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Colson P, Fantini J, Delerce J, Bader W, Levasseur A, Pontarotti P, Devaux C, Raoult D. "Outlaw" mutations in quasispecies of SARS-CoV-2 inhibit replication. Emerg Microbes Infect 2024; 13:2368211. [PMID: 38916498 PMCID: PMC11207925 DOI: 10.1080/22221751.2024.2368211] [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: 11/09/2023] [Accepted: 06/10/2024] [Indexed: 06/26/2024]
Abstract
The evolution of SARS-CoV-2, the agent of COVID-19, has been remarkable for its high mutation potential, leading to the appearance of variants. Some mutations have never appeared in the published genomes, which represent consensus, or bona fide genomes. Here we tested the hypothesis that mutations that did not appear in consensus genomes were, in fact, as frequent as the mutations that appeared during the various epidemic episodes, but were not expressed because lethal. To identify these mutations, we analysed the genomes of 90 nasopharyngeal samples and the quasispecies determined by next-generation sequencing. Mutations observed in the quasispecies and not in the consensus genomes were considered to be lethal, what we called "outlaw" mutations. Among these mutations, we analysed the 21 most frequent. Eight of these "outlaws" were in the RNA polymerase and we were able to use a structural biology model and molecular dynamics simulations to demonstrate the functional incapacity of these mutated RNA polymerases. Three other mutations affected the spike, a major protein involved in the pathogenesis of COVID-19. Overall, by analysing the SARS-CoV-2 quasispecies obtained during sequencing, this method made it possible to identify "outlaws," showing areas that could potentially become the target of treatments.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), Marseille, France
| | - Jacques Fantini
- INSERM UMR UA 16, Aix-Marseille Université, Marseille, France
| | | | - Wahiba Bader
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, Marseille, France
| | - Pierre Pontarotti
- IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS), Marseille, France
| | - Christian Devaux
- IHU Méditerranée Infection, Marseille, France
- Department of Biological Sciences, Centre National de la Recherche 16 Scientifique (CNRS), Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, Marseille, France
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2
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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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3
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Chen K, Gao Y, Li J. New-onset and relapsed Graves' disease following COVID-19 vaccination: a comprehensive review of reported cases. Eur J Med Res 2023; 28:232. [PMID: 37443067 DOI: 10.1186/s40001-023-01210-7] [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: 01/08/2023] [Accepted: 07/05/2023] [Indexed: 07/15/2023] Open
Abstract
Global Coronavir us disease 2019 (COVID-19) vaccination efforts are being intensified to combat the pandemic. As the frequency of immunization against COVID-19 has increased, some adverse effects related to vaccination have emerged. Within this context, this article reviewed 62 Graves' disease (GD) cases following COVID-19 vaccination, to probe the potential association between the vaccination and the onset of GD. A comprehensive search of the PubMed, Web of Science, and Scopus databases was conducted to collect GD cases following COVID-19 vaccination up to June 7, 2023. Among the 62 GD cases included in this review, there were 33 (53.2%) new-onset GD and 10 (16.1%) relapsed GD patients following mRNA vaccination, 14 (22.6%) new-onset GD and 4 (6.5%) relapsed GD patients following viral vector vaccination, and 1 (1.6%) relapsed GD patients following inactivated vaccination. Median durations to symptoms onset for new-onset and relapsed GD were 12 (range: 1-60) and 21 (range: 5-30) days following mRNA vaccination, while 7 (range: 1-28) and 14 (range: 10-14) days following viral vector vaccination, respectively. While the definitive pathogenesis of GD following COVID-19 vaccination remains unclear, it might be associated with cross-immune responses triggered by molecular mimicry, and an adjuvant-induced autoimmune/inflammatory syndrome. However, due to the limited number of observed GD cases following COVID-19 vaccination and the lack of systematic experimental studies, a causal relationship between COVID-19 vaccination and the onset of GD has not been definitively confirmed. It should be highlighted that most of GD patients following COVID-19 vaccination experienced positive outcomes after treatment. In the broader context of ending the COVID-19 pandemic and reducing mortality rates, the benefits of COVID-19 vaccination significantly outweigh mild risks such as treatable GD. Adherence to the COVID-19 vaccination schedule is therefore imperative in effectively managing the pandemic.
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Affiliation(s)
- Kan Chen
- Department of Endocrinology and Metabolism, The Institute of Endocrinology, NHC Key Laboratory of Diagnosis and Treatment of Thyroid Disease, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Yiyang Gao
- Department of Endocrinology and Metabolism, The Institute of Endocrinology, NHC Key Laboratory of Diagnosis and Treatment of Thyroid Disease, The First Hospital of China Medical University, Shenyang, Liaoning, China
| | - Jing Li
- Department of Endocrinology and Metabolism, The Institute of Endocrinology, NHC Key Laboratory of Diagnosis and Treatment of Thyroid Disease, The First Hospital of China Medical University, Shenyang, Liaoning, China.
