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Gupta S, Gupta D, Bhatnagar S. Analysis of SARS-CoV-2 genome evolutionary patterns. Microbiol Spectr 2024; 12:e0265423. [PMID: 38197644 PMCID: PMC10846092 DOI: 10.1128/spectrum.02654-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Accepted: 11/20/2023] [Indexed: 01/11/2024] Open
Abstract
The spread of SARS-CoV-2 virus accompanied by public availability of abundant sequence data provides a window for the determination of viral evolutionary patterns. In this study, SARS-CoV-2 genome sequences were collected from seven countries in the period January 2020-December 2022. The sequences were classified into three phases, namely, pre-vaccination, post-vaccination, and recent period. Comparison was performed between these phases based on parameters like mutation rates, selection pressure (dN/dS ratio), and transition to transversion ratios (Ti/Tv). Similar comparisons were performed among SARS-CoV-2 variants. Statistical significance was tested using Graphpad unpaired t-test. The analysis showed an increase in the percent genomic mutation rates post-vaccination and in recent periods across all countries from the pre-vaccination sequences. Mutation rates were highest in NSP3, S, N, and NSP12b before and increased further after vaccination. NSP4 showed the largest change in mutation rates after vaccination. The dN/dS ratios showed purifying selection that shifted toward neutral selection after vaccination. N, ORF8, ORF3a, and ORF10 were under highest positive selection before vaccination. Shift toward neutral selection was driven by E, NSP3, and ORF7a in the after vaccination set. In recent sequences, the largest dN/dS change was observed in E, NSP1, and NSP13. The Ti/Tv ratios decreased with time. C→U and G→U were the most frequent transitions and transversions. However, U→G was the most frequent transversion in recent period. The Omicron variant had the highest genomic mutation rates, while Delta showed the highest dN/dS ratio. Protein-wise dN/dS ratio was also seen to vary across the different variants.IMPORTANCETo the best of our knowledge, there exists no other large-scale study of the genomic and protein-wise mutation patterns during the time course of evolution in different countries. Analyzing the SARS-CoV-2 evolutionary patterns in view of the varying spatial, temporal, and biological signals is important for diagnostics, therapeutics, and pharmacovigilance of SARS-CoV-2.
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Affiliation(s)
- Shubhangi Gupta
- Department of Biological Sciences and Engineering, Computational and Structural Biology Laboratory, Netaji Subhas University of Technology, Dwarka, New Delhi, India
| | - Deepanshu Gupta
- Division of Biotechnology, Computational and Structural Biology Laboratory, Netaji Subhas Institute of Technology, Dwarka, New Delhi, India
| | - Sonika Bhatnagar
- Department of Biological Sciences and Engineering, Computational and Structural Biology Laboratory, Netaji Subhas University of Technology, Dwarka, New Delhi, India
- Division of Biotechnology, Computational and Structural Biology Laboratory, Netaji Subhas Institute of Technology, Dwarka, New Delhi, India
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2
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Lo Presti A, Di Martino A, Ambrosio L, De Sabato L, Knijn A, Vaccari G, Di Bartolo I, Morabito S, Terregino C, Fusaro A, Monne I, Giussani E, Tramuto F, Maida CM, Mazzucco W, Costantino C, Rueca M, Giombini E, Gruber CEM, Capobianchi MR, Palamara AT, Stefanelli P. Tracking the Selective Pressure Profile and Gene Flow of SARS-CoV-2 Delta Variant in Italy from April to October 2021 and Frequencies of Key Mutations from Three Representative Italian Regions. Microorganisms 2023; 11:2644. [PMID: 38004656 PMCID: PMC10673055 DOI: 10.3390/microorganisms11112644] [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: 09/19/2023] [Revised: 10/19/2023] [Accepted: 10/20/2023] [Indexed: 11/26/2023] Open
Abstract
The SARS-CoV-2 Delta variant of concern (VOC) was often associated with serious clinical course of the COVID-19 disease. Herein, we investigated the selective pressure, gene flow and evaluation on the frequencies of mutations causing amino acid substitutions in the Delta variant in three Italian regions. A total of 1500 SARS-CoV-2 Delta genomes, collected in Italy from April to October 2021 were investigated, including a subset of 596 from three Italian regions. The selective pressure and the frequency of amino acid substitutions and the prediction of their possible impact on the stability of the proteins were investigated. Delta variant dataset, in this study, identified 68 sites under positive selection: 16 in the spike (23.5%), 11 in nsp2 (16.2%) and 10 in nsp12 (14.7%) genes. Three of the positive sites in the spike were located in the receptor-binding domain (RBD). In Delta genomes from the three regions, 6 changes were identified as very common (>83.7%), 4 as common (>64.0%), 21 at low frequency (2.1%-25.0%) and 29 rare (≤2.0%). The detection of positive selection on key mutations may represent a model to identify recurrent signature mutations of the virus.
