1
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El-Maradny YA, Badawy MA, Mohamed KI, Ragab RF, Moharm HM, Abdallah NA, Elgammal EM, Rubio-Casillas A, Uversky VN, Redwan EM. Unraveling the role of the nucleocapsid protein in SARS-CoV-2 pathogenesis: From viral life cycle to vaccine development. Int J Biol Macromol 2024; 279:135201. [PMID: 39216563 DOI: 10.1016/j.ijbiomac.2024.135201] [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: 05/30/2024] [Revised: 08/24/2024] [Accepted: 08/28/2024] [Indexed: 09/04/2024]
Abstract
BACKGROUND The nucleocapsid protein (N protein) is the most abundant protein in SARS-CoV-2. Viral RNA and this protein are bound by electrostatic forces, forming cytoplasmic helical structures known as nucleocapsids. Subsequently, these nucleocapsids interact with the membrane (M) protein, facilitating virus budding into early secretory compartments. SCOPE OF REVIEW Exploring the role of the N protein in the SARS-CoV-2 life cycle, pathogenesis, post-sequelae consequences, and interaction with host immunity has enhanced our understanding of its function and potential strategies for preventing SARS-CoV-2 infection. MAJOR CONCLUSION This review provides an overview of the N protein's involvement in SARS-CoV-2 infectivity, highlighting its crucial role in the virus-host protein interaction and immune system modulation, which in turn influences viral spread. GENERAL SIGNIFICANCE Understanding these aspects identifies the N protein as a promising target for developing effective antiviral treatments and vaccines against SARS-CoV-2.
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Affiliation(s)
- Yousra A El-Maradny
- Pharmaceutical and Fermentation Industries Development Center, City of Scientific Research and Technological Applications (SRTA-City), New Borg EL-Arab, Alexandria 21934, Egypt; Microbiology and Immunology, Faculty of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), El Alamein 51718, Egypt.
| | - Moustafa A Badawy
- Industrial Microbiology and Applied Chemistry program, Faculty of Science, Alexandria University, Egypt.
| | - Kareem I Mohamed
- Microbiology and Immunology, Faculty of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), El Alamein 51718, Egypt.
| | - Renad F Ragab
- Microbiology and Immunology, Faculty of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), El Alamein 51718, Egypt.
| | - Hamssa M Moharm
- Genetics, Biotechnology Department, Faculty of Agriculture, Alexandria University, Egypt.
| | - Nada A Abdallah
- Medicinal Plants Department, Faculty of Agriculture, Alexandria University, Egypt.
| | - Esraa M Elgammal
- Microbiology and Immunology, Faculty of Pharmacy, Arab Academy for Science, Technology and Maritime Transport (AASTMT), El Alamein 51718, Egypt.
| | - Alberto Rubio-Casillas
- Autlan Regional Hospital, Health Secretariat, Autlan, JAL 48900, Mexico; Biology Laboratory, Autlan Regional Preparatory School, University of Guadalajara, Autlan, JAL 48900, Mexico.
| | - Vladimir N Uversky
- Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL 33612, USA.
| | - Elrashdy M Redwan
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia; Centre of Excellence in Bionanoscience Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia; Therapeutic and Protective Proteins Laboratory, Protein Research Department, Genetic Engineering and Biotechnology Research Institute, City of Scientific Research and Technological Applications (SRTA-City), New Borg EL-Arab, 21934 Alexandria, Egypt.
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2
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Nguyen A, Zhao H, Myagmarsuren D, Srinivasan S, Wu D, Chen J, Piszczek G, Schuck P. Modulation of biophysical properties of nucleocapsid protein in the mutant spectrum of SARS-CoV-2. eLife 2024; 13:RP94836. [PMID: 38941236 PMCID: PMC11213569 DOI: 10.7554/elife.94836] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/30/2024] Open
Abstract
Genetic diversity is a hallmark of RNA viruses and the basis for their evolutionary success. Taking advantage of the uniquely large genomic database of SARS-CoV-2, we examine the impact of mutations across the spectrum of viable amino acid sequences on the biophysical phenotypes of the highly expressed and multifunctional nucleocapsid protein. We find variation in the physicochemical parameters of its extended intrinsically disordered regions (IDRs) sufficient to allow local plasticity, but also observe functional constraints that similarly occur in related coronaviruses. In biophysical experiments with several N-protein species carrying mutations associated with major variants, we find that point mutations in the IDRs can have nonlocal impact and modulate thermodynamic stability, secondary structure, protein oligomeric state, particle formation, and liquid-liquid phase separation. In the Omicron variant, distant mutations in different IDRs have compensatory effects in shifting a delicate balance of interactions controlling protein assembly properties, and include the creation of a new protein-protein interaction interface in the N-terminal IDR through the defining P13L mutation. A picture emerges where genetic diversity is accompanied by significant variation in biophysical characteristics of functional N-protein species, in particular in the IDRs.
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Affiliation(s)
- Ai Nguyen
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Dulguun Myagmarsuren
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Sanjana Srinivasan
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, United States
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, United States
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3
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Zhao H, Syed AM, Khalid MM, Nguyen A, Ciling A, Wu D, Yau WM, Srinivasan S, Esposito D, Doudna J, Piszczek G, Ott M, Schuck P. Assembly of SARS-CoV-2 nucleocapsid protein with nucleic acid. Nucleic Acids Res 2024; 52:6647-6661. [PMID: 38587193 PMCID: PMC11194069 DOI: 10.1093/nar/gkae256] [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] [Received: 11/22/2023] [Revised: 03/18/2024] [Accepted: 03/27/2024] [Indexed: 04/09/2024] Open
Abstract
The viral genome of SARS-CoV-2 is packaged by the nucleocapsid (N-)protein into ribonucleoprotein particles (RNPs), 38 ± 10 of which are contained in each virion. Their architecture has remained unclear due to the pleomorphism of RNPs, the high flexibility of N-protein intrinsically disordered regions, and highly multivalent interactions between viral RNA and N-protein binding sites in both N-terminal (NTD) and C-terminal domain (CTD). Here we explore critical interaction motifs of RNPs by applying a combination of biophysical techniques to ancestral and mutant proteins binding different nucleic acids in an in vitro assay for RNP formation, and by examining nucleocapsid protein variants in a viral assembly assay. We find that nucleic acid-bound N-protein dimers oligomerize via a recently described protein-protein interface presented by a transient helix in its long disordered linker region between NTD and CTD. The resulting hexameric complexes are stabilized by multivalent protein-nucleic acid interactions that establish crosslinks between dimeric subunits. Assemblies are stabilized by the dimeric CTD of N-protein offering more than one binding site for stem-loop RNA. Our study suggests a model for RNP assembly where N-protein scaffolding at high density on viral RNA is followed by cooperative multimerization through protein-protein interactions in the disordered linker.
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Affiliation(s)
- Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Abdullah M Syed
- Gladstone Institutes, San Francisco, CA 94158, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Mir M Khalid
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Ai Nguyen
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Alison Ciling
- Gladstone Institutes, San Francisco, CA 94158, USA
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sanjana Srinivasan
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dominic Esposito
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA
| | - Jennifer A Doudna
- Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
- HHMI, University of California, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720, USA
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Medicine, University of California, San Francisco, CA 94143, USA
- Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
- Center for Biomedical Engineering Technology Acceleration, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
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4
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Stuwe H, Reardon PN, Yu Z, Shah S, Hughes K, Barbar EJ. Phosphorylation in the Ser/Arg-rich region of the nucleocapsid of SARS-CoV-2 regulates phase separation by inhibiting self-association of a distant helix. J Biol Chem 2024; 300:107354. [PMID: 38718862 PMCID: PMC11180338 DOI: 10.1016/j.jbc.2024.107354] [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: 04/01/2024] [Revised: 04/24/2024] [Accepted: 04/30/2024] [Indexed: 06/06/2024] Open
Abstract
The nucleocapsid protein (N) of SARS-CoV-2 is essential for virus replication, genome packaging, evading host immunity, and virus maturation. N is a multidomain protein composed of an independently folded monomeric N-terminal domain that is the primary site for RNA binding and a dimeric C-terminal domain that is essential for efficient phase separation and condensate formation with RNA. The domains are separated by a disordered Ser/Arg-rich region preceding a self-associating Leu-rich helix. Phosphorylation in the Ser/Arg region in infected cells decreases the viscosity of N:RNA condensates promoting viral replication and host immune evasion. The molecular level effect of phosphorylation, however, is missing from our current understanding. Using NMR spectroscopy and analytical ultracentrifugation, we show that phosphorylation destabilizes the self-associating Leu-rich helix 30 amino-acids distant from the phosphorylation site. NMR and gel shift assays demonstrate that RNA binding by the linker is dampened by phosphorylation, whereas RNA binding to the full-length protein is not significantly affected presumably due to retained strong interactions with the primary RNA-binding domain. Introducing a switchable self-associating domain to replace the Leu-rich helix confirms the importance of linker self-association to droplet formation and suggests that phosphorylation not only increases solubility of the positively charged elongated Ser/Arg region as observed in other RNA-binding proteins but can also inhibit self-association of the Leu-rich helix. These data highlight the effect of phosphorylation both at local sites and at a distant self-associating hydrophobic helix in regulating liquid-liquid phase separation of the entire protein.
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Affiliation(s)
- Hannah Stuwe
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | | | - Zhen Yu
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Sahana Shah
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Kaitlyn Hughes
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA
| | - Elisar J Barbar
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, Oregon, USA.
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5
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Ray P, Ledgerwood-Lee M, Brickner H, Clark AE, Garretson A, Graham R, Van Zant W, Carlin AF, Aronoff-Spencer ES. Design and Development of an Antigen Test for SARS-CoV-2 Nucleocapsid Protein to Validate the Viral Quality Assurance Panels. Viruses 2024; 16:662. [PMID: 38793544 PMCID: PMC11125937 DOI: 10.3390/v16050662] [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: 03/30/2024] [Revised: 04/19/2024] [Accepted: 04/21/2024] [Indexed: 05/26/2024] Open
Abstract
The continuing mutability of the SARS-CoV-2 virus can result in failures of diagnostic assays. To address this, we describe a generalizable bioinformatics-to-biology pipeline developed for the calibration and quality assurance of inactivated SARS-CoV-2 variant panels provided to Radical Acceleration of Diagnostics programs (RADx)-radical program awardees. A heuristic genetic analysis based on variant-defining mutations demonstrated the lowest genetic variance in the Nucleocapsid protein (Np)-C-terminal domain (CTD) across all SARS-CoV-2 variants. We then employed the Shannon entropy method on (Np) sequences collected from the major variants, verifying the CTD with lower entropy (less prone to mutations) than other Np regions. Polyclonal and monoclonal antibodies were raised against this target CTD antigen and used to develop an Enzyme-linked immunoassay (ELISA) test for SARS-CoV-2. Blinded Viral Quality Assurance (VQA) panels comprised of UV-inactivated SARS-CoV-2 variants (XBB.1.5, BF.7, BA.1, B.1.617.2, and WA1) and distractor respiratory viruses (CoV 229E, CoV OC43, RSV A2, RSV B, IAV H1N1, and IBV) were assembled by the RADx-rad Diagnostics core and tested using the ELISA described here. The assay tested positive for all variants with high sensitivity (limit of detection: 1.72-8.78 ng/mL) and negative for the distractor virus panel. Epitope mapping for the monoclonal antibodies identified a 20 amino acid antigenic peptide on the Np-CTD that an in-silico program also predicted for the highest antigenicity. This work provides a template for a bioinformatics pipeline to select genetic regions with a low propensity for mutation (low Shannon entropy) to develop robust 'pan-variant' antigen-based assays for viruses prone to high mutational rates.