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Bader W, Delerce J, Aherfi S, La Scola B, Colson P. Quasispecies Analysis of SARS-CoV-2 of 15 Different Lineages during the First Year of the Pandemic Prompts Scratching under the Surface of Consensus Genome Sequences. Int J Mol Sci 2022; 23:15658. [PMID: 36555300 PMCID: PMC9779826 DOI: 10.3390/ijms232415658] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/01/2022] [Accepted: 12/02/2022] [Indexed: 12/14/2022] Open
Abstract
The tremendous majority of SARS-CoV-2 genomic data so far neglected intra-host genetic diversity. Here, we studied SARS-CoV-2 quasispecies based on data generated by next-generation sequencing (NGS) of complete genomes. SARS-CoV-2 raw NGS data had been generated for nasopharyngeal samples collected between March 2020 and February 2021 by the Illumina technology on a MiSeq instrument, without prior PCR amplification. To analyze viral quasispecies, we designed and implemented an in-house Excel file (“QuasiS”) that can characterize intra-sample nucleotide diversity along the genomes using data of the mapping of NGS reads. We compared intra-sample genetic diversity and global genetic diversity available from Nextstrain. Hierarchical clustering of all samples based on the intra-sample genetic diversity was performed and visualized with the Morpheus web application. NGS mapping data from 110 SARS-CoV-2-positive respiratory samples characterized by a mean depth of 169 NGS reads/nucleotide position and for which consensus genomes that had been obtained were classified into 15 viral lineages were analyzed. Mean intra-sample nucleotide diversity was 0.21 ± 0.65%, and 5357 positions (17.9%) exhibited significant (>4%) diversity, in ≥2 genomes for 1730 (5.8%) of them. ORF10, spike, and N genes had the highest number of positions exhibiting diversity (0.56%, 0.34%, and 0.24%, respectively). Nine hot spots of intra-sample diversity were identified in the SARS-CoV-2 NSP6, NSP12, ORF8, and N genes. Hierarchical clustering delineated a set of six genomes of different lineages characterized by 920 positions exhibiting intra-sample diversity. In addition, 118 nucleotide positions (0.4%) exhibited diversity at both intra- and inter-patient levels. Overall, the present study illustrates that the SARS-CoV-2 consensus genome sequences are only an incomplete and imperfect representation of the entire viral population infecting a patient, and that quasispecies analysis may allow deciphering more accurately the viral evolutionary pathways.
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Affiliation(s)
- Wahiba Bader
- IHU Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
| | - Jeremy Delerce
- IHU Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France
| | - Sarah Aherfi
- IHU Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
| | - Bernard La Scola
- IHU Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
| | - Philippe Colson
- IHU Méditerranée Infection, 19–21 Boulevard Jean Moulin, 13005 Marseille, France
- Microbes Evolution Phylogeny and Infections (MEPHI), Institut de Recherche pour le Développement (IRD), Aix-Marseille University, 27 Boulevard Jean Moulin, 13005 Marseille, France
- Assistance Publique-Hôpitaux de Marseille (AP-HM), 264 rue Saint-Pierre, 13005 Marseille, France
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5
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Hao Y, Wang Y, Wang M, Zhou L, Shi J, Cao J, Wang D. The origins of COVID-19 pandemic: A brief overview. Transbound Emerg Dis 2022; 69:3181-3197. [PMID: 36218169 PMCID: PMC9874793 DOI: 10.1111/tbed.14732] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 09/26/2022] [Accepted: 10/04/2022] [Indexed: 02/06/2023]
Abstract
The novel coronavirus disease (COVID-19) outbreak that emerged at the end of 2019 has now swept the world for more than 2 years, causing immeasurable damage to the lives and economies of the world. It has drawn so much attention to discovering how the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated and entered the human body. The current argument revolves around two contradictory theories: a scenario of laboratory spillover events and human contact with zoonotic diseases. Here, we reviewed the transmission, pathogenesis, possible hosts, as well as the genome and protein structure of SARS-CoV-2, which play key roles in the COVID-19 pandemic. We believe the coronavirus was originally transmitted to human by animals rather than by a laboratory leak. However, there still needs more investigations to determine the source of the pandemic. Understanding how COVID-19 emerged is vital to developing global strategies for mitigating future outbreaks.
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Affiliation(s)
- Ying‐Jian Hao
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - Yu‐Lan Wang
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - Mei‐Yue Wang
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - Lan Zhou
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - Jian‐Yun Shi
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - Ji‐Min Cao
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
| | - De‐Ping Wang
- Key Laboratory of Cellular Physiology, Ministry of Education, Department of PhysiologyShanxi Medical UniversityTaiyuanChina
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6
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Colson P, Gautret P, Delerce J, Chaudet H, Pontarotti P, Forterre P, Tola R, Bedotto M, Delorme L, Bader W, Levasseur A, Lagier J, Million M, Yahi N, Fantini J, La Scola B, Fournier P, Raoult D. The emergence, spread and vanishing of a French SARS-CoV-2 variant exemplifies the fate of RNA virus epidemics and obeys the Mistigri rule. J Med Virol 2022; 95:e28102. [PMID: 36031728 PMCID: PMC9539255 DOI: 10.1002/jmv.28102] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/25/2022] [Accepted: 08/25/2022] [Indexed: 01/11/2023]
Abstract
The nature and dynamics of mutations associated with the emergence, spread, and vanishing of SARS-CoV-2 variants causing successive waves are complex. We determined the kinetics of the most common French variant ("Marseille-4") for 10 months since its onset in July 2020. Here, we analyzed and classified into subvariants and lineages 7453 genomes obtained by next-generation sequencing. We identified two subvariants, Marseille-4A, which contains 22 different lineages of at least 50 genomes, and Marseille-4B. Their average lifetime was 4.1 ± 1.4 months, during which 4.1 ± 2.6 mutations accumulated. Growth rate was 0.079 ± 0.045, varying from 0.010 to 0.173. Most of the lineages exhibited a bell-shaped distribution. Several beneficial mutations at unpredicted sites initiated a new outbreak, while the accumulation of other mutations resulted in more viral heterogenicity, increased diversity and vanishing of the lineages. Marseille-4B emerged when the other Marseille-4 lineages vanished. Its ORF8 gene was knocked out by a stop codon, as reported in SARS-CoV-2 of mink and in the Alpha variant. This subvariant was associated with increased hospitalization and death rates, suggesting that ORF8 is a nonvirulence gene. We speculate that the observed heterogenicity of a lineage may predict the end of the outbreak.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée InfectionMarseilleFrance,Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI)Aix‐Marseille UniversityMarseilleFrance
