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Karousis ED. The art of hijacking: how Nsp1 impacts host gene expression during coronaviral infections. Biochem Soc Trans 2024; 52:481-490. [PMID: 38385526 PMCID: PMC10903449 DOI: 10.1042/bst20231119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 02/14/2024] [Accepted: 02/14/2024] [Indexed: 02/23/2024]
Abstract
Non-structural protein 1 (Nsp1) is one of the first proteins produced during coronaviral infections. It plays a pivotal role in hijacking and rendering the host gene expression under the service of the virus. With a focus on SARS-CoV-2, this review presents how Nsp1 selectively inhibits host protein synthesis and induces mRNA degradation of host but not viral mRNAs and blocks nuclear mRNA export. The clinical implications of this protein are highlighted by showcasing the pathogenic role of Nsp1 through the repression of interferon expression pathways and the features of viral variants with mutations in the Nsp1 coding sequence. The ability of SARS-CoV-2 Nsp1 to hinder host immune responses at an early step, the absence of homology to any human proteins, and the availability of structural information render this viral protein an ideal drug target with therapeutic potential.
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Affiliation(s)
- Evangelos D Karousis
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- Department of Chemistry, Biochemistry and Pharmaceutical Sciences, University of Bern, Bern, Switzerland
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2
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Jeronimo PMC, Aksenen CF, Duarte IO, Lins RD, Miyajima F. Evolutionary deletions within the SARS-CoV-2 genome as signature trends for virus fitness and adaptation. J Virol 2024; 98:e0140423. [PMID: 38088350 PMCID: PMC10804945 DOI: 10.1128/jvi.01404-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2024] Open
Abstract
Coronaviruses are large RNA viruses that can infect and spread among humans and animals. Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), responsible for coronavirus disease 2019, has evolved since its first detection in December 2019. Deletions are a common occurrence in SARS-CoV-2 evolution, particularly in specific genomic sites, and may be associated with the emergence of highly competent lineages. While deletions typically have a negative impact on viral fitness, some persist and become fixed in viral populations, indicating that they may confer advantageous benefits for the virus's adaptive evolution. This work presents a literature review and data analysis on structural losses in the SARS-CoV-2 genome and the potential relevance of specific signatures for enhanced viral fitness and spread.
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Affiliation(s)
| | - Cleber Furtado Aksenen
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Ceara, Eusebio, Brazil
| | - Igor Oliveira Duarte
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Ceara, Eusebio, Brazil
| | - Roberto D. Lins
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Pernambuco, Recife, Brazil
| | - Fabio Miyajima
- Fiocruz Genomic Network, Oswaldo Cruz Foundation (FIOCRUZ), branch Ceara, Eusebio, Brazil
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3
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Karousis ED, Schubert K, Ban N. Coronavirus takeover of host cell translation and intracellular antiviral response: a molecular perspective. EMBO J 2024; 43:151-167. [PMID: 38200146 PMCID: PMC10897431 DOI: 10.1038/s44318-023-00019-8] [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: 06/01/2023] [Revised: 11/01/2023] [Accepted: 11/24/2023] [Indexed: 01/12/2024] Open
Abstract
Coronaviruses are a group of related RNA viruses that cause respiratory diseases in humans and animals. Understanding the mechanisms of translation regulation during coronaviral infections is critical for developing antiviral therapies and preventing viral spread. Translation of the viral single-stranded RNA genome in the host cell cytoplasm is an essential step in the life cycle of coronaviruses, which affects the cellular mRNA translation landscape in many ways. Here we discuss various viral strategies of translation control, including how members of the Betacoronavirus genus shut down host cell translation and suppress host innate immune functions, as well as the role of the viral non-structural protein 1 (Nsp1) in the process. We also outline the fate of viral RNA, considering stress response mechanisms triggered in infected cells, and describe how unique viral RNA features contribute to programmed ribosomal -1 frameshifting, RNA editing, and translation shutdown evasion.
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Affiliation(s)
- Evangelos D Karousis
- Multidisciplinary Center for Infectious Diseases, University of Bern, Bern, Switzerland
- Department of Chemistry and Biochemistry, University of Bern, Bern, Switzerland
| | - Katharina Schubert
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland
| | - Nenad Ban
- Department of Biology, Institute of Molecular Biology and Biophysics, ETH Zurich, Zurich, Switzerland.
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4
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Nguyen H, Nguyen HL, Lan PD, Thai NQ, Sikora M, Li MS. Interaction of SARS-CoV-2 with host cells and antibodies: experiment and simulation. Chem Soc Rev 2023; 52:6497-6553. [PMID: 37650302 DOI: 10.1039/d1cs01170g] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of the devastating global COVID-19 pandemic announced by WHO in March 2020. Through unprecedented scientific effort, several vaccines, drugs and antibodies have been developed, saving millions of lives, but the fight against COVID-19 continues as immune escape variants of concern such as Delta and Omicron emerge. To develop more effective treatments and to elucidate the side effects caused by vaccines and therapeutic agents, a deeper understanding of the molecular interactions of SARS-CoV-2 with them and human cells is required. With special interest in computational approaches, we will focus on the structure of SARS-CoV-2 and the interaction of its spike protein with human angiotensin-converting enzyme-2 (ACE2) as a prime entry point of the virus into host cells. In addition, other possible viral receptors will be considered. The fusion of viral and human membranes and the interaction of the spike protein with antibodies and nanobodies will be discussed, as well as the effect of SARS-CoV-2 on protein synthesis in host cells.
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Affiliation(s)
- Hung Nguyen
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
| | - Hoang Linh Nguyen
- Institute of Fundamental and Applied Sciences, Duy Tan University, Ho Chi Minh City 700000, Vietnam
- Faculty of Environmental and Natural Sciences, Duy Tan University, Da Nang 550000, Vietnam
| | - Pham Dang Lan
- Life Science Lab, Institute for Computational Science and Technology, Quang Trung Software City, Tan Chanh Hiep Ward, District 12, 729110 Ho Chi Minh City, Vietnam
- Faculty of Physics and Engineering Physics, VNUHCM-University of Science, 227, Nguyen Van Cu Street, District 5, 749000 Ho Chi Minh City, Vietnam
| | - Nguyen Quoc Thai
- Dong Thap University, 783 Pham Huu Lau Street, Ward 6, Cao Lanh City, Dong Thap, Vietnam
| | - Mateusz Sikora
- Malopolska Centre of Biotechnology, Jagiellonian University, Kraków, Poland
- Department of Theoretical Biophysics, Max Planck Institute of Biophysics, Frankfurt am Main, Germany
| | - Mai Suan Li
- Institute of Physics, Polish Academy of Sciences, al. Lotnikow 32/46, 02-668 Warsaw, Poland.
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5
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Li X, Yan H, Wong G, Ouyang W, Cui J. Identifying featured indels associated with SARS-CoV-2 fitness. Microbiol Spectr 2023; 11:e0226923. [PMID: 37698427 PMCID: PMC10580940 DOI: 10.1128/spectrum.02269-23] [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: 06/01/2023] [Accepted: 07/14/2023] [Indexed: 09/13/2023] Open
Abstract
As an RNA virus, severe acute respiratory coronavirus 2 (SARS-CoV-2) is known for frequent substitution mutations, and substitutions in important genome regions are often associated with viral fitness. However, whether indel mutations are related to viral fitness is generally ignored. Here we developed a computational methodology to investigate indels linked to fitness occurring in over 9 million SARS-CoV-2 genomes. Remarkably, by analyzing 31,642,404 deletion records and 1,981,308 insertion records, our pipeline identified 26,765 deletion types and 21,054 insertion types and discovered 65 indel types with a significant association with Pango lineages. We proposed the concept of featured indels representing the population of specific Pango lineages and variants as substitution mutations and termed these 65 indels as featured indels. The selective pressure of all indel types is assessed using the Bayesian model to explore the importance of indels. Our results exhibited higher selective pressure of indels like substitution mutations, which are important for assessing viral fitness and consistent with previous studies in vitro. Evaluation of the growth rate of each viral lineage indicated that indels play key roles in SARS-CoV-2 evolution and deserve more attention as substitution mutations. IMPORTANCE The fitness of indels in pathogen genome evolution has rarely been studied. We developed a computational methodology to investigate the severe acute respiratory coronavirus 2 genomes and analyze over 33 million records of indels systematically, ultimately proposing the concept of featured indels that can represent specific Pango lineages and identifying 65 featured indels. Machine learning model based on Bayesian inference and viral lineage growth rate evaluation suggests that these featured indels exhibit selection pressure comparable to replacement mutations. In conclusion, indels are not negligible for evaluating viral fitness.
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Affiliation(s)
- Xiang Li
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
- AI for Science, Shanghai Artificial Intelligence Laboratory, Shanghai, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Hongliang Yan
- AI for Science, Shanghai Artificial Intelligence Laboratory, Shanghai, China
| | - Gary Wong
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
| | - Wanli Ouyang
- AI for Science, Shanghai Artificial Intelligence Laboratory, Shanghai, China
| | - Jie Cui
- CAS Key Laboratory of Molecular Virology & Immunology, Shanghai Institute of Immunity and Infection, Chinese Academy of Sciences, Shanghai, China
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6
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Tardivat Y, Sosnowski P, Tidu A, Westhof E, Eriani G, Martin F. SARS-CoV-2 NSP1 induces mRNA cleavages on the ribosome. Nucleic Acids Res 2023; 51:8677-8690. [PMID: 37503833 PMCID: PMC10484668 DOI: 10.1093/nar/gkad627] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 07/10/2023] [Accepted: 07/17/2023] [Indexed: 07/29/2023] Open
Abstract
In severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the non-structural protein NSP1 inhibits translation of host mRNAs by binding to the mRNA entry channel of the ribosome and, together with the 5'-untranslated region (UTR) of the viral mRNAs, allows the evasion of that inhibition. Here, we show that NSP1 mediates endonucleolytic cleavages of both host and viral mRNAs in the 5'UTR, but with different cleavage patterns. The first pattern is observed in host mRNAs with cleavages interspersed regularly and close to the 5' cap (6-11 nt downstream of the cap). Those cleavage positions depend more on the position relative to the 5' cap than on the sequence itself. The second cleavage pattern occurs at high NSP1 concentrations and only in SARS-CoV-2 RNAs, with the cleavages clustered at positions 45, 46 and 49. Both patterns of cleavage occur with the mRNA and NSP1 bound to the ribosome, with the SL1 hairpin at the 5' end sufficient to protect from NSP1-mediated degradation at low NSP1 concentrations. We show further that the N-terminal domain of NSP1 is necessary and sufficient for efficient cleavage. We suggest that in the ribosome-bound NSP1 protein the catalytic residues of the N-terminal domain are unmasked by the remodelling of the α1- and α2-helices of the C-terminal domain.
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Affiliation(s)
- Yann Tardivat
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l’ARN, CNRS UPR9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Piotr Sosnowski
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l’ARN, CNRS UPR9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Antonin Tidu
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l’ARN, CNRS UPR9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Eric Westhof
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l’ARN, CNRS UPR9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Gilbert Eriani
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l’ARN, CNRS UPR9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
| | - Franck Martin
- Université de Strasbourg, Institut de Biologie Moléculaire et Cellulaire, Architecture et Réactivité de l’ARN, CNRS UPR9002, 2, allée Konrad Roentgen, F-67084 Strasbourg, France
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7
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Zhang P, Liu D, Ji L, Dong F. SARS-CoV-2 genomic characterization and evolution in China. Heliyon 2023; 9:e18980. [PMID: 37636456 PMCID: PMC10450859 DOI: 10.1016/j.heliyon.2023.e18980] [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: 01/27/2023] [Revised: 07/25/2023] [Accepted: 08/03/2023] [Indexed: 08/29/2023] Open
Abstract
The pandemic caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) affected global health worldwide due to its high contagiousness. During the viral spread, many mutations occurred within the virus genome. China has adopted nonpharmaceutical intervention (NPI) to contain COVID-19 outbreaks. In order to understand the evolution and genomic variation of SARS-CoV-2 in China under this policy, a total of 524 sequences downloaded from Global Initiative on Sharing All Influenza Data (GISAID) between 2019 and 2022 were included in this study. The time-scaled evolutionary analysis showed that these sequences clustered in three groups (Group A-C). Group B and C accounted for the majority of the sequences whose divergence times were around 2020 and distributed in multiple regions. Group A was mainly composed of G variants, which were mainly isolated from several regions. Moreover, we found that 191 sites had mutations with no less than 3 times, including 30 amino acids that were deleted. Finally, we found that spike and nucleocapsid genes underwent positive selection evolution, indicating that the mutations within spike and nucleocapsid genes increased the SARS-CoV-2 contagiousness. Hence, this study preliminarily elucidates the evolutionary characteristics and genomic mutations of SARS-CoV-2 under the implementation of the NPI policy in China, providing scientific basis for further understanding the control effect of the NPI policy on the epidemic.
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Affiliation(s)
- Peng Zhang
- Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang, 313000, China
| | - Dongzi Liu
- State Key Laboratory of Virology, College of Life Sciences, Wuhan University, Wuhan, 430072, China
| | - Lei Ji
- Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang, 313000, China
| | - Fenfen Dong
- Huzhou Center for Disease Control and Prevention, 999 Changxing Road, Huzhou, Zhejiang, 313000, China
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8
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Broni E, Miller WA. Computational Analysis Predicts Correlations among Amino Acids in SARS-CoV-2 Proteomes. Biomedicines 2023; 11:512. [PMID: 36831052 PMCID: PMC9953644 DOI: 10.3390/biomedicines11020512] [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: 01/16/2023] [Revised: 02/03/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a serious global challenge requiring urgent and permanent therapeutic solutions. These solutions can only be engineered if the patterns and rate of mutations of the virus can be elucidated. Predicting mutations and the structure of proteins based on these mutations have become necessary for early drug and vaccine design purposes in anticipation of future viral mutations. The amino acid composition (AAC) of proteomes and individual viral proteins provide avenues for exploitation since AACs have been previously used to predict structure, shape and evolutionary rates. Herein, the frequency of amino acid residues found in 1637 complete proteomes belonging to 11 SARS-CoV-2 variants/lineages were analyzed. Leucine is the most abundant amino acid residue in the SARS-CoV-2 with an average AAC of 9.658% while tryptophan had the least abundance of 1.11%. The AAC and ranking of lysine and glycine varied in the proteome. For some variants, glycine had higher frequency and AAC than lysine and vice versa in other variants. Tryptophan was also observed to be the most intolerant to mutation in the various proteomes for the variants used. A correlogram revealed a very strong correlation of 0.999992 between B.1.525 (Eta) and B.1.526 (Iota) variants. Furthermore, isoleucine and threonine were observed to have a very strong negative correlation of -0.912, while cysteine and isoleucine had a very strong positive correlation of 0.835 at p < 0.001. Shapiro-Wilk normality test revealed that AAC values for all the amino acid residues except methionine showed no evidence of non-normality at p < 0.05. Thus, AACs of SARS-CoV-2 variants can be predicted using probability and z-scores. AACs may be beneficial in classifying viral strains, predicting viral disease types, members of protein families, protein interactions and for diagnostic purposes. They may also be used as a feature along with other crucial factors in machine-learning based algorithms to predict viral mutations. These mutation-predicting algorithms may help in developing effective therapeutics and vaccines for SARS-CoV-2.
