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Alsuwairi FA, Alsaleh AN, Alsanea MS, Al-Qahtani AA, Obeid D, Almaghrabi RS, Alahideb BM, AlAbdulkareem MA, Mutabagani MS, Althawadi SI, Altamimi SA, Alshukairi AN, Alhamlan FS. Association of SARS-CoV-2 Nucleocapsid Protein Mutations with Patient Demographic and Clinical Characteristics during the Delta and Omicron Waves. Microorganisms 2023; 11:1288. [PMID: 37317262 PMCID: PMC10224071 DOI: 10.3390/microorganisms11051288] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Revised: 04/22/2023] [Accepted: 04/28/2023] [Indexed: 06/16/2023] Open
Abstract
SARS-CoV-2 genomic mutations outside the spike protein that may increase transmissibility and disease severity have not been well characterized. This study identified mutations in the nucleocapsid protein and their possible association with patient characteristics. We analyzed 695 samples from patients with confirmed COVID-19 in Saudi Arabia between 1 April 2021, and 30 April 2022. Nucleocapsid protein mutations were identified through whole genome sequencing. 𝜒2 tests and t tests assessed associations between mutations and patient characteristics. Logistic regression estimated the risk of intensive care unit (ICU) admission or death. Of the 60 mutations identified, R203K was the most common, followed by G204R, P13L, E31del, R32del, and S33del. These mutations were associated with reduced risk of ICU admission. P13L, E31del, R32del, and S33del were also associated with reduced risk of death. By contrast, D63G, R203M, and D377Y were associated with increased risk of ICU admission. Most mutations were detected in the SR-rich region, which was associated with low risk of death. The C-tail and central linker regions were associated with increased risk of ICU admission, whereas the N-arm region was associated with reduced ICU admission risk. Consequently, mutations in the N protein must be observed, as they may exacerbate viral infection and disease severity. Additional research is needed to validate the mutations' associations with clinical outcomes.
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Affiliation(s)
- Feda A. Alsuwairi
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Asma N. Alsaleh
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh 11451, Saudi Arabia
| | - Madain S. Alsanea
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Ahmed A. Al-Qahtani
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
| | - Dalia Obeid
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
- Public Health Laboratories, Public Health Authority, Riyadh 13351, Saudi Arabia
| | - Reem S. Almaghrabi
- Organ Transplant Center of Excellence, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Basma M. Alahideb
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Maha A. AlAbdulkareem
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Maysoon S. Mutabagani
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Sahar I. Althawadi
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Sara A. Altamimi
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
| | - Abeer N. Alshukairi
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Medicine, King Faisal Specialist Hospital and Research Center, Jeddah 23433, Saudi Arabia
| | - Fatimah S. Alhamlan
- Department of Infection and Immunity, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
- College of Medicine, Alfaisal University, Riyadh 11533, Saudi Arabia
- Department of Pathology and Laboratory Medicine, King Faisal Specialist Hospital and Research Center, Riyadh 11211, Saudi Arabia
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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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53
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Markov PV, Ghafari M, Beer M, Lythgoe K, Simmonds P, Stilianakis NI, Katzourakis A. The evolution of SARS-CoV-2. Nat Rev Microbiol 2023; 21:361-379. [PMID: 37020110 DOI: 10.1038/s41579-023-00878-2] [Citation(s) in RCA: 265] [Impact Index Per Article: 265.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/01/2023] [Indexed: 04/07/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused millions of deaths and substantial morbidity worldwide. Intense scientific effort to understand the biology of SARS-CoV-2 has resulted in daunting numbers of genomic sequences. We witnessed evolutionary events that could mostly be inferred indirectly before, such as the emergence of variants with distinct phenotypes, for example transmissibility, severity and immune evasion. This Review explores the mechanisms that generate genetic variation in SARS-CoV-2, underlying the within-host and population-level processes that underpin these events. We examine the selective forces that likely drove the evolution of higher transmissibility and, in some cases, higher severity during the first year of the pandemic and the role of antigenic evolution during the second and third years, together with the implications of immune escape and reinfections, and the increasing evidence for and potential relevance of recombination. In order to understand how major lineages, such as variants of concern (VOCs), are generated, we contrast the evidence for the chronic infection model underlying the emergence of VOCs with the possibility of an animal reservoir playing a role in SARS-CoV-2 evolution, and conclude that the former is more likely. We evaluate uncertainties and outline scenarios for the possible future evolutionary trajectories of SARS-CoV-2.
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Affiliation(s)
- Peter V Markov
- European Commission, Joint Research Centre (JRC), Ispra, Italy.
- London School of Hygiene & Tropical Medicine, University of London, London, UK.
| | - Mahan Ghafari
- Big Data Institute, University of Oxford, Oxford, UK
| | - Martin Beer
- Institute of Diagnostic Virology, Friedrich-Loeffler-Institut, Insel Riems, Germany
| | | | - Peter Simmonds
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Nikolaos I Stilianakis
- European Commission, Joint Research Centre (JRC), Ispra, Italy
- Department of Biometry and Epidemiology, University of Erlangen-Nuremberg, Erlangen, Germany
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Mayer ADM, Gröhs Ferrareze PA, de Oliveira LFV, Gregianini TS, Neves CLAM, Caldana GD, Kmetzsch L, Thompson CE. Genomic characterization and molecular evolution of SARS-CoV-2 in Rio Grande do Sul State, Brazil. Virology 2023; 582:1-11. [PMID: 36989935 PMCID: PMC10018445 DOI: 10.1016/j.virol.2023.03.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Revised: 03/08/2023] [Accepted: 03/10/2023] [Indexed: 03/18/2023]
Abstract
SARS-CoV-2 is the virus responsible for the COVID-19 and has afflicted the world since the end of 2019. Different lineages have been discovered and the Gamma lineage, which started the second wave of infections, was first described in Brazil, one of the most affected countries by pandemic. Therefore, this study analyzed SARS-CoV-2 sequenced genomes from Esteio city in Rio Grande do Sul, Southern Brazil. We also comparatively analyzed genomes of the two first years of the pandemic from Rio Grande do Sul state for understanding their genomic and evolutionary patterns. The phylogenomic analysis showed monophyletic groups for Alpha, Gamma, Delta and Omicron, as well as for other circulating lineages in the state. Molecular evolutionary analysis identified several sites under adaptive selection in membrane and nucleocapsid proteins which could be related to a prevalent stabilizing effect on membrane protein structure, as well as majoritarily destabilizing effects on C-terminal nucleocapsid domain.
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Affiliation(s)
- Amanda de Menezes Mayer
- Center of Biotechnology, Graduate Program in Cell and Molecular Biology (PPGBCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Patrícia Aline Gröhs Ferrareze
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | | | - Tatiana Schäffer Gregianini
- Laboratório Central de Saúde Pública do Centro Estadual de Vigilância em Saúde da Secretaria de Saúde do Estado do Rio Grande do Sul (LACEN/CEVS/SES-RS), Porto Alegre, RS, Brazil
| | | | - Gabriel Dickin Caldana
- Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil
| | - Lívia Kmetzsch
- Center of Biotechnology, Graduate Program in Cell and Molecular Biology (PPGBCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil
| | - Claudia Elizabeth Thompson
- Center of Biotechnology, Graduate Program in Cell and Molecular Biology (PPGBCM), Universidade Federal do Rio Grande do Sul (UFRGS), Porto Alegre, RS, Brazil; Graduate Program in Health Sciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, RS, Brazil; Department of Pharmacosciences, Universidade Federal de Ciências da Saúde de Porto Alegre (UFCSPA), Porto Alegre, Brazil.