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Affiliation(s)
- Alessandra Lo Presti
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
| | - Angela Di Martino
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
| | - Luigina Ambrosio
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
| | - Luca De Sabato
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Arnold Knijn
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Gabriele Vaccari
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Ilaria Di Bartolo
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Stefano Morabito
- Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (L.D.S.); (A.K.); (G.V.); (I.D.B.); (S.M.)
| | - Calogero Terregino
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padova, Italy; (C.T.); (A.F.); (I.M.); (E.G.)
| | - Alice Fusaro
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padova, Italy; (C.T.); (A.F.); (I.M.); (E.G.)
| | - Isabella Monne
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padova, Italy; (C.T.); (A.F.); (I.M.); (E.G.)
| | - Edoardo Giussani
- Division of Comparative Biomedical Sciences, Istituto Zooprofilattico Sperimentale delle Venezie, 35020 Padova, Italy; (C.T.); (A.F.); (I.M.); (E.G.)
| | - Fabio Tramuto
- Clinical Epidemiology Unit and Regional Reference Laboratory, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (F.T.); (C.M.M.); (W.M.); (C.C.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy
| | - Carmelo Massimo Maida
- Clinical Epidemiology Unit and Regional Reference Laboratory, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (F.T.); (C.M.M.); (W.M.); (C.C.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy
| | - Walter Mazzucco
- Clinical Epidemiology Unit and Regional Reference Laboratory, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (F.T.); (C.M.M.); (W.M.); (C.C.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy
| | - Claudio Costantino
- Clinical Epidemiology Unit and Regional Reference Laboratory, University Hospital “P. Giaccone”, 90127 Palermo, Italy; (F.T.); (C.M.M.); (W.M.); (C.C.)
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D’Alessandro”, University of Palermo, 90127 Palermo, Italy
| | - Martina Rueca
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (M.R.); (E.G.); (C.E.M.G.); (M.R.C.)
| | - Emanuela Giombini
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (M.R.); (E.G.); (C.E.M.G.); (M.R.C.)
| | - Cesare Ernesto Maria Gruber
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (M.R.); (E.G.); (C.E.M.G.); (M.R.C.)
| | - Maria Rosaria Capobianchi
- Laboratory of Virology, National Institute for Infectious Diseases “Lazzaro Spallanzani” (IRCCS), 00149 Rome, Italy; (M.R.); (E.G.); (C.E.M.G.); (M.R.C.)
- Saint Camillus International University of Health Sciences, Via di Sant’Alessandro, 8, 00131 Rome, Italy
- Department of Infectious Tropical Diseases and Microbiology, Sacro Cuore Don Calabria Hospital I.R.C.C.S., Via Don A. Sempreboni 5, 37024 Negrar di Valpolicella, Italy
| | - Anna Teresa Palamara
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
| | - Paola Stefanelli
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Rome, Italy; (A.D.M.); (L.A.); (A.T.P.); (P.S.)
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Vilain M, Aris-Brosou S. Machine Learning Algorithms Associate Case Numbers with SARS-CoV-2 Variants Rather Than with Impactful Mutations. Viruses 2023; 15:1226. [PMID: 37376526 DOI: 10.3390/v15061226] [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: 04/03/2023] [Revised: 05/12/2023] [Accepted: 05/13/2023] [Indexed: 06/29/2023] Open
Abstract
During the SARS-CoV-2 pandemic, much effort has been geared towards creating models to predict case numbers. These models typically rely on epidemiological data, and as such overlook viral genomic information, which could be assumed to improve predictions, as different variants show varying levels of virulence. To test this hypothesis, we implemented simple models to predict future case numbers based on the genomic sequences of the Alpha and Delta variants, which were co-circulating in Texas and Minnesota early during the pandemic. Sequences were encoded, matched with case numbers at a future time based on collection date, and used to train two algorithms: one based on random forests and one based on a feed-forward neural network. While prediction accuracies were ≥93%, explainability analyses showed that the models were not associating case numbers with mutations known to have an impact on virulence, but with individual variants. This work highlights the necessity of gaining a better understanding of the data used for training and of conducting explainability analysis to assess whether model predictions are misleading.
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Affiliation(s)
- Matthieu Vilain
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
| | - Stéphane Aris-Brosou
- Department of Biology, University of Ottawa, Ottawa, ON K1N 6N5, Canada
- Department of Mathematics and Statistics, University of Ottawa, Ottawa, ON K1N 6N5, Canada
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4
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Azizogli AR, Pai V, Coppola F, Jafari R, Dodd-o JB, Harish R, Balasubramanian B, Kashyap J, Acevedo-Jake AM, Král P, Kumar VA. Scalable Inhibitors of the Nsp3-Nsp4 Coupling in SARS-CoV-2. ACS OMEGA 2023; 8:5349-5360. [PMID: 36798146 PMCID: PMC9923439 DOI: 10.1021/acsomega.2c06384] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/03/2022] [Accepted: 11/29/2022] [Indexed: 06/18/2023]
Abstract
The human Betacoronavirus SARS-CoV-2 is a novel pathogen claiming millions of lives and causing a global pandemic that has disrupted international healthcare systems, economies, and communities. The virus is fast mutating and presenting more infectious but less lethal versions. Currently, some small-molecule therapeutics have received FDA emergency use authorization for the treatment of COVID-19, including Lagevrio (molnupiravir) and Paxlovid (nirmaltrevir/ritonavir), which target the RNA-dependent RNA polymerase and the 3CLpro main protease, respectively. Proteins downstream in the viral replication process, specifically the nonstructural proteins (Nsps1-16), are potential drug targets due to their crucial functions. Of these Nsps, Nsp4 is a particularly promising drug target due to its involvement in the SARS-CoV viral replication and double-membrane vesicle formation (mediated via interaction with Nsp3). Given the degree of sequence conservation of these two Nsps across the Betacoronavirus clade, their protein-protein interactions and functions are likely to be conserved as well in SARS-CoV-2. Through AlphaFold2 and its recent advancements, protein structures were generated of Nsp3 and 4 lumenal loops of interest. Then, using a combination of molecular docking suites and an existing library of lead-like compounds, we virtually screened 7 million ligands to identify five putative ligand inhibitors of Nsp4, which could present an alternative pharmaceutical approach against SARS-CoV-2. These ligands exhibit promising lead-like properties (ideal molecular weight and log P profiles), maintain fixed-Nsp4-ligand complexes in molecular dynamics (MD) simulations, and tightly associate with Nsp4 via hydrophobic interactions. Additionally, alternative peptide inhibitors based on Nsp3 were designed and shown in MD simulations to provide a highly stable binding to the Nsp4 protein. Finally, these therapeutics were attached to dendrimer structures to promote their multivalent binding with Nsp4, especially its large flexible luminal loop (Nsp4LLL). The therapeutics tested in this study represent many different approaches for targeting large flexible protein structures, especially those localized to the ER. This study is the first work targeting the membrane rearrangement system of viruses and will serve as a potential avenue for treating viruses with similar replicative function.