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Affiliation(s)
- Partha Ray
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Melissa Ledgerwood-Lee
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Howard Brickner
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Alex E. Clark
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Aaron Garretson
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Rishi Graham
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Westley Van Zant
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
| | - Aaron F. Carlin
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
- Department of Pathology, University of California, San Diego, CA 92093, USA
| | - Eliah S. Aronoff-Spencer
- Department of Medicine, Division of Infectious Diseases and Global Public Health, University of California, San Diego, CA 92093, USA; (P.R.); (M.L.-L.); (H.B.); (A.E.C.); (A.G.); (R.G.); (W.V.Z.); (A.F.C.)
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6
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Nguyen A, Zhao H, Myagmarsuren D, Srinivasan S, Wu D, Chen J, Piszczek G, Schuck P. Modulation of Biophysical Properties of Nucleocapsid Protein in the Mutant Spectrum of SARS-CoV-2. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.21.568093. [PMID: 38045241 PMCID: PMC10690151 DOI: 10.1101/2023.11.21.568093] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Genetic diversity is a hallmark of RNA viruses and the basis for their evolutionary success. Taking advantage of the uniquely large genomic database of SARS-CoV-2, we examine the impact of mutations across the spectrum of viable amino acid sequences on the biophysical phenotypes of the highly expressed and multifunctional nucleocapsid protein. We find variation in the physicochemical parameters of its extended intrinsically disordered regions (IDRs) sufficient to allow local plasticity, but also exhibiting functional constraints that similarly occur in related coronaviruses. In biophysical experiments with several N-protein species carrying mutations associated with major variants, we find that point mutations in the IDRs can have nonlocal impact and modulate thermodynamic stability, secondary structure, protein oligomeric state, particle formation, and liquid-liquid phase separation. In the Omicron variant, distant mutations in different IDRs have compensatory effects in shifting a delicate balance of interactions controlling protein assembly properties, and include the creation of a new protein-protein interaction interface in the N-terminal IDR through the defining P13L mutation. A picture emerges where genetic diversity is accompanied by significant variation in biophysical characteristics of functional N-protein species, in particular in the IDRs.
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Affiliation(s)
- Ai Nguyen
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Dulguun Myagmarsuren
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sanjana Srinivasan
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
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7
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Cubuk J, Alston J, Incicco JJ, Holehouse A, Hall K, Stuchell-Brereton M, Soranno A. The disordered N-terminal tail of SARS-CoV-2 Nucleocapsid protein forms a dynamic complex with RNA. Nucleic Acids Res 2024; 52:2609-2624. [PMID: 38153183 PMCID: PMC10954482 DOI: 10.1093/nar/gkad1215] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 11/17/2023] [Accepted: 12/11/2023] [Indexed: 12/29/2023] Open
Abstract
The SARS-CoV-2 Nucleocapsid (N) protein is responsible for condensation of the viral genome. Characterizing the mechanisms controlling nucleic acid binding is a key step in understanding how condensation is realized. Here, we focus on the role of the RNA binding domain (RBD) and its flanking disordered N-terminal domain (NTD) tail, using single-molecule Förster Resonance Energy Transfer and coarse-grained simulations. We quantified contact site size and binding affinity for nucleic acids and concomitant conformational changes occurring in the disordered region. We found that the disordered NTD increases the affinity of the RBD for RNA by about 50-fold. Binding of both nonspecific and specific RNA results in a modulation of the tail configurations, which respond in an RNA length-dependent manner. Not only does the disordered NTD increase affinity for RNA, but mutations that occur in the Omicron variant modulate the interactions, indicating a functional role of the disordered tail. Finally, we found that the NTD-RBD preferentially interacts with single-stranded RNA and that the resulting protein:RNA complexes are flexible and dynamic. We speculate that this mechanism of interaction enables the Nucleocapsid protein to search the viral genome for and bind to high-affinity motifs.
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Affiliation(s)
- Jasmine Cubuk
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA
| | - Jhullian J Alston
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA
| | - J Jeremías Incicco
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA
| | - Kathleen B Hall
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA
| | - Melissa D Stuchell-Brereton
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA
| | - Andrea Soranno
- Department of Biochemistry and Molecular Biophysics, Washington University in St Louis, 660 St Euclid Ave, 63110 Saint Louis, MO, USA
- Center for Biomolecular Condensates, Washington University in St Louis, 1 Brookings Drive, 63130 Saint Louis, MO, USA
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8
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Kubinski HC, Despres HW, Johnson BA, Schmidt MM, Jaffrani SA, Mills MG, Lokugamage K, Dumas CM, Shirley DJ, Estes LK, Pekosz A, Crothers JW, Roychoudhury P, Greninger AL, Jerome KR, Di Genova BM, Walker DH, Ballif BA, Ladinsky MS, Bjorkman PJ, Menachery VD, Bruce EA. Variant mutation in SARS-CoV-2 nucleocapsid enhances viral infection via altered genomic encapsidation. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.08.584120. [PMID: 38559000 PMCID: PMC10979914 DOI: 10.1101/2024.03.08.584120] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
The evolution of SARS-CoV-2 variants and their respective phenotypes represents an important set of tools to understand basic coronavirus biology as well as the public health implications of individual mutations in variants of concern. While mutations outside of Spike are not well studied, the entire viral genome is undergoing evolutionary selection, particularly the central disordered linker region of the nucleocapsid (N) protein. Here, we identify a mutation (G215C), characteristic of the Delta variant, that introduces a novel cysteine into this linker domain, which results in the formation of a disulfide bond and a stable N-N dimer. Using reverse genetics, we determined that this cysteine residue is necessary and sufficient for stable dimer formation in a WA1 SARS-CoV-2 background, where it results in significantly increased viral growth both in vitro and in vivo. Finally, we demonstrate that the N:G215C virus packages more nucleocapsid per virion and that individual virions are larger, with elongated morphologies.
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Affiliation(s)
- Hannah C. Kubinski
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - Hannah W. Despres
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - Bryan A. Johnson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA
- Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX, USA
| | - Madaline M. Schmidt
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - Sara A. Jaffrani
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - Margaret G. Mills
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA 98195, USA
| | - Kumari Lokugamage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Caroline M. Dumas
- Department of Biology, University of Vermont 109 Carrigan Drive, 120A Marsh Life Sciences, Burlington VT 05404, USA
| | - David J. Shirley
- Faraday, Inc. Data Science Department. Burlington VT, 05405, USA
| | - Leah K. Estes
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Andrew Pekosz
- W. Harry Feinstone Department of Molecular Microbiology and Immunology, The Johns Hopkins Bloomberg School of Public Health, Baltimore, MD, USA
| | - Jessica W. Crothers
- Department of Pathology and Laboratory Medicine, Robert Larner, MD College of Medicine, University of Vermont, Burlington, VT, USA
| | - Pavitra Roychoudhury
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA 98195, USA
| | - Alexander L. Greninger
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA 98195, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA 98109, USA
| | - Keith R. Jerome
- Virology Division, Department of Laboratory Medicine and Pathology, University of Washington, Seattle WA 98195, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA 98109, USA
| | - Bruno Martorelli Di Genova
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
| | - David H. Walker
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Bryan A. Ballif
- Department of Biology, University of Vermont 109 Carrigan Drive, 120A Marsh Life Sciences, Burlington VT 05404, USA
| | - Mark S. Ladinsky
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA. 91125, USA
| | - Pamela J. Bjorkman
- Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA. 91125, USA
| | - Vineet D. Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- World Reference Center of Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, USA
- Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, Texas, USA
| | - Emily A. Bruce
- Department of Microbiology and Molecular Genetics, Robert Larner, M.D. College of Medicine, University of Vermont, Burlington VT, 05405, USA
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9
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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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10
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Eskew MW, Reardon P, Benight AS. DNA-based assay for calorimetric determination of protein concentrations in pure or mixed solutions. PLoS One 2024; 19:e0298969. [PMID: 38427623 PMCID: PMC10906865 DOI: 10.1371/journal.pone.0298969] [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] [Received: 10/07/2023] [Accepted: 02/01/2024] [Indexed: 03/03/2024] Open
Abstract
It was recently reported that values of the transition heat capacities, as measured by differential scanning calorimetry, for two globular proteins and a short DNA hairpin in NaCl buffer are essentially equivalent, at equal concentrations (mg/mL). To validate the broad applicability of this phenomenon, additional evidence for this equivalence is presented that reveals it does not depend on DNA sequence, buffer salt, or transition temperature (Tm). Based on the equivalence of transition heat capacities, a calorimetric method was devised to determine protein concentrations in pure and complex solutions. The scheme uses direct comparisons between the thermodynamic stability of a short DNA hairpin standard of known concentration, and thermodynamic stability of protein solutions of unknown concentrations. Sequences of two DNA hairpins were designed to confer a near 20°C difference in their Tm values. In all cases, evaluated protein concentrations determined from the DNA standard curves agreed with the UV-Vis concentration for monomeric proteins. For multimeric proteins evaluated concentrations were greater than determined by UV-Vis suggesting the calorimetric approach can also be an indicator of molecular stoichiometry.