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Affiliation(s)
- Emmanuel Broni
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
| | - Whelton A. Miller
- Department of Medicine, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
- Department of Molecular Pharmacology & Neuroscience, Loyola University Medical Center, Loyola University Chicago, Maywood, IL 60153, USA
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Structural insights into the activity regulation of full-length non-structural protein 1 from SARS-CoV-2. Structure 2023; 31:128-137.e5. [PMID: 36610391 PMCID: PMC9817231 DOI: 10.1016/j.str.2022.12.006] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/17/2022] [Accepted: 12/05/2022] [Indexed: 01/09/2023]
Abstract
Non-structural protein 1 (Nsp1) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is a major virulence factor and thus an attractive drug target. The last 33 amino acids of Nsp1 have been shown to bind within the mRNA entry tunnel of the 40S ribosomal subunit, shutting off host gene expression. Here, we report the solution-state structure of full-length Nsp1, which features an α/β fold formed by a six-stranded, capped β-barrel-like globular domain (N-terminal domain [NTD]), flanked by short N-terminal and long C-terminal flexible tails. The NTD has been found to be critical for 40S-mediated viral mRNA recognition and promotion of viral gene expression. We find that in free Nsp1, the NTD mRNA-binding surface is occluded by interactions with the acidic C-terminal tail, suggesting a mechanism of activity regulation based on the interplay between the folded NTD and the disordered C-terminal region. These results are relevant for drug-design efforts targeting Nsp1.
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10
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Libich DS, Baudin A. Order and disorder bound together in SARS-CoV-2 Nsp1 suppress host translation. Structure 2023; 31:121-122. [PMID: 36736295 PMCID: PMC9893522 DOI: 10.1016/j.str.2023.01.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
In this issue of Structure, Wang et al. investigate the interplay between folded and disordered regions of the SARS-CoV-2 non-structural protein 1 (Nsp1) that promotes the suppression of host protein translation. Their investigation will lead to novel avenues to therapeutically target critical viral functions necessary for host immune-response suppression.
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Affiliation(s)
- David S Libich
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; The Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA.
| | - Antoine Baudin
- Greehey Children's Cancer Research Institute, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA; The Department of Biochemistry and Structural Biology, The University of Texas Health Science Center at San Antonio, San Antonio, TX 78229, USA
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11
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Ghaleh SS, Rahimian K, Mahmanzar M, Mahdavi B, Tokhanbigli S, Sisakht MM, Farhadi A, Bakhtiari MM, Kuehu DL, Deng Y. SARS-CoV-2 Non-structural protein 1(NSP1) mutation virulence and natural selection: Evolutionary trends in the six continents. Virus Res 2023; 323:199016. [PMID: 36473671 PMCID: PMC9721189 DOI: 10.1016/j.virusres.2022.199016] [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: 10/07/2022] [Revised: 11/27/2022] [Accepted: 11/28/2022] [Indexed: 12/12/2022]
Abstract
OBJECTIVE Rapid transmission and reproduction of RNA viruses prepare conducive conditions to have a high rate of mutations in their genetic sequence. The viral mutations make adapt the severe acute respiratory syndrome coronavirus 2 in the host environment and help the evolution of the virus then also caused a high mortality rate by the virus that threatens worldwide health. Mutations and adaptation help the virus to escape confrontations that are done against it. METHODS In the present study, we analyzed 6,510,947 sequences of non-structural protein 1 as one of the conserved regions of the virus to find out frequent mutations and substitute amino acids in comparison with the wild type. NSP1 mutations rate divided into continents were different. RESULTS Based on this continental categorization, E87D in global vision and also in Europe notably increased. The E87D mutation has signed up to January 2022 as the first frequent mutation observed. The remarkable mutations, H110Y and R24C have the second and third frequencies, respectively. CONCLUSION According to the important role of non-structural protein 1 on the host mRNA translation, developing drug design against the protein could be so hopeful to find more effective ways the control and then treatment of the global pandemic coronavirus disease 2019.
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Affiliation(s)
| | - Karim Rahimian
- Bioinformatics and Computational Omics Lab (BioCOOL), Department of Biophysics. Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Mohammadamin Mahmanzar
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Bahar Mahdavi
- Department of Molecular Biotechnology, Cell Science Research Center, Royan Institute for Biotechnology, ACECR, Isfahan, Iran
| | - Samaneh Tokhanbigli
- Department of Molecular and Cellular Sciences, Faculty of Advanced Sciences and Technology, pharmaceutical Sciences Branch, Islamic Azad University, Tehran, Iran (IAUPS)
| | - Mahsa Mollapour Sisakht
- Department of Biochemistry, Erasmus University Medical Center, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Amin Farhadi
- Department of Biology, Payame Noor University, Tehran, Iran
| | - Mahsa Mousakhan Bakhtiari
- Pediatric Cell Therapy Research Center, Children's Medical Center, Tehran University of Medical Sciences, Tehran, Iran
| | - Donna Lee Kuehu
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA
| | - Youping Deng
- Department of Quantitative Health Sciences, John A. Burns School of Medicine, University of Hawaii at Manoa, Honolulu, HI 96813, USA.
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12
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Gu SH, Song DH, Yun H, Kim J, Lee S, Lee H, Lee TH, Kang SM, Jung YS, Hur G, Lee D. Molecular characterization of SARS-CoV-2 from the saliva of patients in the Republic of Korea in 2020. Health Sci Rep 2022; 5:e856. [PMID: 36210871 PMCID: PMC9528954 DOI: 10.1002/hsr2.856] [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: 03/02/2022] [Revised: 09/07/2022] [Accepted: 09/13/2022] [Indexed: 11/06/2022] Open
Abstract
Background and aims Despite global vaccination efforts, the number of confirmed cases of coronavirus disease 2019 (COVID‐19) remains high. To overcome the crisis precipitated by the ongoing pandemic, characteristic studies such as virus diagnosis, isolation, and genome analysis of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) are necessary. Herein, we report the isolation and molecular characterization of SARS‐CoV‐2 from the saliva of patients who had tested positive for COVID‐19 at Proving Ground in Taean County, Republic of Korea, in 2020. Methods We analyzed the whole‐genome sequence of SARS‐CoV‐2 isolated from the saliva samples of patients through next‐generation sequencing. We also successfully isolated SARS‐CoV‐2 from the saliva samples of two patients by using cell culture, which was used to study the cytopathic effects and viral replication in Vero E6 cells. Results Whole‐genome sequences of the isolates, SARS‐CoV‐2 ADD‐2 and ADD‐4, obtained from saliva were identical, and phylogenetic analysis using Bayesian inference methods showed SARS‐CoV‐2 GH clade (B.1.497) genome‐specific clustering. Typical coronavirus‐like particles, with diameters of 70–120 nm, were observed in the SARS‐CoV‐2 infected Vero E6 cells using transmission electron microscopy. Conclusion In conclusion, this report provides insights into the molecular diagnosis, isolation, genetic characteristics, and diversity of SARS‐CoV‐2 isolated from the saliva of patients. Further studies are needed to explore and monitor the evolution and characteristics of SARS‐CoV‐2 variants.
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Affiliation(s)
- Se Hun Gu
- Chem‐Bio Technology CenterAgency for Defense DevelopmentDaejeonRepublic of Korea
| | - Dong Hyun Song
- Chem‐Bio Technology CenterAgency for Defense DevelopmentDaejeonRepublic of Korea
| | - Hyeongseok Yun
- Chem‐Bio Technology CenterAgency for Defense DevelopmentDaejeonRepublic of Korea
| | - Jung‐Eun Kim
- Chem‐Bio Technology CenterAgency for Defense DevelopmentDaejeonRepublic of Korea
| | - Seung‐Ho Lee
- Chem‐Bio Technology CenterAgency for Defense DevelopmentDaejeonRepublic of Korea
| | - Hyunjin Lee
- Chem‐Bio Technology CenterAgency for Defense DevelopmentDaejeonRepublic of Korea
| | - Tae Ho Lee
- Institute of Health and EnvironmentDaejeonRepublic of Korea
| | - Seol Muk Kang
- Defense Test and Evaluation Research InstituteAgency for Defense DevelopmentTaeanRepublic of Korea
| | - Yu Sub Jung
- Defense Test and Evaluation Research InstituteAgency for Defense DevelopmentTaeanRepublic of Korea
| | - Gyeunghaeng Hur
- Chem‐Bio Technology CenterAgency for Defense DevelopmentDaejeonRepublic of Korea
| | - Daesang Lee
- Chem‐Bio Technology CenterAgency for Defense DevelopmentDaejeonRepublic of Korea
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13
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Mahmud S, Afrose S, Biswas S, Nagata A, Paul GK, Mita MA, Hasan MR, Shimu MSS, Zaman S, Uddin MS, Islam MS, Saleh MA. Plant-derived compounds effectively inhibit the main protease of SARS-CoV-2: An in silico approach. PLoS One 2022; 17:e0273341. [PMID: 35998194 PMCID: PMC9398018 DOI: 10.1371/journal.pone.0273341] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Accepted: 08/06/2022] [Indexed: 11/23/2022] Open
Abstract
The current coronavirus disease 2019 (COVID-19) pandemic, caused by the coronavirus 2 (SARS-CoV-2), involves severe acute respiratory syndrome and poses unprecedented challenges to global health. Structure-based drug design techniques have been developed targeting the main protease of the SARS-CoV-2, responsible for viral replication and transcription, to rapidly identify effective inhibitors and therapeutic targets. Herein, we constructed a phytochemical dataset of 1154 compounds using deep literature mining and explored their potential to bind with and inhibit the main protease of SARS-CoV-2. The three most effective phytochemicals Cosmosiine, Pelargonidin-3-O-glucoside, and Cleomiscosin A had binding energies of -8.4, -8.4, and -8.2 kcal/mol, respectively, in the docking analysis. These molecules could bind to Gln189, Glu166, Cys145, His41, and Met165 residues on the active site of the targeted protein, leading to specific inhibition. The pharmacological characteristics and toxicity of these compounds, examined using absorption, distribution, metabolism, excretion, and toxicity (ADMET) analyses, revealed no carcinogenicity or toxicity. Furthermore, the complexes were simulated with molecular dynamics for 100 ns to calculate the root mean square deviation (RMSD), root mean square fluctuation (RMSF), radius of gyration (Rg), solvent-accessible surface area (SASA), and hydrogen profiles from the simulation trajectories. Our analysis validated the rigidity of the docked protein-ligand. Taken together, our computational study findings might help develop potential drugs to combat the main protease of the SARS-CoV-2 and help alleviate the severity of the pandemic.
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Affiliation(s)
- Shafi Mahmud
- Division of Genome Sciences and Cancer, The John Curtin School of Medical Research, and The Shine-Dalgarno Centre for RNA Innovation, The Australian National University, Canberra, Australian Capital Territory, Australia
| | - Shamima Afrose
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Suvro Biswas
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Abir Nagata
- Department of Regenerative Dermatology, Graduate School of Medicine, Osaka University, Suita, Osaka, Japan
| | - Gobindo Kumar Paul
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Mohasana Akter Mita
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Robiul Hasan
- Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | | | - Shahriar Zaman
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md. Salah Uddin
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
| | - Md Sayeedul Islam
- Department of Biological Sciences, Graduate School of Science, Osaka University, Toyonaka, Osaka, Japan
| | - Md. Abu Saleh
- Microbiology Laboratory, Department of Genetic Engineering and Biotechnology, University of Rajshahi, Rajshahi, Bangladesh
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14
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Umair M, Ikram A, Rehman Z, Haider SA, Ammar M, Badar N, Ali Q, Rana MS, Salman M. Genomic diversity of SARS-CoV-2 in Pakistan during the fourth wave of pandemic. J Med Virol 2022; 94:4869-4877. [PMID: 35754094 PMCID: PMC9349642 DOI: 10.1002/jmv.27957] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2022] [Revised: 05/13/2022] [Accepted: 06/24/2022] [Indexed: 12/04/2022]
Abstract
The emergence of different variants of concern of severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) has resulted in upsurges of coronavirus disease 2019 (COVID‐19) cases around the globe. Pakistan faced the fourth wave of COVID‐19 from July to August 2021 with 314,786 cases. To understand the genomic diversity of circulating SARS‐CoV‐2 strains during the fourth wave of the pandemic in Pakistan, this study was conducted. The samples from 140 COVID‐19‐positive patients were subjected to whole‐genome sequencing using the iSeq Sequencer by Illumina. The results showed that 97% (n = 136) of isolates belonged to the delta variant while three isolates belonged to alpha and only one isolate belonged to the beta variant. Among delta variant cases, 20.5% (n = 28) isolates were showing B.1.617.2 while 23.5% (n = 25), 17.59% (n = 19), 14.81% (n = 16), and 13.89% (n = 15) of isolates were showing AY.108, AY.43 AY.127, and AY.125 lineages, respectively. Islamabad was found to be the most affected city with 65% (n = 89) of delta variant cases, followed by Karachi (17%, n = 23), and Rawalpindi (10%, n = 14). Apart from the characteristic spike mutations (T19R, L452R, T478K, P681R, and D950N) of the delta variant, the sublineages exhibited other spike mutations as E156del, G142D, T95I, A222V, G446V, K529N, N532S, Q613H, and V483A. The phylogenetic analysis revealed the introductions from Singapore, the United Kingdom, and Germany. This study highlights the circulation of delta variants (B.1.617.2 and sublineages) during the fourth wave of pandemic in Pakistan.
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Affiliation(s)
- Massab Umair
- National Institute of Health, Islamabad, Pakistan
| | - Aamer Ikram
- National Institute of Health, Islamabad, Pakistan
| | - Zaira Rehman
- National Institute of Health, Islamabad, Pakistan
| | | | | | - Nazish Badar
- National Institute of Health, Islamabad, Pakistan
| | - Qasim Ali
- National Institute of Health, Islamabad, Pakistan
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15
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Jin Y, Ouyang M, Yu T, Zhuang J, Wang W, Liu X, Duan F, Guo D, Peng X, Pan JA. Genome-Wide Analysis of the Indispensable Role of Non-structural Proteins in the Replication of SARS-CoV-2. Front Microbiol 2022; 13:907422. [PMID: 35722274 PMCID: PMC9198553 DOI: 10.3389/fmicb.2022.907422] [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: 03/29/2022] [Accepted: 04/21/2022] [Indexed: 11/27/2022] Open
Abstract
Understanding the process of replication and transcription of SARS-CoV-2 is essential for antiviral strategy development. The replicase polyprotein is indispensable for viral replication. However, whether all nsps derived from the replicase polyprotein of SARS-CoV-2 are indispensable is not fully understood. In this study, we utilized the SARS-CoV-2 replicon as the system to investigate the role of each nsp in viral replication. We found that except for nsp16, all the nsp deletions drastically impair the replication of the replicon, and nsp14 could recover the replication deficiency caused by its deletion in the viral replicon. Due to the unsuccessful expressions of nsp1, nsp3, and nsp16, we could not draw a conclusion about their in trans-rescue functions. Our study provided a new angle to understand the role of each nsp in viral replication and transcription, helping the evaluation of nsps as the target for antiviral drug development.