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Affiliation(s)
- Abdul-Rahman Azizogli
- Department
of Biological Sciences, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Varun Pai
- Department
of Biological Sciences, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Francesco Coppola
- Department
of Chemistry, University of Illinois at
Chicago, Chicago, Illinois 60607, United States
| | - Roya Jafari
- Department
of Chemistry, University of Illinois at
Chicago, Chicago, Illinois 60607, United States
| | - Joseph B. Dodd-o
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Rohan Harish
- Department
of Electrical and Computer Engineering, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Bhavani Balasubramanian
- Department
of Chemistry and Environmental Sciences, New Jersey Institute of Technology, Newark, New Jersey 07102, United States
| | - Jatin Kashyap
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Amanda M. Acevedo-Jake
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
| | - Petr Král
- Department
of Chemistry, University of Illinois at
Chicago, Chicago, Illinois 60607, United States
- Departments
of Physics, Pharmaceutical Sciences, and Chemical Engineering, University of Illinois at Chicago, Chicago, Illinois 60607, United States
| | - Vivek A. Kumar
- Department
of Biological Sciences, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
- Department
of Biomedical Engineering, New Jersey Institute
of Technology, Newark, New Jersey 07102, United States
- Department
of Chemical and Materials Engineering, New
Jersey Institute of Technology, Newark, New Jersey 07102, United States
- Department
of Endodontics, Rutgers School of Dental
Medicine, Newark, New Jersey 07103, United States
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5
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González-Vázquez LD, Arenas M. Molecular Evolution of SARS-CoV-2 during the COVID-19 Pandemic. Genes (Basel) 2023; 14:407. [PMID: 36833334 PMCID: PMC9956206 DOI: 10.3390/genes14020407] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2022] [Revised: 01/27/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) produced diverse molecular variants during its recent expansion in humans that caused different transmissibility and severity of the associated disease as well as resistance to monoclonal antibodies and polyclonal sera, among other treatments. In order to understand the causes and consequences of the observed SARS-CoV-2 molecular diversity, a variety of recent studies investigated the molecular evolution of this virus during its expansion in humans. In general, this virus evolves with a moderate rate of evolution, in the order of 10-3-10-4 substitutions per site and per year, which presents continuous fluctuations over time. Despite its origin being frequently associated with recombination events between related coronaviruses, little evidence of recombination was detected, and it was mostly located in the spike coding region. Molecular adaptation is heterogeneous among SARS-CoV-2 genes. Although most of the genes evolved under purifying selection, several genes showed genetic signatures of diversifying selection, including a number of positively selected sites that affect proteins relevant for the virus replication. Here, we review current knowledge about the molecular evolution of SARS-CoV-2 in humans, including the emergence and establishment of variants of concern. We also clarify relationships between the nomenclatures of SARS-CoV-2 lineages. We conclude that the molecular evolution of this virus should be monitored over time for predicting relevant phenotypic consequences and designing future efficient treatments.
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Affiliation(s)
- Luis Daniel González-Vázquez
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
| | - Miguel Arenas
- Biomedical Research Center (CINBIO), University of Vigo, 36310 Vigo, Spain
- Department of Biochemistry, Genetics and Immunology, University of Vigo, 36310 Vigo, Spain
- Galicia Sur Health Research Institute (IIS Galicia Sur), 36310 Vigo, Spain
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6
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Cheng N, Liu M, Li W, Sun B, Liu D, Wang G, Shi J, Li L. Protein post-translational modification in SARS-CoV-2 and host interaction. Front Immunol 2023; 13:1068449. [PMID: 36713387 PMCID: PMC9880545 DOI: 10.3389/fimmu.2022.1068449] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/27/2022] [Indexed: 01/14/2023] Open
Abstract
SARS-CoV-2 can cause lung diseases, such as pneumonia and acute respiratory distress syndrome, and multi-system dysfunction. Post-translational modifications (PTMs) related to SARS-CoV-2 are conservative and pathogenic, and the common PTMs are glycosylation, phosphorylation, and acylation. The glycosylation of SARS-CoV-2 mainly occurs on spike (S) protein, which mediates the entry of the virus into cells through interaction with angiotensin-converting enzyme 2. SARS-CoV-2 utilizes glycans to cover its epitopes and evade the immune response through glycosylation of S protein. Phosphorylation of SARS-CoV-2 nucleocapsid (N) protein improves its selective binding to viral RNA and promotes viral replication and transcription, thereby increasing the load of the virus in the host. Succinylated N and membrane(M) proteins of SARS-CoV-2 synergistically affect virus particle assembly. N protein regulates its affinity for other proteins and the viral genome through acetylation. The acetylated envelope (E) protein of SARS-CoV-2 interacts with bromodomain-containing protein 2/4 to influence the host immune response. Both palmitoylation and myristoylation sites on S protein can affect the virus infectivity. Papain-like protease is a domain of NSP3 that dysregulates host inflammation by deubiquitination and impinges host IFN-I antiviral immune responses by deISGylation. Ubiquitination of ORF7a inhibits host IFN-α signaling by blocking STAT2 phosphorylation. The methylation of N protein can inhibit the formation of host stress granules and promote the binding of N protein to viral RNA, thereby promoting the production of virus particles. NSP3 macrodomain can reverse the ADP-ribosylation of host proteins, and inhibit the cascade immune response with IFN as the core, thereby promoting the intracellular replication of SARS-CoV-2. On the whole, PTMs have fundamental roles in virus entry, replication, particle assembly, and host immune response. Mutations in various SARS-CoV-2 variants, which lead to changes in PTMs at corresponding sites, cause different biological effects. In this paper, we mainly reviewed the effects of PTMs on SARS-CoV-2 and host cells, whose application is to inform the strategies for inhibiting viral infection and facilitating antiviral treatment and vaccine development for COVID-19.