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55
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Carabelli AM, Peacock TP, Thorne LG, Harvey WT, Hughes J, Peacock SJ, Barclay WS, de Silva TI, Towers GJ, Robertson DL. SARS-CoV-2 variant biology: immune escape, transmission and fitness. Nat Rev Microbiol 2023; 21:162-177. [PMID: 36653446 PMCID: PMC9847462 DOI: 10.1038/s41579-022-00841-7] [Citation(s) in RCA: 238] [Impact Index Per Article: 238.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2022] [Indexed: 01/19/2023]
Abstract
In late 2020, after circulating for almost a year in the human population, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) exhibited a major step change in its adaptation to humans. These highly mutated forms of SARS-CoV-2 had enhanced rates of transmission relative to previous variants and were termed 'variants of concern' (VOCs). Designated Alpha, Beta, Gamma, Delta and Omicron, the VOCs emerged independently from one another, and in turn each rapidly became dominant, regionally or globally, outcompeting previous variants. The success of each VOC relative to the previously dominant variant was enabled by altered intrinsic functional properties of the virus and, to various degrees, changes to virus antigenicity conferring the ability to evade a primed immune response. The increased virus fitness associated with VOCs is the result of a complex interplay of virus biology in the context of changing human immunity due to both vaccination and prior infection. In this Review, we summarize the literature on the relative transmissibility and antigenicity of SARS-CoV-2 variants, the role of mutations at the furin spike cleavage site and of non-spike proteins, the potential importance of recombination to virus success, and SARS-CoV-2 evolution in the context of T cells, innate immunity and population immunity. SARS-CoV-2 shows a complicated relationship among virus antigenicity, transmission and virulence, which has unpredictable implications for the future trajectory and disease burden of COVID-19.
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Affiliation(s)
| | - Thomas P Peacock
- Department of Infectious Disease, St Mary's Medical School, Imperial College London, London, UK
| | - Lucy G Thorne
- Division of Infection and Immunity, University College London, London, UK
| | - William T Harvey
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
- Roslin Institute, University of Edinburgh, Edinburgh, UK
| | - Joseph Hughes
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK
| | - Sharon J Peacock
- Department of Medicine, University of Cambridge, Addenbrookes Hospital, Cambridge, UK
| | - Wendy S Barclay
- Department of Infectious Disease, St Mary's Medical School, Imperial College London, London, UK
| | - Thushan I de Silva
- Department of Infection, Immunity and Cardiovascular Disease, Medical School, University of Sheffield, Sheffield, UK
| | - Greg J Towers
- Division of Infection and Immunity, University College London, London, UK
| | - David L Robertson
- MRC-University of Glasgow Centre for Virus Research, University of Glasgow, Glasgow, UK.
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Schindewolf C, Lokugamage K, Vu MN, Johnson BA, Scharton D, Plante JA, Kalveram B, Crocquet-Valdes PA, Sotcheff S, Jaworski E, Alvarado RE, Debbink K, Daugherty MD, Weaver SC, Routh AL, Walker DH, Plante KS, Menachery VD. SARS-CoV-2 Uses Nonstructural Protein 16 To Evade Restriction by IFIT1 and IFIT3. J Virol 2023; 97:e0153222. [PMID: 36722972 PMCID: PMC9973020 DOI: 10.1128/jvi.01532-22] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Accepted: 01/13/2023] [Indexed: 02/02/2023] Open
Abstract
Understanding the molecular basis of innate immune evasion by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an important consideration for designing the next wave of therapeutics. Here, we investigate the role of the nonstructural protein 16 (NSP16) of SARS-CoV-2 in infection and pathogenesis. NSP16, a ribonucleoside 2'-O-methyltransferase (MTase), catalyzes the transfer of a methyl group to mRNA as part of the capping process. Based on observations with other CoVs, we hypothesized that NSP16 2'-O-MTase function protects SARS-CoV-2 from cap-sensing host restriction. Therefore, we engineered SARS-CoV-2 with a mutation that disrupts a conserved residue in the active site of NSP16. We subsequently show that this mutant is attenuated both in vitro and in vivo, using a hamster model of SARS-CoV-2 infection. Mechanistically, we confirm that the NSP16 mutant is more sensitive than wild-type SARS-CoV-2 to type I interferon (IFN-I) in vitro. Furthermore, silencing IFIT1 or IFIT3, IFN-stimulated genes that sense a lack of 2'-O-methylation, partially restores fitness to the NSP16 mutant. Finally, we demonstrate that sinefungin, an MTase inhibitor that binds the catalytic site of NSP16, sensitizes wild-type SARS-CoV-2 to IFN-I treatment and attenuates viral replication. Overall, our findings highlight the importance of SARS-CoV-2 NSP16 in evading host innate immunity and suggest a target for future antiviral therapies. IMPORTANCE Similar to other coronaviruses, disruption of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) NSP16 function attenuates viral replication in a type I interferon-dependent manner. In vivo, our results show reduced disease and viral replication at late times in the hamster lung, but an earlier titer deficit for the NSP16 mutant (dNSP16) in the upper airway. In addition, our results confirm a role for IFIT1 but also demonstrate the necessity of IFIT3 in mediating dNSP16 attenuation. Finally, we show that targeting NSP16 activity with a 2'-O-methyltransferase inhibitor in combination with type I interferon offers a novel avenue for antiviral development.
