.)
| | - Galina Vladimirovna Trunova
- Federal State Budgetary Institution National Medical Research Radiological Center (FSBI NMRRC) of the Ministry of Health of the Russian Federation, P.A. Hertsen Moscow, Oncology Research Institute, 125284 Moscow, Russia;
| | - Sergei Vladimirovich Dolinnyi
- Faculty of Medicine, Peoples’ Friendship University of Russia (RUDN University), 117198 Moscow, Russia; (L.V.G.); (S.V.D.)
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135
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Lanz-Mendoza H, Gálvez D, Contreras-Garduño J. The plasticity of immune memory in invertebrates. J Exp Biol 2024; 227:jeb246158. [PMID: 38449328 DOI: 10.1242/jeb.246158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Whether specific immune protection after initial pathogen exposure (immune memory) occurs in invertebrates has long been uncertain. The absence of antibodies, B-cells and T-cells, and the short lifespans of invertebrates led to the hypothesis that immune memory does not occur in these organisms. However, research in the past two decades has supported the existence of immune memory in several invertebrate groups, including Ctenophora, Cnidaria, Nematoda, Mollusca and Arthropoda. Interestingly, some studies have demonstrated immune memory that is specific to the parasite strain. Nonetheless, other work does not provide support for immune memory in invertebrates or offers only partial support. Moreover, the expected biphasic immune response, a characteristic of adaptive immune memory in vertebrates, varies within and between invertebrate species. This variation may be attributed to the influence of biotic or abiotic factors, particularly parasites, on the outcome of immune memory. Despite its critical importance for survival, the role of phenotypic plasticity in immune memory has not been systematically examined in the past two decades. Additionally, the features of immune responses occurring in diverse environments have yet to be fully characterized.
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Affiliation(s)
- Humberto Lanz-Mendoza
- Centro de Investigaciones sobre Enfermedades Infecciosas, INSP, 62100 Cuernavaca, Morelos, Mexico
| | - Dumas Gálvez
- Coiba Scientific Station, City of Knowledge, Calle Gustavo Lara, Boulevard 145B, Clayton 0843-01853, Panama
- Programa Centroamericano de Maestría en Entomología, Universidad de Panamá, Estafeta universitaria, Avenida Simón Bolívar, 0824, Panama
- Sistema Nacional de Investigación, Edificio 205, Ciudad del Saber, 0816-02852, Panama
| | - Jorge Contreras-Garduño
- Escuela Nacional de Estudios Superiores, Unidad Morelia, UNAM, 58190 Morelia, Mexico
- Institute for Evolution and Biodiversity, University of Münster, 48149 Münster, Germany
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136
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Gonzalez-Parra G, Mahmud MS, Kadelka C. Learning from the COVID-19 pandemic: a systematic review of mathematical vaccine prioritization models. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2024:2024.03.04.24303726. [PMID: 38496570 PMCID: PMC10942533 DOI: 10.1101/2024.03.04.24303726] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
As the world becomes ever more connected, the chance of pandemics increases as well. The recent COVID-19 pandemic and the concurrent global mass vaccine roll-out provides an ideal setting to learn from and refine our understanding of infectious disease models for better future preparedness. In this review, we systematically analyze and categorize mathematical models that have been developed to design optimal vaccine prioritization strategies of an initially limited vaccine. As older individuals are disproportionately affected by COVID-19, the focus is on models that take age explicitly into account. The lower mobility and activity level of older individuals gives rise to non-trivial trade-offs. Secondary research questions concern the optimal time interval between vaccine doses and spatial vaccine distribution. This review showcases the effect of various modeling assumptions on model outcomes. A solid understanding of these relationships yields better infectious disease models and thus public health decisions during the next pandemic.
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Affiliation(s)
- Gilberto Gonzalez-Parra
- Instituto de Matemática Multidisciplinar, Universitat Politècnica de València, València, Spain
- Department of Mathematics, New Mexico Tech, 801 Leroy Place, Socorro, 87801, NM, USA
| | - Md Shahriar Mahmud
- Department of Mathematics, Iowa State University, 411 Morrill Rd, Ames, 50011, IA, USA
| | - Claus Kadelka
- Department of Mathematics, Iowa State University, 411 Morrill Rd, Ames, 50011, IA, USA
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137
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White CL, Glover MA, Gandhapudi SK, Richards KA, Sant AJ. Flublok Quadrivalent Vaccine Adjuvanted with R-DOTAP Elicits a Robust and Multifunctional CD4 T Cell Response That Is of Greater Magnitude and Functional Diversity Than Conventional Adjuvant Systems. Vaccines (Basel) 2024; 12:281. [PMID: 38543915 PMCID: PMC10975948 DOI: 10.3390/vaccines12030281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2024] [Revised: 02/20/2024] [Accepted: 02/29/2024] [Indexed: 04/01/2024] Open
Abstract
It is clear that new approaches are needed to promote broadly protective immunity to viral pathogens, particularly those that are prone to mutation and escape from antibody-mediated immunity. CD4+ T cells, known to target many viral proteins and highly conserved peptide epitopes, can contribute greatly to protective immunity through multiple mechanisms. Despite this potential, CD4+ T cells are often poorly recruited by current vaccine strategies. Here, we have analyzed a promising new adjuvant (R-DOTAP), as well as conventional adjuvant systems AddaVax with or without an added TLR9 agonist CpG, to promote CD4+ T cell responses to the licensed vaccine Flublok containing H1, H3, and HA-B proteins. Our studies, using a preclinical mouse model of vaccination, revealed that the addition of R-DOTAP to Flublok dramatically enhances the magnitude and functionality of CD4+ T cells specific for HA-derived CD4+ T cell epitopes, far outperforming conventional adjuvant systems based on cytokine EliSpot assays and multiparameter flow cytometry. The elicited CD4+ T cells specific for HA-derived epitopes produce IL-2, IFN-γ, IL-4/5, and granzyme B and have multifunctional potential. Hence, R-DOTAP, which has been verified safe by human studies, can offer exciting opportunities as an immune stimulant for next-generation prophylactic recombinant protein-based vaccines.