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Affiliation(s)
- Nana Cheng
- China-Japan Union Hospital, Jilin University, Changchun, Jilin Province, China
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, Jilin Province, China
| | - Mingzhu Liu
- China-Japan Union Hospital, Jilin University, Changchun, Jilin Province, China
| | - Wanting Li
- China-Japan Union Hospital, Jilin University, Changchun, Jilin Province, China
| | - BingYue Sun
- First Affiliated Hospital of Jilin University, Changchun, China
| | - Dandan Liu
- First Affiliated Hospital of Jilin University, Changchun, China
| | - Guoqing Wang
- Department of Pathogenobiology, The Key Laboratory of Zoonosis Research, Chinese Ministry of Education, College of Basic Medical Science, Jilin University, Changchun, China
| | - Jingwei Shi
- China-Japan Union Hospital, Jilin University, Changchun, Jilin Province, China
| | - Lisha Li
- The Key Laboratory of Pathobiology, Ministry of Education, College of Basic Medical Sciences, Jilin University, Changchun, Jilin Province, China
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Ku X, Zhang C, Li P, Yu X, Sun Q, Xu F, Qian P, He Q. Epidemiological and genetic characteristics of porcine circovirus 3 in 15 provinces and municipalities of China between 2016 and 2020. Virol J 2022; 19:187. [PMID: 36376944 PMCID: PMC9661739 DOI: 10.1186/s12985-022-01893-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 09/26/2022] [Indexed: 11/16/2022] Open
Abstract
Porcine circovirus 3 (PCV3) is a newly emerging virus and has been found associated with porcine dermatitis and nephropathy syndrome in pigs. Compared with PCV2, research into PCV3 cap gene sequencing is deficient. To investigate the prevalence and genotype distribution of PCV3, we collected 1291 samples from 211 pig farms throughout 15 provinces and municipalities. 312 out of 1291 samples were tested positive by PCR. We further sequenced and analyzed 164 PCR-positive samples. The majority (61.8%) of isolates we sequenced belong to genotype PCV3c. PCV3c is also the dominant genotype in Hubei, Hunan, Hebei province and Chongqing city. We found 3 sites under positive selection and located in predicted epitope peptide, revealing that the pig’s immunity may be a reason those sites are undergoing highly positive selection.
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8
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Lu D, Liu D, Wang X, Liu Y, Liu Y, Ren R, Pang G. Kinetics of Drug Molecule Interactions with a Newly Developed Nano-Gold-Modified Spike Protein Electrochemical Receptor Sensor. BIOSENSORS 2022; 12:888. [PMID: 36291025 PMCID: PMC9599096 DOI: 10.3390/bios12100888] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/17/2022] [Revised: 10/15/2022] [Accepted: 10/16/2022] [Indexed: 06/16/2023]
Abstract
In March 2020, the World Health Organization (WHO) declared COVID-19 a pandemic, and the spike protein has been reported to be an important drug target for anti-COVID-19 treatment. As such, in this study, we successfully developed a novel electrochemical receptor biosensor by immobilizing the SARS-CoV-2 spike protein and using AuNPs-HRP as an electrochemical signal amplification system. Moreover, the time-current method was used to quantify seven antiviral drug compounds, such as arbidol and chloroquine diphosphate. The results show that the spike protein and the drugs are linearly correlated within a certain concentration range and that the detection sensitivity of the sensor is extremely high. In the low concentration range of linear response, the kinetics of receptor-ligand interactions are similar to that of an enzymatic reaction. Among the investigated drug molecules, bromhexine exhibits the smallest Ka value, and thus, is most sensitively detected by the sensor. Hydroxychloroquine exhibits the largest Ka value. Molecular docking simulations of the spike protein with six small-molecule drugs show that residues of this protein, such as Asp, Trp, Asn, and Gln, form hydrogen bonds with the -OH or -NH2 groups on the branched chains of small-molecule drugs. The electrochemical receptor biosensor can directly quantify the interaction between the spike protein and drugs such as abidor and hydroxychloroquine and perform kinetic studies with a limit of detection 3.3 × 10-20 mol/L, which provides a new research method and idea for receptor-ligand interactions and pharmacodynamic evaluation.