| | - Philippe Gautret
- IHU Méditerranée InfectionMarseilleFrance,Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance,Institut de Recherche pour le Développement (IRD), Vecteurs—Infections Tropicales et Méditerranéennes (VITROME)Aix‐Marseille UniversityMarseilleFrance
| | | | - Hervé Chaudet
- IHU Méditerranée InfectionMarseilleFrance,Institut de Recherche pour le Développement (IRD), Vecteurs—Infections Tropicales et Méditerranéennes (VITROME)Aix‐Marseille UniversityMarseilleFrance,French Armed Forces Center for Epidemiology and Public Health (CESPA), Camp de Sainte MartheMarseilleFrance
| | - Pierre Pontarotti
- IHU Méditerranée InfectionMarseilleFrance,Centre national de la recherche scientifique (CNRS)MarseilleFrance
| | - Patrick Forterre
- Département de MicrobiologieInstitut PasteurParisFrance,Institute for Integrative Biology of the Cell (I2BC)Université Paris‐Saclay, CEA, CNRSGif‐sur‐YvetteFrance
| | - Raphael Tola
- IHU Méditerranée InfectionMarseilleFrance,Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance
| | | | - Léa Delorme
- IHU Méditerranée InfectionMarseilleFrance,Institut de Recherche pour le Développement (IRD), Vecteurs—Infections Tropicales et Méditerranéennes (VITROME)Aix‐Marseille UniversityMarseilleFrance,French Armed Forces Center for Epidemiology and Public Health (CESPA), Camp de Sainte MartheMarseilleFrance
| | - Wahiba Bader
- IHU Méditerranée InfectionMarseilleFrance,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI)Aix‐Marseille UniversityMarseilleFrance
| | - Anthony Levasseur
- IHU Méditerranée InfectionMarseilleFrance,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI)Aix‐Marseille UniversityMarseilleFrance
| | - Jean‐Christophe Lagier
- IHU Méditerranée InfectionMarseilleFrance,Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI)Aix‐Marseille UniversityMarseilleFrance
| | - Matthieu Million
- IHU Méditerranée InfectionMarseilleFrance,Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI)Aix‐Marseille UniversityMarseilleFrance
| | - Nouara Yahi
- INSERM UMR_S 1072Aix‐Marseille UniversitéMarseilleFrance
| | | | - Bernard La Scola
- IHU Méditerranée InfectionMarseilleFrance,Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI)Aix‐Marseille UniversityMarseilleFrance
| | - Pierre‐Edouard Fournier
- IHU Méditerranée InfectionMarseilleFrance,Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI)Aix‐Marseille UniversityMarseilleFrance
| | - Didier Raoult
- IHU Méditerranée InfectionMarseilleFrance,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI)Aix‐Marseille UniversityMarseilleFrance
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7
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Hameedi MA, T Prates E, Garvin MR, Mathews II, Amos BK, Demerdash O, Bechthold M, Iyer M, Rahighi S, Kneller DW, Kovalevsky A, Irle S, Vuong VQ, Mitchell JC, Labbe A, Galanie S, Wakatsuki S, Jacobson D. Structural and functional characterization of NEMO cleavage by SARS-CoV-2 3CLpro. Nat Commun 2022; 13:5285. [PMID: 36075915 PMCID: PMC9453703 DOI: 10.1038/s41467-022-32922-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 08/23/2022] [Indexed: 11/15/2022] Open
Abstract
In addition to its essential role in viral polyprotein processing, the SARS-CoV-2 3C-like protease (3CLpro) can cleave human immune signaling proteins, like NF-κB Essential Modulator (NEMO) and deregulate the host immune response. Here, in vitro assays show that SARS-CoV-2 3CLpro cleaves NEMO with fine-tuned efficiency. Analysis of the 2.50 Å resolution crystal structure of 3CLpro C145S bound to NEMO226-234 reveals subsites that tolerate a range of viral and host substrates through main chain hydrogen bonds while also enforcing specificity using side chain hydrogen bonds and hydrophobic contacts. Machine learning- and physics-based computational methods predict that variation in key binding residues of 3CLpro-NEMO helps explain the high fitness of SARS-CoV-2 in humans. We posit that cleavage of NEMO is an important piece of information to be accounted for, in the pathology of COVID-19.
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Affiliation(s)
- Mikhail A Hameedi
- SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, Structural Molecular Biology, Menlo Park, CA, 94025, USA
- SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, Biosciences, Menlo Park, CA, 94025, USA
- Department of Structural Biology, Stanford University, Stanford, CA, 94305, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
| | - Erica T Prates
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Michael R Garvin
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Irimpan I Mathews
- SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, Structural Molecular Biology, Menlo Park, CA, 94025, USA
| | - B Kirtley Amos
- Department of Horticulture, University of Kentucky, Lexington, KY, USA
| | - Omar Demerdash
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Mark Bechthold
- Department of Structural Biology, Stanford University, Stanford, CA, 94305, USA
| | - Mamta Iyer
- Chapman University School of Pharmacy, Irvine, CA, 92618, USA
| | - Simin Rahighi
- Chapman University School of Pharmacy, Irvine, CA, 92618, USA
| | - Daniel W Kneller
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Andrey Kovalevsky
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
- Neutron Scattering Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Stephan Irle
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, TN, 37831, USA
| | - Van-Quan Vuong
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Julie C Mitchell
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Audrey Labbe
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
| | - Stephanie Galanie
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA
- Department of Process Research and Development, Merck & Co., Inc., Rahway, NJ, 07065, USA
| | - Soichi Wakatsuki
- SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, Structural Molecular Biology, Menlo Park, CA, 94025, USA.