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Affiliation(s)
- Chantelle L. White
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA; (C.L.W.); (M.A.G.); (K.A.R.)
| | - Maryah A. Glover
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA; (C.L.W.); (M.A.G.); (K.A.R.)
| | - Siva K. Gandhapudi
- Department of Microbiology, Immunology and Molecular Genetics, University of Kentucky School of Medicine, Lexington, KY 40508, USA;
| | - Katherine A. Richards
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA; (C.L.W.); (M.A.G.); (K.A.R.)
| | - Andrea J. Sant
- David H. Smith Center for Vaccine Biology and Immunology, Department of Microbiology and Immunology, University of Rochester, Rochester, NY 14642, USA; (C.L.W.); (M.A.G.); (K.A.R.)
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138
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Chen H, Zhuang Z, Xu N, Feng Y, Fang K, Tan C, Tan Y. Simple, Visual, Point-of-Care SARS-CoV-2 Detection Incorporating Recombinase Polymerase Amplification and Target DNA-Protein Crosslinking Enhanced Chemiluminescence. BIOSENSORS 2024; 14:135. [PMID: 38534242 DOI: 10.3390/bios14030135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Revised: 12/14/2023] [Accepted: 12/26/2023] [Indexed: 03/28/2024]
Abstract
The ongoing COVID-19 pandemic, driven by persistent SARS-CoV-2 transmission, threatens human health worldwide, underscoring the urgent need for an efficient, low-cost, rapid SARS-CoV-2 detection method. Herein, we developed a point-of-care SARS-CoV-2 detection method incorporating recombinase polymerase amplification (RPA) and DNA-protein crosslinking chemiluminescence (DPCL) (RPADPCL). RPADPCL involves the crosslinking of biotinylated double-stranded RPA DNA products with horseradish peroxidase (HRP)-labeled streptavidin (SA-HRP). Modified products are captured using SA-labeled magnetic beads, and then analyzed using a chemiluminescence detector and smartphone after the addition of a chemiluminescent substrate. Under optimal conditions, the RPADPCL limit of detection (LOD) was observed to be 6 copies (within the linear detection range of 1-300 copies) for a plasmid containing the SARS-CoV-2 N gene and 15 copies (within the linear range of 10-500 copies) for in vitro transcribed (IVT) SARS-CoV-2 RNA. The proposed method is convenient, specific, visually intuitive, easy to use, and does not require external excitation. The effective RPADPCL detection of SARS-CoV-2 in complex matrix systems was verified by testing simulated clinical samples containing 10% human saliva or a virus transfer medium (VTM) spiked with a plasmid containing a SARS-CoV-2 N gene sequence or SARS-CoV-2 IVT RNA. Consequently, this method has great potential for detecting targets in clinical samples.
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Affiliation(s)
- Hui Chen
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Zhiyuan Zhuang
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Naihan Xu
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- School of Food and Drug, Shenzhen Polytechnic University, Shenzhen 518055, China
| | - Ying Feng
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Kaixin Fang
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Chunyan Tan
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Ying Tan
- State Key Laboratory of Chemical Oncogenomics, Institute of Biomedical and Health Engineering, Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
- Department of Chemistry, Tsinghua University, Beijing 100084, China
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Álvarez-Herrera M, Sevilla J, Ruiz-Rodriguez P, Vergara A, Vila J, Cano-Jiménez P, González-Candelas F, Comas I, Coscollá M. VIPERA: Viral Intra-Patient Evolution Reporting and Analysis. Virus Evol 2024; 10:veae018. [PMID: 38510921 PMCID: PMC10953798 DOI: 10.1093/ve/veae018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Revised: 02/02/2024] [Accepted: 03/05/2024] [Indexed: 03/22/2024] Open
Abstract
Viral mutations within patients nurture the adaptive potential of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during chronic infections, which are a potential source of variants of concern. However, there is no integrated framework for the evolutionary analysis of intra-patient SARS-CoV-2 serial samples. Herein, we describe Viral Intra-Patient Evolution Reporting and Analysis (VIPERA), a new software that integrates the evaluation of the intra-patient ancestry of SARS-CoV-2 sequences with the analysis of evolutionary trajectories of serial sequences from the same viral infection. We have validated it using positive and negative control datasets and have successfully applied it to a new case, which revealed population dynamics and evidence of adaptive evolution. VIPERA is available under a free software license at https://github.com/PathoGenOmics-Lab/VIPERA.