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Affiliation(s)
- Yunyun Jin
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Muzi Ouyang
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Ting Yu
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Jiaxin Zhuang
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Wenhao Wang
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Xue Liu
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Fangfang Duan
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Deyin Guo
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Xiaoxue Peng
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
| | - Ji-An Pan
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-sen University, Shenzhen, China
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16
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Kumar P, Schexnaydre E, Rafie K, Kurata T, Terenin I, Hauryliuk V, Carlson LA. Clinically observed deletions in SARS-CoV-2 Nsp1 affect its stability and ability to inhibit translation. FEBS Lett 2022; 596:1203-1213. [PMID: 35434785 PMCID: PMC9081967 DOI: 10.1002/1873-3468.14354] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/21/2022] [Accepted: 03/23/2022] [Indexed: 11/11/2022]
Abstract
Nonstructural protein 1 (Nsp1) of SARS‐CoV‐2 inhibits host cell translation through an interaction between its C‐terminal domain and the 40S ribosome. The N‐terminal domain (NTD) of Nsp1 is a target of recurring deletions, some of which are associated with altered COVID‐19 disease progression. Here, we characterize the efficiency of translational inhibition by clinically observed Nsp1 deletion variants. We show that a frequent deletion of residues 79–89 severely reduces the ability of Nsp1 to inhibit translation while not abrogating Nsp1 binding to the 40S. Notably, while the SARS‐CoV‐2 5′ untranslated region enhances translation of mRNA, it does not protect from Nsp1‐mediated inhibition. Finally, thermal stability measurements and structure predictions reveal a correlation between stability of the NTD and the efficiency of translation inhibition.
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Affiliation(s)
- Pravin Kumar
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University, SE-901 87, Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87, Umeå, Sweden
| | - Erin Schexnaydre
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University, SE-901 87, Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87, Umeå, Sweden
| | - Karim Rafie
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University, SE-901 87, Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87, Umeå, Sweden
| | - Tatsuaki Kurata
- Department of Experimental Medicine, University of Lund, 221 84, Lund, Sweden
| | - Ilya Terenin
- Lomonosov Moscow State University, Belozersky Institute of Physico-Chemical Biology, Leninskie Gory 1, Bldg. 40, Moscow, 119992, Russia
| | - Vasili Hauryliuk
- Department of Experimental Medicine, University of Lund, 221 84, Lund, Sweden.,Department of Molecular Biology, Umeå University, SE-901 87, Umeå, Sweden.,University of Tartu, Institute of Technology, 50411, Tartu, Estonia
| | - Lars-Anders Carlson
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87, Umeå, Sweden.,Wallenberg Centre for Molecular Medicine, Umeå University, SE-901 87, Umeå, Sweden.,Laboratory for Molecular Infection Medicine Sweden (MIMS), Umeå University, SE-901 87, Umeå, Sweden
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17
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Eriani G, Martin F. Viral and cellular translation during SARS‐CoV‐2 infection. FEBS Open Bio 2022; 12:1584-1601. [PMID: 35429230 PMCID: PMC9110871 DOI: 10.1002/2211-5463.13413] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/30/2022] [Accepted: 04/14/2022] [Indexed: 11/16/2022] Open
Abstract
SARS‐CoV‐2 is a betacoronavirus that emerged in China in December 2019 and which is the causative agent of the Covid‐19 pandemic. This enveloped virus contains a large positive‐sense single‐stranded RNA genome. In this review, we summarize the current knowledge on the molecular mechanisms for the translation of both viral transcripts and cellular messenger RNAs. Non‐structural proteins are encoded by the genomic RNA and are produced in the early steps of infection. In contrast, the structural proteins are produced from subgenomic RNAs that are translated in the late phase of the infectious program. Non‐structural protein 1 (NSP1) is a key molecule that regulates both viral and cellular translation. In addition, NSP1 interferes with multiple steps of the interferon I pathway and thereby blocks host antiviral responses. Therefore, NSP1 is a drug target of choice for the development of antiviral therapies.
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Affiliation(s)
- Gilbert Eriani
- Université de Strasbourg Institut de Biologie Moléculaire et Cellulaire Architecture et Réactivité de l’ARN CNRS UPR9002 2, allée Konrad Roentgen F‐67084 Strasbourg France
| | - Franck Martin
- Université de Strasbourg Institut de Biologie Moléculaire et Cellulaire Architecture et Réactivité de l’ARN CNRS UPR9002 2, allée Konrad Roentgen F‐67084 Strasbourg France
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18
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Abstract
SARS-CoV-2 continues adapting to human hosts during the current worldwide pandemic since 2019. This virus evolves through multiple means, such as single nucleotide mutations and structural variations, which has brought great difficulty to disease prevention and control of COVID-19. Structural variation, including multiple nucleotide changes like insertions and deletions, has a greater impact relative to single nucleotide mutation on both genome structures and protein functions. In this study, we found that deletion occurred frequently in not only SARS-CoV-2 but also in other SARS-related coronaviruses. These deletions showed obvious location bias and formed 45 recurrent deletion regions in the viral genome. Some of these deletions showed proliferation advantages, including four high-frequency deletions (nsp6 Δ106-109, S Δ69-70, S Δ144, and Δ28271) that were detected in around 50% of SARS-CoV-2 genomes and other 19 median-frequency deletions. In addition, the association between deletions and the WHO reported variants of concern (VOC) and variants of interest (VOI) of SARS-CoV-2 indicated that these variants had a unique combination of deletion patterns. In the spike (S) protein, the deletions in SARS-CoV-2 were mainly in the N-terminal domain. Some deletions, such as S Δ144/145 and S Δ243-244, have been confirmed to block the binding sites of neutralizing antibodies. Overall, this study revealed a conservative regional pattern and the potential effect of some deletions in SARS-CoV-2 over the whole genome, providing important evidence for potential epidemic control and vaccine development. IMPORTANCE Mutations in SARS-CoV-2 were studied extensively, while only the structure variations on the spike protein were discussed well in previous studies. To study the role of structural variations in virus evolution, we described the distribution of structure variations on the whole genome. Conserved patterns were found of deletions among SARS-CoV-2, SARS-CoV-2-like, and SARS-CoV-like viruses. There were 45 recurrent deletion regions (RDRs) in SARS-CoV-2 generated through the integration of deleted positions. In these regions, four high-frequency deletions parallelly appeared in multiple strains. Furthermore, in the spike protein, the deletions in SARS-CoV-2 were mainly in the N-terminal domain, blocking the binding sites of some neutralizing antibodies, while the structural variations in SARS-related coronavirus were mainly in the N-terminal domain and receptor binding domain. The receptor binding domain is highly related to hosting recognition. The deletions in the receptor binding domain may play a role in host adaption.
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19
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Xue W, Ding C, Qian K, Liao Y. The Interplay Between Coronavirus and Type I IFN Response. Front Microbiol 2022; 12:805472. [PMID: 35317429 PMCID: PMC8934427 DOI: 10.3389/fmicb.2021.805472] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Accepted: 12/24/2021] [Indexed: 12/14/2022] Open
Abstract
In the past few decades, newly evolved coronaviruses have posed a global threat to public health and animal breeding. To control and prevent the coronavirus-related diseases, understanding the interaction of the coronavirus and the host immune system is the top priority. Coronaviruses have evolved multiple mechanisms to evade or antagonize the host immune response to ensure their replication. As the first line and main component of innate immune response, type I IFN response is able to restrict virus in the initial infection stage; it is thus not surprising that the primary aim of the virus is to evade or antagonize the IFN response. Gaining a profound understanding of the interaction between coronaviruses and type I IFN response will shed light on vaccine development and therapeutics. In this review, we provide an update on the current knowledge on strategies employed by coronaviruses to evade type I IFN response.
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Affiliation(s)
- Wenxiang Xue
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Chan Ding
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Kun Qian
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, China
| | - Ying Liao
- Department of Avian Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
- *Correspondence: Ying Liao,
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20
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Vora SM, Fontana P, Mao T, Leger V, Zhang Y, Fu TM, Lieberman J, Gehrke L, Shi M, Wang L, Iwasaki A, Wu H. Targeting stem-loop 1 of the SARS-CoV-2 5' UTR to suppress viral translation and Nsp1 evasion. Proc Natl Acad Sci U S A 2022; 119:e2117198119. [PMID: 35149555 PMCID: PMC8892331 DOI: 10.1073/pnas.2117198119] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 01/01/2022] [Indexed: 11/25/2022] Open
Abstract
SARS-CoV-2 is a highly pathogenic virus that evades antiviral immunity by interfering with host protein synthesis, mRNA stability, and protein trafficking. The SARS-CoV-2 nonstructural protein 1 (Nsp1) uses its C-terminal domain to block the messenger RNA (mRNA) entry channel of the 40S ribosome to inhibit host protein synthesis. However, how SARS-CoV-2 circumvents Nsp1-mediated suppression for viral protein synthesis and if the mechanism can be targeted therapeutically remain unclear. Here, we show that N- and C-terminal domains of Nsp1 coordinate to drive a tuned ratio of viral to host translation, likely to maintain a certain level of host fitness while maximizing replication. We reveal that the stem-loop 1 (SL1) region of the SARS-CoV-2 5' untranslated region (5' UTR) is necessary and sufficient to evade Nsp1-mediated translational suppression. Targeting SL1 with locked nucleic acid antisense oligonucleotides inhibits viral translation and makes SARS-CoV-2 5' UTR vulnerable to Nsp1 suppression, hindering viral replication in vitro at a nanomolar concentration, as well as providing protection against SARS-CoV-2-induced lethality in transgenic mice expressing human ACE2. Thus, SL1 allows Nsp1 to switch infected cells from host to SARS-CoV-2 translation, presenting a therapeutic target against COVID-19 that is conserved among immune-evasive variants. This unique strategy of unleashing a virus' own virulence mechanism against itself could force a critical trade-off between drug resistance and pathogenicity.
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Affiliation(s)
- Setu M Vora
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
| | - Pietro Fontana
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
| | - Tianyang Mao
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520
| | - Valerie Leger
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
| | - Ying Zhang
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Tian-Min Fu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
- Department of Biological Chemistry and Pharmacology, The Ohio State University, Columbus, OH 43210
- The Ohio State University Comprehensive Cancer Center, The Ohio State University, Columbus, OH 43210
| | - Judy Lieberman
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
- Department of Pediatrics, Harvard Medical School, Boston, MA 02115
| | - Lee Gehrke
- Institute for Medical Engineering and Science, Massachusetts Institute of Technology, Cambridge, MA 02139
- Department of Microbiology, Blavatnik Institute, Harvard Medical School, MA 02115
| | - Ming Shi
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115;
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
- School of Life Science and Technology, Harbin Institute of Technology, Harbin 150001, China
| | - Longfei Wang
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115;
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
- School of Pharmaceutical Sciences, Wuhan University, Wuhan 430071, China
| | - Akiko Iwasaki
- Department of Immunobiology, Yale University School of Medicine, New Haven, CT 06520;
- HHMI, Chevy Chase, MD 20815
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115;
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, MA 02115
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21
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Boodhoo N, Matsuyama-Kato A, Shojadoost B, Behboudi S, Sharif S. The severe acute respiratory syndrome coronavirus 2 non-structural proteins 1 and 15 proteins mediate antiviral immune evasion. CURRENT RESEARCH IN VIROLOGICAL SCIENCE 2022; 3:100021. [PMID: 35187506 PMCID: PMC8837493 DOI: 10.1016/j.crviro.2022.100021] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/03/2022] [Accepted: 02/10/2022] [Indexed: 12/11/2022]
Abstract
Infection with pathogenic viruses is often sensed by innate receptors such as Toll-Like Receptors (TLRs) which stimulate type I and III interferons (IFNs) responses, to generate an antiviral state within many cell types. To counteract these antiviral systems, many viruses, including severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), encode non-structural proteins (NSPs) that mediate immune evasion. Using an overexpression system in A549 cells, we demonstrated a significant increase (p ≤ 0.0001) in Vesicular Stomatitis Virus (VSV)-EGFP reporter virus replication in cell lines overexpressing either the SARS-CoV-2 NSP1 or NSP15 when compared to control A549 cells. The increase in VSV-EGFP virus output was associated with a decrease in TLR2, TLR4 and TLR9 protein expression and a lack of antiviral protein production. Truncation of both NSP1 and NSP15 led to an increase in cellular TLR2, TLR4 and TLR9 as well as a decrease in TLR2 expression respectively. This observation can be attributed to the presence of a functional domain in NSP1 and NSP15 between amino acid (aa) 120–180 and aa 230–346, respectively. Both TLR3 and TLR9 ligands but not TLR2 ligand were highly effective at overcoming NSP1 and NSP15 functional interference based on significant decrease (p ≤ 0.0001) in VSV-EGFP virus replication. NSP1 or NSP15 intracellular interactions are likely low affinity interactions that can be easily disrupted by stimulating cells with specific TLR3 and TLR9 ligands. This report provides insights into the role of SARS-CoV-2 NSP1 and NSP15 in limiting specific TLR pathway activation, as an evasive mechanism against host innate responses.
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Affiliation(s)
- Nitish Boodhoo
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Ayumi Matsuyama-Kato
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Bahram Shojadoost
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Shahriar Behboudi
- The Pirbright Institute, Pirbright, Woking, United Kingdom.,Faculty of Health and Medical Sciences, School of Veterinary Medicine, University of Surrey, Guildford, Surrey, United Kingdom
| | - Shayan Sharif
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON, N1G 2W1, Canada
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22
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Rapid SARS-CoV-2 Intra-Host and Within-Household Emergence of Novel Haplotypes. Viruses 2022; 14:v14020399. [PMID: 35215992 PMCID: PMC8877413 DOI: 10.3390/v14020399] [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: 01/18/2022] [Revised: 02/11/2022] [Accepted: 02/13/2022] [Indexed: 12/13/2022] Open
Abstract
In February 2020, the municipality of Vo', a small town near Padua (Italy) was quarantined due to the first coronavirus disease 19 (COVID-19)-related death detected in Italy. To investigate the viral prevalence and clinical features, the entire population was swab tested in two sequential surveys. Here we report the analysis of 87 viral genomes, which revealed that the unique ancestor haplotype introduced in Vo' belongs to lineage B, carrying the mutations G11083T and G26144T. The viral sequences allowed us to investigate the viral evolution while being transmitted within and across households and the effectiveness of the non-pharmaceutical interventions implemented in Vo'. We report, for the first time, evidence that novel viral haplotypes can naturally arise intra-host within an interval as short as two weeks, in approximately 30% of the infected individuals, regardless of symptom severity or immune system deficiencies. Moreover, both phylogenetic and minimum spanning network analyses converge on the hypothesis that the viral sequences evolved from a unique common ancestor haplotype that was carried by an index case. The lockdown extinguished both the viral spread and the emergence of new variants.