- SLAC National Accelerator Laboratory, Stanford Synchrotron Radiation Lightsource, Biosciences, Menlo Park, CA, 94025, USA.
- Department of Structural Biology, Stanford University, Stanford, CA, 94305, USA.
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA.
| | - Daniel Jacobson
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA.
- Biosciences Division, Oak Ridge National Laboratory, Oak Ridge, TN, USA.
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8
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Okendo J, Musanabaganwa C, Mwangi P, Nyaga M, Onywera H. SARS-CoV-2-positive patients display considerable differences in proteome diversity in urine, nasopharyngeal, gargle solution and bronchoalveolar lavage fluid samples. PLoS One 2022; 17:e0271870. [PMID: 35939435 PMCID: PMC9359582 DOI: 10.1371/journal.pone.0271870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 07/09/2022] [Indexed: 11/18/2022] Open
Abstract
Proteome profile changes post-severe acute respiratory syndrome coronavirus 2 (post-SARS-CoV-2) infection in different body sites of humans remains an active scientific investigation whose solutions stand a chance of providing more information on what constitutes SARS-CoV-2 pathogenesis. While proteomics has been used to understand SARS-CoV-2 pathogenesis, there are limited data about the status of proteome profile in different human body sites infected by the SARS-CoV-2 virus. To bridge this gap, our study aims to characterize the proteins secreted in urine, bronchoalveolar lavage fluid (BALF), gargle solution, and nasopharyngeal samples and assess the proteome differences in these body samples collected from SARS-CoV-2-positive patients. We downloaded publicly available proteomic data from (https://www.ebi.ac.uk/pride/). The data we downloaded had the following identifiers: (i) PXD019423, n = 3 from Charles Tanford Protein Center in Germany. (ii) IPX0002166000, n = 15 from Beijing Proteome Research Centre, China. (iii) IPX0002429000, n = 5 from Huazhong University of Science and Technology, China, and (iv) PXD022889, n = 18 from Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905 USA. MaxQuant was used for the human peptide spectral matching using human and SARS-CoV-2 proteome database which we downloaded from the UniProt database (access date 13th October 2021). The individuals infected with SARS-CoV-2 viruses displayed a different proteome diversity from the different body sites we investigated. Overally, we identified 1809 proteins across the four sample types we compared. Urine and BALF samples had significantly more abundant SARS-CoV-2 proteins than the other body sites we compared. Urine samples had 257(33.7%) unique proteins, followed by nasopharyngeal with 250(32.8%) unique proteins. Gargle solution and BALF had 38(5%) and 73(9.6%) unique proteins respectively. Urine, gargle solution, nasopharyngeal, and bronchoalveolar lavage fluid samples have different protein diversity in individuals infected with SARS-CoV-2. Moreover, our data also demonstrated that a given body site is characterized by a unique set of proteins in SARS-CoV-2 seropositive individuals.
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Affiliation(s)
- Javan Okendo
- Systems and Chemical Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- * E-mail:
| | | | - Peter Mwangi
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Martin Nyaga
- Next Generation Sequencing Unit and Division of Virology, Faculty of Health Sciences, University of the Free State, Bloemfontein, South Africa
| | - Harris Onywera
- Division of Medical Virology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Division of Medical Microbiology, Department of Pathology, Institute of Infectious Disease and Molecular Medicine, Faculty of Health Sciences, University of Cape Town, Cape Town, South Africa
- Research, Innovations and Academics Unit, Tunacare Services Health Providers Limited, Nairobi, Kenya
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9
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Liu Y, Ye Q. Safety and Efficacy of the Common Vaccines against COVID-19. Vaccines (Basel) 2022; 10:vaccines10040513. [PMID: 35455262 PMCID: PMC9027683 DOI: 10.3390/vaccines10040513] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/15/2022] [Accepted: 03/23/2022] [Indexed: 02/04/2023] Open
Abstract
The worldwide pandemic of coronavirus disease 2019 (COVID-19) has imposed a challenge on human health worldwide, and vaccination represents a vital strategy to control the pandemic. To date, multiple COVID-19 vaccines have been granted emergency use authorization, including inactivated vaccines, adenovirus-vectored vaccines, and nucleic acid vaccines. These vaccines have different technical principles, which will necessarily lead to differences in safety and efficacy. Therefore, we aim to implement a systematic review by synthesizing clinical experimental data combined with mass vaccination data and conducting a synthesis to evaluate the safety and efficacy of COVID-19 vaccines. Compared with other vaccines, adverse reactions after vaccination with inactivated vaccines are relatively low. The efficacy of inactivated vaccines is approximately 60%, adenovirus-vectored vaccines are 65%, and mRNA vaccines are 90%, which are always efficient against asymptomatic severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection, symptomatic COVID-19, COVID-19 hospitalization, severe or critical hospitalization, and death. RNA-based vaccines have a number of advantages and are one of the most promising vaccines identified to date and are particularly important during a pandemic. However, further improvements are required. In time, all the antibody levels weaken gradually, so a booster dose is needed to maintain immunity. Compared with homologous prime-boost immunization, heterologous prime-boost immunization prompts more robust humoral and cellular immune responses.