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Affiliation(s)
- Craig Schindewolf
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
| | - Kumari Lokugamage
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Michelle N. Vu
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Bryan A. Johnson
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Dionna Scharton
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, USA
| | - Jessica A. Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, USA
| | - Birte Kalveram
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | | | - Stephanea Sotcheff
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Elizabeth Jaworski
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Rojelio E. Alvarado
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Translational Sciences, University of Texas Medical Branch, Galveston, Texas, USA
| | - Kari Debbink
- Department of Microbiology and Immunology, Johns Hopkins University, Baltimore, Maryland, USA
| | - Matthew D. Daugherty
- Department of Molecular Biology, University of California, San Diego, California, USA
| | - Scott C. Weaver
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, USA
| | - Andrew L. Routh
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - David H. Walker
- Department of Pathology, University of Texas Medical Branch, Galveston, Texas, USA
- Center for Biodefense and Emerging Infectious Disease, University of Texas Medical Branch, Galveston, Texas, USA
| | - Kenneth S. Plante
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, USA
| | - Vineet D. Menachery
- Department of Microbiology and Immunology, University of Texas Medical Branch, Galveston, Texas, USA
- Institute for Human Infections and Immunity, University of Texas Medical Branch, Galveston, Texas, USA
- World Reference Center for Emerging Viruses and Arboviruses, University of Texas Medical Branch, Galveston, Texas, USA
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Intragenomic rearrangements involving 5'-untranslated region segments in SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses. Virol J 2023; 20:36. [PMID: 36829234 PMCID: PMC9957694 DOI: 10.1186/s12985-023-01998-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2022] [Accepted: 02/21/2023] [Indexed: 02/26/2023] Open
Abstract
BACKGROUND Variation of the betacoronavirus SARS-CoV-2 has been the bane of COVID-19 control. Documented variation includes point mutations, deletions, insertions, and recombination among closely or distantly related coronaviruses. Here, we describe yet another aspect of genome variation by beta- and alphacoronaviruses that was first documented in an infectious isolate of the betacoronavirus SARS-CoV-2, obtained from 3 patients in Hong Kong that had a 5'-untranslated region segment at the end of the ORF6 gene that in its new location translated into an ORF6 protein with a predicted modified carboxyl terminus. While comparing the amino acid sequences of translated ORF8 genes in the GenBank database, we found a subsegment of the same 5'-UTR-derived amino acid sequence modifying the distal end of ORF8 of an isolate from the United States and decided to carry out a systematic search. METHODS Using the nucleotide and in the case of SARS-CoV-2 also the translated amino acid sequence in three reading frames of the genomic termini of coronaviruses as query sequences, we searched for 5'-UTR sequences in regions other than the 5'-UTR in SARS-CoV-2 and reference strains of alpha-, beta-, gamma-, and delta-coronaviruses. RESULTS We here report numerous genomic insertions of 5'-untranslated region sequences into coding regions of SARS-CoV-2, other betacoronaviruses, and alphacoronaviruses, but not delta- or gammacoronaviruses. To our knowledge this is the first systematic description of such insertions. In many cases, these insertions would change viral protein sequences and further foster genomic flexibility and viral adaptability through insertion of transcription regulatory sequences in novel positions within the genome. Among human Embecorivus betacoronaviruses, for instance, from 65% to all of the surveyed sequences in publicly available databases contain inserted 5'-UTR sequences. CONCLUSION The intragenomic rearrangements involving 5'-untranslated region sequences described here, which in several cases affect highly conserved genes with a low propensity for recombination, may underlie the generation of variants homotypic with those of concern or interest and with potentially differing pathogenic profiles. Intragenomic rearrangements thus add to our appreciation of how variants of SARS-CoV-2 and other beta- and alphacoronaviruses may arise.
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Zheng Y, Gao C. Phase Separation: The Robust Modulator of Innate Antiviral Signaling and SARS-CoV-2 Infection. Pathogens 2023; 12:pathogens12020243. [PMID: 36839515 PMCID: PMC9962166 DOI: 10.3390/pathogens12020243] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/28/2023] [Accepted: 02/01/2023] [Indexed: 02/05/2023] Open
Abstract
SARS-CoV-2 has been a pandemic threat to human health and the worldwide economy, but efficient treatments are still lacking. Type I and III interferons are essential for controlling viral infection, indicating that antiviral innate immune signaling is critical for defense against viral infection. Phase separation, one of the basic molecular processes, governs multiple cellular activities, such as cancer progression, microbial infection, and signaling transduction. Notably, recent studies suggest that phase separation regulates antiviral signaling such as the RLR and cGAS-STING pathways. Moreover, proper phase separation of viral proteins is essential for viral replication and pathogenesis. These observations indicate that phase separation is a critical checkpoint for virus and host interaction. In this study, we summarize the recent advances concerning the regulation of antiviral innate immune signaling and SARS-CoV-2 infection by phase separation. Our review highlights the emerging notion that phase separation is the robust modulator of innate antiviral signaling and viral infection.
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SARS-CoV-2 Omicron (B.1.1.529) Variant: A Challenge with COVID-19. Diagnostics (Basel) 2023; 13:diagnostics13030559. [PMID: 36766664 PMCID: PMC9913917 DOI: 10.3390/diagnostics13030559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 01/17/2023] [Accepted: 01/24/2023] [Indexed: 02/05/2023] Open
Abstract
Since the beginning of the coronavirus disease 2019 (COVID-19) pandemic, there have been multiple peaks of the SARS-CoV-2 (severe acute respiratory syndrome coronavirus virus 2) infection, mainly due to the emergence of new variants, each with a new set of mutations in the viral genome, which have led to changes in the pathogenicity, transmissibility, and morbidity. The Omicron variant is the most recent variant of concern (VOC) to emerge and was recognized by the World Health Organization (WHO) on 26 November 2021. The Omicron lineage is phylogenetically distinct from earlier variants, including the previously dominant Delta SARS-CoV-2 variant. The reverse transcription-polymerase chain reaction (RT-PCR) test, rapid antigen assays, and chest computed tomography (CT) scans can help diagnose the Omicron variant. Furthermore, many agents are expected to have therapeutic benefits for those infected with the Omicron variant, including TriSb92, molnupiravir, nirmatrelvir, and their combination, corticosteroids, and interleukin-6 (IL-6) receptor blockers. Despite being milder than previous variants, the Omicron variant threatens many lives, particularly among the unvaccinated, due to its higher transmissibility, pathogenicity, and infectivity. Mounting evidence has reported the most common clinical manifestations of the Omicron variant to be fever, runny nose, sore throat, severe headache, and fatigue. This review summarizes the essential features of the Omicron variant, including its history, genome, transmissibility, clinical manifestations, diagnosis, management, and the effectiveness of existing vaccines against this VOC.
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Kurhade C, Zou J, Xia H, Liu M, Chang HC, Ren P, Xie X, Shi PY. Low neutralization of SARS-CoV-2 Omicron BA.2.75.2, BQ.1.1 and XBB.1 by parental mRNA vaccine or a BA.5 bivalent booster. Nat Med 2023; 29:344-347. [PMID: 36473500 DOI: 10.1038/s41591-022-02162-x] [Citation(s) in RCA: 210] [Impact Index Per Article: 210.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 11/30/2022] [Indexed: 12/12/2022]
Abstract
The newly emerged severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron sublineages, including the BA.2-derived BA.2.75.2 and the BA.5-derived BQ.1.1 and XBB.1, have accumulated additional spike mutations that may affect vaccine effectiveness. Here we report neutralizing activities of three human serum panels collected from individuals 23-94 days after dose 4 of a parental mRNA vaccine; 14-32 days after a BA.5 bivalent booster from individuals with 2-4 previous doses of parental mRNA vaccine; or 14-32 days after a BA.5 bivalent booster from individuals with previous SARS-CoV-2 infection and 2-4 doses of parental mRNA vaccine. The results showed that a BA.5 bivalent booster elicited a high neutralizing titer against BA.4/5 measured at 14-32 days after boost; however, the BA.5 bivalent booster did not produce robust neutralization against the newly emerged BA.2.75.2, BQ.1.1 or XBB.1. Previous infection substantially enhanced the magnitude and breadth of BA.5 bivalent booster-elicited neutralization. Our data support a vaccine update strategy that future boosters should match newly emerged circulating SARS-CoV-2 variants.
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Affiliation(s)
- Chaitanya Kurhade
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jing Zou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Hongjie Xia
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Mingru Liu
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Hope C Chang
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Ping Ren
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Institute for Drug Discovery, University of Texas Medical Branch, Galveston, TX, USA.
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA.
- Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
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61
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Kurhade C, Xie X, Shi PY. Reverse genetic systems of SARS-CoV-2 for antiviral research. Antiviral Res 2023; 210:105486. [PMID: 36657881 PMCID: PMC9776485 DOI: 10.1016/j.antiviral.2022.105486] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 12/06/2022] [Accepted: 12/08/2022] [Indexed: 12/24/2022]
Abstract
Reverse genetic systems are widely used to engineer recombinant viruses with desired mutations. In response to the COVID-19 pandemic, four types of reverse genetic systems have been developed for SARS-CoV-2: (i) a full-length infectious clone that can be used to prepare recombinant SARS-CoV-2 at biosafety level 3 (BSL3), (ii) a trans-complementation system that can be used to produce single-round infectious SARS-CoV-2 at BSL2, (iii) an attenuated SARS-CoV-2 vaccine candidate (with deletions of viral accessory genes) that may be developed for veterinary use as well as for antiviral screening at BSL2, and (iv) replicon systems with deletions of viral structural genes that can be used at BSL2. Each of these genetic systems has its advantages and disadvantages that can be used to address different questions for basic and translational research. Due to the long genomic size and bacteria-toxic sequences of SARS-CoV-2, several experimental approaches have been established to rescue recombinant viruses and replicons, including (i) in vitro DNA ligation, (ii) bacterial artificial chromosome (BAC) system, (iii) yeast artificial chromosome (YAC) system, and (iv) circular polymerase extension reaction (CPER). This review summarizes the current status of SARS-CoV-2 genetic systems and their applications for studying viral replication, pathogenesis, vaccines, and therapeutics.
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Affiliation(s)
- Chaitanya Kurhade
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Drug Discovery, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Structural Biology & Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
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62
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Tugaeva KV, Sysoev AA, Kapitonova AA, Smith JLR, Zhu P, Cooley RB, Antson AA, Sluchanko NN. Human 14-3-3 Proteins Site-selectively Bind the Mutational Hotspot Region of SARS-CoV-2 Nucleoprotein Modulating its Phosphoregulation. J Mol Biol 2023; 435:167891. [PMID: 36427566 PMCID: PMC9683861 DOI: 10.1016/j.jmb.2022.167891] [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: 10/06/2022] [Revised: 11/06/2022] [Accepted: 11/11/2022] [Indexed: 11/27/2022]
Abstract
Phosphorylation of SARS-CoV-2 nucleoprotein recruits human cytosolic 14-3-3 proteins playing a well-recognized role in replication of many viruses. Here we use genetic code expansion to demonstrate that 14-3-3 binding is triggered by phosphorylation of SARS-CoV-2 nucleoprotein at either of two pseudo-repeats centered at Ser197 and Thr205. According to fluorescence anisotropy measurements, the pT205-motif,presentin SARS-CoV-2 but not in SARS-CoV, is preferred over the pS197-motif by all seven human 14-3-3 isoforms, which collectively display an unforeseen pT205/pS197 peptide binding selectivity hierarchy. Crystal structures demonstrate that pS197 and pT205 are mutually exclusive 14-3-3-binding sites, whereas SAXS and biochemical data obtained on the full protein-protein complex indicate that 14-3-3 binding occludes the Ser/Arg-rich region of the nucleoprotein, inhibiting its dephosphorylation. This Ser/Arg-rich region is highly prone to mutations, as exemplified by the Omicron and Delta variants, with our data suggesting that the strength of 14-3-3/nucleoprotein interaction can be linked with the replicative fitness of the virus.
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Affiliation(s)
- Kristina V Tugaeva
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Andrey A Sysoev
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Anna A Kapitonova
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia
| | - Jake L R Smith
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Phillip Zhu
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Richard B Cooley
- Department of Biochemistry and Biophysics, Oregon State University, Corvallis, OR 97331, USA
| | - Alfred A Antson
- York Structural Biology Laboratory, Department of Chemistry, University of York, York YO10 5DD, United Kingdom
| | - Nikolai N Sluchanko
- A.N. Bach Institute of Biochemistry, Federal Research Center of Biotechnology of the Russian Academy of Sciences, 119071 Moscow, Russia.
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63
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Haque S, Khatoon F, Ashgar SS, Faidah H, Bantun F, Jalal NA, Qashqari FSI, Kumar V. Energetic and frustration analysis of SARS-CoV-2 nucleocapsid protein mutations. Biotechnol Genet Eng Rev 2023:1-21. [PMID: 36708355 DOI: 10.1080/02648725.2023.2170031] [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: 08/07/2022] [Accepted: 01/11/2023] [Indexed: 01/29/2023]
Abstract
The ongoing COVID-19 spreads worldwide with the ability to evolve in diverse human populations. The nucleocapsid (N) protein is one of the mutational hotspots in the SARS-CoV-2 genome. The N protein is an abundant RNA-binding protein critical for viral genome packaging. It comprises two large domains including the N-terminal domain (NTD) and the C-terminal domain (CTD) linked by the centrally located linker region. Mutations in N protein have been reported to increase the severity of disease by modulating viral transmissibility, replication efficiency as well as virulence properties of the virus in different parts of the world. To study the effect of N protein missense mutations on protein stability, function, and pathogenicity, we analyzed 228 mutations from each domain of N protein. Further, we have studied the effect of mutations on local residual frustration changes in N protein. Out of 228 mutations, 11 mutations were predicted to be deleterious and destabilized. Among these mutations, R32C, R191C, and R203 M mutations fall into disordered regions and show significant change in frustration state. Overall, this work reveals that by altering the energetics and residual frustration, N protein mutations might affect the stability, function, and pathogenicity of the SARS-CoV-2.
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Affiliation(s)
- Shafiul Haque
- Research and Scientific Studies Unit, College of Nursing and Allied Health Sciences, Jazan University, Jazan, Saudi Arabia
- Gilbert and Rose-Marie Chagoury School of Medicine, Lebanese American University, Beirut, Lebanon
- Centre of Medical and Bio-Allied Health Sciences Research, Ajman University, Ajman, United Arab Emirates
| | - Fatima Khatoon
- Amity Institute of Neuropsychology & Neurosciences (AINN), Amity University, Noida, India
| | - Sami S Ashgar
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Hani Faidah
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Farkad Bantun
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Naif A Jalal
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Fadi S I Qashqari
- Department of Microbiology, Faculty of Medicine, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Vijay Kumar
- Amity Institute of Neuropsychology & Neurosciences (AINN), Amity University, Noida, India
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64
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Rak A, Gorbunov N, Kostevich V, Sokolov A, Prokopenko P, Rudenko L, Isakova-Sivak I. Assessment of Immunogenic and Antigenic Properties of Recombinant Nucleocapsid Proteins of Five SARS-CoV-2 Variants in a Mouse Model. Viruses 2023; 15:230. [PMID: 36680269 PMCID: PMC9861333 DOI: 10.3390/v15010230] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2023] [Revised: 01/10/2023] [Accepted: 01/11/2023] [Indexed: 01/17/2023] Open
Abstract
COVID-19 cases caused by new variants of highly mutable SARS-CoV-2 continue to be identified worldwide. Effective control of the spread of new variants can be achieved through targeting of conserved viral epitopes. In this regard, the SARS-CoV-2 nucleocapsid (N) protein, which is much more conserved than the evolutionarily influenced spike protein (S), is a suitable antigen. The recombinant N protein can be considered not only as a screening antigen but also as a basis for the development of next-generation COVID-19 vaccines, but little is known about induction of antibodies against the N protein via different SARS-CoV-2 variants. In addition, it is important to understand how antibodies produced against the antigen of one variant can react with the N proteins of other variants. Here, we used recombinant N proteins from five SARS-CoV-2 strains to investigate their immunogenicity and antigenicity in a mouse model and to obtain and characterize a panel of hybridoma-derived monoclonal anti-N antibodies. We also analyzed the variable epitopes of the N protein that are potentially involved in differential recognition of antiviral antibodies. These results will further deepen our knowledge of the cross-reactivity of the humoral immune response in COVID-19.