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Affiliation(s)
- Miguel Álvarez-Herrera
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia—CSIC), FISABIO Joint Research Unit ‘Infection and Public Health’, C/Agustín Escardino, 9, Paterna 46980, Spain
| | - Jordi Sevilla
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia—CSIC), FISABIO Joint Research Unit ‘Infection and Public Health’, C/Agustín Escardino, 9, Paterna 46980, Spain
| | - Paula Ruiz-Rodriguez
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia—CSIC), FISABIO Joint Research Unit ‘Infection and Public Health’, C/Agustín Escardino, 9, Paterna 46980, Spain
| | - Andrea Vergara
- Department of Clinical Microbiology, CDB, Hospital Clínic of Barcelona; University of Barcelona; ISGlobal, C. de Villarroel, 170, Barcelona 08007, Spain
- CIBER of Infectious Diseases (CIBERINFEC), Av. Monforte de Lemos, 3-5, Madrid 28029, Spain
| | - Jordi Vila
- Department of Clinical Microbiology, CDB, Hospital Clínic of Barcelona; University of Barcelona; ISGlobal, C. de Villarroel, 170, Barcelona 08007, Spain
- CIBER of Infectious Diseases (CIBERINFEC), Av. Monforte de Lemos, 3-5, Madrid 28029, Spain
| | - Pablo Cano-Jiménez
- Institute of Biomedicine of Valencia (IBV-CSIC), C/ Jaime Roig, 11, Valencia 46010, Spain
| | - Fernando González-Candelas
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia—CSIC), FISABIO Joint Research Unit ‘Infection and Public Health’, C/Agustín Escardino, 9, Paterna 46980, Spain
- CIBER of Epidemiology and Public Health (CIBERESP), Av. Monforte de Lemos, 3-5, Madrid 28029, Spain
| | - Iñaki Comas
- Institute of Biomedicine of Valencia (IBV-CSIC), C/ Jaime Roig, 11, Valencia 46010, Spain
- CIBER of Epidemiology and Public Health (CIBERESP), Av. Monforte de Lemos, 3-5, Madrid 28029, Spain
| | - Mireia Coscollá
- Institute for Integrative Systems Biology (I2SysBio, University of Valencia—CSIC), FISABIO Joint Research Unit ‘Infection and Public Health’, C/Agustín Escardino, 9, Paterna 46980, Spain
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Song T, Cooper L, Galván Achi J, Wang X, Dwivedy A, Rong L, Wang X. Polyvalent Nanobody Structure Designed for Boosting SARS-CoV-2 Inhibition. J Am Chem Soc 2024; 146:5894-5900. [PMID: 38408177 PMCID: PMC10965196 DOI: 10.1021/jacs.3c11760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/28/2024]
Abstract
Coronavirus transmission and mutations have brought intensive challenges on pandemic control and disease treatment. Developing robust and versatile antiviral drugs for viral neutralization is highly desired. Here, we created a new polyvalent nanobody (Nb) structure that shows the effective inhibition of SARS-CoV-2 infections. Our polyvalent Nb structure, called "PNS", is achieved by first conjugating single-stranded DNA (ssDNA) and the receptor-binding domain (RBD)-targeting Nb with retained binding ability to SARS-CoV-2 spike protein and then coalescing the ssDNA-Nb conjugates around a gold nanoparticle (AuNP) via DNA hybridization with a desired Nb density that offers spatial pattern-matching with that of the Nb binding sites on the trimeric spike. The surface plasmon resonance (SPR) assays show that the PNS binds the SARS-CoV-2 trimeric spike proteins with a ∼1000-fold improvement in affinity than that of monomeric Nbs. Furthermore, our viral entry inhibition assays using the PNS against SARS-CoV-2 WA/2020 and two recent variants of interest (BQ1.1 and XBB) show an over 400-fold enhancement in viral inhibition compared to free Nbs. Our PNS strategy built on a new DNA-protein conjugation chemistry provides a facile approach to developing robust virus inhibitors by using a corresponding virus-targeting Nb with a desired Nb density.