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10
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Colson P, Delerce J, Beye M, Levasseur A, Boschi C, Houhamdi L, Tissot-Dupont H, Yahi N, Million M, La Scola B, Fantini J, Raoult D, Fournier PE. First cases of infection with the 21L/BA.2 Omicron variant in Marseille, France. J Med Virol 2022; 94:3421-3430. [PMID: 35243660 PMCID: PMC9088623 DOI: 10.1002/jmv.27695] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 02/28/2022] [Accepted: 03/01/2022] [Indexed: 11/22/2022]
Abstract
The SARS‐CoV‐2 21K/BA.1, 21L/BA.2, and BA.3 Omicron variants have recently emerged worldwide. To date, the 21L/BA.2 Omicron variant has remained very minority globally but became predominant in Denmark instead of the 21K/BA.1 variant. Here, we describe the first cases diagnosed with this variant in south‐eastern France. We identified 13 cases using variant‐specific qPCR and next‐generation sequencing between 28/11/2021 and 31/01/2022, the first two cases being diagnosed in travelers returning from Tanzania. Overall, viral genomes displayed a mean (±standard deviation) number of 65.9 ± 2.5 (range, 61–69) nucleotide substitutions and 31.0 ± 8.3 (27–50) nucleotide deletions, resulting in 49.6 ± 2.2 (45–52) amino acid substitutions (including 28 in the spike protein) and 12.4 ± 1.1 (12–15) amino acid deletions. Phylogeny showed the distribution in three different clusters of these genomes, which were most closely related to genomes from England and South Africa, from Singapore and Nepal, or from France and Denmark. Structural predictions highlighted a significant enlargement and flattening of the surface of the 21L/BA.2 N‐terminal domain of the spike protein compared to that of the 21K/BA.1 Omicron variant, which may facilitate initial viral interactions with lipid rafts. Close surveillance is needed at global, country, and center scales to monitor the incidence and clinical outcome of the 21L/BA.2 Omicron variant.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), 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
| | - Jérémy Delerce
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Mamadou Beye
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France
| | - Anthony Levasseur
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Céline Boschi
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), 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
| | - Linda Houhamdi
- 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
| | - Hervé Tissot-Dupont
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), 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
| | - Nouara Yahi
- Aix-Marseille Université, INSERM UMR S 1072, 51 boulevard Pierre Dramard, 13015, Marseille, France
| | - Matthieu Million
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), 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
| | - Bernard La Scola
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), 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 S 1072, 51 boulevard Pierre Dramard, 13015, Marseille, France
| | - Didier Raoult
- IHU Méditerranée Infection, 19-21 boulevard Jean Moulin, 13005, Marseille, France.,Aix-Marseille Univ., Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI), 27 boulevard Jean Moulin, 13005, Marseille, France
| | - Pierre-Edouard Fournier
- 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 Univ., Institut de Recherche pour le Développement (IRD), Vecteurs - Infections Tropicales et Méditerranéennes (VITROME), 27 boulevard Jean Moulin, 13005, Marseille, France
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11
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Prates ET, Garvin MR, Jones P, Miller JI, Sullivan KA, Cliff A, Gazolla JGFM, Shah MB, Walker AM, Lane M, Rentsch CT, Justice A, Pavicic M, Romero J, Jacobson D. Antiviral Strategies Against SARS-CoV-2: A Systems Biology Approach. Methods Mol Biol 2022; 2452:317-351. [PMID: 35554915 DOI: 10.1007/978-1-0716-2111-0_19] [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] [Indexed: 06/15/2023]
Abstract
The unprecedented scientific achievements in combating the COVID-19 pandemic reflect a global response informed by unprecedented access to data. We now have the ability to rapidly generate a diversity of information on an emerging pathogen and, by using high-performance computing and a systems biology approach, we can mine this wealth of information to understand the complexities of viral pathogenesis and contagion like never before. These efforts will aid in the development of vaccines, antiviral medications, and inform policymakers and clinicians. Here we detail computational protocols developed as SARS-CoV-2 began to spread across the globe. They include pathogen detection, comparative structural proteomics, evolutionary adaptation analysis via network and artificial intelligence methodologies, and multiomic integration. These protocols constitute a core framework on which to build a systems-level infrastructure that can be quickly brought to bear on future pathogens before they evolve into pandemic proportions.
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Affiliation(s)
- Erica T Prates
- Oak Ridge National Laboratory, Computational Systems Biology, Oak Ridge, TN, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
| | - Michael R Garvin
- Oak Ridge National Laboratory, Computational Systems Biology, Oak Ridge, TN, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
| | - Piet Jones
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA
| | - J Izaak Miller
- Oak Ridge National Laboratory, Computational Systems Biology, Oak Ridge, TN, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
| | - Kyle A Sullivan
- Oak Ridge National Laboratory, Computational Systems Biology, Oak Ridge, TN, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
| | - Ashley Cliff
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Joao Gabriel Felipe Machado Gazolla
- Oak Ridge National Laboratory, Computational Systems Biology, Oak Ridge, TN, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
| | - Manesh B Shah
- Genome Science and Technology, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Angelica M Walker
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Matthew Lane
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Christopher T Rentsch
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK
- VA Connecticut Healthcare/General Internal Medicine, West Haven, CT, USA
| | - Amy Justice
- VA Connecticut Healthcare/General Internal Medicine, West Haven, CT, USA
- Yale University School of Medicine, New Haven, CT, USA
| | - Mirko Pavicic
- Oak Ridge National Laboratory, Computational Systems Biology, Oak Ridge, TN, USA
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA
| | - Jonathon Romero
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Daniel Jacobson
- Oak Ridge National Laboratory, Computational Systems Biology, Oak Ridge, TN, USA.
- National Virtual Biotechnology Laboratory, US Department of Energy, Washington, DC, USA.
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA.
- Genome Science and Technology, University of Tennessee Knoxville, Knoxville, TN, USA.
- Department of Psychology, NeuroNet Research Center, University of Tennessee Knoxville, Knoxville, TN, USA.