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23
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Chakraborty C, Sharma AR, Bhattacharya M, Lee SS. A Detailed Overview of Immune Escape, Antibody Escape, Partial Vaccine Escape of SARS-CoV-2 and Their Emerging Variants With Escape Mutations. Front Immunol 2022; 13:801522. [PMID: 35222380 PMCID: PMC8863680 DOI: 10.3389/fimmu.2022.801522] [Citation(s) in RCA: 66] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 01/05/2022] [Indexed: 01/08/2023] Open
Abstract
The infective SARS-CoV-2 is more prone to immune escape. Presently, the significant variants of SARS-CoV-2 are emerging in due course of time with substantial mutations, having the immune escape property. Simultaneously, the vaccination drive against this virus is in progress worldwide. However, vaccine evasion has been noted by some of the newly emerging variants. Our review provides an overview of the emerging variants' immune escape and vaccine escape ability. We have illustrated a broad view related to viral evolution, variants, and immune escape ability. Subsequently, different immune escape approaches of SARS-CoV-2 have been discussed. Different innate immune escape strategies adopted by the SARS-CoV-2 has been discussed like, IFN-I production dysregulation, cytokines related immune escape, immune escape associated with dendritic cell function and macrophages, natural killer cells and neutrophils related immune escape, PRRs associated immune evasion, and NLRP3 inflammasome associated immune evasion. Simultaneously we have discussed the significant mutations related to emerging variants and immune escape, such as mutations in the RBD region (N439K, L452R, E484K, N501Y, K444R) and other parts (D614G, P681R) of the S-glycoprotein. Mutations in other locations such as NSP1, NSP3, NSP6, ORF3, and ORF8 have also been discussed. Finally, we have illustrated the emerging variants' partial vaccine (BioNTech/Pfizer mRNA/Oxford-AstraZeneca/BBIBP-CorV/ZF2001/Moderna mRNA/Johnson & Johnson vaccine) escape ability. This review will help gain in-depth knowledge related to immune escape, antibody escape, and partial vaccine escape ability of the virus and assist in controlling the current pandemic and prepare for the next.
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Affiliation(s)
- Chiranjib Chakraborty
- Department of Biotechnology, School of Life Science and Biotechnology, Adamas University, Kolkata, India
| | - Ashish Ranjan Sharma
- Institute for Skeletal Aging and Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, South Korea
| | | | - Sang-Soo Lee
- Institute for Skeletal Aging and Orthopedic Surgery, Hallym University-Chuncheon Sacred Heart Hospital, Chuncheon-si, South Korea
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Liu X, Guo L, Xu T, Lu X, Ma M, Sheng W, Wu Y, Peng H, Cao L, Zheng F, Huang S, Yang Z, Du J, Shi M, Guo D. A comprehensive evolutionary and epidemiological characterization of insertion and deletion mutations in SARS-CoV-2 genomes. Virus Evol 2022; 7:veab104. [PMID: 35039785 PMCID: PMC8754802 DOI: 10.1093/ve/veab104] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Revised: 11/29/2021] [Accepted: 12/11/2021] [Indexed: 12/19/2022] Open
Abstract
SARS-CoV-2, which causes the current pandemic of respiratory illness, is evolving continuously and generating new variants. Nevertheless, most of the sequence analyses thus far focused on nucleotide substitutions despite the fact that insertions and deletions (indels) are equally important in the evolution of SARS-CoV-2. In this study, we analyzed 1,099,664 high-quality sequences of SARS-CoV-2 genomes to re-construct the evolutionary and epidemiological histories of indels. Our analysis revealed 289 circulating indel types (237 deletion and 52 insertion types, each represented by more than ten genomic sequences), among which eighteen were recurrent indel types, each represented by more than 500 genome sequences. Although indels were identified across the entire genome, most of them were identified in nsp6, S, ORF8, and N genes, among which ORF8 indel types had the highest frequencies of frameshift. Geographical and temporal analyses of these variants revealed a few alterations of dominant indel types, each accompanied by geographic expansion to different countries and continents, which resulted in the fixation of several types of indels in the field, including the current variants of concern. Evolutionary and structural analyses revealed that indels involving S N-terminal domain regions were linked to the 3/4 variants of concern, resulting in significantly altered S protein that might contribute to the selective advantage of the corresponding variant. In sum, our study highlights the important role of insertions and deletions in the evolution and spread of SARS-CoV-2.
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Affiliation(s)
- Xue Liu
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Liping Guo
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Tiefeng Xu
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Xiaoyu Lu
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Mingpeng Ma
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Wenyu Sheng
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Yinxia Wu
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Hong Peng
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Liu Cao
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Fuxiang Zheng
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Siyao Huang
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Zixiao Yang
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Jie Du
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Mang Shi
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
| | - Deyin Guo
- Centre for Infection and Immunity Study (CIIS), School of Medicine (Shenzhen), Shenzhen Campus of Sun Yat-sen University, Sun Yat-sen University, Shenzhen, Guangdong 518107, China
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Panzera Y, Ramos N, Calleros L, Marandino A, Tomás G, Techera C, Grecco S, Frabasile S, Fuques E, Coppola L, Goñi N, Ramas V, Sorhouet C, Bormida V, Burgueño A, Brasesco M, Garland MR, Molinari S, Perez MT, Somma R, Somma S, Morel MN, Mogdasy C, Chiparelli H, Arbiza J, Delfraro A, Pérez R. Transmission cluster of COVID-19 cases from Uruguay: emergence and spreading of a novel SARS-CoV-2 ORF6 deletion. Mem Inst Oswaldo Cruz 2022; 116:e210275. [PMID: 35019072 PMCID: PMC8752050 DOI: 10.1590/0074-02760210275] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Accepted: 11/03/2021] [Indexed: 01/07/2023] Open
Abstract
BACKGROUND Evolutionary changes in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) include indels in non-structural, structural, and accessory open reading frames (ORFs) or genes. OBJECTIVES We track indels in accessory ORFs to infer evolutionary gene patterns and epidemiological links between outbreaks. METHODS Genomes from Coronavirus disease 2019 (COVID-19) case-patients were Illumina sequenced using ARTIC_V3. The assembled genomes were analysed to detect substitutions and indels. FINDINGS We reported the emergence and spread of a unique 4-nucleotide deletion in the accessory ORF6, an interesting gene with immune modulation activity. The deletion in ORF6 removes one repeat unit of a two 4-nucleotide repeat, which shows that directly repeated sequences in the SARS-CoV-2 genome are associated with indels, even outside the context of extended repeat regions. The 4-nucleotide deletion produces a frameshifting change that results in a protein with two inserted amino acids, increasing the coding information of this accessory ORF. Epidemiological and genomic data indicate that the deletion variant has a single common ancestor and was initially detected in a health care outbreak and later in other COVID-19 cases, establishing a transmission cluster in the Uruguayan population. MAIN CONCLUSIONS Our findings provide evidence for the origin and spread of deletion variants and emphasise indels’ importance in epidemiological studies, including differentiating consecutive outbreaks occurring in the same health facility.
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Affiliation(s)
- Yanina Panzera
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Natalia Ramos
- Universidad de la República, Facultad de Ciencias, Instituto de Biología e Instituto de Química Biológica, Sección Virología, Montevideo, Uruguay
| | - Lucía Calleros
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Ana Marandino
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Gonzalo Tomás
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Claudia Techera
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Sofía Grecco
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Sandra Frabasile
- Universidad de la República, Facultad de Ciencias, Instituto de Biología e Instituto de Química Biológica, Sección Virología, Montevideo, Uruguay
| | - Eddie Fuques
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
| | - Leticia Coppola
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Natalia Goñi
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Viviana Ramas
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Cecilia Sorhouet
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Victoria Bormida
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Analía Burgueño
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - María Brasesco
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Maria Rosa Garland
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Sylvia Molinari
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Maria Teresa Perez
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Rosina Somma
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Silvana Somma
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Maria Noelia Morel
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Cristina Mogdasy
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Héctor Chiparelli
- Ministerio de Salud Pública, Centro Nacional de Referencia de Influenza y Otros Virus Respiratorios, Departamento de Laboratorios de Salud Pública, Montevideo, Uruguay
| | - Juan Arbiza
- Universidad de la República, Facultad de Ciencias, Instituto de Biología e Instituto de Química Biológica, Sección Virología, Montevideo, Uruguay
| | - Adriana Delfraro
- Universidad de la República, Facultad de Ciencias, Instituto de Biología e Instituto de Química Biológica, Sección Virología, Montevideo, Uruguay
| | - Ruben Pérez
- Universidad de la República, Facultad de Ciencias, Instituto de Biología, Departamento de Biología Animal, Sección Genética Evolutiva, Montevideo, Uruguay
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26
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Gong YN, Lee KM, Shih SR. Evolution and Epidemiology of SARS-CoV-2 Virus. Methods Mol Biol 2022; 2452:3-18. [PMID: 35554897 DOI: 10.1007/978-1-0716-2111-0_1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
A novel coronavirus (CoV) that emerged in Wuhan, Hubei province in China, in December 2019, has rapidly spread worldwide. Named as the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), this virus has been responsible for infecting about 153 million people and causing 3 million deaths by May 2021. There is obvious interest in gaining novel insights into the epidemiologic evolution of this virus; however, inappropriate application and interpretation of genomic and phylogenetic analyses has led to dangerous outcomes and misunderstandings. This chapter focuses on not only introducing this virus, its genomic characteristics and molecular mechanisms but also describing the application and interpretation of phylogenetic tree analyses, in order to provide useful information to better understand the evolution and epidemiology of this virus. In addition, recombinant region and genetic ancestry of SARS-CoV-2 remain unknown. It is urgently required to collect samples and obtain related viral genetic data from animal sources for identifying the intermediate host of SARS-CoV-2 that is responsible for its cross-species transmission.
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Affiliation(s)
- Yu-Nong Gong
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Kuo-Ming Lee
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan
- Division of Infectious Diseases, Department of Pediatrics, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan
| | - Shin-Ru Shih
- Research Center for Emerging Viral Infections, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
- Department of Laboratory Medicine, Linkou Chang Gung Memorial Hospital, Taoyuan, Taiwan.
- Department of Medical Biotechnology and Laboratory Science, College of Medicine, Chang Gung University, Taoyuan, Taiwan.
- Research Center for Chinese Herbal Medicine, Research Center for Food and Cosmetic Safety, and Graduate Institute of Health Industry Technology, College of Human Ecology, Chang Gung University of Science and Technology, Taoyuan, Taiwan.
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27
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Vasudevan S, Baraniuk JN. Understanding COVID-19 Pathogenesis: A Drug-Repurposing Effort to Disrupt Nsp-1 Binding to Export Machinery Receptor Complex. Pathogens 2021; 10:1634. [PMID: 34959589 PMCID: PMC8709492 DOI: 10.3390/pathogens10121634] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 12/06/2021] [Accepted: 12/15/2021] [Indexed: 11/16/2022] Open
Abstract
Non-structural protein 1 (Nsp1) is a virulence factor found in all beta coronaviruses (b-CoVs). Recent studies have shown that Nsp1 of SARS-CoV-2 virus interacts with the nuclear export receptor complex, which includes nuclear RNA export factor 1 (NXF1) and nuclear transport factor 2-like export factor 1 (NXT1). The NXF1-NXT1 complex plays a crucial role in the transport of host messenger RNA (mRNA). Nsp1 interferes with the proper binding of NXF1 to mRNA export adaptors and its docking to the nuclear pore complex. We propose that drugs targeting the binding surface between Nsp1 and NXF1-NXT1 may be a useful strategy to restore host antiviral gene expression. Exploring this strategy forms the main goals of this paper. Crystal structures of Nsp1 and the heterodimer of NXF1-NXT1 have been determined. We modeled the docking of Nsp1 to the NXF1-NXT1 complex, and discovered repurposed drugs that may interfere with this binding. To our knowledge, this is the first attempt at drug-repurposing of this complex. We used structural analysis to screen 1993 FDA-approved drugs for docking to the NXF1-NXT1 complex. The top hit was ganirelix, with a docking score of -14.49. Ganirelix competitively antagonizes the gonadotropin releasing hormone receptor (GNRHR) on pituitary gonadotrophs, and induces rapid, reversible suppression of gonadotropin secretion. The conformations of Nsp1 and GNRHR make it unlikely that they interact with each other. Additional drug leads were inferred from the structural analysis of this complex, which are discussed in the paper. These drugs offer several options for therapeutically blocking Nsp1 binding to NFX1-NXT1, which may normalize nuclear export in COVID-19 infection.
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Affiliation(s)
- Sona Vasudevan
- Department of Biochemistry, Molecular and Cellular Biology, Georgetown University Medical Center, 3900 Reservoir Road NW, Washington, DC 20057, USA
| | - James N Baraniuk
- Division of Rheumatology, Immunology and Allergy, Department of Medicine, Georgetown University Medical Center, 3900 Reservoir Road NW, Washington, DC 20007, USA
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28
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Perez-Gomez R. The Development of SARS-CoV-2 Variants: The Gene Makes the Disease. J Dev Biol 2021; 9:58. [PMID: 34940505 PMCID: PMC8705434 DOI: 10.3390/jdb9040058] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Revised: 11/22/2021] [Accepted: 11/30/2021] [Indexed: 12/15/2022] Open
Abstract
A novel coronavirus (SARS-CoV-2) emerged towards the end of 2019 that caused a severe respiratory disease in humans called COVID-19. It led to a pandemic with a high rate of morbidity and mortality that is ongoing and threatening humankind. Most of the mutations occurring in SARS-CoV-2 are synonymous or deleterious, but a few of them produce improved viral functions. The first known mutation associated with higher transmissibility, D614G, was detected in early 2020. Since then, the virus has evolved; new mutations have occurred, and many variants have been described. Depending on the genes affected and the location of the mutations, they could provide altered infectivity, transmissibility, or immune escape. To date, mutations that cause variations in the SARS-CoV-2 spike protein have been among the most studied because of the protein's role in the initial virus-cell contact and because it is the most variable region in the virus genome. Some concerning mutations associated with an impact on viral fitness have been described in the Spike protein, such as D614G, N501Y, E484K, K417N/T, L452R, and P681R, among others. To understand the impact of the infectivity and antigenicity of the virus, the mutation landscape of SARS-CoV-2 has been under constant global scrutiny. The virus variants are defined according to their origin, their genetic profile (some characteristic mutations prevalent in the lineage), and the severity of the disease they produce, which determines the level of concern. If they increase fitness, new variants can outcompete others in the population. The Alpha variant was more transmissible than previous versions and quickly spread globally. The Beta and Gamma variants accumulated mutations that partially escape the immune defenses and affect the effectiveness of vaccines. Nowadays, the Delta variant, identified around March 2021, has spread and displaced the other variants, becoming the most concerning of all lineages that have emerged. The Delta variant has a particular genetic profile, bearing unique mutations, such as T478K in the spike protein and M203R in the nucleocapsid. This review summarizes the current knowledge of the different mutations that have appeared in SARS-CoV-2, mainly on the spike protein. It analyzes their impact on the protein function and, subsequently, on the level of concern of different variants and their importance in the ongoing pandemic.