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Affiliation(s)
- Tingjie Song
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Laura Cooper
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Jazmin Galván Achi
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Xiaojing Wang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Abhisek Dwivedy
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
| | - Lijun Rong
- Department of Microbiology and Immunology, College of Medicine, University of Illinois at Chicago, Chicago, Illinois 60612, United States
| | - Xing Wang
- Carl R. Woese Institute for Genomic Biology, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Holonyak Micro and Nanotechnology Lab, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Chemistry, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
- Department of Bioengineering, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801, United States
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141
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Chaki SP, Kahl-McDonagh MM, Neuman BW, Zuelke KA. Validating the inactivation of viral pathogens with a focus on SARS-CoV-2 to safely transfer samples from high-containment laboratories. Front Cell Infect Microbiol 2024; 14:1292467. [PMID: 38510962 PMCID: PMC10951993 DOI: 10.3389/fcimb.2024.1292467] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 02/19/2024] [Indexed: 03/22/2024] Open
Abstract
Introduction Pathogen leak from a high-containment laboratory seriously threatens human safety, animal welfare, and environmental security. Transportation of pathogens from a higher (BSL4 or BSL3) to a lower (BSL2) containment laboratory for downstream experimentation requires complete pathogen inactivation. Validation of pathogen inactivation is necessary to ensure safety during transportation. This study established a validation strategy for virus inactivation. Methods SARS-CoV-2 wild type, delta, and omicron variants underwent heat treatment at 95°C for 10 minutes using either a hot water bath or a thermocycler. To validate the inactivation process, heat-treated viruses, and untreated control samples were incubated with A549-hACE2 and Vero E6-TMPRSS2-T2A-ACE2 cells. The cells were monitored for up to 72 hours for any cytopathic effects, visually and under a microscope, and for virus genome replication via RT-qPCR. The quality of post-treated samples was assessed for suitability in downstream molecular testing applications. Results Heat treatment at 95°C for 10 minutes effectively inactivated SARS-CoV-2 variants. The absence of cytopathic effects, coupled with the inability of virus genome replication, validated the efficacy of the inactivation process. Furthermore, the heat-treated samples proved to be qualified for COVID-19 antigen testing, RT-qPCR, and whole-genome sequencing. Discussion By ensuring the safety of sample transportation for downstream experimentation, this validation approach enhances biosecurity measures. Considerations for potential limitations, comparisons with existing inactivation methods, and broader implications of the findings are discussed.
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Affiliation(s)
- Sankar Prasad Chaki
- Global Health Research Complex, Division of Research, Texas A&M University, College Station, TX, United States
| | - Melissa M. Kahl-McDonagh
- Global Health Research Complex, Division of Research, Texas A&M University, College Station, TX, United States
| | - Benjamin W. Neuman
- Global Health Research Complex, Division of Research, Texas A&M University, College Station, TX, United States
- Department of Biological Sciences, Texas A&M University, College Station, TX, United States
- Department of Molecular Pathogenesis and Immunology, Texas A&M University, College Station, TX, United States
| | - Kurt A. Zuelke
- Global Health Research Complex, Division of Research, Texas A&M University, College Station, TX, United States
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Delgado S, Somovilla P, Ferrer-Orta C, Martínez-González B, Vázquez-Monteagudo S, Muñoz-Flores J, Soria ME, García-Crespo C, de Ávila AI, Durán-Pastor A, Gadea I, López-Galíndez C, Moran F, Lorenzo-Redondo R, Verdaguer N, Perales C, Domingo E. Incipient functional SARS-CoV-2 diversification identified through neural network haplotype maps. Proc Natl Acad Sci U S A 2024; 121:e2317851121. [PMID: 38416684 DOI: 10.1073/pnas.2317851121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 01/08/2024] [Indexed: 03/01/2024] Open
Abstract
Since its introduction in the human population, SARS-CoV-2 has evolved into multiple clades, but the events in its intrahost diversification are not well understood. Here, we compare three-dimensional (3D) self-organized neural haplotype maps (SOMs) of SARS-CoV-2 from thirty individual nasopharyngeal diagnostic samples obtained within a 19-day interval in Madrid (Spain), at the time of transition between clades 19 and 20. SOMs have been trained with the haplotype repertoire present in the mutant spectra of the nsp12- and spike (S)-coding regions. Each SOM consisted of a dominant neuron (displaying the maximum frequency), surrounded by a low-frequency neuron cloud. The sequence of the master (dominant) neuron was either identical to that of the reference Wuhan-Hu-1 genome or differed from it at one nucleotide position. Six different deviant haplotype sequences were identified among the master neurons. Some of the substitutions in the neural clouds affected critical sites of the nsp12-nsp8-nsp7 polymerase complex and resulted in altered kinetics of RNA synthesis in an in vitro primer extension assay. Thus, the analysis has identified mutations that are relevant to modification of viral RNA synthesis, present in the mutant clouds of SARS-CoV-2 quasispecies. These mutations most likely occurred during intrahost diversification in several COVID-19 patients, during an initial stage of the pandemic, and within a brief time period.