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Affiliation(s)
- Matthew W. Eskew
- ThermoCap Laboratories Inc, Portland, Oregon, United States of America
- Department of Chemistry, Portland State University, Portland, Oregon, United States of America
| | - Patrick Reardon
- OSU NMR Facility, Oregon State University, Corvallis, Oregon, United States of America
| | - Albert S. Benight
- ThermoCap Laboratories Inc, Portland, Oregon, United States of America
- Department of Chemistry, Portland State University, Portland, Oregon, United States of America
- Department of Physics, Portland State University, Portland, Oregon, United States of America
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11
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Gerashchenko GV, Hryshchenko NV, Melnichuk NS, Marchyshak TV, Chernushyn SY, Demchyshina IV, Chernenko LM, Kuzin IV, Tkachuk ZY, Kashuba VI, Tukalo MA. Genetic characteristics of SARS-CoV-2 virus variants observed upon three waves of the COVID-19 pandemic in Ukraine between February 2021-January 2022. Heliyon 2024; 10:e25618. [PMID: 38380034 PMCID: PMC10877268 DOI: 10.1016/j.heliyon.2024.e25618] [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: 04/25/2023] [Revised: 12/06/2023] [Accepted: 01/31/2024] [Indexed: 02/22/2024] Open
Abstract
The aim of our study was to identify and characterize the SARS-CoV-2 variants in COVID-19 patients' samples collected from different regions of Ukraine to determine the relationship between SARS-CoV-2 phylogenetics and COVID-19 epidemiology. Patients and methods Samples were collected from COVID-19 patients during 2021 and the beginning of 2022 (401 patients). The SARS-CoV-2 genotyping was performed by parallel whole genome sequencing. Results The obtained SARS-CoV-2 genotypes showed that three waves of the COVID-19 pandemic in Ukraine were represented by three main variants of concern (VOC), named Alpha, Delta and Omicron; each VOC successfully replaced the earlier variant. The VOC Alpha strain was presented by one B.1.1.7 lineage, while VOC Delta showed a spectrum of 25 lineages that had different prevalence in 19 investigated regions of Ukraine. The VOC Omicron in the first half of the pandemic was represented by 13 lines that belonged to two different clades representing B.1 and B.2 Omicron strains. Each of the three epidemic waves (VOC Alpha, Delta, and Omicron) demonstrated their own course of disease, associated with genetic changes in the SARS-CoV-2 genome. The observed epidemiological features are associated with the genetic characteristics of the different VOCs, such as point mutations, deletions and insertions in the viral genome. A phylogenetic and transmission analysis showed the different mutation rates; there were multiple virus sources with a limited distribution between regions. Conclusions The evolution of SARS-CoV-2 virus and high levels of morbidity due to COVID-19 are still registered in the world. Observed multiple virus sourses with the limited distribution between regions indicates the high efficiency of the anti-epidemic policy pursued by the Ministry of Health of Ukraine to prevent the spread of the epidemic, despite the low level of vaccination of the Ukrainian population.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Zenovii Yu Tkachuk
- Institute of Molecular Biology and Genetics of NAS of Ukraine, Kyiv, Ukraine
| | - Vladimir I. Kashuba
- Institute of Molecular Biology and Genetics of NAS of Ukraine, Kyiv, Ukraine
| | - Mykhailo A. Tukalo
- Institute of Molecular Biology and Genetics of NAS of Ukraine, Kyiv, Ukraine
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12
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Kim Y, Maltseva N, Tesar C, Jedrzejczak R, Endres M, Ma H, Dugan HL, Stamper CT, Chang C, Li L, Changrob S, Zheng NY, Huang M, Ramanathan A, Wilson P, Michalska K, Joachimiak A. Epitopes recognition of SARS-CoV-2 nucleocapsid RNA binding domain by human monoclonal antibodies. iScience 2024; 27:108976. [PMID: 38327783 PMCID: PMC10847736 DOI: 10.1016/j.isci.2024.108976] [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: 09/08/2023] [Revised: 11/02/2023] [Accepted: 01/16/2024] [Indexed: 02/09/2024] Open
Abstract
Coronavirus nucleocapsid protein (NP) of SARS-CoV-2 plays a central role in many functions important for virus proliferation including packaging and protecting genomic RNA. The protein shares sequence, structure, and architecture with nucleocapsid proteins from betacoronaviruses. The N-terminal domain (NPRBD) binds RNA and the C-terminal domain is responsible for dimerization. After infection, NP is highly expressed and triggers robust host immune response. The anti-NP antibodies are not protective and not neutralizing but can effectively detect viral proliferation soon after infection. Two structures of SARS-CoV-2 NPRBD were determined providing a continuous model from residue 48 to 173, including RNA binding region and key epitopes. Five structures of NPRBD complexes with human mAbs were isolated using an antigen-bait sorting. Complexes revealed a distinct complement-determining regions and unique sets of epitope recognition. This may assist in the early detection of pathogens and designing peptide-based vaccines. Mutations that significantly increase viral load were mapped on developed, full length NP model, likely impacting interactions with host proteins and viral RNA.
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Affiliation(s)
- Youngchang Kim
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Natalia Maltseva
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Christine Tesar
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Robert Jedrzejczak
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Michael Endres
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Heng Ma
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Haley L. Dugan
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
| | - Christopher T. Stamper
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
| | - Changsoo Chang
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Lei Li
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
| | - Siriruk Changrob
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
| | - Nai-Ying Zheng
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
| | - Min Huang
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
| | - Arvind Ramanathan
- Data Science and Learning Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Patrick Wilson
- Gale and Ira Drukier Institute for Children’s Health, Weill Cornell Medicine, New York, NY 10021, USA
| | - Karolina Michalska
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
| | - Andrzej Joachimiak
- Center for Structural Biology of Infectious Diseases, Consortium for Advanced Science and Engineering, University of Chicago, Chicago, IL 60367, USA
- Structural Biology Center, X-ray Science Division, Argonne National Laboratory, Lemont, IL 60439, USA
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60367, USA
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13
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Xu Z, Peng Q, Song J, Zhang H, Wei D, Demongeot J, Zeng Q. Bioinformatic analysis of defective viral genomes in SARS-CoV-2 and its impact on population infection characteristics. Front Immunol 2024; 15:1341906. [PMID: 38348041 PMCID: PMC10859446 DOI: 10.3389/fimmu.2024.1341906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2023] [Accepted: 01/12/2024] [Indexed: 02/15/2024] Open
Abstract
DVGs (Defective Viral Genomes) are prevalent in RNA virus infections. In this investigation, we conducted an analysis of high-throughput sequencing data and observed widespread presence of DVGs in SARS-CoV-2. Comparative analysis between SARS-CoV-2 and diverse DNA viruses revealed heightened susceptibility to damage and increased sequencing sample heterogeneity within the SARS-CoV-2 genome. Whole-genome sequencing depth variability analysis exhibited a higher coefficient of variation for SARS-CoV-2, while DVG analysis indicated a significant proportion of recombination sites, signifying notable genome heterogeneity and suggesting that a large proportion of assembled virus particles contain incomplete RNA sequences. Moreover, our investigation explored the sequencing depth and DVG content differences among various strains. Our findings revealed that as the virus evolves, there is a notable increase in the proportion of intact genomes within virus particles, as evidenced by third-generation sequencing data. Specifically, the proportion of intact genome in the Omicron strain surpassed that of the Delta and Alpha strains. This observation effectively elucidates the heightened infectiousness of the Omicron strain compared to the Delta and Alpha strains. We also postulate that this improvement in completeness stems from enhanced virus assembly capacity, as the Omicron strain can promptly facilitate the binding of RNA and capsid protein, thereby reducing the exposure time of vulnerable virus RNA in the host environment and significantly mitigating its degradation. Finally, employing mathematical modeling, we simulated the impact of DVG effects under varying environmental factors on infection characteristics and population evolution. Our findings provide an explanation for the close association between symptom severity and the extent of virus invasion, as well as the substantial disparity in population infection characteristics caused by the same strain under distinct environmental conditions. This study presents a novel approach for future virus research and vaccine development.
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Affiliation(s)
- Zhaobin Xu
- Department of Life Science, Dezhou University, Dezhou, China
| | - Qingzhi Peng
- Department of Life Science, Dezhou University, Dezhou, China
| | - Jian Song
- Department of Life Science, Dezhou University, Dezhou, China
| | - Hongmei Zhang
- Department of Life Science, Dezhou University, Dezhou, China
| | - Dongqing Wei
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Shanghai Jiao Tong University, Shanghai, China
- Joint International Research Laboratory of Metabolic & Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
- Zhongjing Research and Industrialization Institute of Chinese Medicine, Zhongguancun Scientific Park, Meixi, Nanyang, Henan, China
- Peng Cheng National Laboratory, Shenzhen, Guangdong, China
| | - Jacques Demongeot
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, Faculty of Medicine, University Grenoble Alpes (UGA), F-38700 La Tronche, France
| | - Qiangcheng Zeng
- Department of Life Science, Dezhou University, Dezhou, China
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14
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Ravi V, Shamim U, Khan MA, Swaminathan A, Mishra P, Singh R, Bharali P, Chauhan NS, Pandey R. Unraveling the genetic evolution of SARS-CoV-2 Recombinants using mutational dynamics across the different lineages. Front Med (Lausanne) 2024; 10:1294699. [PMID: 38288302 PMCID: PMC10823376 DOI: 10.3389/fmed.2023.1294699] [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: 09/15/2023] [Accepted: 12/18/2023] [Indexed: 01/31/2024] Open
Abstract
Introduction Recombination serves as a common strategy employed by RNA viruses for their genetic evolution. Extensive genomic surveillance during the COVID-19 pandemic has reported SARS-CoV-2 Recombinant strains indicating recombination events during the viral evolution. This study introspects the phenomenon of genome recombination by tracing the footprint of prominent lineages of SARS-CoV-2 at different time points in the context of on-going evolution and emergence of Recombinants. Method Whole genome sequencing was carried out for 2,516 SARS-CoV-2 (discovery cohort) and 1,126 (validation cohort) using nasopharyngeal samples collected between the time period of March 2020 to August 2022, as part of the genomic surveillance program. The sequences were classified according to the different lineages of SARS-CoV-2 prevailing in India at respective time points. Results Mutational diversity and abundance evaluation across the 12 lineages identified 58 Recombinant sequences as harboring the least number of mutations (n = 111), with 14 low-frequency unique mutations with major chunk of mutations coming from the BA.2. The spontaneously/dynamically increasing and decreasing trends of mutations highlight the loss of mutations in the Recombinants that were associated with the SARS-CoV-2 replication efficiency, infectivity, and disease severity, rendering them functionally with low infectivity and pathogenicity. Linkage disequilibrium (LD) analysis revealed that mutations comprising the LD blocks of BA.1, BA.2, and Recombinants were found as minor alleles or as low-frequency alleles in the LD blocks from the previous SARS-CoV-2 variant samples, especially Pre-VOC. Moreover, a dissipation in the size of LD blocks as well as LD decay along with a high negative regression coefficient (R squared) value was demonstrated in the Omicron and BA.1 and BA.2 lineages, which corroborated with the breakpoint analysis. Conclusion Together, the findings help to understand the evolution and emergence of Recombinants after the Omicron lineages, for sustenance and adaptability, to maintain the epidemic spread of SARS-CoV-2 in the host population already high in immunity levels.