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Affiliation(s)
- Dingqiang Lu
- College of Biotechnology & Food Science, Tianjin University of Commerce, Tianjin 300134, China
- Tianjin Key Laboratory of Food Biotechnology, Tianjin 300134, China
| | - Danyang Liu
- College of Biotechnology & Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Xinqian Wang
- College of Biotechnology & Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Yujiao Liu
- College of Biotechnology & Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Yixuan Liu
- College of Biotechnology & Food Science, Tianjin University of Commerce, Tianjin 300134, China
| | - Ruijuan Ren
- Tianjin Institute for Food Safety Inspection Technology, Tianjin 300134, China
| | - Guangchang Pang
- College of Biotechnology & Food Science, Tianjin University of Commerce, Tianjin 300134, China
- Tianjin Key Laboratory of Food Biotechnology, Tianjin 300134, China
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9
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Colson P, Gautret P, Delerce J, Chaudet H, Pontarotti P, Forterre P, Tola R, Bedotto M, Delorme L, Bader W, Levasseur A, Lagier J, Million M, Yahi N, Fantini J, La Scola B, Fournier P, Raoult D. The emergence, spread and vanishing of a French SARS-CoV-2 variant exemplifies the fate of RNA virus epidemics and obeys the Mistigri rule. J Med Virol 2022; 95:e28102. [PMID: 36031728 PMCID: PMC9539255 DOI: 10.1002/jmv.28102] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 07/25/2022] [Accepted: 08/25/2022] [Indexed: 01/11/2023]
Abstract
The nature and dynamics of mutations associated with the emergence, spread, and vanishing of SARS-CoV-2 variants causing successive waves are complex. We determined the kinetics of the most common French variant ("Marseille-4") for 10 months since its onset in July 2020. Here, we analyzed and classified into subvariants and lineages 7453 genomes obtained by next-generation sequencing. We identified two subvariants, Marseille-4A, which contains 22 different lineages of at least 50 genomes, and Marseille-4B. Their average lifetime was 4.1 ± 1.4 months, during which 4.1 ± 2.6 mutations accumulated. Growth rate was 0.079 ± 0.045, varying from 0.010 to 0.173. Most of the lineages exhibited a bell-shaped distribution. Several beneficial mutations at unpredicted sites initiated a new outbreak, while the accumulation of other mutations resulted in more viral heterogenicity, increased diversity and vanishing of the lineages. Marseille-4B emerged when the other Marseille-4 lineages vanished. Its ORF8 gene was knocked out by a stop codon, as reported in SARS-CoV-2 of mink and in the Alpha variant. This subvariant was associated with increased hospitalization and death rates, suggesting that ORF8 is a nonvirulence gene. We speculate that the observed heterogenicity of a lineage may predict the end of the outbreak.
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Affiliation(s)
- Philippe Colson
- IHU Méditerranée InfectionMarseilleFrance,Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI)Aix‐Marseille UniversityMarseilleFrance
| | - Philippe Gautret
- IHU Méditerranée InfectionMarseilleFrance,Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance,Institut de Recherche pour le Développement (IRD), Vecteurs—Infections Tropicales et Méditerranéennes (VITROME)Aix‐Marseille UniversityMarseilleFrance
| | | | - Hervé Chaudet
- IHU Méditerranée InfectionMarseilleFrance,Institut de Recherche pour le Développement (IRD), Vecteurs—Infections Tropicales et Méditerranéennes (VITROME)Aix‐Marseille UniversityMarseilleFrance,French Armed Forces Center for Epidemiology and Public Health (CESPA), Camp de Sainte MartheMarseilleFrance
| | - Pierre Pontarotti
- IHU Méditerranée InfectionMarseilleFrance,Centre national de la recherche scientifique (CNRS)MarseilleFrance
| | - Patrick Forterre
- Département de MicrobiologieInstitut PasteurParisFrance,Institute for Integrative Biology of the Cell (I2BC)Université Paris‐Saclay, CEA, CNRSGif‐sur‐YvetteFrance
| | - Raphael Tola
- IHU Méditerranée InfectionMarseilleFrance,Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance
| | | | - Léa Delorme
- IHU Méditerranée InfectionMarseilleFrance,Institut de Recherche pour le Développement (IRD), Vecteurs—Infections Tropicales et Méditerranéennes (VITROME)Aix‐Marseille UniversityMarseilleFrance,French Armed Forces Center for Epidemiology and Public Health (CESPA), Camp de Sainte MartheMarseilleFrance
| | - Wahiba Bader
- IHU Méditerranée InfectionMarseilleFrance,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI)Aix‐Marseille UniversityMarseilleFrance
| | - Anthony Levasseur
- IHU Méditerranée InfectionMarseilleFrance,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI)Aix‐Marseille UniversityMarseilleFrance
| | - Jean‐Christophe Lagier
- IHU Méditerranée InfectionMarseilleFrance,Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI)Aix‐Marseille UniversityMarseilleFrance
| | - Matthieu Million
- IHU Méditerranée InfectionMarseilleFrance,Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI)Aix‐Marseille UniversityMarseilleFrance
| | - Nouara Yahi
- INSERM UMR_S 1072Aix‐Marseille UniversitéMarseilleFrance
| | | | - Bernard La Scola
- IHU Méditerranée InfectionMarseilleFrance,Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI)Aix‐Marseille UniversityMarseilleFrance
| | - Pierre‐Edouard Fournier
- IHU Méditerranée InfectionMarseilleFrance,Assistance Publique‐Hôpitaux de Marseille (AP‐HM)MarseilleFrance,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI)Aix‐Marseille UniversityMarseilleFrance
| | - Didier Raoult
- IHU Méditerranée InfectionMarseilleFrance,Institut de Recherche pour le Développement (IRD), Microbes Evolution Phylogeny and Infections (MEPHI)Aix‐Marseille UniversityMarseilleFrance
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10
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Agius JE, Johnson-Mackinnon JC, Fong W, Gall M, Lam C, Basile K, Kok J, Arnott A, Sintchenko V, Rockett RJ. SARS-CoV-2 Within-Host and in vitro Genomic Variability and Sub-Genomic RNA Levels Indicate Differences in Viral Expression Between Clinical Cohorts and in vitro Culture. Front Microbiol 2022; 13:824217. [PMID: 35663867 PMCID: PMC9161297 DOI: 10.3389/fmicb.2022.824217] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Accepted: 04/18/2022] [Indexed: 12/23/2022] Open