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Affiliation(s)
- Soledad Delgado
- Departamento de Sistemas Informáticos, Escuela Técnica Superior de Ingeniería de Sistemas Informáticos, Universidad Politécnica de Madrid, Madrid 28031, Spain
| | - Pilar Somovilla
- Microbes in Health and Welfare Program, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
- Departamento de Biología Molecular, Universidad Autónoma de Madrid, Madrid 28049, Spain
| | - Cristina Ferrer-Orta
- Structural and Molecular Biology Department, Institut de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona 08028, Spain
| | - Brenda Martínez-González
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid 28040, Spain
| | - Sergi Vázquez-Monteagudo
- Structural and Molecular Biology Department, Institut de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona 08028, Spain
| | | | - María Eugenia Soria
- Microbes in Health and Welfare Program, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid 28040, Spain
| | - Carlos García-Crespo
- Microbes in Health and Welfare Program, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
| | - Ana Isabel de Ávila
- Microbes in Health and Welfare Program, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
| | - Antoni Durán-Pastor
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
| | - Ignacio Gadea
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid 28040, Spain
| | - Cecilio López-Galíndez
- Unidad de Virología Molecular, Laboratorio de Referencia e Investigación en retrovirus, Centro Nacional de Microbiología, Instituto de salud Carlos III, Majadahonda 28222, Spain
| | - Federico Moran
- Departamento de Bioquímica y Biología Molecular, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Ramon Lorenzo-Redondo
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Center for Pathogen Genomics and Microbial Evolution, Northwestern University Havey Institute for Global Health, Chicago, IL 60611
| | - Nuria Verdaguer
- Structural and Molecular Biology Department, Institut de Biología Molecular de Barcelona, Consejo Superior de Investigaciones Científicas, Barcelona 08028, Spain
| | - Celia Perales
- Department of Molecular and Cell Biology, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
- Department of Clinical Microbiology, Instituto de Investigación Sanitaria-Fundación Jiménez Díaz University Hospital, Universidad Autónoma de Madrid, Madrid 28040, Spain
| | - Esteban Domingo
- Microbes in Health and Welfare Program, Centro de Biología Molecular "Severo Ochoa" (CSIC-UAM), Consejo Superior de Investigaciones Científicas, Madrid 28049, Spain
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Woodruff MC, Faliti CE, Sanz I. Systems biology of B cells in COVID-19. Semin Immunol 2024; 72:101875. [PMID: 38489999 DOI: 10.1016/j.smim.2024.101875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 03/04/2024] [Accepted: 03/04/2024] [Indexed: 03/17/2024]
Abstract
The integration of multi-'omic datasets into complex systems-wide assessments has become a mainstay in immunologic investigation. This focus on high-dimensional data collection and analysis was on full display in the investigation of COVID-19, the respiratory illness resulting from infection by the novel coronavirus SARS-CoV-2. Particularly in the area of B cell biology, tremendous efforts in both cellular and serologic investigation have resulted in an increasingly detailed mapping of the coordinated effector, memory, and antibody secreting cell responses that underpin the development of humoral immunity in response to primary viral infection. Further, the rapid development and deployment of effective vaccines has allowed for the assessment of developing memory responses across a wide variety of immune contexts, including in patients with compromised immune function. The result has been a period of rapid gains in the understanding of B cell biology unrestricted to the study of COVID-19. Here, we outline the systems-level technologies that have been routinely implemented in these investigations throughout the pandemic, and discuss how their use has led to clear and applicable gains in pursuance of the amelioration of human infectious disease and beyond.
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Affiliation(s)
- Matthew C Woodruff
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA; Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA.
| | - Caterina E Faliti
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA; Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA.
| | - Ignacio Sanz
- Department of Medicine, Division of Rheumatology, Lowance Center for Human Immunology, Emory University, Atlanta, GA, USA; Emory Autoimmunity Center of Excellence, Emory University, Atlanta, GA, USA
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Satapathy P. Global spread of COVID-19's JN.1 variant: Implications and public health responses. New Microbes New Infect 2024; 57:101225. [PMID: 38357690 PMCID: PMC10864788 DOI: 10.1016/j.nmni.2024.101225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/16/2024] Open
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145
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García-López R, Taboada B, Zárate S, Muñoz-Medina JE, Salas-Lais AG, Herrera-Estrella A, Boukadida C, Vazquez-Perez JA, Gómez-Gil B, Sanchez-Flores A, Arias CF. Exploration of low-frequency allelic variants of SARS-CoV-2 genomes reveals coinfections in Mexico occurred during periods of VOCs turnover. Microb Genom 2024; 10:001220. [PMID: 38512312 PMCID: PMC11004493 DOI: 10.1099/mgen.0.001220] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 03/04/2024] [Indexed: 03/22/2024] Open
Abstract
A total of 14 973 alleles in 29 661 sequenced samples collected between March 2021 and January 2023 by the Mexican Consortium for Genomic Surveillance (CoViGen-Mex) and collaborators were used to construct a thorough map of mutations of the Mexican SARS-CoV-2 genomic landscape containing Intra-Patient Minor Allelic Variants (IPMAVs), which are low-frequency alleles not ordinarily present in a genomic consensus sequence. This additional information proved critical in identifying putative coinfecting variants included alongside the most common variants, B.1.1.222, B.1.1.519, and variants of concern (VOCs) Alpha, Gamma, Delta, and Omicron. A total of 379 coinfection events were recorded in the dataset (a rate of 1.28 %), resulting in the first such catalogue in Mexico. The most common putative coinfections occurred during the spread of Delta or after the introduction of Omicron BA.2 and its descendants. Coinfections occurred constantly during periods of variant turnover when more than one variant shared the same niche and high infection rate was observed, which was dependent on the local variants and time. Coinfections might occur at a higher frequency than customarily reported, but they are often ignored as only the consensus sequence is reported for lineage identification.