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Affiliation(s)
- Varsha Ravi
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Uzma Shamim
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Md Abuzar Khan
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Aparna Swaminathan
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Pallavi Mishra
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
| | - Rajender Singh
- CSIR-Central Drug Research Institute, (CSIR-CDRI), Lucknow, Lucknow, India
| | - Pankaj Bharali
- CSIR-North East Institute of Science and Technology (CSIR-NEIST), Jorhat, Assam, India
| | - Nar Singh Chauhan
- Department of Biochemistry, Maharshi Dayanand University, Rohtak, India
| | - Rajesh Pandey
- Division of Immunology and Infectious Disease Biology, INtegrative GENomics of HOst-PathogEn (INGEN-HOPE) Laboratory, CSIR-Institute of Genomics and Integrative Biology (CSIR-IGIB), Delhi, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
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15
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Schuck P, Zhao H. Diversity of short linear interaction motifs in SARS-CoV-2 nucleocapsid protein. mBio 2023; 14:e0238823. [PMID: 38018991 PMCID: PMC10746173 DOI: 10.1128/mbio.02388-23] [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: 09/01/2023] [Accepted: 10/16/2023] [Indexed: 11/30/2023] Open
Abstract
IMPORTANCE Short linear motifs (SLiMs) are 3-10 amino acid long binding motifs in intrinsically disordered protein regions (IDRs) that serve as ubiquitous protein-protein interaction modules in eukaryotic cells. Through molecular mimicry, viruses hijack these sequence motifs to control host cellular processes. It is thought that the small size of SLiMs and the high mutation frequencies of viral IDRs allow rapid host adaptation. However, a salient characteristic of RNA viruses, due to high replication errors, is their obligate existence as mutant swarms. Taking advantage of the uniquely large genomic database of SARS-CoV-2, here, we analyze the role of sequence diversity in the presentation of SLiMs, focusing on the highly abundant, multi-functional nucleocapsid protein. We find that motif mimicry is a highly dynamic process that produces an abundance of motifs transiently present in subsets of mutant species. This diversity allows the virus to efficiently explore eukaryotic motifs and evolve the host-virus interface.
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Affiliation(s)
- Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, Maryland, USA
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16
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Rak A, Isakova-Sivak I, Rudenko L. Overview of Nucleocapsid-Targeting Vaccines against COVID-19. Vaccines (Basel) 2023; 11:1810. [PMID: 38140214 PMCID: PMC10747980 DOI: 10.3390/vaccines11121810] [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: 11/04/2023] [Revised: 11/30/2023] [Accepted: 12/01/2023] [Indexed: 12/24/2023] Open
Abstract
The new SARS-CoV-2 coronavirus, which emerged in late 2019, is a highly variable causative agent of COVID-19, a contagious respiratory disease with potentially severe complications. Vaccination is considered the most effective measure to prevent the spread and complications of this infection. Spike (S) protein-based vaccines were very successful in preventing COVID-19 caused by the ancestral SARS-CoV-2 strain; however, their efficacy was significantly reduced when coronavirus variants antigenically different from the original strain emerged in circulation. This is due to the high variability of this major viral antigen caused by escape from the immunity caused by the infection or vaccination with spike-targeting vaccines. The nucleocapsid protein (N) is a much more conserved SARS-CoV-2 antigen than the spike protein and has therefore attracted the attention of scientists as a promising target for broad-spectrum vaccine development. Here, we summarized the current data on various N-based COVID-19 vaccines that have been tested in animal challenge models or clinical trials. Despite the high conservatism of the N protein, escape mutations gradually occurring in the N sequence can affect its protective properties. During the three years of the pandemic, at least 12 mutations have arisen in the N sequence, affecting more than 40 known immunogenic T-cell epitopes, so the antigenicity of the N protein of recent SARS-CoV-2 variants may be altered. This fact should be taken into account as a limitation in the development of cross-reactive vaccines based on N-protein.
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Affiliation(s)
- Alexandra Rak
- Department of Virology, Institute of Experimental Medicine, St. Petersburg 197022, Russia; (I.I.-S.); (L.R.)
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17
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Adly AN, Bi M, Carlson CR, Syed AM, Ciling A, Doudna JA, Cheng Y, Morgan DO. Assembly of SARS-CoV-2 ribonucleosomes by truncated N ∗ variant of the nucleocapsid protein. J Biol Chem 2023; 299:105362. [PMID: 37863261 PMCID: PMC10665939 DOI: 10.1016/j.jbc.2023.105362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/05/2023] [Accepted: 10/11/2023] [Indexed: 10/22/2023] Open
Abstract
The nucleocapsid (N) protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) compacts the RNA genome into viral ribonucleoprotein (vRNP) complexes within virions. Assembly of vRNPs is inhibited by phosphorylation of the N protein serine/arginine (SR) region. Several SARS-CoV-2 variants of concern carry N protein mutations that reduce phosphorylation and enhance the efficiency of viral packaging. Variants of the dominant B.1.1 viral lineage also encode a truncated N protein, termed N∗ or Δ(1-209), that mediates genome packaging despite lacking the N-terminal RNA-binding domain and SR region. Here, we use mass photometry and negative stain electron microscopy to show that purified Δ(1-209) and viral RNA assemble into vRNPs that are remarkably similar in size and shape to those formed with full-length N protein. We show that assembly of Δ(1-209) vRNPs requires the leucine-rich helix of the central disordered region and that this helix promotes N protein oligomerization. We also find that fusion of a phosphomimetic SR region to Δ(1-209) inhibits RNA binding and vRNP assembly. Our results provide new insights into the mechanisms by which RNA binding promotes N protein self-association and vRNP assembly, and how this process is modulated by phosphorylation.
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Affiliation(s)
- Armin N Adly
- Department of Physiology, University of California, San Francisco, California, USA
| | - Maxine Bi
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA
| | | | - Abdullah M Syed
- J. David Gladstone Institutes, San Francisco, California, USA
| | - Alison Ciling
- J. David Gladstone Institutes, San Francisco, California, USA
| | - Jennifer A Doudna
- J. David Gladstone Institutes, San Francisco, California, USA; Department of Molecular and Cell Biology, University of California, Berkeley, California, USA; Howard Hughes Medical Institute, University of California, Berkeley, California, USA; Innovative Genomics Institute, University of California, Berkeley, California, USA; California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, California, USA; MBIB Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Yifan Cheng
- Department of Biochemistry & Biophysics, University of California, San Francisco, California, USA; Howard Hughes Medical Institute, University of California, San Francisco, California, USA
| | - David O Morgan
- Department of Physiology, University of California, San Francisco, California, USA.
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18
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Arya R, Tripathi P, Nayak K, Ganesh J, Bihani SC, Ghosh B, Prashar V, Kumar M. Insights into the evolution of mutations in SARS-CoV-2 non-spike proteins. Microb Pathog 2023; 185:106460. [PMID: 37995880 DOI: 10.1016/j.micpath.2023.106460] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 10/16/2023] [Accepted: 11/17/2023] [Indexed: 11/25/2023]
Abstract
The COVID-19 pandemic has been driven by the emergence of SARS-CoV-2 variants with mutations across all the viral proteins. Although mutations in the spike protein have received significant attention, understanding the prevalence and potential impact of mutations in other viral proteins is essential for comprehending the evolution of SARS-CoV-2. Here, we conducted a comprehensive analysis of approximately 14 million sequences of SARS-CoV-2 deposited in the GISAID database until December 2022 to identify prevalent mutations in the non-spike proteins at the global and country levels. Additionally, we evaluated the energetics of each mutation to better understand their impact on protein stability. While the consequences of many mutations remain unclear, we discuss potential structural and functional significance of some mutations. Our study highlights the ongoing evolutionary process of SARS-CoV-2 and underscores the importance of understanding changes in non-spike proteins.
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Affiliation(s)
- Rimanshee Arya
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Preeti Tripathi
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Karthik Nayak
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; School of Chemical Sciences, UM-DAE Centre for Excellence in Basic Sciences, University of Mumbai, Vidyanagari, Mumbai, 400098, India
| | - Janani Ganesh
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Subhash C Bihani
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India
| | - Biplab Ghosh
- Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India; Beamline Development & Application Section, Bhabha Atomic Research Centre, Mumbai, 400085, India
| | - Vishal Prashar
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India.
| | - Mukesh Kumar
- Protein Crystallography Section, Bhabha Atomic Research Centre, Mumbai, 400085, India; Homi Bhabha National Institute, Anushakti Nagar, Mumbai, 400094, India.
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19
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Zhao H, Syed AM, Khalid MM, Nguyen A, Ciling A, Wu D, Yau WM, Srinivasan S, Esposito D, Doudna JA, Piszczek G, Ott M, Schuck P. Assembly reactions of SARS-CoV-2 nucleocapsid protein with nucleic acid. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.11.22.568361. [PMID: 38045338 PMCID: PMC10690241 DOI: 10.1101/2023.11.22.568361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
The viral genome of SARS-CoV-2 is packaged by the nucleocapsid (N-) protein into ribonucleoprotein particles (RNPs), 38±10 of which are contained in each virion. Their architecture has remained unclear due to the pleomorphism of RNPs, the high flexibility of N-protein intrinsically disordered regions, and highly multivalent interactions between viral RNA and N-protein binding sites in both N-terminal (NTD) and C-terminal domain (CTD). Here we explore critical interaction motifs of RNPs by applying a combination of biophysical techniques to mutant proteins binding different nucleic acids in an in vitro assay for RNP formation, and by examining mutant proteins in a viral assembly assay. We find that nucleic acid-bound N-protein dimers oligomerize via a recently described protein-protein interface presented by a transient helix in its long disordered linker region between NTD and CTD. The resulting hexameric complexes are stabilized by multi-valent protein-nucleic acid interactions that establish crosslinks between dimeric subunits. Assemblies are stabilized by the dimeric CTD of N-protein offering more than one binding site for stem-loop RNA. Our study suggests a model for RNP assembly where N-protein scaffolding at high density on viral RNA is followed by cooperative multimerization through protein-protein interactions in the disordered linker.