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Affiliation(s)
- Alexandra Rak
- Department of Virology, Institute of Experimental Medicine, Saint Petersburg 197022, Russia
| | - Nikolay Gorbunov
- Department of Molecular Genetics, Institute of Experimental Medicine, Saint Petersburg 197022, Russia
| | - Valeria Kostevich
- Department of Molecular Genetics, Institute of Experimental Medicine, Saint Petersburg 197022, Russia
| | - Alexey Sokolov
- Department of Molecular Genetics, Institute of Experimental Medicine, Saint Petersburg 197022, Russia
| | - Polina Prokopenko
- Department of Virology, Institute of Experimental Medicine, Saint Petersburg 197022, Russia
| | - Larisa Rudenko
- Department of Virology, Institute of Experimental Medicine, Saint Petersburg 197022, Russia
| | - Irina Isakova-Sivak
- Department of Virology, Institute of Experimental Medicine, Saint Petersburg 197022, Russia
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65
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Cheng N, Liu M, Li W, Sun B, Liu D, Wang G, Shi J, Li L. Protein post-translational modification in SARS-CoV-2 and host interaction. Front Immunol 2023; 13:1068449. [PMID: 36713387 PMCID: PMC9880545 DOI: 10.3389/fimmu.2022.1068449] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/27/2022] [Indexed: 01/14/2023] Open
Abstract
SARS-CoV-2 can cause lung diseases, such as pneumonia and acute respiratory distress syndrome, and multi-system dysfunction. Post-translational modifications (PTMs) related to SARS-CoV-2 are conservative and pathogenic, and the common PTMs are glycosylation, phosphorylation, and acylation. The glycosylation of SARS-CoV-2 mainly occurs on spike (S) protein, which mediates the entry of the virus into cells through interaction with angiotensin-converting enzyme 2. SARS-CoV-2 utilizes glycans to cover its epitopes and evade the immune response through glycosylation of S protein. Phosphorylation of SARS-CoV-2 nucleocapsid (N) protein improves its selective binding to viral RNA and promotes viral replication and transcription, thereby increasing the load of the virus in the host. Succinylated N and membrane(M) proteins of SARS-CoV-2 synergistically affect virus particle assembly. N protein regulates its affinity for other proteins and the viral genome through acetylation. The acetylated envelope (E) protein of SARS-CoV-2 interacts with bromodomain-containing protein 2/4 to influence the host immune response. Both palmitoylation and myristoylation sites on S protein can affect the virus infectivity. Papain-like protease is a domain of NSP3 that dysregulates host inflammation by deubiquitination and impinges host IFN-I antiviral immune responses by deISGylation. Ubiquitination of ORF7a inhibits host IFN-α signaling by blocking STAT2 phosphorylation. The methylation of N protein can inhibit the formation of host stress granules and promote the binding of N protein to viral RNA, thereby promoting the production of virus particles. NSP3 macrodomain can reverse the ADP-ribosylation of host proteins, and inhibit the cascade immune response with IFN as the core, thereby promoting the intracellular replication of SARS-CoV-2. On the whole, PTMs have fundamental roles in virus entry, replication, particle assembly, and host immune response. Mutations in various SARS-CoV-2 variants, which lead to changes in PTMs at corresponding sites, cause different biological effects. In this paper, we mainly reviewed the effects of PTMs on SARS-CoV-2 and host cells, whose application is to inform the strategies for inhibiting viral infection and facilitating antiviral treatment and vaccine development for COVID-19.
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Affiliation(s)
- Nana Cheng
- China-Japan Union Hospital, Jilin University, Changchun, Jilin Province, China
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, Jilin Province, China
| | - Mingzhu Liu
- China-Japan Union Hospital, Jilin University, Changchun, Jilin Province, China
| | - Wanting Li
- China-Japan Union Hospital, Jilin University, Changchun, Jilin Province, China
| | - BingYue Sun
- First Affiliated Hospital of Jilin University, Changchun, China
| | - Dandan Liu
- First Affiliated Hospital of Jilin University, Changchun, China
| | - Guoqing Wang
- Department of Pathogenobiology, The Key Laboratory of Zoonosis Research, Chinese Ministry of Education, College of Basic Medical Science, Jilin University, Changchun, China
| | - Jingwei Shi
- China-Japan Union Hospital, Jilin University, Changchun, Jilin Province, China
| | - Lisha Li
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, Jilin Province, China
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66
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Bai H, Ata G, Sun Q, Rahman SU, Tao S. Natural selection pressure exerted on "Silent" mutations during the evolution of SARS-CoV-2: Evidence from codon usage and RNA structure. Virus Res 2023; 323:198966. [PMID: 36244617 PMCID: PMC9561399 DOI: 10.1016/j.virusres.2022.198966] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 10/08/2022] [Accepted: 10/10/2022] [Indexed: 01/25/2023]
Abstract
From the first emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) till now, multiple mutations that caused synonymous and nonsynonymous substitutions have accumulated. Among them, synonymous substitutions were regarded as "silent" mutations that received less attention than nonsynonymous substitutions that cause amino acid variations. However, the importance of synonymous substitutions can not be neglected. This research focuses on synonymous substitutions on SARS-CoV-2 and proves that synonymous substitutions were under purifying selection in its evolution. The evidence of purifying selection is provided by comparing the mutation number per site in coding and non-coding regions. We then study the two forces of purifying selection: synonymous codon usage and RNA secondary structure. Results show that the codon usage optimization leads to an adapted codon usage towards humans. Furthermore, our results show that the maintenance of RNA secondary structure causes the purifying of synonymous substitutions in the structural region. These results explain the selection pressure on synonymous substitutions during the evolution of SARS-CoV-2.
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Affiliation(s)
- Haoxiang Bai
- College of Life Sciences, Northwest A&F University, Yangling, China; Bioinformatics Center, Northwest A&F University, Yangling, China
| | - Galal Ata
- College of Life Sciences, Northwest A&F University, Yangling, China; Bioinformatics Center, Northwest A&F University, Yangling, China
| | - Qing Sun
- College of Life Sciences, Northwest A&F University, Yangling, China; Bioinformatics Center, Northwest A&F University, Yangling, China
| | - Siddiq Ur Rahman
- Department of Computer Science and Bioinformatics, Khushal Khan Khattak University, Karak, Khyber Pakhtunkhwa, Pakistan
| | - Shiheng Tao
- College of Life Sciences, Northwest A&F University, Yangling, China; Bioinformatics Center, Northwest A&F University, Yangling, China.