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Affiliation(s)
- Raquel Perez-Gomez
- Translational Genomics Group, Institut Universitari de Biotecnologia y Biomedicina BIOTECMED, Universitat de Valencia, 46100 Valencia, Spain
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29
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Setaro AC, Gaglia MM. All hands on deck: SARS-CoV-2 proteins that block early anti-viral interferon responses. CURRENT RESEARCH IN VIROLOGICAL SCIENCE 2021; 2:100015. [PMID: 34786565 PMCID: PMC8588586 DOI: 10.1016/j.crviro.2021.100015] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Revised: 11/02/2021] [Accepted: 11/09/2021] [Indexed: 12/11/2022]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection is responsible for the current pandemic coronavirus disease of 2019 (COVID-19). Like other pathogens, SARS-CoV-2 infection can elicit production of the type I and III interferon (IFN) cytokines by the innate immune response. A rapid and robust type I and III IFN response can curb viral replication and improve clinical outcomes of SARS-CoV-2 infection. To effectively replicate in the host, SARS-CoV-2 has evolved mechanisms for evasion of this innate immune response, which could also modulate COVID-19 pathogenesis. In this review, we discuss studies that have reported the identification and characterization of SARS-CoV-2 proteins that inhibit type I IFNs. We focus especially on the mechanisms of nsp1 and ORF6, which are the two most potent and best studied SARS-CoV-2 type I IFN inhibitors. We also discuss naturally occurring mutations in these SARS-CoV-2 IFN antagonists and the impact of these mutations in vitro and on clinical presentation. As SARS-CoV-2 continues to spread and evolve, researchers will have the opportunity to study natural mutations in IFN antagonists and assess their role in disease. Additional studies that look more closely at previously identified antagonists and newly arising mutants may inform future therapeutic interventions for COVID-19.
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Key Words
- 3CLpro, 3-chymotrypsin like protease
- COVID-19, coronavirus disease of 2019
- IFN, interferon
- IFNAR, interferon alpha/beta receptor
- IFNLR, interferon lambda receptor
- IRF, interferon response factor
- ISRE, interferon stimulated response element
- Immune evasion
- MAVS, mitochondrial antiviral-signaling protein
- MDA-5, melanoma differentiation-associated protein 5
- ORF, open reading frame
- ORF6
- PLpro, papain-like protease
- RIG-I, retinoic acid-inducible gene I
- SARS-CoV-2
- SARS-CoV-2, SARS coronavirus 2
- SRP, signal recognition particle
- STAT, signal transducer and regulator of transcription
- SeV, Sendai virus
- TAB1, TGF-beta activated kinase 1 binding protein 1
- TAK1, TGF-beta activated kinase 1
- TBK1, TANK-binding kinase 1
- TLR, toll-like receptor
- TRIF, TIR domain-containing adapter-inducing interferon beta
- Type I interferon
- UTR, untranslated region
- eIF, eukaryotic initiation factor
- nsp, non-structural protein
- nsp1
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Affiliation(s)
- Alessandra C Setaro
- Program in Immunology, Tufts Graduate School of Biomedical Sciences, USA.,Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Tufts University, MA, USA
| | - Marta M Gaglia
- Program in Immunology, Tufts Graduate School of Biomedical Sciences, USA.,Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Tufts University, MA, USA
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30
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Zanchi FB, Mariúba LA, Nascimento V, Souza V, Corado A, Nascimento F, Costa ÁK, Duarte D, Silva G, Mejía M, Pessoa K, Gonçalves L, Brandão MJ, Jesus M, Glória J, Silva M, Mattos T, da Costa C, Naveca FG. Structural analysis of SARS-Cov-2 nonstructural protein 1 polymorphisms found in the Brazilian Amazon. Exp Biol Med (Maywood) 2021; 246:2332-2337. [PMID: 34749522 DOI: 10.1177/15353702211021348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
The coronavirus disease COVID-19 has been the cause of millions of deaths worldwide. Among the SARS-CoV-2 proteins, the non-structural protein 1 (NSP1) has great importance during the virus infection process and is present in both alpha and beta-CoVs. Therefore, monitoring of NSP1 polymorphisms is crucial in order to understand their role during infection and virus-induced pathogenicity. Herein, we analyzed how mutations detected in the circulating SARS-CoV-2 in the population of the city of Manaus, Amazonas state, Brazil could modify the tertiary structure of the NSP1 protein. Three mutations were detected in the SARS-CoV-2 NSP1 gene: deletion of the amino acids KSF from positions 141 to 143 (delKSF), SARS-CoV-2, lineage B.1.195; and two substitutions, R29H and R43C, SARS-CoV-2 lineage B.1.1.28 and B.1.1.33, respectively. The delKSF was found in 47 samples, whereas R29H and R43C were found in two samples, one for each mutation. The NSP1 structures carrying the mutations R43C and R29H on the N-terminal portion (e.g. residues 10 to 127) showed minor backbone divergence compared to the Wuhan model. However, the NSP1 C-terminal region (residues 145 to 180) was severely affected in the delKSF and R29H mutants. The intermediate variable region (residues 144 to 148) leads to changes in the C-terminal region, particularly in the delKSF structure. New investigations must be carried out to analyze how these changes affect NSP1 activity during the infection. Our results reinforce the need for continuous genomic surveillance of SARS-CoV-2 to better understand virus evolution and assess the potential impact of the viral mutations on the approved vaccines and future therapies.
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Affiliation(s)
- Fernando Berton Zanchi
- Laboratório de Bioinformática e Química Medicinal, Fundação Oswaldo Cruz, FIOCRUZ, Unidade Rondônia, Porto Velho, RO 76812-245, Brazil.,Programa de Pós-Graduação em Biologia Experimental, Universidade Federal de Rondônia (UNIR), Porto Velho, RO 76801-059, Brazil.,Instituto Nacional de Epidemiologia na Amazônia Ocidental - EPIAMO, Porto Velho, RO 76812-245, Brazil
| | - Luis André Mariúba
- Programa Multi-institucional de Pós-graduação em Biotecnologia, Universidade Federal do Amazonas (PPGBIOTEC-UFAM), Manaus, AM 69067-005, Brazil.,Programa de Pós-graduação em Imunologia Básica e Aplicada, Universidade Federal do Amazonas (PPGIBA-UFAM), Manaus, AM 69067-005, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Oswaldo Cruz, Programa de Pós-Graduação em Biologia Celular e Molecular, Rio de Janeiro, RJ 21040-360, Brazil
| | - Valdinete Nascimento
- Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Oswaldo Cruz, Programa de Pós-Graduação em Biologia Celular e Molecular, Rio de Janeiro, RJ 21040-360, Brazil.,Rede Genômica de Vigilância em Saúde do Estado do Amazonas, Manaus, AM 69057-070, Brazil
| | - Victor Souza
- Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Oswaldo Cruz, Programa de Pós-Graduação em Biologia Celular e Molecular, Rio de Janeiro, RJ 21040-360, Brazil.,Rede Genômica de Vigilância em Saúde do Estado do Amazonas, Manaus, AM 69057-070, Brazil
| | - André Corado
- Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Oswaldo Cruz, Programa de Pós-Graduação em Biologia Celular e Molecular, Rio de Janeiro, RJ 21040-360, Brazil
| | - Fernanda Nascimento
- Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane, Programa de Pós-Graduação em Biologia da Interação Patógeno-Hospedeiro, Manaus, AM 69057-070, Brazil
| | - Ágatha Kelly Costa
- Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil
| | - Débora Duarte
- Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil
| | - George Silva
- Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil
| | - Matilde Mejía
- Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil
| | - Karina Pessoa
- Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane, Programa de Pós-Graduação em Biologia da Interação Patógeno-Hospedeiro, Manaus, AM 69057-070, Brazil
| | - Luciana Gonçalves
- Fundação de Vigilância em Saúde do Amazonas, Manaus, AM 69093-018, Brazil
| | - Maria Júlia Brandão
- Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil
| | - Michele Jesus
- Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil
| | - Juliane Glória
- Programa Multi-institucional de Pós-graduação em Biotecnologia, Universidade Federal do Amazonas (PPGBIOTEC-UFAM), Manaus, AM 69067-005, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil
| | - Marineide Silva
- Fundação de Vigilância em Saúde do Amazonas, Manaus, AM 69093-018, Brazil
| | - Tirza Mattos
- Fundação de Vigilância em Saúde do Amazonas, Manaus, AM 69093-018, Brazil
| | - Cristiano da Costa
- Fundação de Vigilância em Saúde do Amazonas, Manaus, AM 69093-018, Brazil
| | - Felipe Gomes Naveca
- Programa de Pós-graduação em Imunologia Básica e Aplicada, Universidade Federal do Amazonas (PPGIBA-UFAM), Manaus, AM 69067-005, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane (ILMD-FIOCRUZ), Manaus, AM 69057-070, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Oswaldo Cruz, Programa de Pós-Graduação em Biologia Celular e Molecular, Rio de Janeiro, RJ 21040-360, Brazil.,Rede Genômica de Vigilância em Saúde do Estado do Amazonas, Manaus, AM 69057-070, Brazil.,Fundação Oswaldo Cruz, Fiocruz, Instituto Leônidas e Maria Deane, Programa de Pós-Graduação em Biologia da Interação Patógeno-Hospedeiro, Manaus, AM 69057-070, Brazil
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31
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Mendez AS, Ly M, González-Sánchez AM, Hartenian E, Ingolia NT, Cate JH, Glaunsinger BA. The N-terminal domain of SARS-CoV-2 nsp1 plays key roles in suppression of cellular gene expression and preservation of viral gene expression. Cell Rep 2021; 37:109841. [PMID: 34624207 PMCID: PMC8481097 DOI: 10.1016/j.celrep.2021.109841] [Citation(s) in RCA: 59] [Impact Index Per Article: 19.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 08/16/2021] [Accepted: 09/24/2021] [Indexed: 01/23/2023] Open
Abstract
Nonstructural protein 1 (nsp1) is a coronavirus (CoV) virulence factor that restricts cellular gene expression by inhibiting translation through blocking the mRNA entry channel of the 40S ribosomal subunit and by promoting mRNA degradation. We perform a detailed structure-guided mutational analysis of severe acute respiratory syndrome (SARS)-CoV-2 nsp1, revealing insights into how it coordinates these activities against host but not viral mRNA. We find that residues in the N-terminal and central regions of nsp1 not involved in docking into the 40S mRNA entry channel nonetheless stabilize its association with the ribosome and mRNA, both enhancing its restriction of host gene expression and enabling mRNA containing the SARS-CoV-2 leader sequence to escape translational repression. These data support a model in which viral mRNA binding functionally alters the association of nsp1 with the ribosome, which has implications for drug targeting and understanding how engineered or emerging mutations in SARS-CoV-2 nsp1 could attenuate the virus.
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Affiliation(s)
- Aaron S Mendez
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Michael Ly
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Angélica M González-Sánchez
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; Comparative Biochemistry Graduate Program, University of California, Berkeley, Berkeley, CA, USA
| | - Ella Hartenian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA
| | - Jamie H Cate
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA; Department of Chemistry, University of California, Berkeley, Berkeley, CA, USA; Molecular Biophysics & Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA, USA
| | - Britt A Glaunsinger
- Department of Plant & Microbial Biology, University of California, Berkeley, Berkeley, CA, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA; California Institute for Quantitative Biosciences, University of California, Berkeley, Berkeley, CA, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA; Howard Hughes Medical Institute, Berkeley, CA, USA.
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32
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Ramesh S, Govindarajulu M, Parise RS, Neel L, Shankar T, Patel S, Lowery P, Smith F, Dhanasekaran M, Moore T. Emerging SARS-CoV-2 Variants: A Review of Its Mutations, Its Implications and Vaccine Efficacy. Vaccines (Basel) 2021; 9:1195. [PMID: 34696303 PMCID: PMC8537675 DOI: 10.3390/vaccines9101195] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 09/26/2021] [Accepted: 10/08/2021] [Indexed: 12/21/2022] Open
Abstract
The widespread increase in multiple severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) variants is causing a significant health concern in the United States and worldwide. These variants exhibit increased transmissibility, cause more severe disease, exhibit evasive immune properties, impair neutralization by antibodies from vaccinated individuals or convalescence sera, and reinfection. The Centers for Disease Control and Prevention (CDC) has classified SARS-CoV-2 variants into variants of interest, variants of concern, and variants of high consequence. Currently, four variants of concern (B.1.1.7, B.1.351, P.1, and B.1.617.2) and several variants of interests (B.1.526, B.1.525, and P.2) are characterized and are essential for close monitoring. In this review, we discuss the different SARS-CoV-2 variants, emphasizing variants of concern circulating the world and highlight the various mutations and how these mutations affect the characteristics of the virus. In addition, we discuss the most common vaccines and the various studies concerning the efficacy of these vaccines against different variants of concern.
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Affiliation(s)
- Sindhu Ramesh
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Manoj Govindarajulu
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Rachel S. Parise
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Logan Neel
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Tharanath Shankar
- Department of Internal Medicine, Ramaiah Medical College and Hospital, Bengaluru 560054, Karnataka, India;
| | - Shriya Patel
- Department of Neuroscience, Middlebury College, Middlebury, VT 05753, USA;
| | - Payton Lowery
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Forrest Smith
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Muralikrishnan Dhanasekaran
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
| | - Timothy Moore
- Department of Drug Discovery and Development, Auburn University Harrison School of Pharmacy, Auburn, AL 36849, USA; (S.R.); (M.G.); (R.S.P.); (L.N.); (P.L.); (F.S.); (M.D.)
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33
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Zannoli S, Dirani G, Taddei F, Gatti G, Poggianti I, Denicolò A, Arfilli V, Manera M, Mancini A, Battisti A, Sambri V. A deletion in the N gene may cause diagnostic escape in SARS-CoV-2 samples. Diagn Microbiol Infect Dis 2021; 102:115540. [PMID: 34649189 PMCID: PMC8447549 DOI: 10.1016/j.diagmicrobio.2021.115540] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 09/07/2021] [Accepted: 09/12/2021] [Indexed: 11/28/2022]
Abstract
Five SARS-CoV-2-positive samples showed N-gene drop-out with a RT-PCR multiplex test. WGS found all samples to harbor a deletion in the same region of the N gene, which is likely to impair the efficiency of amplification. This highlights the need for a continued surveillance of viral evolution and diagnostic test performance.