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Affiliation(s)
- Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892
| | - Abdullah M. Syed
- Gladstone Institutes, San Francisco, CA 94158
- Innovative Genomics Institute, University of California, Berkeley, CA 94720
| | | | - Ai Nguyen
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892
| | - Alison Ciling
- Gladstone Institutes, San Francisco, CA 94158
- Innovative Genomics Institute, University of California, Berkeley, CA 94720
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Wai-Ming Yau
- Laboratory of Chemical Physics, National Institute of Diabetes and Digestive and Kidney Diseases, National Institutes of Health, Bethesda, MD 20892
| | - Sanjana Srinivasan
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892
| | - Dominic Esposito
- Protein Expression Laboratory, Frederick National Laboratory for Cancer Research, Frederick, MD 21702
| | - Jennifer A. Doudna
- Gladstone Institutes, San Francisco, CA 94158
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- HHMI, University of California, Berkeley, CA 94720
- Department of Chemistry, University of California, Berkeley, CA 94720
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720
- California Institute for Quantitative Biosciences (QB3), University of California, Berkeley, CA 94720
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892
| | - Melanie Ott
- Gladstone Institutes, San Francisco, CA 94158
- Department of Medicine, University of California, San Francisco, CA 94143
- Chan Zuckerberg Biohub, San Francisco, CA 94158
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892
- Center for Biomedical Engineering Technology Acceleration, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892
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20
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Equestre M, Marcantonio C, Marascio N, Centofanti F, Martina A, Simeoni M, Suffredini E, La Rosa G, Bonanno Ferraro G, Mancini P, Veneri C, Matera G, Quirino A, Costantino A, Taffon S, Tritarelli E, Campanella C, Pisani G, Nisini R, Spada E, Verde P, Ciccaglione AR, Bruni R. Characterization of SARS-CoV-2 Variants in Military and Civilian Personnel of an Air Force Airport during Three Pandemic Waves in Italy. Microorganisms 2023; 11:2711. [PMID: 38004723 PMCID: PMC10672769 DOI: 10.3390/microorganisms11112711] [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: 10/07/2023] [Revised: 11/01/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
We investigated SARS-CoV-2 variants circulating, from November 2020 to March 2022, among military and civilian personnel at an Air Force airport in Italy in order to classify viral isolates in a potential hotspot for virus spread. Positive samples were subjected to Next-Generation Sequencing (NGS) of the whole viral genome and Sanger sequencing of the spike coding region. Phylogenetic analysis classified viral isolates and traced their evolutionary relationships. Clusters were identified using 70% cut-off. Sequencing methods yielded comparable results in terms of variant classification. In 2020 and 2021, we identified several variants, including B.1.258 (4/67), B.1.177 (9/67), Alpha (B.1.1.7, 9/67), Gamma (P.1.1, 4/67), and Delta (4/67). In 2022, only Omicron and its sub-lineage variants were observed (37/67). SARS-CoV-2 isolates were screened to detect naturally occurring resistance in genomic regions, the target of new therapies, comparing them to the Wuhan Hu-1 reference strain. Interestingly, 2/30 non-Omicron isolates carried the G15S 3CLpro substitution responsible for reduced susceptibility to protease inhibitors. On the other hand, Omicron isolates carried unusual substitutions A1803V, D1809N, and A949T on PLpro, and the D216N on 3CLpro. Finally, the P323L substitution on RdRp coding regions was not associated with the mutational pattern related to polymerase inhibitor resistance. This study highlights the importance of continuous genomic surveillance to monitor SARS-CoV-2 evolution in the general population, as well as in restricted communities.
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Affiliation(s)
- Michele Equestre
- Department of Neurosciences, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Cinzia Marcantonio
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (C.M.); (F.C.); (A.C.); (S.T.); (E.T.); (R.N.); (E.S.); (A.R.C.); (R.B.)
| | - Nadia Marascio
- Clinical Microbiology Unit, Department of Health Sciences, “Magna Grecia” University, 88100 Catanzaro, Italy; (G.M.); (A.Q.)
| | - Federica Centofanti
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (C.M.); (F.C.); (A.C.); (S.T.); (E.T.); (R.N.); (E.S.); (A.R.C.); (R.B.)
| | - Antonio Martina
- Center for Immunobiologicals Research and Evaluation, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.M.); (M.S.); (G.P.)
| | - Matteo Simeoni
- Center for Immunobiologicals Research and Evaluation, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.M.); (M.S.); (G.P.)
| | - Elisabetta Suffredini
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy;
| | - Giuseppina La Rosa
- Department of Environment and Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (G.L.R.); (G.B.F.); (P.M.); (C.V.)
| | - Giusy Bonanno Ferraro
- Department of Environment and Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (G.L.R.); (G.B.F.); (P.M.); (C.V.)
| | - Pamela Mancini
- Department of Environment and Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (G.L.R.); (G.B.F.); (P.M.); (C.V.)
| | - Carolina Veneri
- Department of Environment and Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (G.L.R.); (G.B.F.); (P.M.); (C.V.)
| | - Giovanni Matera
- Clinical Microbiology Unit, Department of Health Sciences, “Magna Grecia” University, 88100 Catanzaro, Italy; (G.M.); (A.Q.)
| | - Angela Quirino
- Clinical Microbiology Unit, Department of Health Sciences, “Magna Grecia” University, 88100 Catanzaro, Italy; (G.M.); (A.Q.)
| | - Angela Costantino
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (C.M.); (F.C.); (A.C.); (S.T.); (E.T.); (R.N.); (E.S.); (A.R.C.); (R.B.)
| | - Stefania Taffon
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (C.M.); (F.C.); (A.C.); (S.T.); (E.T.); (R.N.); (E.S.); (A.R.C.); (R.B.)
| | - Elena Tritarelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (C.M.); (F.C.); (A.C.); (S.T.); (E.T.); (R.N.); (E.S.); (A.R.C.); (R.B.)
| | - Carmelo Campanella
- Clinical Analysis and Molecular Biology Laboratory Rome, Institute of Aerospace Medicine, 00185 Rome, Italy;
| | - Giulio Pisani
- Center for Immunobiologicals Research and Evaluation, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.M.); (M.S.); (G.P.)
| | - Roberto Nisini
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (C.M.); (F.C.); (A.C.); (S.T.); (E.T.); (R.N.); (E.S.); (A.R.C.); (R.B.)
| | - Enea Spada
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (C.M.); (F.C.); (A.C.); (S.T.); (E.T.); (R.N.); (E.S.); (A.R.C.); (R.B.)
| | - Paola Verde
- Aerospace Medicine Department, Aerospace Test Division, Militay Airport Mario De Bernardi, Pratica di Mare, 00040 Rome, Italy;
| | - Anna Rita Ciccaglione
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (C.M.); (F.C.); (A.C.); (S.T.); (E.T.); (R.N.); (E.S.); (A.R.C.); (R.B.)
| | - Roberto Bruni
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (C.M.); (F.C.); (A.C.); (S.T.); (E.T.); (R.N.); (E.S.); (A.R.C.); (R.B.)
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Skuza K, Rutyna P, Krzowski L, Rabalski L, Lepionka T. Surveillance of SARS-CoV-2 Genetic Variants in the Polish Armed Forces Using Whole Genome Sequencing Analysis. Int J Mol Sci 2023; 24:14851. [PMID: 37834302 PMCID: PMC10573488 DOI: 10.3390/ijms241914851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2023] [Revised: 09/26/2023] [Accepted: 09/30/2023] [Indexed: 10/15/2023] Open
Abstract
Military operations involve the global movement of personnel and equipment, increasing the risk of spreading infectious pathogens such as SARS-CoV-2. Given the continuous engagement of the Polish Armed Forces in overseas operations, an active surveillance program targeting Variants of Concern (VOC) of SARS-CoV-2 was implemented among military personnel. Screening using RT-qPCR tests was conducted on 1699 soldiers between November 2021 and May 2022. Of these, 84 SARS-CoV-2 positive samples met the criteria for whole genome sequencing analysis and variant identification. Whole genome sequencing was performed using two advanced next-generation sequencing (NGS) technologies: sequencing by synthesis and nanopore sequencing. Our analysis revealed eleven SARS-CoV-2 lineages belonging to 21K, 21L, and 21J. The predominant lineage was BA.1.1 (57% of the samples), followed by BA.1 (23%) and BA.2 (6%). Notably, all identified lineages detected in post-deployment screening tests were classified as VOC and were already present in Poland, showing the effectiveness of the Military Sanitary Inspection measures in mitigating the COVID-19 spread. Pre-departure and post-mission screening and isolation successfully prevented SARS-CoV-2 VOC exportation and importation. Proactive measures are vital in minimizing the impact of COVID-19 in military settings, emphasizing the need for continued vigilance and response strategies.
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Affiliation(s)
- Katarzyna Skuza
- Biological Threats Identification and Countermeasure Center, General Karol Kaczkowski Military Institute of Hygiene and Epidemiology, Lubelska 4, 24-100 Pulawy, Poland;
| | - Pawel Rutyna
- Chair and Department of Medical Microbiology, Medical University of Lublin, 1 Chodzki, 20-093 Lublin, Poland;
| | - Lukasz Krzowski
- Biomedical Engineering Centre, Institute of Optoeletronics. Military University of Technology, 2 Gen. Sylwestra Kaliskiego, 00-908 Warsaw, Poland;
| | - Lukasz Rabalski
- Biological Threats Identification and Countermeasure Center, General Karol Kaczkowski Military Institute of Hygiene and Epidemiology, Lubelska 4, 24-100 Pulawy, Poland;
- Department of Recombinant Vaccines, Intercollegiate Faculty of Biotechnology University of Gdansk and Medical University of Gdansk, Abrahama 58, 80-307 Gdansk, Poland
| | - Tomasz Lepionka
- Biological Threats Identification and Countermeasure Center, General Karol Kaczkowski Military Institute of Hygiene and Epidemiology, Lubelska 4, 24-100 Pulawy, Poland;
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22
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Eskew MW, Reardon PW, Benight AS. Calorimetric analysis using DNA thermal stability to determine protein concentration. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.25.559360. [PMID: 37808849 PMCID: PMC10557601 DOI: 10.1101/2023.09.25.559360] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
It was recently reported for two globular proteins and a short DNA hairpin in NaCl buffer that values of the transition heat capacities, Cp,DNA and Cp,PRO, for equal concentrations (mg/mL) of DNA and proteins, are essentially equivalent (differ by less than 1%). Additional evidence for this equivalence is presented that reveals this phenomenon does not depend on DNA sequence, buffer salt, or Tm. Sequences of two DNA hairpins were designed to confer a near 20°C difference in their Tm's. For the molecules, in NaCl and CsCl buffer the evaluated Cp,PRO and Cp,DNA were equivalent. Based on the equivalence of transition heat capacities, a calorimetric method was devised to determine protein concentrations in pure and complex solutions. The scheme uses direct comparisons between the thermodynamic stability of a short DNA hairpin standard of known concentration, and thermodynamic stability of protein solutions of unknown concentrations. In all cases, evaluated protein concentrations determined from the DNA standard curve agreed with the UV-Vis concentration for monomeric proteins. For samples of multimeric proteins, streptavidin (tetramer), Herpes Simplex Virus glycoprotein D (trimer/dimer), and a 16 base pair DNA duplex (dimer), evaluated concentrations were greater than determined by UV-Vis by factors of 3.94, 2.65, and 2.15, respectively.