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12
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Amiri-Dashatan N, Koushki M, Rezaei-Tavirani M. Mass Spectrometry-Based Proteomics Research to Fight COVID-19: An Expert Review on Hopes and Challenges. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022; 26:19-34. [PMID: 35005991 DOI: 10.1089/omi.2021.0182] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The COVID-19 pandemic caused by the severe acute respiratory syndrome (SARS)-CoV-2 infection is a systemic disease and a major planetary health burden. While SARS-CoV-2 impacts host biology extensively, our knowledge of these alterations from a systems perspective remains incomplete. Moreover, there is currently only a limited description of this systemic disease. For precision diagnosis and treatment of SARS-CoV-2, multiomics technologies and systems science research offer significant prospects. This expert review offers a critical analysis of the prospects and challenges of the emerging mass spectrometry-based proteomics approaches to the study of COVID-19 as seen through a systems medicine lens. We also discuss the ways in which proteomics is poised to offer hope for diagnostics and therapeutics innovation on SARS-CoV-2 infection as the disease transitions from a pandemic to an endemic disease, and thus further challenging the health systems and services worldwide in the coming decade. Proteomics is an important high-throughput technology platform to achieve a functional overview of the ways in which COVID-19 changes host biology, and hence, can help identify possible points of entry for innovation in medicines and vaccines, among others.
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Affiliation(s)
- Nasrin Amiri-Dashatan
- Proteomics Research Center, Shahid Beheshti University of Medical Sciences, Tehran, Iran.,Zanjan Metabolic Diseases Research Center, Zanjan University of Medical Sciences, Zanjan, Iran
| | - Mehdi Koushki
- Department of Clinical Biochemistry, School of Medicine, Zanjan University of Medical Sciences, Zanjan, Iran
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13
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Zhu Z, Zhang S, Wang P, Chen X, Bi J, Cheng L, Zhang X. A comprehensive review of the analysis and integration of omics data for SARS-CoV-2 and COVID-19. Brief Bioinform 2021; 23:6412396. [PMID: 34718395 PMCID: PMC8574485 DOI: 10.1093/bib/bbab446] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 09/06/2021] [Accepted: 09/28/2021] [Indexed: 12/14/2022] Open
Abstract
Since the first report of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) in December 2019, over 100 million people have been infected by COVID-19, millions of whom have died. In the latest year, a large number of omics data have sprung up and helped researchers broadly study the sequence, chemical structure and function of SARS-CoV-2, as well as molecular abnormal mechanisms of COVID-19 patients. Though some successes have been achieved in these areas, it is necessary to analyze and mine omics data for comprehensively understanding SARS-CoV-2 and COVID-19. Hence, we reviewed the current advantages and limitations of the integration of omics data herein. Firstly, we sorted out the sequence resources and database resources of SARS-CoV-2, including protein chemical structure, potential drug information and research literature resources. Next, we collected omics data of the COVID-19 hosts, including genomics, transcriptomics, microbiology and potential drug information data. And subsequently, based on the integration of omics data, we summarized the existing data analysis methods and the related research results of COVID-19 multi-omics data in recent years. Finally, we put forward SARS-CoV-2 (COVID-19) multi-omics data integration research direction and gave a case study to mine deeper for the disease mechanisms of COVID-19.
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Affiliation(s)
- Zijun Zhu
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China, 150081
| | - Sainan Zhang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China, 150081
| | - Ping Wang
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China, 150081
| | - Xinyu Chen
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China, 150081
| | - Jianxing Bi
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China, 150081
| | - Liang Cheng
- College of Bioinformatics Science and Technology, Harbin Medical University, Harbin, Heilongjiang, China, 150081.,NHC and CAMS Key Laboratory of Molecular Probe and Targeted Theranostics, Harbin Medical University, Harbin, Heilongjiang, China, 150028
| | - Xue Zhang
- NHC and CAMS Key Laboratory of Molecular Probe and Targeted Theranostics, Harbin Medical University, Harbin, Heilongjiang, China, 150028.,McKusick-Zhang Center for Genetic Medicine, Peking Union Medical College, Beijing, China, 100005
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14
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Maio M, Lahn M, Di Giacomo AM, Covre A, Calabrò L, Ibrahim R, Fox B. A vision of immuno-oncology: the Siena think tank of the Italian network for tumor biotherapy (NIBIT) foundation. J Exp Clin Cancer Res 2021; 40:240. [PMID: 34301276 PMCID: PMC8298945 DOI: 10.1186/s13046-021-02023-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Accepted: 06/18/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND The yearly Think Tank Meeting of the Italian Network for Tumor Biotherapy (NIBIT) Foundation, brings together in Siena, Tuscany (Italy), experts in immuno-oncology to review the learnings from current immunotherapy treatments, and to propose new pre-clinical and clinical investigations in selected research areas. MAIN: While immunotherapies in non-small cell lung cancer and melanoma led to practice changing therapies, the same therapies had only modest benefit for patients with other malignancies, such as mesothelioma and glioblastoma. One way to improve on current immunotherapies is to alter the sequence of each combination agent. Matching the immunotherapy to the host's immune response may thus improve the activity of the current treatments. A second approach is to combine current immunotherapies with novel agents targeting complementary mechanisms. Identifying the appropriate novel agents may require different approaches than the traditional laboratory-based discovery work. For example, artificial intelligence-based research may help focusing the search for innovative and most promising combination partners. CONCLUSION Novel immunotherapies are needed in cancer patients with resistance to or relapse after current immunotherapeutic drugs. Such new treatments may include targeted agents or monoclonal antibodies to overcome the immune-suppressive tumor microenvironment. The mode of combining the novel treatments, including vaccines, needs to be matched to the patient's immune status for achieving the maximum benefit. In this scenario, specific attention should be also paid nowadays to the immune intersection between COVID-19 and cancer.