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Affiliation(s)
- Silvia Zannoli
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Italy.
| | - Giorgio Dirani
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Italy
| | - Francesca Taddei
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Italy
| | - Giulia Gatti
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Italy
| | - Ilaria Poggianti
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Italy
| | - Agnese Denicolò
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Italy
| | | | - Martina Manera
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Italy
| | - Andrea Mancini
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Italy
| | - Arianna Battisti
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Italy
| | - Vittorio Sambri
- Unit of Microbiology, The Great Romagna Area Hub Laboratory, Italy; Department of Experimental, Diagnostic and Specialty Medicine (DIMES), University of Bologna
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34
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Small molecule interactions with the SARS-CoV-2 main protease: In silico all-atom microsecond MD simulations, PELE Monte Carlo simulations, and determination of in vitro activity inhibition. J Mol Graph Model 2021; 110:108050. [PMID: 34655918 PMCID: PMC8504156 DOI: 10.1016/j.jmgm.2021.108050] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/16/2021] [Accepted: 10/08/2021] [Indexed: 12/20/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has caused the ongoing COVID-19 pandemic. With some notable exceptions, safe and effective vaccines, which are now being widely distributed globally, have largely begun to stabilise the situation. However, emerging variants of concern and vaccine hesitancy are apparent obstacles to eradication. Therefore, the need for the development of potent antivirals is still of importance. In this context, the SARS-CoV-2 main protease (Mpro) is a critical target and numerous clinical trials, predominantly in the private domain, are currently in progress. Here, our aim was to extend our previous studies, with hypericin and cyanidin-3-O-glucoside, as potential inhibitors of the SARS-CoV-2 Mpro. Firstly, we performed all-atom microsecond molecular dynamics simulations, which highlight the stability of the ligands in the Mpro active site over the duration of the trajectories. We also invoked PELE Monte Carlo simulations which indicate that both hypericin and cyanidin-3-O-glucoside preferentially interact with the Mpro active site and known allosteric sites. For further validation, we performed an in vitro enzymatic activity assay that demonstrated that hypericin and cyanidin-3-O-glucoside inhibit Mpro activity in a dose-dependent manner at biologically relevant (μM) concentrations. However, both ligands are much less potent than the well-known covalent antiviral GC376, which was used as a positive control in our experiments. Nevertheless, the biologically relevant activity of hypericin and cyanidin-3-O-glucoside is encouraging. In particular, a synthetic version of hypericin has FDA orphan drug designation, which could simplify potential clinical evaluation in the context of COVID-19.
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35
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Faggioni G, Stefanelli P, Giordani F, Fillo S, Anselmo A, Vera Fain V, Fortunato A, Petralito G, Molinari F, Lo Presti A, Di Martino A, Palomba S, De Santis R, Rezza G, Lista F. Identification and characterization of SARS-CoV-2 clusters in the EU/EEA in the first pandemic wave: additional elements to trace the route of the virus. INFECTION GENETICS AND EVOLUTION 2021; 96:105108. [PMID: 34637920 PMCID: PMC8501518 DOI: 10.1016/j.meegid.2021.105108] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Revised: 10/01/2021] [Accepted: 10/06/2021] [Indexed: 12/20/2022]
Abstract
A high-quality dataset of 3289 complete SARS-CoV-2 genomes collected in Europe and European Economic Area (EAA) in the early phase of the first wave of the pandemic was analyzed. Among all single nucleotide mutations, 41 had a frequency ≥ 1%, and the phylogenetic analysis showed at least 6 clusters with a specific mutational profile. These clusters were differentially distributed in the EU/EEA, showing a statistically significant association with the geographic origin. The analysis highlighted that the mutations C14408T and C14805T played an important role in clusters selection and further virus spread. Moreover, the molecular analysis suggests that the SARS-CoV-2 strain responsible for the first Italian confirmed COVID-19 case was already circulating outside the country.
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Affiliation(s)
| | - Paola Stefanelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | | | - Silvia Fillo
- Scientific Department, Army Medical Center, Rome, Italy
| | - Anna Anselmo
- Scientific Department, Army Medical Center, Rome, Italy
| | | | | | | | | | | | - Angela Di Martino
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Stefano Palomba
- General Directorate of Military Medical Services, Medical Situation Awareness Branch, Rome, Italy
| | | | - Giovanni Rezza
- Health Prevention Directorate, Ministry of Health, Rome, Italy
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36
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Mou K, Mukhtar F, Khan MT, Darwish DB, Peng S, Muhammad S, Al-Sehemi AG, Wei DQ. Emerging Mutations in Nsp1 of SARS-CoV-2 and Their Effect on the Structural Stability. Pathogens 2021; 10:pathogens10101285. [PMID: 34684233 PMCID: PMC8539063 DOI: 10.3390/pathogens10101285] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/19/2021] [Accepted: 10/01/2021] [Indexed: 01/31/2023] Open
Abstract
The genome of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) encodes 16 non-structural (Nsp) and 4 structural proteins. Among the Nsps, Nsp1 inhibits host gene expression and also evades the immune system. This protein has been proposed as a target for vaccine development and also for drug design. Owing to its important role, the current study aimed to identify mutations in Nsp1 and their effect on protein stability and flexibility. This is the first comprehensive study in which 295,000 complete genomes have been screened for mutations after alignment with the Wuhan-Hu-1 reference genome (Accession NC_045512), using the CoVsurver app. The sequences harbored 933 mutations in the entire coding region of Nsp1. The most frequently occurring mutation in the 180-amino-acid Nsp1 protein was R24C (n = 1122), followed by D75E (n = 890), D48G (n = 881), H110Y (n = 860), and D144A (n = 648). Among the 933 non-synonymous mutations, 529 exhibited a destabilizing effect. Similarly, a gain in flexibility was observed in 542 mutations. The majority of the most frequent mutations were detected in the loop regions. These findings imply that Nsp1 mutations might be useful to exploit SARS-CoV-2's pathogenicity. Genomic sequencing of SARS-CoV-2 on a regular basis will further assist in analyzing variations among the drug targets and to test the diagnostic accuracy. This wide range of mutations and their effect on Nsp1's stability may have some consequences for the host's innate immune response to SARS-CoV-2 infection and also for the vaccines' efficacy. Based on this mutational information, geographically strain-specific drugs, vaccines, and antibody combinations could be a useful strategy against SARS-CoV-2 infection.
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Affiliation(s)
- Kejie Mou
- Department of Neurosurgery, Bishan Hospital of Chongqing, Chongqing 402760, China;
| | - Farwa Mukhtar
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, KM Defence Road, Lahore 58810, Pakistan;
| | - Muhammad Tahir Khan
- Institute of Molecular Biology and Biotechnology (IMBB), The University of Lahore, KM Defence Road, Lahore 58810, Pakistan;
- Correspondence: (M.T.K.); (D.-Q.W.)
| | - Doaa B. Darwish
- Botany Department, Faculty of Science, Mansoura University, Mansoura 35516, Egypt;
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk 71491, Saudi Arabia
| | - Shaoliang Peng
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen 518055, China;
| | - Shabbir Muhammad
- Department of Physics, College of Science, King Khalid University, Abha 61413, Saudi Arabia;
| | - Abdullah G. Al-Sehemi
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha 61413, Saudi Arabia;
- Department of Chemistry, College of Science, King Khalid University, Abha 61413, Saudi Arabia
| | - Dong-Qing Wei
- Peng Cheng Laboratory, Vanke Cloud City Phase I Building 8, Xili Street, Nashan District, Shenzhen 518055, China;
- State Key Laboratory of Microbial Metabolism, Shanghai-Islamabad-Belgrade Joint Innovation Center on Antibacterial Resistances, Joint International Research Laboratory of Metabolic & Developmental Sciences and School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200030, China
- Correspondence: (M.T.K.); (D.-Q.W.)
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37
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Wang Y, Kirkpatrick J, Zur Lage S, Korn SM, Neißner K, Schwalbe H, Schlundt A, Carlomagno T. 1H, 13C, and 15N backbone chemical-shift assignments of SARS-CoV-2 non-structural protein 1 (leader protein). BIOMOLECULAR NMR ASSIGNMENTS 2021; 15:287-295. [PMID: 33770349 PMCID: PMC7996116 DOI: 10.1007/s12104-021-10019-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 03/13/2021] [Indexed: 05/30/2023]
Abstract
The current COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has become a worldwide health crisis, necessitating coordinated scientific research and urgent identification of new drug targets for treatment of COVID-19 lung disease. The covid19-nmr consortium seeks to support drug development by providing publicly accessible NMR data on the viral RNA elements and proteins. The SARS-CoV-2 genome comprises a single RNA of about 30 kb in length, in which 14 open reading frames (ORFs) have been annotated, and encodes approximately 30 proteins. The first two-thirds of the SARS-CoV-2 genome is made up of two large overlapping open-reading-frames (ORF1a and ORF1b) encoding a replicase polyprotein, which is subsequently cleaved to yield 16 so-called non-structural proteins. The non-structural protein 1 (Nsp1), which is considered to be a major virulence factor, suppresses host immune functions by associating with host ribosomal complexes at the very end of its C-terminus. Furthermore, Nsp1 facilitates initiation of viral RNA translation via an interaction of its N-terminal domain with the 5' untranslated region (UTR) of the viral RNA. Here, we report the near-complete backbone chemical-shift assignments of full-length SARS-CoV-2 Nsp1 (19.8 kDa), which reveal the domain organization, secondary structure and backbone dynamics of Nsp1, and which will be of value to further NMR-based investigations of both the biochemical and physiological functions of Nsp1.
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Affiliation(s)
- Ying Wang
- Centre of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
| | - John Kirkpatrick
- Centre of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Susanne Zur Lage
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany
| | - Sophie M Korn
- Institute for Molecular Biosciences, St Lucia, QLD, 4072, Australia
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Konstantin Neißner
- Institute for Molecular Biosciences, St Lucia, QLD, 4072, Australia
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, 60438, Frankfurt, Germany
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Andreas Schlundt
- Institute for Molecular Biosciences, St Lucia, QLD, 4072, Australia
- Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt, Germany
| | - Teresa Carlomagno
- Centre of Biomolecular Drug Research (BMWZ), Leibniz University Hannover, Schneiderberg 38, 30167, Hannover, Germany.
- Group of NMR-Based Structural Chemistry, Helmholtz Centre for Infection Research, Inhoffenstrasse 7, 38124, Braunschweig, Germany.
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38
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Selvaraj C, Dinesh DC, Krafcikova P, Boura E, Aarthy M, Pravin MA, Singh SK. Structural Understanding of SARS-CoV-2 Drug Targets, Active Site Contour Map Analysis and COVID-19 Therapeutics. Curr Mol Pharmacol 2021; 15:418-433. [PMID: 34488601 DOI: 10.2174/1874467214666210906125959] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Revised: 03/11/2021] [Accepted: 03/17/2021] [Indexed: 11/22/2022]
Abstract
The most iconic word of the year 2020 is 'COVID-19', the shortened name for coronavirus disease 2019. The pandemic, caused by Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), is responsible for multiple worldwide lockdowns, an economic crisis, and a substantial increase in hospitalizations for viral pneumonia along with respiratory failure and multiorgan dysfunctions. Recently, the first few vaccines were approved by World Health Organization (WHO) and can eventually save millions of lives. Even though, few emergency use drugs like Remdesivir and several other repurposed drugs, still there is no approved drug for COVID-19. The coronaviral encoded proteins involved in host-cell entry, replication, and host-cell invading mechanism are potentially therapeutic targets. This perspective review provides the molecular overview of SARS-CoV-2 life cycle for summarizing potential drug targets, structural insights, active site contour map analyses of those selected SARS-CoV-2 protein targets for drug discovery, immunology, and pathogenesis.
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Affiliation(s)
- Chandrabose Selvaraj
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi-630004, Tamil Nadu. India
| | | | - Petra Krafcikova
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2, 166 10 Prague 6. Czech Republic
| | - Evzen Boura
- Institute of Organic Chemistry and Biochemistry AS CR, v.v.i., Flemingovo nam. 2, 166 10 Prague 6. Czech Republic
| | - Murali Aarthy
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi-630004, Tamil Nadu. India
| | - Muthuraja Arun Pravin
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi-630004, Tamil Nadu. India
| | - Sanjeev Kumar Singh
- Computer Aided Drug Design and Molecular Modeling Lab, Department of Bioinformatics, Science Block, Alagappa University, Karaikudi-630004, Tamil Nadu. India
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Zhao K, Ke Z, Hu H, Liu Y, Li A, Hua R, Guo F, Xiao J, Zhang Y, Duan L, Yan XF, Gao YG, Liu B, Xia Y, Li Y. Structural Basis and Function of the N Terminus of SARS-CoV-2 Nonstructural Protein 1. Microbiol Spectr 2021; 9:e0016921. [PMID: 34132580 PMCID: PMC8552758 DOI: 10.1128/spectrum.00169-21] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Accepted: 05/12/2021] [Indexed: 11/20/2022] Open
Abstract
Nonstructural protein 1 (Nsp1) of severe acute respiratory syndrome coronaviruses (SARS-CoVs) is an important pathogenic factor that inhibits host protein translation by means of its C terminus. However, its N-terminal function remains elusive. Here, we determined the crystal structure of the N terminus (amino acids [aa] 11 to 125) of SARS-CoV-2 Nsp1 at a 1.25-Å resolution. Further functional assays showed that the N terminus of SARS-CoVs Nsp1 alone loses the ability to colocalize with ribosomes and inhibit protein translation. The C terminus of Nsp1 can colocalize with ribosomes, but its protein translation inhibition ability is significantly weakened. Interestingly, fusing the C terminus of Nsp1 with enhanced green fluorescent protein (EGFP) or other proteins in place of its N terminus restored the protein translation inhibitory ability to a level equivalent to that of full-length Nsp1. Thus, our results suggest that the N terminus of Nsp1 is able to stabilize the binding of the Nsp1 C terminus to ribosomes and act as a nonspecific barrier to block the mRNA channel, thus abrogating host mRNA translation.