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Affiliation(s)
- Rodrigo García-López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Blanca Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Selene Zárate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Mexico City, Mexico
| | - José Esteban Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Angel Gustavo Salas-Lais
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Alfredo Herrera-Estrella
- Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Centro de Investigación y de Estudios Avanzados del IPN, Irapuato, Guanajuato, Mexico
| | - Celia Boukadida
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Joel Armando Vazquez-Perez
- Laboratorio de Biología Molecular de Enfermedades Emergentes y EPOC, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Mexico City, Mexico
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo AC, Unidad Mazatlán, Mazatlán, Sinaloa, Mexico
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
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Zhu J, Guo G, Liu J, Li X, Yang X, Liu M, Fu C, Zeng J, Li J. One-pot synthesized Au@Pt nanostars-based lateral flow immunoassay for colorimetric and photothermal dual-mode detection of SARS-CoV-2 nucleocapsid antibody. Anal Chim Acta 2024; 1292:342241. [PMID: 38309851 DOI: 10.1016/j.aca.2024.342241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/06/2024] [Accepted: 01/11/2024] [Indexed: 02/05/2024]
Abstract
In addition to confirming virus infection, quantitative identification of the antibodies to severe acute respiratory syndrome coronavirus 2(SARS-CoV-2) also evaluates persons immunity to guide personal protection. However, portable assays for fast and accurate quantification of SARS-CoV-2 antibodies remain challenging. In this work, we synthesized Au@Pt star-like nanoparticles (NPs) quickly and easily by a one-pot wet-chemical approach, allowing the stellate Au core to be partially decorated by Pt nanoshells. The nanoparticles were used as probe in a lateral flow immunoassay (LFIA) that operated in both colorimetric and photothermal dual modes, which could detect the antibodies to the SARS-CoV-2 nucleocapsid (N) protein with high sensitivity. Due to the sharp tips on the external region of nanostars and surface plasmon coupling effect between the Au core and Pt shell, the NIR absorption capacity and photothermal performance of these NPs were exceptional. Under optimal conditions, the colorimetric mode's detection limit for SARS-CoV-2 N protein antibody was 1 ng mL-1, which is significantly lower by 2-order of magnitude compared to commercially available colloidal gold strips. And the detection limit for the photothermal mode was as low as 24.91 pg mL-1, which was approximately 40-fold more sensitive than colorimetric detection. Moreover, the method demonstrated favorable specificity, reproducibility and stability. Finally, the approach was employed for the successful identification of actual serum samples. Therefore, the dual-mode LFIA can be applied for screening and tracking the early immunological reaction to SARS-CoV-2, and it has great promise for clinical application.
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Affiliation(s)
- Jinyue Zhu
- College of Chemistry and Chemical Engineering and State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao, 266580, PR China
| | - Gengchen Guo
- College of Chemistry and Chemical Engineering and State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao, 266580, PR China
| | - Jianting Liu
- Huangdao Customs of the People's Republic of China, 266580, PR China
| | - Xiang Li
- College of Chemistry and Chemical Engineering and State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao, 266580, PR China
| | - Xianning Yang
- College of Chemistry and Chemical Engineering and State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao, 266580, PR China
| | - Min Liu
- College of Chemistry and Chemical Engineering and State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao, 266580, PR China
| | - Chunhui Fu
- Qingdao Henderson Biological Technology Co., Ltd, Qingdao, 266109, PR China
| | - Jingbin Zeng
- College of Chemistry and Chemical Engineering and State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao, 266580, PR China.
| | - Jingwen Li
- College of Chemistry and Chemical Engineering and State Key Laboratory of Heavy Oil Processing, China University of Petroleum (East China), Qingdao, 266580, PR China.
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147
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Yao Z, Zhang L, Duan Y, Tang X, Lu J. Molecular insights into the adaptive evolution of SARS-CoV-2 spike protein. J Infect 2024; 88:106121. [PMID: 38367704 DOI: 10.1016/j.jinf.2024.106121] [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: 12/01/2023] [Revised: 02/02/2024] [Accepted: 02/10/2024] [Indexed: 02/19/2024]
Abstract
The COVID-19 pandemic, caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has substantially damaged the global economy and human health. The spike (S) protein of coronaviruses plays a pivotal role in viral entry by binding to host cell receptors. Additionally, it acts as the primary target for neutralizing antibodies in those infected and is the central focus for currently utilized or researched vaccines. During the virus's adaptation to the human host, the S protein of SARS-CoV-2 has undergone significant evolution. As the COVID-19 pandemic has unfolded, new mutations have arisen and vanished, giving rise to distinctive amino acid profiles within variant of concern strains of SARS-CoV-2. Notably, many of these changes in the S protein have been positively selected, leading to substantial alterations in viral characteristics, such as heightened transmissibility and immune evasion capabilities. This review aims to provide an overview of our current understanding of the structural implications associated with key amino acid changes in the S protein of SARS-CoV-2. These research findings shed light on the intricate and dynamic nature of viral evolution, underscoring the importance of continuous monitoring and analysis of viral genomes. Through these molecular-level investigations, we can attain deeper insights into the virus's adaptive evolution, offering valuable guidance for designing vaccines and developing antiviral drugs to combat the ever-evolving viral threats.