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67
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Zhou Y, Zhi H, Teng Y. The outbreak of SARS-CoV-2 Omicron lineages, immune escape, and vaccine effectivity. J Med Virol 2023; 95:e28138. [PMID: 36097349 PMCID: PMC9538491 DOI: 10.1002/jmv.28138] [Citation(s) in RCA: 56] [Impact Index Per Article: 56.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 08/03/2022] [Accepted: 09/07/2022] [Indexed: 01/11/2023]
Abstract
As of November 2021, several SARS-CoV-2 variants appeared and became dominant epidemic strains in many countries, including five variants of concern (VOCs) Alpha, Beta, Gamma, Delta, and Omicron defined by the World Health Organization during the COVID-19 pandemic. As of August 2022, Omicron is classified into five main lineages, BA.1, BA.2, BA.3, BA.4, BA.5 and some sublineages (BA.1.1, BA.2.12.1, BA.2.11, BA.2.75, BA.4.6) (https://www.gisaid.org/). Compared to the previous VOCs (Alpha, Beta, Gamma, and Delta), all the Omicron lineages have the most highly mutations in the spike protein, and with 50 mutations accumulated throughout the genome. Early data indicated that Omicron BA.2 sublineage had higher infectivity and more immune escape than the early wild-type (WT) strain, the previous VOCs, and BA.1. Recently, global surveillance data suggest a higher transmissibility of BA.4/BA.5 than BA.1, BA.1.1 and BA.2, and BA.4/BA.5 is becoming dominant strain in many countries globally.
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Affiliation(s)
- Yongbing Zhou
- Department of Clinical Laboratory, Hangzhou Third People's Hospital, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Huilin Zhi
- Department of Dermatology, Hangzhou Third People's Hospital, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yong Teng
- Department of Clinical Laboratory, Hangzhou Third People's Hospital, Affiliated Hangzhou Dermatology Hospital, Zhejiang University School of Medicine, Hangzhou, China
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68
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Escudero-Pérez B, Lawrence P, Castillo-Olivares J. Immune correlates of protection for SARS-CoV-2, Ebola and Nipah virus infection. Front Immunol 2023; 14:1156758. [PMID: 37153606 PMCID: PMC10158532 DOI: 10.3389/fimmu.2023.1156758] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 03/20/2023] [Indexed: 05/09/2023] Open
Abstract
Correlates of protection (CoP) are biological parameters that predict a certain level of protection against an infectious disease. Well-established correlates of protection facilitate the development and licensing of vaccines by assessing protective efficacy without the need to expose clinical trial participants to the infectious agent against which the vaccine aims to protect. Despite the fact that viruses have many features in common, correlates of protection can vary considerably amongst the same virus family and even amongst a same virus depending on the infection phase that is under consideration. Moreover, the complex interplay between the various immune cell populations that interact during infection and the high degree of genetic variation of certain pathogens, renders the identification of immune correlates of protection difficult. Some emerging and re-emerging viruses of high consequence for public health such as SARS-CoV-2, Nipah virus (NiV) and Ebola virus (EBOV) are especially challenging with regards to the identification of CoP since these pathogens have been shown to dysregulate the immune response during infection. Whereas, virus neutralising antibodies and polyfunctional T-cell responses have been shown to correlate with certain levels of protection against SARS-CoV-2, EBOV and NiV, other effector mechanisms of immunity play important roles in shaping the immune response against these pathogens, which in turn might serve as alternative correlates of protection. This review describes the different components of the adaptive and innate immune system that are activated during SARS-CoV-2, EBOV and NiV infections and that may contribute to protection and virus clearance. Overall, we highlight the immune signatures that are associated with protection against these pathogens in humans and could be used as CoP.
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Affiliation(s)
- Beatriz Escudero-Pérez
- WHO Collaborating Centre for Arbovirus and Haemorrhagic Fever Reference and Research, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany
- German Center for Infection Research (DZIF), Partner Site Hamburg-Luebeck-Borstel-Reims, Braunschweig, Germany
- *Correspondence: Beatriz Escudero-Pérez, ; Javier Castillo-Olivares,
| | - Philip Lawrence
- CONFLUENCE: Sciences et Humanités (EA 1598), Université Catholique de Lyon (UCLy), Lyon, France
| | - Javier Castillo-Olivares
- Laboratory of Viral Zoonotics, University of Cambridge, Cambridge, United Kingdom
- *Correspondence: Beatriz Escudero-Pérez, ; Javier Castillo-Olivares,
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69
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Väisänen E, Jiang M, Laine L, Waris M, Julkunen I, Österlund P. Infectious viruses from transfected SARS-CoV-2 genomic RNA. Front Bioeng Biotechnol 2023; 11:1129111. [PMID: 37064222 PMCID: PMC10098207 DOI: 10.3389/fbioe.2023.1129111] [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: 12/21/2022] [Accepted: 03/22/2023] [Indexed: 04/18/2023] Open
Abstract
SARS-CoV-2 emerged at the end of 2019, and like other novel pathogens causing severe symptoms, WHO recommended heightened biosafety measures for laboratories working with the virus. The positive-stranded genomic RNA of coronaviruses has been known to be infectious since the 1970s, and overall, all experiments with the possibility of SARS-CoV-2 propagation are carried out in higher containment level laboratories. However, as SARS-CoV-2 RNA has been routinely handled in BSL-2 laboratories, the question of the true nature of RNA infectiousness has risen along with discussion of appropriate biosafety measures. Here, we studied the ability of native SARS-CoV-2 genomic RNA to produce infectious viruses when transfected into permissive cells and discussed the biosafety control measures related to these assays. In transfection assays large quantities of genomic vRNA of SARS-CoV-2 was required for a successful production of infectious viruses. However, the quantity of vRNA alone was not the only factor, and especially when the transfected RNA was derived from infected cells, even small amounts of genomic vRNA was enough for an infection. Virus replication was found to start rapidly after transfection, and infectious viruses were detected in the cell culture media at 24 h post-transfection. In addition, silica membrane-based kits were shown to be as good as traditional TRI-reagent based methods in extracting high-quality, 30 kb-long genomic vRNA. Taken together, our data indicates that all transfection experiments with samples containing genomic SARS-CoV-2 RNA should be categorized as a propagative work and the work should be conducted only in a higher containment BSL-3 laboratory.
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Affiliation(s)
- Elina Väisänen
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
- Infection and Immunity Unit, Institute of Biomedicine, University of Turku, Turku, Finland
- *Correspondence: Elina Väisänen,
| | - Miao Jiang
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
- Infection and Immunity Unit, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Larissa Laine
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Matti Waris
- Infection and Immunity Unit, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Ilkka Julkunen
- Infection and Immunity Unit, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Pamela Österlund
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
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70
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Mathez G, Pillonel T, Bertelli C, Cagno V. Alpha and Omicron SARS-CoV-2 Adaptation in an Upper Respiratory Tract Model. Viruses 2022; 15:13. [PMID: 36680054 PMCID: PMC9864588 DOI: 10.3390/v15010013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Revised: 12/16/2022] [Accepted: 12/19/2022] [Indexed: 12/24/2022] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently causing an unprecedented pandemic. Although vaccines and antivirals are limiting the spread, SARS-CoV-2 is still under selective pressure in human and animal populations, as demonstrated by the emergence of variants of concern. To better understand the driving forces leading to new subtypes of SARS-CoV-2, we infected an ex vivo cell model of the human upper respiratory tract with Alpha and Omicron BA.1 variants for one month. Although viral RNA was detected during the entire course of the infection, infectious virus production decreased over time. Sequencing analysis did not show any adaptation in the spike protein, suggesting a key role for the adaptive immune response or adaptation to other anatomical sites for the evolution of SARS-CoV-2.