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Affiliation(s)
- Michele Maio
- Center for Immuno-Oncology, Medical Oncology and Immunotherapy, University Hospital of Siena, Viale Mario Bracci, 16, Siena, Italy.
- Italian Network for Tumor Bio-Immunotherapy Foundation Onlus, Siena, Italy.
| | - Michael Lahn
- iOnctura SA, Avenue Secheron 15, Geneva, Switzerland
| | - Anna Maria Di Giacomo
- Center for Immuno-Oncology, Medical Oncology and Immunotherapy, University Hospital of Siena, Viale Mario Bracci, 16, Siena, Italy
- Italian Network for Tumor Bio-Immunotherapy Foundation Onlus, Siena, Italy
| | - Alessia Covre
- Center for Immuno-Oncology, Medical Oncology and Immunotherapy, University Hospital of Siena, Viale Mario Bracci, 16, Siena, Italy
| | - Luana Calabrò
- Center for Immuno-Oncology, Medical Oncology and Immunotherapy, University Hospital of Siena, Viale Mario Bracci, 16, Siena, Italy
| | - Ramy Ibrahim
- Parker Institute for Cancer Immunotherapy, 1 Letterman Drive, San Francisco, 94012, USA
| | - Bernard Fox
- Earle A. Chiles Research Institute at the Robert W. Franz Cancer Center, 4805 NE Glisan St. Suite 2N35, Portland, OR, 97213, USA
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15
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Praissman JL, Wells L. Proteomics-Based Insights Into the SARS-CoV-2-Mediated COVID-19 Pandemic: A Review of the First Year of Research. Mol Cell Proteomics 2021; 20:100103. [PMID: 34089862 PMCID: PMC8176883 DOI: 10.1016/j.mcpro.2021.100103] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 05/24/2021] [Indexed: 02/08/2023] Open
Abstract
In late 2019, a virus subsequently named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged in China and led to a worldwide pandemic of the disease termed coronavirus disease 2019. The global health threat posed by this pandemic led to an extremely rapid and robust mobilization of the scientific and medical communities as evidenced by the publication of more than 10,000 peer-reviewed articles and thousands of preprints in the first year of the pandemic alone. With the publication of the initial genome sequence of SARS-CoV-2, the proteomics community immediately joined this effort publishing, to date, more than 100 peer-reviewed proteomics studies and submitting many more preprints to preprint servers. In this review, we focus on peer-reviewed articles published on the proteome, glycoproteome, and glycome of SARS-CoV-2. At a basic level, proteomic studies provide valuable information on quantitative aspects of viral infection course; information on the identities, sites, and microheterogeneity of post-translational modifications; and, information on protein-protein interactions. At a biological systems level, these studies elucidate host cell and tissue responses, characterize antibodies and other immune system factors in infection, suggest biomarkers that may be useful for diagnosis and disease-course monitoring, and help in the development or repurposing of potential therapeutics. Here, we summarize results from selected early studies to provide a perspective on the current rapidly evolving literature.
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Affiliation(s)
- Jeremy L Praissman
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA
| | - Lance Wells
- Complex Carbohydrate Research Center, University of Georgia, Athens, Georgia, USA.
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16
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Kumar N, Kaushik R, Tennakoon C, Uversky VN, Longhi S, Zhang KYJ, Bhatia S. Comprehensive Intrinsic Disorder Analysis of 6108 Viral Proteomes: From the Extent of Intrinsic Disorder Penetrance to Functional Annotation of Disordered Viral Proteins. J Proteome Res 2021; 20:2704-2713. [PMID: 33719450 DOI: 10.1021/acs.jproteome.1c00011] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Much of our understanding of proteins and proteomes comes from the traditional protein structure-function paradigm. However, in the last 2 decades, both computational and experimental studies have provided evidence that a large fraction of functional proteomes across different domains of life consists of intrinsically disordered proteins, thus triggering a quest to unravel and decipher protein intrinsic disorder. Unlike structured/ordered proteins, intrinsically disordered proteins/regions (IDPs/IDRs) do not possess a well-defined structure under physiological conditions and exist as highly dynamic conformational ensembles. In spite of this peculiarity, these proteins have crucial roles in cell signaling and regulation. To date, studies on the abundance and function of IDPs/IDRs in viruses are rather limited. To fill this gap, we carried out an extensive and thorough bioinformatics analysis of 283 000 proteins from 6108 reference viral proteomes. We analyzed protein intrinsic disorder from multiple perspectives, such as abundance of IDPs/IDRs across diverse virus types, their functional annotations, and subcellular localization in taxonomically divergent hosts. We show that the content of IDPs/IDRs in viral proteomes varies broadly as a function of virus genome types and taxonomically divergent hosts. We have combined the two most commonly used and accurate IDP predictors' results with charge-hydropathy (CH) versus cumulative distribution function (CDF) plots to categorize the viral proteins according to their IDR content and physicochemical properties. Mapping of gene ontology on the disorder content of viral proteins reveals that IDPs are primarily involved in key virus-host interactions and host antiviral immune response downregulation, which are reinforced by the post-translational modifications tied to disorder-enriched viral proteins. The present study offers detailed insights into the prevalence of the intrinsic disorder in viral proteomes and provides appealing targets for the design of novel therapeutics.