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Affiliation(s)
- Kaitao Zhao
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Zunhui Ke
- Department of Blood Transfusion, Wuhan Children’s Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Hongbing Hu
- Department of Blood Transfusion, Wuhan Children’s Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Yahui Liu
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Aixin Li
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Rong Hua
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Fangteng Guo
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Junfeng Xiao
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
| | - Yu Zhang
- Faculty of Science (Medical Science), The University of Sydney, Sydney, New South Wales, Australia
| | - Ling Duan
- Department of Blood Transfusion, Wuhan Children’s Hospital, Tongji Medical College, Huazhong University of Science & Technology, Wuhan, China
| | - Xin-Fu Yan
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Yong-Gui Gao
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Bing Liu
- BioBank, The First Affiliated Hospital of Xi’an Jiaotong University, Xi’an, China
- MRC Centre for Molecular Bacteriology and Infection, Imperial College London, United Kingdom
| | - Yuchen Xia
- State Key Laboratory of Virology and Hubei Province Key Laboratory of Allergy and Immunology, Institute of Medical Virology, School of Basic Medical Sciences, Wuhan University, Wuhan, China
| | - Yan Li
- Department of Pathogen Biology, School of Basic Medicine, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, China
- Tongji-Rongcheng Center for Biomedicine, Huazhong University of Science and Technology, Wuhan, China
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Habibzadeh P, Mofatteh M, Silawi M, Ghavami S, Faghihi MA. Molecular diagnostic assays for COVID-19: an overview. Crit Rev Clin Lab Sci 2021; 58:385-398. [PMID: 33595397 PMCID: PMC7898297 DOI: 10.1080/10408363.2021.1884640] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 01/17/2021] [Accepted: 01/29/2021] [Indexed: 12/26/2022]
Abstract
The coronavirus disease 2019 (COVID-19) pandemic has highlighted the cardinal importance of rapid and accurate diagnostic assays. Since the early days of the outbreak, researchers with different scientific backgrounds across the globe have tried to fulfill the urgent need for such assays, with many assays having been approved and with others still undergoing clinical validation. Molecular diagnostic assays are a major group of tests used to diagnose COVID-19. Currently, the detection of SARS-CoV-2 RNA by reverse transcription polymerase chain reaction (RT-PCR) is the most widely used method. Other diagnostic molecular methods, including CRISPR-based assays, isothermal nucleic acid amplification methods, digital PCR, microarray assays, and next generation sequencing (NGS), are promising alternatives. In this review, we summarize the technical and clinical applications of the different COVID-19 molecular diagnostic assays and suggest directions for the implementation of such technologies in future infectious disease outbreaks.
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Affiliation(s)
- Parham Habibzadeh
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mohammad Mofatteh
- Sir William Dunn School of Pathology, University of Oxford, Oxford, UK
| | - Mohammad Silawi
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Saeid Ghavami
- Max Rady College of Medicine, Rady Faculty of Health Sciences, University of Manitoba, Winnipeg, Canada
| | - Mohammad Ali Faghihi
- Persian BayanGene Research and Training Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Center for Therapeutic Innovation, University of Miami Miller School of Medicine, Miami, FL, USA
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Chen Z, Wang C, Feng X, Nie L, Tang M, Zhang H, Xiong Y, Swisher SK, Srivastava M, Chen J. Interactomes of SARS-CoV-2 and human coronaviruses reveal host factors potentially affecting pathogenesis. EMBO J 2021; 40:e107776. [PMID: 34232536 PMCID: PMC8447597 DOI: 10.15252/embj.2021107776] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Revised: 06/27/2021] [Accepted: 06/30/2021] [Indexed: 12/12/2022] Open
Abstract
Host-virus protein-protein interactions play key roles in the life cycle of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). We conducted a comprehensive interactome study between the virus and host cells using tandem affinity purification and proximity-labeling strategies and identified 437 human proteins as the high-confidence interacting proteins. Further characterization of these interactions and comparison to other large-scale study of cellular responses to SARS-CoV-2 infection elucidated how distinct SARS-CoV-2 viral proteins participate in its life cycle. With these data mining, we discovered potential drug targets for the treatment of COVID-19. The interactomes of two key SARS-CoV-2-encoded viral proteins, NSP1 and N, were compared with the interactomes of their counterparts in other human coronaviruses. These comparisons not only revealed common host pathways these viruses manipulate for their survival, but also showed divergent protein-protein interactions that may explain differences in disease pathology. This comprehensive interactome of SARS-CoV-2 provides valuable resources for the understanding and treating of this disease.
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Affiliation(s)
- Zhen Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Chao Wang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Xu Feng
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Litong Nie
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mengfan Tang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Huimin Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Yun Xiong
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Samuel K Swisher
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Mrinal Srivastava
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
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Jiang Y, Tong K, Yao R, Zhou Y, Lin H, Du L, Jin Y, Cao L, Tan J, Zhang XD, Guo D, Pan JA, Peng X. Genome-wide analysis of protein-protein interactions and involvement of viral proteins in SARS-CoV-2 replication. Cell Biosci 2021; 11:140. [PMID: 34294141 PMCID: PMC8295636 DOI: 10.1186/s13578-021-00644-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 07/01/2021] [Indexed: 12/28/2022] Open
Abstract
BACKGROUND Analysis of viral protein-protein interactions is an essential step to uncover the viral protein functions and the molecular mechanism for the assembly of a viral protein complex. We employed a mammalian two-hybrid system to screen all the viral proteins of SARS-CoV-2 for the protein-protein interactions. RESULTS Our study detected 48 interactions, 14 of which were firstly reported here. Unlike Nsp1 of SARS-CoV, Nsp1 of SARS-CoV-2 has the most interacting partners among all the viral proteins and likely functions as a hub for the viral proteins. Five self-interactions were confirmed, and five interactions, Nsp1/Nsp3.1, Nsp3.1/N, Nsp3.2/Nsp12, Nsp10/Nsp14, and Nsp10/Nsp16, were determined to be positive bidirectionally. Using the replicon reporter system of SARS-CoV-2, we screened all viral Nsps for their impacts on the viral replication and revealed Nsp3.1, the N-terminus of Nsp3, significantly inhibited the replicon reporter gene expression. We found Nsp3 interacted with N through its acidic region at N-terminus, while N interacted with Nsp3 through its NTD, which is rich in the basic amino acids. Furthermore, using purified truncated N and Nsp3 proteins, we determined the direct interactions between Nsp3 and N protein. CONCLUSIONS Our findings provided a basis for understanding the functions of coronavirus proteins and supported the potential of interactions as the target for antiviral drug development.
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Affiliation(s)
- Yiling Jiang
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangming Science City, Shenzhen, 518107, China
| | - Kuijie Tong
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangming Science City, Shenzhen, 518107, China
| | - Roubin Yao
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangming Science City, Shenzhen, 518107, China
| | - Yuanze Zhou
- Nanjing CRYCISION Biotechnology Co., Ltd, Nanjing, 211100, China
| | - Hanwen Lin
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangming Science City, Shenzhen, 518107, China
| | - Liubing Du
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangming Science City, Shenzhen, 518107, China
| | - Yunyun Jin
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangming Science City, Shenzhen, 518107, China
| | - Liu Cao
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangming Science City, Shenzhen, 518107, China
| | - Jingquan Tan
- Nanjing CRYCISION Biotechnology Co., Ltd, Nanjing, 211100, China
| | - Xing-Ding Zhang
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangming Science City, Shenzhen, 518107, China
| | - Deyin Guo
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangming Science City, Shenzhen, 518107, China
| | - Ji-An Pan
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangming Science City, Shenzhen, 518107, China.
| | - Xiaoxue Peng
- The Center for Infection and Immunity Study and Molecular Cancer Research Center, School of Medicine, Sun Yat-Sen University, Guangming Science City, Shenzhen, 518107, China.
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Zella D, Giovanetti M, Benedetti F, Unali F, Spoto S, Guarino M, Angeletti S, Ciccozzi M. The variants question: What is the problem? J Med Virol 2021; 93:6479-6485. [PMID: 34255352 PMCID: PMC8426965 DOI: 10.1002/jmv.27196] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 07/03/2021] [Accepted: 07/08/2021] [Indexed: 12/27/2022]
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) originated in Wuhan, China in early December 2019 has rapidly widespread worldwide. Over the course of the pandemic, due to the advance of whole-genome sequencing technologies, an unprecedented number of genomes have been generated, providing both invaluable insights into the ongoing evolution and epidemiology of the virus and allowing the identification of hundreds of circulating genetic variants during the pandemic. In recent months variants of SARS-CoV-2 that have an increased number of mutations on the Spike protein have brought concern all over the world. These have been called "variants of concerns" (VOCs), and/or "variants of interests" (VOIs) as it has been suggested that their genome mutations might impact transmission, immune control, and virulence. Tracking the spread of emerging SARS-CoV-2 variants is crucial to inform public health efforts and control the ongoing pandemic. In this review, a concise characterization of the SARS-CoV-2 mutational patterns of the main VOCs and VOIs circulating and cocirculating worldwide has been presented to determine the magnitude of the SARS-CoV-2 threat to better understand the virus genetic diversity and its potential impact on vaccination strategy.
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Affiliation(s)
- Davide Zella
- Department of Biochemistry and Molecular Biology, Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Marta Giovanetti
- Laboratório de Flavivírus, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Laboratório de Genética Celular e Molecular, ICB, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Francesca Benedetti
- Department of Biochemistry and Molecular Biology, Institute of Human Virology and Global Virus Network Center, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Francesco Unali
- Area Comunicazione e Brand Management, University Campus Bio-Medico of Rome, Rome, Italy
| | - Silvia Spoto
- Department of Diagnostic and Therapeutic Medicine, University Campus Bio-Medico of Rome, Rome, Italy
| | - Michele Guarino
- Department of Gastrointestinal Diseases, Campus Bio-Medico University, Rome, Italy
| | - Silvia Angeletti
- Unit of Clinical Laboratory Science, University Campus Bio-Medico of Rome, Rome, Italy
| | - Massimo Ciccozzi
- Medical Statistic and Molecular Epidemiology Unit, University of Biomedical Campus, Rome, Italy
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Kelta Wabalo E, Dukessa Dubiwak A, Welde Senbetu M, Sime Gizaw T. Effect of Genomic and Amino Acid Sequence Mutation on Virulence and Therapeutic Target of Severe Acute Respiratory Syndrome Coronavirus-2 (SARS COV-2). Infect Drug Resist 2021; 14:2187-2192. [PMID: 34163183 PMCID: PMC8214021 DOI: 10.2147/idr.s307374] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Accepted: 05/26/2021] [Indexed: 01/08/2023] Open
Abstract
The COVID-19 pandemic is caused by severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2). It is one of the RNA coronaviruses which share the highest mutation rates of RNA viruses when compared with that of their hosts. The collective mutation rate of RNA viruses is up to a million times higher than their hosts and is correlated with enhanced virulence of viruses. The RNA, genomic material of SARS-CoV-2, has the capacity of showing amplified fast changes as the infection spreads. These changes were frequently observed in genes for spike glycoprotein, nucleocapsid, ORF1ab, and ORF8, together with RNA dependent RNA polymerase. In contrast, genes for envelope, membrane, ORF6, ORF7a and ORF7b showed no observable changes in terms of amino acid substitutions. Mutated SARS COV-2 at these particular sites has been associated with viral infectivity, false laboratory results and viral genome mutation and interferes with therapeutic targets. Interferences with therapeutic targets is frequently observed in genes for RdRp. Additionally, mutated viral genes for RdRp render slow fidelity of RdRp protein, resulting in a high mutation rate. Such a high mutation rate might allow new virulent forms of the virus to emerge and influence the disease profile. This review aimed to elaborate on the effect of genomic and amino acid sequence mutations on the virulence and therapeutic targets of SARS COV-2. To achieve this objective, multiple literatures have been reviewed.
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Affiliation(s)
- Endriyas Kelta Wabalo
- Department of Biomedical Sciences, Faculty of Medical Sciences, Institute of Health, Jimma University, Jimma, Ethiopia
| | - Abebe Dukessa Dubiwak
- Department of Biomedical Sciences, Faculty of Medical Sciences, Institute of Health, Jimma University, Jimma, Ethiopia
| | - Mengistu Welde Senbetu
- Department of Biomedical Sciences, Faculty of Medical Sciences, Institute of Health, Jimma University, Jimma, Ethiopia
| | - Tariku Sime Gizaw
- Department of Biomedical Sciences, Faculty of Medical Sciences, Institute of Health, Jimma University, Jimma, Ethiopia
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Singh R, Bhardwaj VK, Das P, Purohit R. A computational approach for rational discovery of inhibitors for non-structural protein 1 of SARS-CoV-2. Comput Biol Med 2021; 135:104555. [PMID: 34144270 PMCID: PMC8184359 DOI: 10.1016/j.compbiomed.2021.104555] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2021] [Revised: 06/03/2021] [Accepted: 06/03/2021] [Indexed: 12/21/2022]
Abstract
Background Non-structural protein 1 (Nsp1), a virulence agent of SARS-CoV-2, has emerged as an important target for drug discovery. Nsp1 shuts down the host gene function by associating with the 40S ribosomal subunit. Methods Molecular interactions, drug-likeness, physiochemical property predictions, and robust molecular dynamics (MD) simulations were employed to discover novel Nsp1 inhibitors. In this study, we evaluated a series of molecules based on the plant (Cedrus deodara) derived α,β,γ-Himachalenes scaffolds. Results The results obtained from estimated affinity and ligand efficiency suggested that BCH10, BCH15, BCH16, and BCH17 could act as potential inhibitors of Nsp1. Moreover, MD simulations comprising various MD driven time-dependent analyses and thermodynamic free energy calculations also suggested stable protein-ligand complexes and strong interactions with the binding site. Furthermore, the selected molecules passed drug likeliness parameters and the physiochemical property analysis showed acceptable bioactivity scores. Conclusion The structural parameters of dynamic simulations revealed that the reported molecules could act as lead compounds against SARS-CoV-2 Nsp1 protein.
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Affiliation(s)
- Rahul Singh
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India
| | - Vijay Kumar Bhardwaj
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Pralay Das
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India; Natural Product Chemistry and Process Development, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palam-pur, India
| | - Rituraj Purohit
- Structural Bioinformatics Lab, CSIR-Institute of Himalayan Bioresource Technology (CSIR-IHBT), Palampur, HP, 176061, India; Biotechnology Division, CSIR-IHBT, Palampur, HP, 176061, India; Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India.