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Affiliation(s)
- Zhuocheng Yao
- College of Marine Life Sciences, Ocean University of China, Qingdao 266003, China
| | - Lin Zhang
- College of Fishery, Ocean University of China, Qingdao 266003, China
| | - Yuange Duan
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China.
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Kahrizi MS, Nasiri K, Ebrahimzadeh F, Yaseri AF, Ghodratizadeh S, Gholamrezaei M, Rahat Dahmardeh A, Adili A, Amjidifar R, Hemmatzadeh M, Arabi M, Maghsoudi MR, Mohammadi H. Lymphopenia associated with survivin and its downstream pathway in COVID-19 serving as a potential route in COVID-19 pathogenesis. Adv Med Sci 2024; 69:190-197. [PMID: 38521459 DOI: 10.1016/j.advms.2024.03.006] [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: 12/14/2022] [Revised: 02/16/2024] [Accepted: 03/20/2024] [Indexed: 03/25/2024]
Abstract
PURPOSE Starting in 2019, coronavirus disease 2019 (COVID-19) caused an epidemic that was growing rapidly and has harmed millions of people globally. It has been demonstrated that survivin regulates lymphocyte survival, a main route involved in COVID-19 pathogenesis. Survivin belongs to the inhibitor of apoptosis protein (IAP) family, and its primary functions comprise regulating mitosis and inhibiting apoptosis. Since lower survivin expression has been shown to increase the sensitivity of lymphocytes to apoptotic induction, we looked into the function of survivin and its corresponding pathways in COVID-19 pathogenesis. MATERIALS AND METHODS The expression of survivin, X-linked inhibitor of apoptosis protein (XIAP), caspases 3, 7, 9, and poly (ADP-ribose) polymerase (PARP) was evaluated at both mRNA and protein levels in peripheral blood mononuclear cells (PBMCs) derived from healthy donors and patients with severe and moderate COVID-19 by qRT-PCR and Western blotting, respectively. Then, we enforced apoptosis to COVID-19 patient-derived lymphocytes, and the percent was assessed by flow cytometry. RESULTS Survivin and XIAP were less expressed in PBMCs derived from COVID-19 patients as apoptosis inhibitors than PARP, cleaved-PARP, caspase 9, and cleaved caspases 3 and 7, according to the results of real-time PCR and Western blot analysis. Additionally, according to the flow cytometry results, the down-regulation of survivin served as a potential factor in the lymphocyte depletion observed in patients with COVID-19. CONCLUSION The role of survivin and its related pathway was first discovered in the development of COVID-19 and may serve as a potential prognostic and therapeutic target.
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Affiliation(s)
| | - Kamyar Nasiri
- Department of Dentistry, Islamic Azad University, Tehran, Iran
| | - Farnoosh Ebrahimzadeh
- Department of Internal Medicine, Faculty of Medicine, Mashhad University of Medical Sciences, Mashhad, Iran
| | | | - Soroush Ghodratizadeh
- Department of Biochemistry, Faculty of Medicine, Urmia University of Medical Sciences, Urmia, Iran
| | - Mostafa Gholamrezaei
- Department of Parasitology and Mycology, School of Medicine, Shahid Sadoughi University of Medical Sciences, Yazd, Iran
| | - Alireza Rahat Dahmardeh
- Department of Anesthesiology and Critical Care, School of Medicine, Zahedan University of Medical Sciences, Zahedan, Iran
| | - Ali Adili
- Department of Oncology, Tabriz University of Medical Sciences, Tabriz, Iran; Senior Adult Oncology Department, Moffitt Cancer Center, University of South, Florida, USA
| | - Rosita Amjidifar
- Department of Microbiology, Islamic Azad University of Iran, Ahar, Iran
| | - Maryam Hemmatzadeh
- Department of Immunology, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Mohsen Arabi
- Department of Physiology, Pharmacology and Medical Physics, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran
| | - Mohammad Reza Maghsoudi
- Faculty of Emergency Medicine & Toxicology, Emergency Department, Alborz University of Medical Sciences, Karaj, Iran
| | - Hamed Mohammadi
- Non-Communicable Diseases Research Center, Alborz University of Medical Sciences, Karaj, Iran; Department of Immunology, School of Medicine, Alborz University of Medical Sciences, Karaj, Iran.