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Affiliation(s)
- Naveen Kumar
- Diagnostics & Vaccines Group, ICAR-National Institute of High Security Animal Diseases, Bhopal 462022, India
| | - Rahul Kaushik
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | | | - Vladimir N Uversky
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida 33612, United States.,Federal Research Center 'Pushchino Scientific Center for Biological Research of the Russian Academy of Sciences', Institute for Biological Instrumentation of the Russian Academy of Sciences, Pushchino 142290, Moscow Region, Russia
| | - Sonia Longhi
- Laboratoire Architecture et Fonction des Macromolecules Biologiques (AFMB), UMR 7257, Aix Marseille Université, CNRS, 13288 Marseille, France
| | - Kam Y J Zhang
- Laboratory for Structural Bioinformatics, Center for Biosystems Dynamics Research, RIKEN, 1-7-22 Suehiro, Yokohama, Kanagawa 230-0045, Japan
| | - Sandeep Bhatia
- Diagnostics & Vaccines Group, ICAR-National Institute of High Security Animal Diseases, Bhopal 462022, India
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Fung SY, Siu KL, Lin H, Yeung ML, Jin DY. SARS-CoV-2 main protease suppresses type I interferon production by preventing nuclear translocation of phosphorylated IRF3. Int J Biol Sci 2021; 17:1547-1554. [PMID: 33907518 PMCID: PMC8071772 DOI: 10.7150/ijbs.59943] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 03/12/2021] [Indexed: 12/17/2022] Open
Abstract
Suppression of type I interferon (IFN) response is one pathological outcome of the infection of highly pathogenic human coronaviruses. To effect this, severe acute respiratory syndrome coronavirus (SARS-CoV) and SARS-CoV-2 encode multiple IFN antagonists. In this study, we reported on the IFN antagonism of SARS-CoV-2 main protease NSP5. NSP5 proteins of both SARS-CoV and SARS-CoV-2 counteracted Sendai virus-induced IFN production. NSP5 variants G15S and K90R commonly seen in circulating strains of SARS-CoV-2 retained the IFN-antagonizing property. The suppressive effect of NSP5 on IFN-β gene transcription induced by RIG-I, MAVS, TBK1 and IKKϵ suggested that NSP5 likely acts at a step downstream of IRF3 phosphorylation in the cytoplasm. NSP5 did not influence steady-state expression or phosphorylation of IRF3, suggesting that IRF3, regardless of its phosphorylation state, might not be the substrate of NSP5 protease. However, nuclear translocation of phosphorylated IRF3 was severely compromised in NSP5-expressing cells. Taken together, our work revealed a new mechanism by which NSP5 proteins encoded by SARS-CoV and SARS-CoV-2 antagonize IFN production by retaining phosphorylated IRF3 in the cytoplasm. Our findings have implications in rational design and development of antiviral agents against SARS-CoV-2.
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Affiliation(s)
- Sin-Yee Fung
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Kam-Leung Siu
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Huayue Lin
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
| | - Man Lung Yeung
- Department of Microbiology, The University of Hong Kong, Pokfulam, Hong Kong.,Department of Clinical Microbiology and Infection Control, The University of Hong Kong-Shenzhen Hospital, Shenzhen, China
| | - Dong-Yan Jin
- School of Biomedical Sciences, The University of Hong Kong, Pokfulam, Hong Kong
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Garvin MR, T Prates E, Pavicic M, Jones P, Amos BK, Geiger A, Shah MB, Streich J, Felipe Machado Gazolla JG, Kainer D, Cliff A, Romero J, Keith N, Brown JB, Jacobson D. Potentially adaptive SARS-CoV-2 mutations discovered with novel spatiotemporal and explainable AI models. Genome Biol 2020; 21:304. [PMID: 33357233 PMCID: PMC7756312 DOI: 10.1186/s13059-020-02191-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 10/29/2020] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND A mechanistic understanding of the spread of SARS-CoV-2 and diligent tracking of ongoing mutagenesis are of key importance to plan robust strategies for confining its transmission. Large numbers of available sequences and their dates of transmission provide an unprecedented opportunity to analyze evolutionary adaptation in novel ways. Addition of high-resolution structural information can reveal the functional basis of these processes at the molecular level. Integrated systems biology-directed analyses of these data layers afford valuable insights to build a global understanding of the COVID-19 pandemic. RESULTS Here we identify globally distributed haplotypes from 15,789 SARS-CoV-2 genomes and model their success based on their duration, dispersal, and frequency in the host population. Our models identify mutations that are likely compensatory adaptive changes that allowed for rapid expansion of the virus. Functional predictions from structural analyses indicate that, contrary to previous reports, the Asp614Gly mutation in the spike glycoprotein (S) likely reduced transmission and the subsequent Pro323Leu mutation in the RNA-dependent RNA polymerase led to the precipitous spread of the virus. Our model also suggests that two mutations in the nsp13 helicase allowed for the adaptation of the virus to the Pacific Northwest of the USA. Finally, our explainable artificial intelligence algorithm identified a mutational hotspot in the sequence of S that also displays a signature of positive selection and may have implications for tissue or cell-specific expression of the virus. CONCLUSIONS These results provide valuable insights for the development of drugs and surveillance strategies to combat the current and future pandemics.
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Affiliation(s)
- Michael R Garvin
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Erica T Prates
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Mirko Pavicic
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Piet Jones
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA
| | - B Kirtley Amos
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
- Department of Horticulture, N-318 Ag Sciences Center, University of Kentucky, Lexington, KY, USA
| | - Armin Geiger
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Manesh B Shah
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Jared Streich
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | | | - David Kainer
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
| | - Ashley Cliff
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Jonathon Romero
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA
| | - Nathan Keith
- Lawrence Berkeley National Laboratory, Environmental Genomics & Systems Biology, Berkeley, CA, USA
| | - James B Brown
- Lawrence Berkeley National Laboratory, Environmental Genomics & Systems Biology, Berkeley, CA, USA
| | - Daniel Jacobson
- Oak Ridge National Laboratory, Biosciences Division, Oak Ridge, TN, USA.
- The Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee Knoxville, Knoxville, TN, USA.
- Department of Psychology, University of Tennessee Knoxville, Knoxville, TN, USA.
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