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Affiliation(s)
- Matthew W. Eskew
- ThermoCap Laboratories Inc, Portland, Oregon
- Department of Chemistry, Portland State University, Portland, Oregon
| | | | - Albert S. Benight
- ThermoCap Laboratories Inc, Portland, Oregon
- Department of Chemistry, Portland State University, Portland, Oregon
- Department of Physics, Portland State University, Portland, Oregon
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23
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Schuck P, Zhao H. Diversity of Short Linear Interaction Motifs in SARS-CoV-2 Nucleocapsid Protein. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.01.551467. [PMID: 37790474 PMCID: PMC10542142 DOI: 10.1101/2023.08.01.551467] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
Abstract
Molecular mimicry of short linear interaction motifs has emerged as a key mechanism for viral proteins binding host domains and hijacking host cell processes. Here, we examine the role of RNA-virus sequence diversity in the dynamics of the virus-host interface, by analyzing the uniquely vast sequence record of viable SARS-CoV-2 species with focus on the multi-functional nucleocapsid protein. We observe the abundant presentation of motifs encoding several essential host protein interactions, alongside a majority of possibly non-functional and randomly occurring motif sequences absent in subsets of viable virus species. A large number of motifs emerge ex nihilo through transient mutations relative to the ancestral consensus sequence. The observed mutational landscape implies an accessible motif space that spans at least 25% of known eukaryotic motifs. This reveals motif mimicry as a highly dynamic process with the capacity to broadly explore host motifs, allowing the virus to rapidly evolve the virus-host interface.
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Affiliation(s)
- Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
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24
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Wang Y, Ling X, Zhang C, Zou J, Luo B, Luo Y, Jia X, Jia G, Zhang M, Hu J, Liu T, Wang Y, Lu K, Li D, Ma J, Liu C, Su Z. Modular characterization of SARS-CoV-2 nucleocapsid protein domain functions in nucleocapsid-like assembly. MOLECULAR BIOMEDICINE 2023; 4:16. [PMID: 37211575 DOI: 10.1186/s43556-023-00129-z] [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: 01/13/2023] [Accepted: 04/09/2023] [Indexed: 05/23/2023] Open
Abstract
SARS-CoV-2 and its variants, with the Omicron subvariant XBB currently prevailing the global infections, continue to pose threats on public health worldwide. This non-segmented positive-stranded RNA virus encodes the multi-functional nucleocapsid protein (N) that plays key roles in viral infection, replication, genome packaging and budding. N protein consists of two structural domains, NTD and CTD, and three intrinsically disordered regions (IDRs) including the NIDR, the serine/arginine rich motif (SRIDR), and the CIDR. Previous studies revealed functions of N protein in RNA binding, oligomerization, and liquid-liquid phase separation (LLPS), however, characterizations of individual domains and their dissected contributions to N protein functions remain incomplete. In particular, little is known about N protein assembly that may play essential roles in viral replication and genome packing. Here, we present a modular approach to dissect functional roles of individual domains in SARS-CoV-2 N protein that reveals inhibitory or augmented modulations of protein assembly and LLPS in the presence of viral RNAs. Intriguingly, full-length N protein (NFL) assembles into ring-like architecture whereas the truncated SRIDR-CTD-CIDR (N182-419) promotes filamentous assembly. Moreover, LLPS droplets of NFL and N182-419 are significantly enlarged in the presence of viral RNAs, and we observed filamentous structures in the N182-419 droplets using correlative light and electron microscopy (CLEM), suggesting that the formation of LLPS droplets may promote higher-order assembly of N protein for transcription, replication and packaging. Together this study expands our understanding of the multiple functions of N protein in SARS-CoV-2.
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Affiliation(s)
- Yan Wang
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Xiaobin Ling
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Chong Zhang
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Jian Zou
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Bingnan Luo
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Yongbo Luo
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Xinyu Jia
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Guowen Jia
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Minghua Zhang
- College of Polymer Science and Engineering, Sichuan University, Chengdu, 610065, Sichuan, China
| | - Junchao Hu
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Ting Liu
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Yuanfeiyi Wang
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Kefeng Lu
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China
| | - Dan Li
- Bio-X Institutes, Key Laboratory for the Genetics of Developmental and Neuropsychiatric Disorders, Ministry of Education, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jinbiao Ma
- State Key Laboratory of Genetic Engineering, Collaborative Innovation Center of Genetics and Development, Department of Biochemistry and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, China.
| | - Cong Liu
- Interdisciplinary Research Center On Biology and Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 201210, China.
- State Key Laboratory of Bio-Organic and Natural Products Chemistry, Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences, Shanghai, 200032, China.
| | - Zhaoming Su
- The State Key Laboratory of Biotherapy, Frontiers Medical Center of Tianfu Jincheng Laboratory, National Clinical Research Center for Geriatrics and Department of Geriatrics, West China Hospital, Sichuan University, Chengdu, 610044, Sichuan, China.
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25
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Saldivar-Espinoza B, Garcia-Segura P, Novau-Ferré N, Macip G, Martínez R, Puigbò P, Cereto-Massagué A, Pujadas G, Garcia-Vallve S. The Mutational Landscape of SARS-CoV-2. Int J Mol Sci 2023; 24:ijms24109072. [PMID: 37240420 DOI: 10.3390/ijms24109072] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2023] [Revised: 05/12/2023] [Accepted: 05/16/2023] [Indexed: 05/28/2023] Open
Abstract
Mutation research is crucial for detecting and treating SARS-CoV-2 and developing vaccines. Using over 5,300,000 sequences from SARS-CoV-2 genomes and custom Python programs, we analyzed the mutational landscape of SARS-CoV-2. Although almost every nucleotide in the SARS-CoV-2 genome has mutated at some time, the substantial differences in the frequency and regularity of mutations warrant further examination. C>U mutations are the most common. They are found in the largest number of variants, pangolin lineages, and countries, which indicates that they are a driving force behind the evolution of SARS-CoV-2. Not all SARS-CoV-2 genes have mutated in the same way. Fewer non-synonymous single nucleotide variations are found in genes that encode proteins with a critical role in virus replication than in genes with ancillary roles. Some genes, such as spike (S) and nucleocapsid (N), show more non-synonymous mutations than others. Although the prevalence of mutations in the target regions of COVID-19 diagnostic RT-qPCR tests is generally low, in some cases, such as for some primers that bind to the N gene, it is significant. Therefore, ongoing monitoring of SARS-CoV-2 mutations is crucial. The SARS-CoV-2 Mutation Portal provides access to a database of SARS-CoV-2 mutations.
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Affiliation(s)
- Bryan Saldivar-Espinoza
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Pol Garcia-Segura
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Nil Novau-Ferré
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Guillem Macip
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | | | - Pere Puigbò
- Department of Biology, University of Turku, 20500 Turku, Finland
- Department of Biochemistry and Biotechnology, Rovira i Virgili University, 43007 Tarragona, Spain
- Eurecat, Technology Centre of Catalonia, Unit of Nutrition and Health, 43204 Reus, Spain
| | - Adrià Cereto-Massagué
- EURECAT Centre Tecnològic de Catalunya, Centre for Omic Sciences (COS), Joint Unit Universitat Rovira i Virgili-EURECAT, Unique Scientific and Technical Infrastructures (ICTS), 43204 Reus, Spain
| | - Gerard Pujadas
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
| | - Santiago Garcia-Vallve
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, 43007 Tarragona, Spain
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26
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Cissé OH, Curran S, Folco HD, Liu Y, Bishop L, Wang H, Fischer ER, Davis AS, Babb-Biernacki S, Doyle VP, Richards JK, Hassan SA, Dekker JP, Khil PP, Brenchley JM, Grewal S, Cushion M, Ma L, Kovacs JA. The Host Adapted Fungal Pathogens of Pneumocystis Genus Utilize Genic Regional Centromeres. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.12.540427. [PMID: 37425787 PMCID: PMC10327204 DOI: 10.1101/2023.05.12.540427] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
Centromeres are genomic regions that coordinate accurate chromosomal segregation during mitosis and meiosis. Yet, despite their essential function, centromeres evolve rapidly across eukaryotes. Centromeres are often the sites of chromosomal breaks which contribute to genome shuffling and promote speciation by inhibiting gene flow. How centromeres form in strongly host-adapted fungal pathogens has yet to be investigated. Here, we characterized the centromere structures in closely related species of mammalian-specific pathogens of the fungal phylum of Ascomycota. Methods allowing reliable continuous culture of Pneumocystis species do not currently exist, precluding genetic manipulation. CENP-A, a variant of histone H3, is the epigenetic marker that defines centromeres in most eukaryotes. Using heterologous complementation, we show that the Pneumocystis CENP-A ortholog is functionally equivalent to CENP-ACnp1 of Schizosaccharomyces pombe. Using organisms from a short-term in vitro culture or infected animal models and ChIP-seq, we identified centromeres in three Pneumocystis species that diverged ~100 million years ago. Each species has a unique short regional centromere (< 10kb) flanked by heterochromatin in 16-17 monocentric chromosomes. They span active genes and lack conserved DNA sequence motifs and repeats. CENP-C, a scaffold protein that links the inner centromere to the kinetochore appears dispensable in one species, suggesting a kinetochore rewiring. Despite the loss of DNA methyltransferases, 5-methylcytosine DNA methylation occurs in these species, though not related to centromere function. These features suggest an epigenetic specification of centromere function.
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Affiliation(s)
- Ousmane H Cissé
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Shelly Curran
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - H Diego Folco
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Yueqin Liu
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Lisa Bishop
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Honghui Wang
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Elizabeth R Fischer
- Microscopy Unit, Research Technologies Branch, Rocky Mountain Laboratories, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Hamilton, Montana, USA
| | - A Sally Davis
- Diagnostic Medicine/Pathobiology, Kansas State University College of Veterinary Medicine, Manhattan, USA
| | - Spenser Babb-Biernacki
- Museum of Natural Science and Department of Biological Sciences, Louisiana State University, Baton Rouge, Louisiana, USA
| | - Vinson P Doyle
- Department of Plant Pathology and Crop Physiology, Lousiana State University AgCenter, Baton Rouge, Louisiana, USA
| | - Jonathan K Richards
- Department of Plant Pathology and Crop Physiology, Lousiana State University AgCenter, Baton Rouge, Louisiana, USA
| | - Sergio A Hassan
- Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - John P Dekker
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, National Institute of Allergy, and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Pavel P Khil
- Bacterial Pathogenesis and Antimicrobial Resistance Unit, National Institute of Allergy, and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
- Department of Laboratory Medicine, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Jason M Brenchley
- Laboratory of Viral Diseases, National Institute of Allergy, and Infectious Diseases, National Institutes of Health, Bethesda, Maryland, USA
| | - Shiv Grewal
- Laboratory of Biochemistry and Molecular Biology, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Melanie Cushion
- Department of Internal Medicine, College of Medicine, University of Cincinnati, Cincinnati, Ohio, USA
| | - Liang Ma
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
| | - Joseph A Kovacs
- Critical Care Medicine Department, Clinical Center, National Institutes of Health, Bethesda, Maryland, USA
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27
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Zhao H, Wu D, Hassan SA, Nguyen A, Chen J, Piszczek G, Schuck P. A conserved oligomerization domain in the disordered linker of coronavirus nucleocapsid proteins. SCIENCE ADVANCES 2023; 9:eadg6473. [PMID: 37018390 PMCID: PMC10075959 DOI: 10.1126/sciadv.adg6473] [Citation(s) in RCA: 17] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2023] [Accepted: 03/07/2023] [Indexed: 06/01/2023]
Abstract
The nucleocapsid (N-)protein of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has a key role in viral assembly and scaffolding of the viral RNA. It promotes liquid-liquid phase separation (LLPS), forming dense droplets that support the assembly of ribonucleoprotein particles with as-of-yet unknown macromolecular architecture. Combining biophysical experiments, molecular dynamics simulations, and analysis of the mutational landscape, we describe a heretofore unknown oligomerization site that contributes to LLPS, is required for the assembly of higher-order protein-nucleic acid complexes, and is coupled to large-scale conformational changes of N-protein upon nucleic acid binding. The self-association interface is located in a leucine-rich sequence of the intrinsically disordered linker between N-protein folded domains and formed by transient helices assembling into trimeric coiled-coils. Critical residues stabilizing hydrophobic and electrostatic interactions between adjacent helices are highly protected against mutations in viable SARS-CoV-2 genomes, and the oligomerization motif is conserved across related coronaviruses, thus presenting a target for antiviral therapeutics.