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Baker TL, Greiner JV. Guidelines for Reopening a Nation in a SARS-CoV-2 Pandemic: A Path Forward. MEDICINA (KAUNAS, LITHUANIA) 2021; 57:496. [PMID: 34068853 PMCID: PMC8153561 DOI: 10.3390/medicina57050496] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 04/26/2021] [Accepted: 05/04/2021] [Indexed: 02/06/2023]
Abstract
Background and Objectives: Action, not fear, is the path forward in the coronavirus infectious disease 2019 (COVID-19) pandemic. Since early 2020, the world's nations have faced conundrums over severe acute respiratory syndrome corona virus type 2 (SARS-CoV-2) infections resulting in COVID-19 resulting in national closures, and thus, a clear understandable plan that nations can implement is required to reopen. The healthcare benefits of reopening a nation more likely than not exceed the benefits of continued pandemic-related closure. Pandemic-related closures have resulted in countless delayed or avoided urgent care evaluations. Furthermore, routine care of acute and chronic illnesses, including evaluations, diagnoses, and treatments, has also been delayed. Isolation, loss of income, and fear have resulted in mental health conditions or exacerbated existing conditions. The magnitude of untoward ramifications is unknown and may ultimately represent an inestimable degree of danger and morbidity, and even death. The pandemic of SARS-CoV-2 has created an atmosphere of fear of COVID-19 that has directly and indirectly injured the world's population. Since this has resulted in increasing morbidity and mortality, creating economic chaos, and near systemic collapse of educational systems with no well described plan forward, it is the purpose of this study to provide guidelines that provide a path forward to safely open a nation. Physicians often equipped by their education, training, and experiences across disciplines are uniquely positioned to comprehend, coordinate, and teach other physicians, business owners, and municipal and government leaders from guidelines. As such, physicians may take the lead in a path forward to reopening a nation, including opening businesses, educational facilities, and religious establishments, while minimizing the risk of SARS-CoV-2 infection. Materials and Methods: Reviews of the literature among the disciplines of environmental air, sanitation, social interaction, medical testing, vaccination, protection, and disease prevention and safety allowed for the conceptualization and eventual genesis of identifiable interventions which either reduce the viral load in the environment or inactivate the virus from replication. Each of the guidelines was selected based on the principle that it involved the elimination or inactivation of the viral particle. With a reduction in viral load or inactivation of replication, the implementation of these guidelines is expected to allow for reopening a nation with an increased level of safety. Results: The guidelines identified, including air exchange (ventilation), air filtration, personal protective filtering devices (masks), hand hygiene, social distancing, screening and testing, vaccines, high-risk patient protection, medical management, and adjunctive therapies, are described and referenced. Conclusions: In that the pandemic is primarily a public health issue, the path forward is best coordinated by local, regional, and national physicians. Many physicians with a breadth of experiences are uniquely positioned to coordinate the implementation of these interdisciplinary guidelines. Using these guidelines as a planned, coordinated action, not fear, is a path forward. Nations have a decision to make: closuring versus opening.
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Affiliation(s)
- Terrance L. Baker
- Johns Hopkins Community Physician, Baltimore, MD 21287, USA;
- School of Nursing, University of Maryland, Baltimore, MD 20742, USA
- School of Nursing, State University of New York at Stony Brook, Brookhaven, NY 11794, USA
- Sollay Medical Center, Sollay Kenyan Foundation, Katani Hospital, Katani, Kenya
| | - Jack V. Greiner
- Eye Research Institute of Massachusetts Eye & Ear, 20 Staniford St., W239, Boston, MA 02114, USA
- Department of Ophthalmology, Harvard Medical School, Boston, MA 02115, USA
- Department of Ophthalmology, Tufts University School of Medicine, Boston, MA 02155, USA
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Majumdar P, Niyogi S. SARS-CoV-2 mutations: the biological trackway towards viral fitness. Epidemiol Infect 2021; 149:e110. [PMID: 33928885 PMCID: PMC8134885 DOI: 10.1017/s0950268821001060] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Revised: 03/26/2021] [Accepted: 04/27/2021] [Indexed: 01/10/2023] Open
Abstract
The outbreak of pneumonia-like respiratory disorder at China and its rapid transmission world-wide resulted in public health emergency, which brought lineage B betacoronaviridae SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2) into spotlight. The fairly high mutation rate, frequent recombination and interspecies transmission in betacoronaviridae are largely responsible for their temporal changes in infectivity and virulence. Investigation of global SARS-CoV-2 genotypes revealed considerable mutations in structural, non-structural, accessory proteins as well as untranslated regions. Among the various types of mutations, single-nucleotide substitutions are the predominant ones. In addition, insertion, deletion and frame-shift mutations are also reported, albeit at a lower frequency. Among the structural proteins, spike glycoprotein and nucleocapsid phosphoprotein accumulated a larger number of mutations whereas envelope and membrane proteins are mostly conserved. Spike protein and RNA-dependent RNA polymerase variants, D614G and P323L in combination became dominant world-wide. Divergent genetic variants created serious challenge towards the development of therapeutics and vaccines. This review will consolidate mutations in different SARS-CoV-2 proteins and their implications on viral fitness.
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Affiliation(s)
| | - Sougata Niyogi
- Dinabandhu Andrews Institute of Technology and Management, Block-S, 1/406A, Patuli, Kolkata, West Bengal700094, India
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48
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Peacock TP, Penrice-Randal R, Hiscox JA, Barclay WS. SARS-CoV-2 one year on: evidence for ongoing viral adaptation. J Gen Virol 2021; 102:001584. [PMID: 33855951 PMCID: PMC8290271 DOI: 10.1099/jgv.0.001584] [Citation(s) in RCA: 99] [Impact Index Per Article: 33.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2021] [Accepted: 03/16/2021] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 is thought to have originated in the human population from a zoonotic spillover event. Infection in humans results in a variety of outcomes ranging from asymptomatic cases to the disease COVID-19, which can have significant morbidity and mortality, with over two million confirmed deaths worldwide as of January 2021. Over a year into the pandemic, sequencing analysis has shown that variants of SARS-CoV-2 are being selected as the virus continues to circulate widely within the human population. The predominant drivers of genetic variation within SARS-CoV-2 are single nucleotide polymorphisms (SNPs) caused by polymerase error, potential host factor driven RNA modification, and insertion/deletions (indels) resulting from the discontinuous nature of viral RNA synthesis. While many mutations represent neutral 'genetic drift' or have quickly died out, a subset may be affecting viral traits such as transmissibility, pathogenicity, host range, and antigenicity of the virus. In this review, we summarise the current extent of genetic change in SARS-CoV-2, particularly recently emerging variants of concern, and consider the phenotypic consequences of this viral evolution that may impact the future trajectory of the pandemic.
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Affiliation(s)
- Thomas P. Peacock
- Department of Infectious Diseases, St Marys Medical School, Imperial College London, UK
| | | | - Julian A. Hiscox
- Institute of Infection, Veterinary and Ecology Sciences, University of Liverpool, UK
- A*STAR Infectious Diseases Laboratories (A*STAR ID Labs), Agency for Science, Technology and Research (A*STAR), Singapore
| | - Wendy S. Barclay
- Department of Infectious Diseases, St Marys Medical School, Imperial College London, UK
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Benvenuto D, Benedetti F, Demir AB, Ciccozzi M, Zella D. Analysis of Three Mutations in Italian Strains of SARS-CoV-2: Implications for Pathogenesis. Chemotherapy 2021; 66:33-37. [PMID: 33735872 PMCID: PMC8089447 DOI: 10.1159/000515342] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 01/28/2021] [Indexed: 11/19/2022]
Abstract
Background Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an enveloped virus initially detected in Wuhan in December 2019, responsible for coronavirus disease 2019 (COVID-19), a respiratory syndrome currently affecting >220 countries around the world, with >80 million cases registered and >1.8 million deaths. Objective As several vaccines are still being developed and 2 have been approved, it is particularly important to perform evolutionary surveillance to identify mutations potentially affecting vaccine efficacy. Methods DynaMut server has been used to evaluate the impact of the mutation found on SARS-CoV-2 isolates available on GISAID. Results In this article, we analyze whole genomes sequenced from Italian patients, and we report the characterization of 3 mutations, one of which presents in the spike protein. Conclusion The mutations analyzed in this article can be useful to evaluate the evolution of SARS-CoV-2.
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Affiliation(s)
- Domenico Benvenuto
- Medical Statistic and Molecular Epidemiology Unit, Campus Bio-Medico University, Rome, Italy
| | - Francesca Benedetti
- Institute of Human Virology and Global Virus Network Center, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Ayse Banu Demir
- Department of Medical Biology, School of Medicine, Izmir University of Economics, Izmir, Turkey
| | - Massimo Ciccozzi
- Medical Statistic and Molecular Epidemiology Unit, Campus Bio-Medico University, Rome, Italy
| | - Davide Zella
- Institute of Human Virology and Global Virus Network Center, Department of Biochemistry and Molecular Biology, University of Maryland School of Medicine, Baltimore, Maryland, USA,
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50
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Lin JW, Tang C, Wei HC, Du B, Chen C, Wang M, Zhou Y, Yu MX, Cheng L, Kuivanen S, Ogando NS, Levanov L, Zhao Y, Li CL, Zhou R, Li Z, Zhang Y, Sun K, Wang C, Chen L, Xiao X, Zheng X, Chen SS, Zhou Z, Yang R, Zhang D, Xu M, Song J, Wang D, Li Y, Lei S, Zeng W, Yang Q, He P, Zhang Y, Zhou L, Cao L, Luo F, Liu H, Wang L, Ye F, Zhang M, Li M, Fan W, Li X, Li K, Ke B, Xu J, Yang H, He S, Pan M, Yan Y, Zha Y, Jiang L, Yu C, Liu Y, Xu Z, Li Q, Jiang Y, Sun J, Hong W, Wei H, Lu G, Vapalahti O, Luo Y, Wei Y, Connor T, Tan W, Snijder EJ, Smura T, Li W, Geng J, Ying B, Chen L. Genomic monitoring of SARS-CoV-2 uncovers an Nsp1 deletion variant that modulates type I interferon response. Cell Host Microbe 2021; 29:489-502.e8. [PMID: 33548198 PMCID: PMC7846228 DOI: 10.1016/j.chom.2021.01.015] [Citation(s) in RCA: 73] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/07/2021] [Accepted: 01/26/2021] [Indexed: 02/05/2023]
Abstract
The SARS-CoV-2 virus, the causative agent of COVID-19, is undergoing constant mutation. Here, we utilized an integrative approach combining epidemiology, virus genome sequencing, clinical phenotyping, and experimental validation to locate mutations of clinical importance. We identified 35 recurrent variants, some of which are associated with clinical phenotypes related to severity. One variant, containing a deletion in the Nsp1-coding region (Δ500-532), was found in more than 20% of our sequenced samples and associates with higher RT-PCR cycle thresholds and lower serum IFN-β levels of infected patients. Deletion variants in this locus were found in 37 countries worldwide, and viruses isolated from clinical samples or engineered by reverse genetics with related deletions in Nsp1 also induce lower IFN-β responses in infected Calu-3 cells. Taken together, our virologic surveillance characterizes recurrent genetic diversity and identified mutations in Nsp1 of biological and clinical importance, which collectively may aid molecular diagnostics and drug design.
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Affiliation(s)
- Jing-Wen Lin
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China.
| | - Chao Tang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Han-Cheng Wei
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Baowen Du
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Chuan Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Minjin Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Yongzhao Zhou
- Department of Respiratory and Critical Care Medicine, Frontier Science Center of Disease Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Ming-Xia Yu
- Department of Clinical Laboratory, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, China
| | - Lu Cheng
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK; Department of Computer Science, School of Science, Aalto University, Aalto FI-00076, Finland
| | - Suvi Kuivanen
- University of Helsinki, Medicum, Department of Virology, Helsinki, Finland
| | - Natacha S Ogando
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Lev Levanov
- University of Helsinki, Medicum, Department of Virology, Helsinki, Finland
| | - Yuancun Zhao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Chang-Ling Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Ran Zhou
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Zhidan Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Yiming Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Ke Sun
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Chengdi Wang
- Department of Respiratory and Critical Care Medicine, Frontier Science Center of Disease Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Li Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Xia Xiao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Xiuran Zheng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Sha-Sha Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Zhen Zhou
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Ruirui Yang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Dan Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Mengying Xu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Junwei Song
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Danrui Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Yupeng Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - ShiKun Lei
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Wanqin Zeng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Qingxin Yang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Ping He
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Yaoyao Zhang
- Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Lifang Zhou
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Ling Cao
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Feng Luo
- Wuhan Chain Medical Labs, Wuhan, Hubei 430011, China
| | - Huayi Liu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Liping Wang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Fei Ye
- NHC Key Laboratory, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Ming Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Mengjiao Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Wei Fan
- Department of Respiratory and Critical Care Medicine, Frontier Science Center of Disease Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China
| | - Xinqiong Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Kaiju Li
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Bowen Ke
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Jiannan Xu
- Sichuan Center for Disease Control and Prevention, No. 6 Zhongxue Rd, Chengdu 610041, China
| | - Huiping Yang
- Sichuan Center for Disease Control and Prevention, No. 6 Zhongxue Rd, Chengdu 610041, China
| | - Shusen He
- Sichuan Center for Disease Control and Prevention, No. 6 Zhongxue Rd, Chengdu 610041, China
| | - Ming Pan
- Sichuan Center for Disease Control and Prevention, No. 6 Zhongxue Rd, Chengdu 610041, China
| | - Yichen Yan
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Yi Zha
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Lingyu Jiang
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Changxiu Yu
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Yingfen Liu
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Zhiyong Xu
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Qingfeng Li
- Department of Clinical Laboratory, Public Health Clinical Center of Chengdu, Chengdu, Sichuan 610041, China
| | - Yongmei Jiang
- Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China
| | - Jiufeng Sun
- Guangdong Provincial Institute of Public Health, Guangdong Provincial Center for Disease Control and Prevention, Guangzhou, Guangdong 511430, China
| | - Wei Hong
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Hongping Wei
- CAS Key Laboratory of Special Pathogens and Biosafety, Centre for Biosafety Mega-Science, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, Hubei 430071, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guangwen Lu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Olli Vapalahti
- University of Helsinki, Medicum, Department of Virology, Helsinki, Finland; University of Helsinki and Helsinki University Hospital, Department of Virology, Helsinki, Finland; Department of Veterinary Biosciences, University of Helsinki, Helsinki, Finland
| | - Yunzi Luo
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Frontier Science Center for Synthetic Biology and Key Laboratory of Systems Bioengineering (Ministry of Education), Collaborative Innovation Center of Chemical Science and Engineering (Tianjin), School of Chemical Engineering and Technology, Tianjin University, Tianjin 300072, China
| | - Yuquan Wei
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China
| | - Thomas Connor
- Microbiomes, Microbes and Informatics Group, Organisms and Environment Division, School of Biosciences, Cardiff University, Cardiff CF10 3AX, UK
| | - Wenjie Tan
- NHC Key Laboratory, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Eric J Snijder
- Molecular Virology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Teemu Smura
- University of Helsinki, Medicum, Department of Virology, Helsinki, Finland; University of Helsinki and Helsinki University Hospital, Department of Virology, Helsinki, Finland.
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, Frontier Science Center of Disease Molecular Network, West China Hospital, Sichuan University, Chengdu 610041, China.
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China.
| | - Binwu Ying
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China.
| | - Lu Chen
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University and Collaborative Innovation Center for Biotherapy, Chengdu, Sichuan 610041, China; Department of Laboratory Medicine and Department of Pediatric Infectious Diseases, Key Laboratory of Birth Defects and Related Diseases of Women and Children of MOE, West China Second University Hospital, Sichuan University, Chengdu 610041, China.
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