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Affiliation(s)
| | | | | | - Valeria Cagno
- Institute of Microbiology, Lausanne University Hospital, University of Lausanne, 1011 Lausanne, Switzerland
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71
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Xie X, Zou J, Kurhade C, Liu M, Ren P, Pei-Yong Shi. Neutralization of SARS-CoV-2 Omicron sublineages by 4 doses of the original mRNA vaccine. Cell Rep 2022; 41:111729. [PMID: 36402138 PMCID: PMC9647030 DOI: 10.1016/j.celrep.2022.111729] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/11/2022] [Accepted: 11/04/2022] [Indexed: 11/11/2022] Open
Abstract
Since the initial emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Omicron BA.1, several Omicron sublineages have emerged, leading to BA.5 as the current dominant sublineage. Here, we report the neutralization of different Omicron sublineages by human sera collected from individuals who had distinct mRNA vaccination and/or BA.1 infection. Four-dose-vaccine sera neutralize the original USA-WA1/2020, Omicron BA.1, BA.2, BA.2.12.1, BA.3, and BA.4/5 viruses with geometric mean titers (GMTs) of 1,554, 357, 236, 236, 165, and 95, respectively; two-dose-vaccine-plus-BA.1-infection sera exhibit GMTs of 2,114, 1,705, 730, 961, 813, and 274, respectively; and three-dose-vaccine-plus-BA.1-infection sera show GMTs of 2,962, 2,038, 983, 1,190, 1,019, and 297, respectively. Thus, the four-dose vaccine elicits the lowest neutralization against BA.5; the two-dose vaccine plus BA.1 infection elicits significantly higher GMTs against Omicron sublineages than the four-dose-vaccine; and the three-dose vaccine plus BA.1 infection elicits slightly higher GMTs (statistically insignificant) than the two-dose vaccine plus BA.1 infection. Finally, the BA.2.75 is more susceptible than BA.5 to four-dose-vaccine-elicited neutralization and three-dose-vaccine-plus-BA.1-infection-elicited neutralization.
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Affiliation(s)
- Xuping Xie
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Jing Zou
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Chaitanya Kurhade
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Mingru Liu
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA
| | - Ping Ren
- Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA.
| | - Pei-Yong Shi
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, TX, USA; Department of Pathology, University of Texas Medical Branch, Galveston, TX, USA; Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX, USA; Sealy Institute for Drug Discovery, University of Texas Medical Branch, Galveston, TX, USA; Institute for Translational Sciences, University of Texas Medical Branch, Galveston, TX, USA; Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX, USA; Sealy Center for Structural Biology and Molecular Biophysics, University of Texas Medical Branch, Galveston, TX, USA.
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72
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Periwal N, Rathod SB, Sarma S, Johar GS, Jain A, Barnwal RP, Srivastava KR, Kaur B, Arora P, Sood V. Time Series Analysis of SARS-CoV-2 Genomes and Correlations among Highly Prevalent Mutations. Microbiol Spectr 2022; 10:e0121922. [PMID: 36069583 PMCID: PMC9603882 DOI: 10.1128/spectrum.01219-22] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 08/03/2022] [Indexed: 12/30/2022] Open
Abstract
The efforts of the scientific community to tame the recent pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) seem to have been diluted by the emergence of new viral strains. Therefore, it is imperative to understand the effect of mutations on viral evolution. We performed a time series analysis on 59,541 SARS-CoV-2 genomic sequences from around the world to gain insights into the kinetics of the mutations arising in the viral genomes. These 59,541 genomes were grouped according to month (January 2020 to March 2021) based on the collection date. Meta-analysis of these data led us to identify significant mutations in viral genomes. Pearson correlation of these mutations led us to the identification of 16 comutations. Among these comutations, some of the individual mutations have been shown to contribute to viral replication and fitness, suggesting a possible role of other unexplored mutations in viral evolution. We observed that the mutations 241C>T in the 5' untranslated region (UTR), 3037C>T in nsp3, 14408C>T in the RNA-dependent RNA polymerase (RdRp), and 23403A>G in spike are correlated with each other and were grouped in a single cluster by hierarchical clustering. These mutations have replaced the wild-type nucleotides in SARS-CoV-2 sequences. Additionally, we employed a suite of computational tools to investigate the effects of T85I (1059C>T), P323L (14408C>T), and Q57H (25563G>T) mutations in nsp2, RdRp, and the ORF3a protein of SARS-CoV-2, respectively. We observed that the mutations T85I and Q57H tend to be deleterious and destabilize the respective wild-type protein, whereas P323L in RdRp tends to be neutral and has a stabilizing effect. IMPORTANCE We performed a meta-analysis on SARS-CoV-2 genomes categorized by collection month and identified several significant mutations. Pearson correlation analysis of these significant mutations identified 16 comutations having absolute correlation coefficients of >0.4 and a frequency of >30% in the genomes used in this study. The correlation results were further validated by another statistical tool called hierarchical clustering, where mutations were grouped in clusters on the basis of their similarity. We identified several positive and negative correlations among comutations in SARS-CoV-2 isolates from around the world which might contribute to viral pathogenesis. The negative correlations among some of the mutations in SARS-CoV-2 identified in this study warrant further investigations. Further analysis of mutations such as T85I in nsp2 and Q57H in ORF3a protein revealed that these mutations tend to destabilize the protein relative to the wild type, whereas P323L in RdRp is neutral and has a stabilizing effect. Thus, we have identified several comutations which can be further characterized to gain insights into SARS-CoV-2 evolution.