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Affiliation(s)
- Huaying Zhao
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Di Wu
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sergio A. Hassan
- Bioinformatics and Computational Biosciences Branch, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ai Nguyen
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
| | - Grzegorz Piszczek
- Biophysics Core Facility, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Peter Schuck
- Laboratory of Dynamics of Macromolecular Assembly, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD 20892, USA
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28
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Takeda K, Noda M, Maruno T, Uchiyama S. Critical Calibration of Mass Photometry for Higher-Mass Samples Such as Adeno-Associated Virus Vectors. J Pharm Sci 2023; 112:1145-1150. [PMID: 36334808 DOI: 10.1016/j.xphs.2022.10.025] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Revised: 10/25/2022] [Accepted: 10/26/2022] [Indexed: 11/11/2022]
Abstract
Mass photometry (MP) is a label-free, single-molecule technique that can determine molecular mass distribution with very low sample consumption in a short time. Because of the established experimental instrument and analytical software, MP measurements may be readily obtained; thus, the application of MP is expanding, especially in the fields of bioscience and biotechnology. However, because the MP data quality is strongly focus-dependent, optical settings must be intrinsically strict. In this study, we report the importance of the critical calibration of the mass photometer, which is required for the accurate estimation of high-molecular mass samples, such as adeno-associated virus vectors. Additionally, a method for optimizing the instrument settings, including the calibration of the stage, is presented.
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Affiliation(s)
| | - Masanori Noda
- U-medico Inc., 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | | | - Susumu Uchiyama
- U-medico Inc., 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan; Department of Biotechnology, Graduate School of Engineering, Osaka University, 2-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.
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29
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Marascio N, Cilburunoglu M, Torun EG, Centofanti F, Mataj E, Equestre M, Bruni R, Quirino A, Matera G, Ciccaglione AR, Yalcinkaya KT. Molecular Characterization and Cluster Analysis of SARS-CoV-2 Viral Isolates in Kahramanmaraş City, Turkey: The Delta VOC Wave within One Month. Viruses 2023; 15:v15030802. [PMID: 36992510 PMCID: PMC10054778 DOI: 10.3390/v15030802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Revised: 03/13/2023] [Accepted: 03/20/2023] [Indexed: 03/31/2023] Open
Abstract
The SARS-CoV-2 pandemic has seriously affected the population in Turkey. Since the beginning, phylogenetic analysis has been necessary to monitor public health measures against COVID-19 disease. In any case, the analysis of spike (S) and nucleocapsid (N) gene mutations was crucial in determining their potential impact on viral spread. We screened S and N regions to detect usual and unusual substitutions, whilst also investigating the clusters among a patient cohort resident in Kahramanmaraş city, in a restricted time span. Sequences were obtained by Sanger methods and genotyped by the PANGO Lineage tool. Amino acid substitutions were annotated comparing newly generated sequences to the NC_045512.2 reference sequence. Clusters were defined using phylogenetic analysis with a 70% cut-off. All sequences were classified as Delta. Eight isolates carried unusual mutations on the S protein, some of them located in the S2 key domain. One isolate displayed the unusual L139S on the N protein, while few isolates carried the T24I and A359S N substitutions able to destabilize the protein. Phylogeny identified nine monophyletic clusters. This study provided additional information about SARS-CoV-2 epidemiology in Turkey, suggesting local transmission of infection in the city by several transmission routes, and highlighting the necessity to improve the power of sequencing worldwide.
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Affiliation(s)
- Nadia Marascio
- Department of Health Sciences, Institute of Microbiology, "Magna Grecia" University, 88100 Catanzaro, Italy
| | - Merve Cilburunoglu
- Microbiology Department, Faculty of Medicine, Kahramanmaras Sutcü Imam University, 46050 Kahramanmaras, Turkey
| | - Elif Gulsum Torun
- Microbiology Department, Faculty of Medicine, Kahramanmaras Sutcü Imam University, 46050 Kahramanmaras, Turkey
| | - Federica Centofanti
- Department of Applied Clinical Sciences and Biotechnology, University of Aquila, 67100 L'Aquila, Italy
| | - Elida Mataj
- Instituti i Shendetit Publik (ISHP), 1000 Tirana, Albania
| | - Michele Equestre
- Department of Neurosciences, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Roberto Bruni
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy
| | - Angela Quirino
- Department of Health Sciences, Institute of Microbiology, "Magna Grecia" University, 88100 Catanzaro, Italy
| | - Giovanni Matera
- Department of Health Sciences, Institute of Microbiology, "Magna Grecia" University, 88100 Catanzaro, Italy
| | | | - Kezban Tulay Yalcinkaya
- Microbiology Department, Faculty of Medicine, Kahramanmaras Sutcü Imam University, 46050 Kahramanmaras, Turkey
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30
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Xu Z, Wei D, Zeng Q, Zhang H, Sun Y, Demongeot J. More or less deadly? A mathematical model that predicts SARS-CoV-2 evolutionary direction. Comput Biol Med 2023; 153:106510. [PMID: 36630829 PMCID: PMC9816089 DOI: 10.1016/j.compbiomed.2022.106510] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 12/18/2022] [Accepted: 12/31/2022] [Indexed: 01/09/2023]
Abstract
SARS-CoV-2 has caused tremendous deaths globally. It is of great value to predict the evolutionary direction of SARS-CoV-2. In this paper, we proposed a novel mathematical model that could predict the evolutionary trend of SARS-CoV-2. We focus on the mutational effects on viral assembly capacity. A robust coarse-grained mathematical model is constructed to simulate the virus dynamics in the host body. Both virulence and transmissibility can be quantified in this model. A delicate equilibrium point that optimizes the transmissibility can be numerically obtained. Based on this model, the virulence of SARS-CoV-2 might further decrease, accompanied by an enhancement of transmissibility. However, this trend is not continuous; its virulence will not disappear but remains at a relatively stable range. A virus assembly model which simulates the virus packing process is also proposed. It can be explained why a few mutations would lead to a significant divergence in clinical performance, both in the overall particle formation quantity and virulence. This research provides a novel mathematical attempt to elucidate the evolutionary driving force in RNA virus evolution.
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Affiliation(s)
- Zhaobin Xu
- Department of Life Science, Dezhou University, Dezhou, 253023, China.
| | - Dongqing Wei
- School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Qiangcheng Zeng
- Department of Life Science, Dezhou University, Dezhou, 253023, China
| | - Hongmei Zhang
- Department of Life Science, Dezhou University, Dezhou, 253023, China
| | - Yinghui Sun
- Department of Life Science, Dezhou University, Dezhou, 253023, China
| | - Jacques Demongeot
- Laboratory AGEIS EA 7407, Team Tools for e-Gnosis Medical, Faculty of Medicine, University Grenoble Alpes (UGA), 38700, La Tronche, France.
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31
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Saldivar-Espinoza B, Macip G, Pujadas G, Garcia-Vallve S. Could nucleocapsid be a next-generation COVID-19 vaccine candidate? Int J Infect Dis 2022; 125:231-232. [PMID: 36347459 PMCID: PMC9636030 DOI: 10.1016/j.ijid.2022.11.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 10/20/2022] [Accepted: 11/01/2022] [Indexed: 11/08/2022] Open
Affiliation(s)
| | | | - Gerard Pujadas
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, Catalonia, Spain.
| | - Santiago Garcia-Vallve
- Departament de Bioquímica i Biotecnologia, Research Group in Cheminformatics & Nutrition, Campus de Sescelades, Universitat Rovira i Virgili, Catalonia, Spain.
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32
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Edich M, Briggs DC, Kippes O, Gao Y, Thorn A. The impact of AlphaFold2 on experimental structure solution. Faraday Discuss 2022; 240:184-195. [PMID: 35943157 PMCID: PMC10231047 DOI: 10.1039/d2fd00072e] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Accepted: 05/03/2022] [Indexed: 01/09/2023]
Abstract
AlphaFold2 is a machine-learning based program that predicts a protein structure based on the amino acid sequence. In this article, we report on the current usages of this new tool and give examples from our work in the Coronavirus Structural Task Force. With its unprecedented accuracy, it can be utilized for the design of expression constructs, de novo protein design and the interpretation of Cryo-EM data with an atomic model. However, these methods are limited by their training data and are of limited use to predict conformational variability and fold flexibility; they also lack co-factors, post-translational modifications and multimeric complexes with oligonucleotides. They also are not always perfect in terms of chemical geometry. Nevertheless, machine learning-based fold prediction is a game changer for structural bioinformatics and experimentalists alike, with exciting developments ahead.
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Affiliation(s)
- Maximilian Edich
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
| | - David C Briggs
- The Francis Crick Institute, 1 Midland Road, London, NW1 1AT, UK
| | - Oliver Kippes
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
| | - Yunyun Gao
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
| | - Andrea Thorn
- Institute for Nanostructure and Solid State Physics, Universität Hamburg, Luruper Chaussee 149, 22761 Hamburg, Germany.