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Katte RH, Ao Y, Xu W, Han Y, Zhong G, Ghimire D, Florence J, Tucker TA, Lu M. Differentiating Cell Entry Potentials of SARS-CoV-2 Omicron Subvariants on Human Lung Epithelium Cells. Viruses 2024; 16:391. [PMID: 38543757 PMCID: PMC10975267 DOI: 10.3390/v16030391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 02/25/2024] [Accepted: 02/28/2024] [Indexed: 04/01/2024] Open
Abstract
The surface spike (S) glycoprotein mediates cell entry of SARS-CoV-2 into the host through fusion at the plasma membrane or endocytosis. Omicron lineages/sublineages have acquired extensive mutations in S to gain transmissibility advantages and altered antigenicity. The fusogenicity, antigenicity, and evasion of Omicron subvariants have been extensively investigated at unprecedented speed to align with the mutation rate of S. Cells that overexpress receptors/cofactors are mostly used as hosts to amplify infection sensitivity to tested variants. However, systematic cell entry comparisons of most prior dominant Omicron subvariants using human lung epithelium cells are yet to be well-studied. Here, with human bronchial epithelium BEAS-2B cells as the host, we compared single-round virus-to-cell entry and cell-to-cell fusion of Omicron BA.1, BA.5, BQ.1.1, CH.1.1, XBB.1.5, and XBB.1.16 based upon split NanoLuc fusion readout assays and the S-pseudotyped lentivirus system. Virus-to-cell entry of tested S variants exhibited cell-type dependence. The parental Omicron BA.1 required more time to develop full entry to HEK293T-ACE2-TMPRSS2 than BEAS-2B cells. Compared to unchanged P681, S-cleavage constructs of P681H/R did not have any noticeable advantages in cell entry. Omicron BA.1 and its descendants entered BEAS-2B cells more efficiently than D614G, and it was slightly less or comparable to that of Delta. Serine protease-pretreated Omicron subvariants enhanced virus-to-cell entry in a dose-dependent manner, suggesting fusion at the plasma membrane persists as a productive cell entry route. Spike-mediated cell-to-cell fusion and total S1/S2 processing of Omicron descendants were similar. Our results indicate no obvious entry or fusion advantages of recent Omicron descendants over preceding variants since Delta, thus supporting immune evasion conferred by antigenicity shifts due to altered S sequences as probably the primary viral fitness driver.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Maolin Lu
- Department of Cellular and Molecular Biology, School of Medicine, University of Texas at Tyler Health Science Center, Tyler, TX 75708, USA; (R.H.K.); (Y.H.); (T.A.T.)
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Tavera Gonzales A, Bazalar Gonzales J, Silvestre Espejo T, Leiva Galarza M, Rodríguez Cueva C, Carhuaricra Huamán D, Luna Espinoza L, Maturrano Hernández A. Possible Spreading of SARS-CoV-2 from Humans to Captive Non-Human Primates in the Peruvian Amazon. Animals (Basel) 2024; 14:732. [PMID: 38473117 DOI: 10.3390/ani14050732] [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: 12/10/2023] [Revised: 02/02/2024] [Accepted: 02/03/2024] [Indexed: 03/14/2024] Open
Abstract
Human-to-animal transmission events of SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2) have been reported in both domestic and wild species worldwide. Despite the high rates of contagion and mortality during the COVID-19 (Coronavirus Diseases 2019) pandemic in Peru, no instances of natural virus infection have been documented in wild animals, particularly in the Amazonian regions where human-wildlife interactions are prevalent. In this study, we conducted a surveillance investigation using viral RNA sequencing of fecal samples collected from 76 captive and semi-captive non-human primates (NHPs) in the Loreto, Ucayali, and Madre de Dios regions between August 2022 and February 2023. We detected a segment of the RNA-dependent RNA polymerase (RdRp) gene of SARS-CoV-2 by metagenomic sequencing in a pooled fecal sample from captive white-fronted capuchins (Cebus unicolor) at a rescue center in Bello Horizonte, Ucayali. Phylogenetic analysis further confirmed that the retrieved partial sequence of the RdRp gene matched the SARS-CoV-2 genome. This study represents the first documented instance of molecular SARS-CoV-2 detection in NHPs in the Peruvian Amazon, underscoring the adverse impact of anthropic activities on the human-NHP interface and emphasizing the importance of ongoing surveillance for early detection and prediction of future emergence of new SARS-CoV-2 variants in animals.
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Affiliation(s)
- Andrea Tavera Gonzales
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
| | - Jhonathan Bazalar Gonzales
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
- Asociación Equipo Primatológico del Perú, Iquitos 16008, Peru
| | - Thalía Silvestre Espejo
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
| | - Milagros Leiva Galarza
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
| | - Carmen Rodríguez Cueva
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
| | - Dennis Carhuaricra Huamán
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
- Programa de Pós-Graduação Interunidades em Bioinformática, Instituto de Matemática e Estatística, Universidade de São Paulo, Rua do Matão 1010, São Paulo 05508-090, Brazil
| | - Luis Luna Espinoza
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
| | - Abelardo Maturrano Hernández
- Research Group in Biotechnology Applied to Animal Health, Production and Conservation (SANIGEN), Laboratorio de Biología y Genética Molecular, Facultad de Medicina Veterinaria, Universidad Nacional Mayor de San Marcos, Lima 15021, Peru
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