Abstract
Background Low frequency intrahost single nucleotide variants (iSNVs) of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) have been increasingly recognised as predictive indicators of positive selection. Particularly as growing numbers of SARS-CoV-2 variants of interest (VOI) and concern (VOC) emerge. However, the dynamics of subgenomic RNA (sgRNA) expression and its impact on genomic diversity and infection outcome remain poorly understood. This study aims to investigate and quantify iSNVs and sgRNA expression in single and longitudinally sampled cohorts over the course of mild and severe SARS-CoV-2 infection, benchmarked against an in vitro infection model. Methods Two clinical cohorts of SARS-CoV-2 positive cases in New South Wales, Australia collected between March 2020 and August 2021 were sequenced. Longitudinal samples from cases hospitalised due to SARS-CoV-2 infection (severe) (n = 16) were analysed and compared with cases that presented with SARS-CoV-2 symptoms but were not hospitalised (mild) (n = 23). SARS-CoV-2 genomic diversity profiles were also examined from daily sampling of culture experiments for three SARS-CoV-2 variants (Lineage A, B.1.351, and B.1.617.2) cultured in VeroE6 C1008 cells (n = 33). Results Intrahost single nucleotide variants were detected in 83% (19/23) of the mild cohort cases and 100% (16/16) of the severe cohort cases. SNP profiles remained relatively fixed over time, with an average of 1.66 SNPs gained or lost, and an average of 4.2 and 5.9 low frequency variants per patient were detected in severe and mild infection, respectively. sgRNA was detected in 100% (25/25) of the mild genomes and 92% (24/26) of the severe genomes. Total sgRNA expressed across all genes in the mild cohort was significantly higher than that of the severe cohort. Significantly higher expression levels were detected in the spike and the nucleocapsid genes. There was significantly less sgRNA detected in the culture dilutions than the clinical cohorts. Discussion and Conclusion The positions and frequencies of iSNVs in the severe and mild infection cohorts were dynamic overtime, highlighting the importance of continual monitoring, particularly during community outbreaks where multiple SARS-CoV-2 variants may co-circulate. sgRNA levels can vary across patients and the overall level of sgRNA reads compared to genomic RNA can be less than 1%. The relative contribution of sgRNA to the severity of illness warrants further investigation given the level of variation between genomes. Further monitoring of sgRNAs will improve the understanding of SARS-CoV-2 evolution and the effectiveness of therapeutic and public health containment measures during the pandemic.
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Affiliation(s)
- Jessica E. Agius
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Institute for Clinical Pathology and Medical Research, Westmead, NSW, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- Sydney Institute for Infectious Diseases, Westmead Institute for Medical Research, Westmead, NSW, Australia
| | - Jessica C. Johnson-Mackinnon
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Institute for Clinical Pathology and Medical Research, Westmead, NSW, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- Sydney Institute for Infectious Diseases, Westmead Institute for Medical Research, Westmead, NSW, Australia
- *Correspondence: Jessica C. Johnson-Mackinnon,
| | - Winkie Fong
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Institute for Clinical Pathology and Medical Research, Westmead, NSW, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
| | - Mailie Gall
- Sydney Institute for Infectious Diseases, Westmead Institute for Medical Research, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology – Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Connie Lam
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Institute for Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Kerri Basile
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology – Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Jen Kok
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Institute for Clinical Pathology and Medical Research, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology – Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Alicia Arnott
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Institute for Clinical Pathology and Medical Research, Westmead, NSW, Australia
- Sydney Institute for Infectious Diseases, Westmead Institute for Medical Research, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology – Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Institute for Clinical Pathology and Medical Research, Westmead, NSW, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- Sydney Institute for Infectious Diseases, Westmead Institute for Medical Research, Westmead, NSW, Australia
- Centre for Infectious Diseases and Microbiology Laboratory Services, NSW Health Pathology – Institute of Clinical Pathology and Medical Research, Westmead, NSW, Australia
| | - Rebecca J. Rockett
- Centre for Infectious Diseases and Microbiology Public Health, Westmead Hospital, Institute for Clinical Pathology and Medical Research, Westmead, NSW, Australia
- Faculty of Medicine and Health, Sydney Medical School, University of Sydney, Sydney, NSW, Australia
- Sydney Institute for Infectious Diseases, Westmead Institute for Medical Research, Westmead, NSW, Australia
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11
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López-Cortés A, Guerrero S, Ortiz-Prado E, Yumiceba V, Vera-Guapi A, León Cáceres Á, Simbaña-Rivera K, Gómez-Jaramillo AM, Echeverría-Garcés G, García-Cárdenas JM, Guevara-Ramírez P, Cabrera-Andrade A, Puig San Andrés L, Cevallos-Robalino D, Bautista J, Armendáriz-Castillo I, Pérez-Villa A, Abad-Sojos A, Ramos-Medina MJ, León-Sosa A, Abarca E, Pérez-Meza ÁA, Nieto-Jaramillo K, Jácome AV, Morillo A, Arias-Erazo F, Fuenmayor-González L, Quiñones LA, Kyriakidis NC. Pulmonary Inflammatory Response in Lethal COVID-19 Reveals Potential Therapeutic Targets and Drugs in Phases III/IV Clinical Trials. Front Pharmacol 2022; 13:833174. [PMID: 35422702 PMCID: PMC9002106 DOI: 10.3389/fphar.2022.833174] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 03/07/2022] [Indexed: 12/26/2022] Open