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33
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Fang FF. As the virus evolves, so too must we: a drug developer's perspective : We need a new paradigm in searching for next-generation countermeasures. Virol J 2022; 19:159. [PMID: 36217145 PMCID: PMC9549815 DOI: 10.1186/s12985-022-01887-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2022] [Accepted: 09/13/2022] [Indexed: 11/26/2022] Open
Abstract
The SARS-CoV-2 virus has been raging globally for over 2 years with no end in sight. It has become clear that this virus possesses enormous genetic plasticity, and it will not be eradicated. Under increasing selective pressure from population immunity, the evolution of SARS-CoV-2 has driven it towards greater infectivity, and evasion of humoral and cellular immunity. Omicron and its expanding army of subvariants and recombinants have impaired vaccine protection and made most antibody drugs obsolete. Antiviral drugs, though presently effective, may select for more resistant strains over time. It may be inevitable, then, that future SARS-CoV-2 variants will be immune to our current virus-directed countermeasures. Thus, to gain control over the virus, we need to adopt a new paradigm in searching for next-generation countermeasures and develop host-directed therapeutics (HDTx) and host-directed antivirals (HDA). Different from the virus-directed countermeasures, HDTx and HDA may offer variant agnostic treatment to reduce the risk and severity of infections. In addition, they may exert more uniform effects against the genetically diverse SARS-CoV-2 quasispecies, thereby diminishing the risk of selecting resistant variants. Some promising HDTx and HDA approaches are summarized here.
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Affiliation(s)
- Fang Flora Fang
- Abimmune Biopharma, Inc., P.O. Box 8793, Rancho Santa Fe, CA, 92037, USA.
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34
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Sokhansanj BA, Rosen GL. Predicting COVID-19 disease severity from SARS-CoV-2 spike protein sequence by mixed effects machine learning. Comput Biol Med 2022; 149:105969. [PMID: 36041271 PMCID: PMC9384346 DOI: 10.1016/j.compbiomed.2022.105969] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 07/11/2022] [Accepted: 08/13/2022] [Indexed: 11/17/2022]
Abstract
Epidemiological studies show that COVID-19 variants-of-concern, like Delta and Omicron, pose different risks for severe disease, but they typically lack sequence-level information for the virus. Studies which do obtain viral genome sequences are generally limited in time, location, and population scope. Retrospective meta-analyses require time-consuming data extraction from heterogeneous formats and are limited to publicly available reports. Fortuitously, a subset of GISAID, the global SARS-CoV-2 sequence repository, includes "patient status" metadata that can indicate whether a sequence record is associated with mild or severe disease. While GISAID lacks data on comorbidities relevant to severity, such as obesity and chronic disease, it does include metadata for age and sex to use as additional attributes in modeling. With these caveats, previous efforts have demonstrated that genotype-patient status models can be fit to GISAID data, particularly when country-of-origin is used as an additional feature. But are these models robust and biologically meaningful? This paper shows that, in fact, temporal and geographic biases in sequences submitted to GISAID, as well as the evolving pandemic response, particularly reduction in severe disease due to vaccination, create complex issues for model development and interpretation. This paper poses a potential solution: efficient mixed effects machine learning using GPBoost, treating country as a random effect group. Training and validation using temporally split GISAID data and emerging Omicron variants demonstrates that GPBoost models are more predictive of the impact of spike protein mutations on patient outcomes than fixed effect XGBoost, LightGBM, random forests, and elastic net logistic regression models.
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Affiliation(s)
- Bahrad A Sokhansanj
- Ecological and Evolutionary Signal Processing & Informatics Laboratory, Drexel University, 3100 Chestnut St., Philadelphia, PA, 19104, United States of America.
| | - Gail L Rosen
- Ecological and Evolutionary Signal Processing & Informatics Laboratory, Drexel University, 3100 Chestnut St., Philadelphia, PA, 19104, United States of America.
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35
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Taboada B, Zárate S, García-López R, Muñoz-Medina JE, Sanchez-Flores A, Herrera-Estrella A, Boukadida C, Gómez-Gil B, Selem Mojica N, Rosales-Rivera M, Salas-Lais AG, Gutiérrez-Ríos RM, Loza A, Rivera-Gutierrez X, Vazquez-Perez JA, Matías-Florentino M, Pérez-García M, Ávila-Ríos S, Hurtado JM, Herrera-Nájera CI, Núñez-Contreras JDJ, Sarquiz-Martínez B, García-Arias VE, Santiago-Mauricio MG, Martínez-Miguel B, Enciso-Ibarra J, Cháidez-Quiróz C, Iša P, Wong-Chew RM, Jiménez-Corona ME, López S, Arias CF. Dominance of Three Sublineages of the SARS-CoV-2 Delta Variant in Mexico. Viruses 2022; 14:1165. [PMID: 35746637 PMCID: PMC9229647 DOI: 10.3390/v14061165] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/24/2022] [Accepted: 05/25/2022] [Indexed: 01/27/2023] Open
Abstract
In this study, we analyzed the sequences of SARS-CoV-2 isolates of the Delta variant in Mexico, which has completely replaced other previously circulating variants in the country due to its transmission advantage. Among all the Delta sublineages that were detected, 81.5 % were classified as AY.20, AY.26, and AY.100. According to publicly available data, these only reached a world prevalence of less than 1%, suggesting a possible Mexican origin. The signature mutations of these sublineages are described herein, and phylogenetic analyses and haplotype networks are used to track their spread across the country. Other frequently detected sublineages include AY.3, AY.62, AY.103, and AY.113. Over time, the main sublineages showed different geographical distributions, with AY.20 predominant in Central Mexico, AY.26 in the North, and AY.100 in the Northwest and South/Southeast. This work describes the circulation, from May to November 2021, of the primary sublineages of the Delta variant associated with the third wave of the COVID-19 pandemic in Mexico and highlights the importance of SARS-CoV-2 genomic surveillance for the timely identification of emerging variants that may impact public health.
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Affiliation(s)
- Blanca Taboada
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico; (R.G.-L.); (M.R.-R.); (A.L.); (X.R.-G.); (P.I.); (S.L.)
| | - Selene Zárate
- Posgrado en Ciencias Genómicas, Universidad Autónoma de la Ciudad de México, Ciudad de México 03100, Mexico
| | - Rodrigo García-López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico; (R.G.-L.); (M.R.-R.); (A.L.); (X.R.-G.); (P.I.); (S.L.)
| | - José Esteban Muñoz-Medina
- Coordinación de Calidad de Insumos y Laboratorios Especializados, Instituto Mexicano del Seguro Social, Ciudad de México 07760, Mexico;
| | - Alejandro Sanchez-Flores
- Unidad Universitaria de Secuenciación Masiva y Bioinformática, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico;
| | - Alfredo Herrera-Estrella
- Centro de Investigación y de Estudios Avanzados del IPN, Laboratorio Nacional de Genómica para la Biodiversidad-Unidad de Genómica Avanzada, Irapuato 36824, Guanajuato, Mexico;
| | - Celia Boukadida
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México 14080, Mexico; (C.B.); (M.M.-F.); (M.P.-G.); (S.Á.-R.)
| | - Bruno Gómez-Gil
- Centro de Investigación en Alimentación y Desarrollo AC, Mazatlán 82000, Sinaloa, Mexico; (B.G.-G.); (J.E.-I.)
| | - Nelly Selem Mojica
- Centro de Ciencias Matemáticas, Universidad Nacional Autónoma de México, Morelia 58089, Michoacan, Mexico;
| | - Mauricio Rosales-Rivera
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico; (R.G.-L.); (M.R.-R.); (A.L.); (X.R.-G.); (P.I.); (S.L.)
- Centro de Investigación en Ciencias, Universidad Autónoma de Estado de Morelos, Cuernavaca 62209, Morelos, Mexico
| | - Angel Gustavo Salas-Lais
- Laboratorio Central de Epidemiología, Instituto Mexicano del Seguro Social, Ciudad de México 02990, Mexico; (A.G.S.-L.); (B.S.-M.)
| | - Rosa María Gutiérrez-Ríos
- Departamento de Microbiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico;
| | - Antonio Loza
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico; (R.G.-L.); (M.R.-R.); (A.L.); (X.R.-G.); (P.I.); (S.L.)
| | - Xaira Rivera-Gutierrez
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico; (R.G.-L.); (M.R.-R.); (A.L.); (X.R.-G.); (P.I.); (S.L.)
| | | | - Margarita Matías-Florentino
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México 14080, Mexico; (C.B.); (M.M.-F.); (M.P.-G.); (S.Á.-R.)
| | - Marissa Pérez-García
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México 14080, Mexico; (C.B.); (M.M.-F.); (M.P.-G.); (S.Á.-R.)
| | - Santiago Ávila-Ríos
- Centro de Investigación en Enfermedades Infecciosas, Instituto Nacional de Enfermedades Respiratorias Ismael Cosío Villegas, Ciudad de México 14080, Mexico; (C.B.); (M.M.-F.); (M.P.-G.); (S.Á.-R.)
| | - Juan Manuel Hurtado
- Unidad de Computo, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico;
| | - Carla Ivón Herrera-Nájera
- Instituto Mexicano del Seguro Social, Unidad de Investigación Médica Yucatán, Mérida 97150, Yucatán, Mexico;
| | | | - Brenda Sarquiz-Martínez
- Laboratorio Central de Epidemiología, Instituto Mexicano del Seguro Social, Ciudad de México 02990, Mexico; (A.G.S.-L.); (B.S.-M.)
| | - Víctor Eduardo García-Arias
- Centro de Investigación Biomédica de Occidente, Instituto Mexicano del Seguro Social, Guadalajara 44340, Jalisco, Mexico;
| | | | - Bernardo Martínez-Miguel
- División de Laboratorios Especializados, Instituto Mexicano del Seguro Social, Ciudad de México 07760, Mexico;
| | - Julissa Enciso-Ibarra
- Centro de Investigación en Alimentación y Desarrollo AC, Mazatlán 82000, Sinaloa, Mexico; (B.G.-G.); (J.E.-I.)
| | - Cristóbal Cháidez-Quiróz
- Laboratorio Nacional para la Investigación en Inocuidad Alimentaria, Centro de Investigación en Alimentación y Desarrollo AC, Culiacán 80129, Sinaloa, Mexico;
| | - Pavel Iša
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico; (R.G.-L.); (M.R.-R.); (A.L.); (X.R.-G.); (P.I.); (S.L.)
| | - Rosa María Wong-Chew
- Laboratorio de Investigación en Enfermedades Infecciosas, División de investigación, Facultad de Medicina, Universidad Nacional Autónoma de Mexico, Ciudad de México 04510, Mexico;
| | - María-Eugenia Jiménez-Corona
- Departamento de Epidemiología, Instituto Nacional de Cardiología Ignacio Chávez, Ciudad de México 14080, Mexico;
| | - Susana López
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico; (R.G.-L.); (M.R.-R.); (A.L.); (X.R.-G.); (P.I.); (S.L.)
| | - Carlos F. Arias
- Departamento de Genética del Desarrollo y Fisiología Molecular, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Cuernavaca 62210, Morelos, Mexico; (R.G.-L.); (M.R.-R.); (A.L.); (X.R.-G.); (P.I.); (S.L.)
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