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Affiliation(s)
- Neha Periwal
- Department of Biochemistry, SCLS, Jamia Hamdard, New Delhi, India
| | - Shravan B. Rathod
- Department of Chemistry, Smt. S. M. Panchal Science College, Talod, Gujarat, India
| | - Sankritya Sarma
- Department of Zoology, Hansraj College, University of Delhi, New Delhi, India
| | | | - Avantika Jain
- Department of Biochemistry, SCLS, Jamia Hamdard, New Delhi, India
- Delhi Institute of Pharmaceutical Sciences and Research, New Delhi, Delhi, India
| | - Ravi P. Barnwal
- Department of Biophysics, Panjab University, Chandigarh, India
| | | | - Baljeet Kaur
- Department of Computer Science, Hansraj College, University of Delhi, New Delhi, India
| | - Pooja Arora
- Department of Zoology, Hansraj College, University of Delhi, New Delhi, India
| | - Vikas Sood
- Department of Biochemistry, SCLS, Jamia Hamdard, New Delhi, India
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73
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Analysis of the mutation dynamics of SARS-CoV-2 genome in the samples from Georgia State of the United States. Gene 2022; 841:146774. [PMID: 35905853 PMCID: PMC9323210 DOI: 10.1016/j.gene.2022.146774] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2022] [Revised: 07/12/2022] [Accepted: 07/24/2022] [Indexed: 11/23/2022]
Abstract
BACKGROUND The COVID-19 is caused by a novel coronavirus SARS-CoV-2, which started from China. It spread rapidly throughout the world and was later declared a pandemic by the WHO. Over the course of time, SARS-CoV-2 has mutated for survival advantages, and this led to multiple variants. Multiple studies on mutations identification in SARS-CoV2 have been published covering extensive sample areas. The purpose of this study was to limit the sample area to the Georgia state in the U.S. and to analyze the genome sequences for mutation profiling across the genome and origin of variants. METHODS The genome sequences (n = 3,970) were obtained from the NCBI database as of June 12, 2021, with the filter of being complete sequenced genomes, homo-sapiens host, and only from Georgia State of the U.S. NextClade, an online tool was used for the analysis of the sequences using Wuhan-Hu-1/2019 as a reference genome. The algorithm was sequence alignment, translation, mutation calling, phylogenetic placement, clade assignment, and quality control (QC). Thirty-six samples with bad QC were removed from the mutational analysis. RESULTS A total 117,743 mutations in the nucleotides were identified (averaging 31.5 mutations per sample). The mutations A23403G, C3037T, C241T, and C14408T were detected in 98% of the samples. Also, a total of 75,517 mutations in the amino acid were identified (averaging 20.2 mutations per sample). The mutations D614G and P314L were identified in >97% samples whereas R203K, G204R, P681H, and N501Y were detected in >50% samples. Analysis also revealed 16 different clades with 20I (49.6%). Clades 20G (24.2%) and 20A (5.5%) being the most abundant, showed that SARS-CoV-2 in the Georgia State originated mainly from Southeast England, other parts of the U.S., and several countries in Western Europe. CONCLUSION Looking at the three most common variants in Georgia State of the U.S., we could determine the primary locations of transmission or origin for the virus, and our analyses indicates that majority of the cases originated from Southeast England (Clade 20I), the U.S. itself (Clade 20G), and from Western Europe (Clade 20C).
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Laine L, Skön M, Väisänen E, Julkunen I, Österlund P. SARS-CoV-2 variants Alpha, Beta, Delta and Omicron show a slower host cell interferon response compared to an early pandemic variant. Front Immunol 2022; 13:1016108. [PMID: 36248817 PMCID: PMC9561549 DOI: 10.3389/fimmu.2022.1016108] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Accepted: 09/15/2022] [Indexed: 11/15/2022] Open
Abstract
Since the start of the pandemic at the end of 2019, arising mutations in SARS-CoV-2 have improved its transmission and ability to circumvent the immunity induced by vaccination and previous COVID-19 infection. Studies on the effects of SARS-CoV-2 genomic mutations on replication and innate immunity will give us valuable insight into the evolution of the virus which can aid in further development of vaccines and new treatment modalities. Here we systematically analyzed the kinetics of virus replication, innate immune activation, and host cell antiviral response patterns in Alpha, Beta, Delta, Kappa, Omicron and two early pandemic SARS-CoV-2 variant-infected human lung epithelial Calu-3 cells. We observed overall comparable replication patterns for these variants with modest variations. Particularly, the sublineages of Omicron BA.1, BA.2 and a recombinant sublineage, XJ, all showed attenuated replication in Calu-3 cells compared to Alpha and Delta. Furthermore, there was relatively weak activation of primary innate immune signaling pathways, however, all variants produced enough interferons to induce the activation of STAT2 and production of interferon stimulated genes (ISGs). While interferon mRNA expression and STAT2 activation correlated with cellular viral RNA levels, ISG production did not. Although clear cut effects of specific SARS-CoV-2 genomic mutations could not be concluded, the variants of concern, including Omicron, showed a lower replication efficiency and a slower interferon response compared to an early pandemic variant in the study.
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Affiliation(s)
- Larissa Laine
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
- *Correspondence: Larissa Laine,
| | - Marika Skön
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Elina Väisänen
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
- Infection and Immunity, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Ilkka Julkunen
- Infection and Immunity, Institute of Biomedicine, University of Turku, Turku, Finland
| | - Pamela Österlund
- Expert Microbiology Unit, Department of Health Security, Finnish Institute for Health and Welfare, Helsinki, Finland
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75
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SARS-CoV-2 Uses Nonstructural Protein 16 to Evade Restriction by IFIT1 and IFIT3. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2022:2022.09.26.509529. [PMID: 36203546 PMCID: PMC9536030 DOI: 10.1101/2022.09.26.509529] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Understanding the molecular basis of innate immune evasion by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an important consideration for designing the next wave of therapeutics. Here, we investigate the role of the nonstructural protein 16 (NSP16) of SARS-CoV-2 in infection and pathogenesis. NSP16, a ribonucleoside 2'- O methyltransferase (MTase), catalyzes the transfer of a methyl group to mRNA as part of the capping process. Based on observations with other CoVs, we hypothesized that NSP16 2'- O MTase function protects SARS-CoV-2 from cap-sensing host restriction. Therefore, we engineered SARS-CoV-2 with a mutation that disrupts a conserved residue in the active site of NSP16. We subsequently show that this mutant is attenuated both in vitro and in vivo , using a hamster model of SARS-CoV-2 infection. Mechanistically, we confirm that the NSP16 mutant is more sensitive to type I interferon (IFN-I) in vitro . Furthermore, silencing IFIT1 or IFIT3, IFN-stimulated genes that sense a lack of 2'- O methylation, partially restores fitness to the NSP16 mutant. Finally, we demonstrate that sinefungin, a methyltransferase inhibitor that binds the catalytic site of NSP16, sensitizes wild-type SARS-CoV-2 to IFN-I treatment. Overall, our findings highlight the importance of SARS-CoV-2 NSP16 in evading host innate immunity and suggest a possible target for future antiviral therapies. Importance Similar to other coronaviruses, disruption of SARS-CoV-2 NSP16 function attenuates viral replication in a type I interferon-dependent manner. In vivo , our results show reduced disease and viral replication at late times in the hamster lung, but an earlier titer deficit for the NSP16 mutant (dNSP16) in the upper airway. In addition, our results confirm a role for IFIT1, but also demonstrate the necessity of IFIT3 in mediating dNSP16 attenuation. Finally, we show that targeting NSP16 activity with a 2'- O methyltransferase inhibitor in combination with type I interferon offers a novel avenue for antiviral development.
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76
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Hossain A, Akter S, Rashid AA, Khair S, Alam ASMRU. Unique mutations in SARS-CoV-2 omicron subvariants' non-spike proteins: Potential impact on viral pathogenesis and host immune evasion. Microb Pathog 2022; 170:105699. [PMID: 35944840 PMCID: PMC9356572 DOI: 10.1016/j.micpath.2022.105699] [Citation(s) in RCA: 33] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 12/20/2022]
Affiliation(s)
- Anamica Hossain
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Shammi Akter
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Alfi Anjum Rashid
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - Sabik Khair
- Department of Microbiology, University of Dhaka, Dhaka, 1000, Bangladesh
| | - A S M Rubayet Ul Alam
- Department of Microbiology, Jashore University of Science and Technology, Jashore, 7408, Bangladesh.
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