Abstract
Background: It is imperative to identify drugs that allow treating symptoms of severe COVID-19. Respiratory failure is the main cause of death in severe COVID-19 patients, and the host inflammatory response at the lungs remains poorly understood. Methods: Therefore, we retrieved data from post-mortem lungs from COVID-19 patients and performed in-depth in silico analyses of single-nucleus RNA sequencing data, inflammatory protein interactome network, and shortest pathways to physiological phenotypes to reveal potential therapeutic targets and drugs in advanced-stage COVID-19 clinical trials. Results: Herein, we analyzed transcriptomics data of 719 inflammatory response genes across 19 cell types (116,313 nuclei) from lung autopsies. The functional enrichment analysis of the 233 significantly expressed genes showed that the most relevant biological annotations were inflammatory response, innate immune response, cytokine production, interferon production, macrophage activation, blood coagulation, NLRP3 inflammasome complex, and the TLR, JAK-STAT, NF-κB, TNF, oncostatin M signaling pathways. Subsequently, we identified 34 essential inflammatory proteins with both high-confidence protein interactions and shortest pathways to inflammation, cell death, glycolysis, and angiogenesis. Conclusion: We propose three small molecules (baricitinib, eritoran, and montelukast) that can be considered for treating severe COVID-19 symptoms after being thoroughly evaluated in COVID-19 clinical trials.
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Affiliation(s)
- Andrés López-Cortés
- Programa de Investigación en Salud Global, Facultad de Ciencias de la Salud, Universidad Internacional SEK, Quito, Ecuador.,Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
| | - Santiago Guerrero
- Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
| | - Esteban Ortiz-Prado
- One Health Research Group, Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | - Verónica Yumiceba
- Institut für Humangenetik Lübeck, Universität zu Lübeck, Lübeck, Germany
| | - Antonella Vera-Guapi
- Integrated Research and Treatment Center, Center for Sepsis Control and Care (CSCC), Jena University Hospital, Jena, Germany
| | - Ángela León Cáceres
- Heidelberg Institute of Global Health, Faculty of Medicine, University of Heidelberg, Heidelberg, Germany
| | - Katherine Simbaña-Rivera
- One Health Research Group, Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador.,Latin American Network for Cancer Research (LAN-CANCER), Lima, Peru
| | - Ana María Gómez-Jaramillo
- Centro de Investigación para la Salud en América Latina (CISeAL), Pontificia Universidad Católica del Ecuador, Quito, Ecuador
| | - Gabriela Echeverría-Garcés
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
| | - Jennyfer M García-Cárdenas
- Escuela de Medicina, Facultad de Ciencias Médicas de la Salud y de la Vida, Universidad Internacional del Ecuador, Quito, Ecuador
| | - Patricia Guevara-Ramírez
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
| | | | | | | | | | - Isaac Armendáriz-Castillo
- Facultade de Ciencias, Universidade da Coruña, A Coruña, Spain.,Instituto Nacional de Investigación en Salud Pública, Quito, Ecuador
| | - Andy Pérez-Villa
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain
| | | | | | | | | | - Álvaro A Pérez-Meza
- Biotechnology Engineering Career, Faculty of Life Sciences, Universidad Regional Amazónica Ikiam, Tena, Ecuador
| | | | - Andrea V Jácome
- Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
| | | | | | | | - Luis Abel Quiñones
- Latin American Network for the Implementation and Validation of Clinical Pharmacogenomics Guidelines (RELIVAF-CYTED), Madrid, Spain.,Laboratory of Chemical Carcinogenesis and Pharmacogenetics, Department of Basic-Clinical Oncology, Faculty of Medicine, University of Chile, Santiago, Chile
| | - Nikolaos C Kyriakidis
- One Health Research Group, Faculty of Medicine, Universidad de Las Américas, Quito, Ecuador
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12
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Zhang L, Yao L, Guo Y, Li X, Ma L, Sun R, Han X, Liu J, Huang J. Oral SARS-CoV-2 Spike Protein Recombinant Yeast Candidate Prompts Specific Antibody and Gut Microbiota Reconstruction in Mice. Front Microbiol 2022; 13:792532. [PMID: 35464985 PMCID: PMC9022078 DOI: 10.3389/fmicb.2022.792532] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2021] [Accepted: 03/07/2022] [Indexed: 11/13/2022] Open
Abstract
A recent study showed that patients with coronavirus disease 2019 (COVID-19) have gastrointestinal symptoms and intestinal flora dysbiosis. Yeast probiotics shape the gut microbiome and improve immune homeostasis. In this study, an oral candidate of yeast-derived spike protein receptor-binding domain (RBD) and fusion peptide displayed on the surface of the yeast cell wall was generated. The toxicity and immune efficacy of oral administration were further performed in Institute of Cancer Research (ICR) mice. No significant difference in body weights, viscera index, and other side effects were detected in the oral-treated group. The detectable RBD-specific immunoglobulin G (IgG) and immunoglobulin A (IgA) of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and more complex microbiota were detected from oral administration mice compared with those of the control group. Interestingly, the recombinant yeast was identified in female fetal of the high-dose group. These results revealed that the displaying yeast could fulfill the agent-driven immunoregulation and gut microbiome reconstitution. The findings will shed light on new dimensions against SARS-CoV-2 infection with the synergistic oral agents as promising non-invasive immunization and restoring gut flora.
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Affiliation(s)
- Lilin Zhang
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Lan Yao
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Yanyu Guo
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Xiaoyang Li
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Li Ma
- Tianjin Institute of Pharmaceutical Research Co., Ltd., Tianjin, China
| | - Ruiqi Sun
- School of Life Sciences, Tianjin University, Tianjin, China
| | - Xueqing Han
- Chinese Academy of Inspection and Quarantine, Beijing, China
| | - Jing Liu
- Tianjin Institute of Pharmaceutical Research Co., Ltd., Tianjin, China
- Jing Liu,
| | - Jinhai Huang
- School of Life Sciences, Tianjin University, Tianjin, China
- *Correspondence: Jinhai Huang,
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13
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Strobelt R, Adler J, Paran N, Yahalom-Ronen Y, Melamed S, Politi B, Shulman Z, Schmiedel D, Shaul Y. Imatinib inhibits SARS-CoV-2 infection by an off-target-mechanism. Sci Rep 2022; 12:5758. [PMID: 35388061 PMCID: PMC8984672 DOI: 10.1038/s41598-022-09664-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Accepted: 03/21/2022] [Indexed: 12/15/2022] Open
Abstract
The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causal agent of the COVID-19 pandemic. More than 274 million individuals have suffered from COVID-19 and over five million people have died from this disease so far. Therefore, there is an urgent need for therapeutic drugs. Repurposing FDA approved drugs should be favored since evaluation of safety and efficacy of de-novo drug design are both costly and time consuming. We report that imatinib, an Abl tyrosine kinase inhibitor, robustly decreases SARS-CoV-2 infection and uncover a mechanism of action. We show that imatinib inhibits the infection of SARS-CoV-2 and its surrogate lentivector pseudotype. In latter, imatinib inhibited both routes of viral entry, endocytosis and membrane-fusion. We utilized a system to quantify in real-time cell-cell membrane fusion mediated by the SARS-CoV-2 surface protein, Spike, and its receptor, hACE2, to demonstrate that imatinib inhibits this process in an Abl1 and Abl2 independent manner. Furthermore, cellular thermal shift assay revealed a direct imatinib-Spike interaction that affects Spike susceptibility to trypsin digest. Collectively, our data suggest that imatinib inhibits Spike mediated viral entry by an off-target mechanism. These findings mark imatinib as a promising therapeutic drug in inhibiting the early steps of SARS-CoV-2 infection.
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Affiliation(s)
- Romano Strobelt
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Julia Adler
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Nir Paran
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Yfat Yahalom-Ronen
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Sharon Melamed
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Boaz Politi
- Department of Infectious Diseases, Israel Institute for Biological Research, Ness Ziona, Israel
| | - Ziv Shulman
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
| | - Dominik Schmiedel
- Department of Immunology, Weizmann Institute of Science, Rehovot, Israel
- Fraunhofer Institute for Cell Therapy and Immunology, Leipzig, Germany
| | - Yosef Shaul
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.
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14
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Genomic stratification and differential natural selection signatures among human norovirus genogroup II isolates. Arch Virol 2022; 167:1235-1245. [PMID: 35322317 PMCID: PMC8942050 DOI: 10.1007/s00705-022-05396-9] [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: 10/05/2021] [Accepted: 01/12/2022] [Indexed: 11/27/2022]
Abstract
Noroviruses (NoVs), which are members of the family Caliciviridae, are the most common cause of gastroenteritis in humans. Ten NoV genogroups have been reported so far. Of these, genogroup II (GII) is the most prevalent, and it causes serious infections worldwide. The complete genome sequences of NoV GII isolates from different geographical regions were retrieved from the public database. The model-based clustering approach, implemented in the STRUCTURE resource, was employed for assessment of genetic composition. The MEGA X and IQ Tree tools were used for phylogenetic analysis. Genome-wide natural selection analysis was performed using maximum-likelihood-based methods. The demographic features of NoV GII genome sequences were assessed using the BEAST package. All of the NoV GII sequences initially clustered into two main subpopulations at significant K = 2, where the genotype GII.4 samples clearly split from the rest of the genotypes. This indicates a marked genetic distinction between norovirus GII.4 and non-GII.4 samples. Phylogenetic analysis showed the presence of five distinct subclades for genotype GII.2 and seven subclades for GII.4 samples. Several isolates with admixed ancestry were identified that constituted distinct subclusters in the phylogenetic tree. No continental-specific genetic distinctions were observed among the NoV GII samples. Significant genomic signatures of both positive and negative natural selection were identified across the NoV GII genes. A differential pattern of positive selection signals was inferred between the GII.4 and non-GII.4 genotypes. The demographic analysis revealed an increase in the effective population size of NoV GII during 2009-2010, followed by a rapid fall in 2015.
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15
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Zhang J, Ejikemeuwa A, Gerzanich V, Nasr M, Tang Q, Simard JM, Zhao RY. Understanding the Role of SARS-CoV-2 ORF3a in Viral Pathogenesis and COVID-19. Front Microbiol 2022; 13:854567. [PMID: 35356515 PMCID: PMC8959714 DOI: 10.3389/fmicb.2022.854567] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2022] [Accepted: 02/09/2022] [Indexed: 12/11/2022] Open
Abstract
The ongoing SARS-CoV-2 pandemic has shocked the world due to its persistence, COVID-19-related morbidity and mortality, and the high mutability of the virus. One of the major concerns is the emergence of new viral variants that may increase viral transmission and disease severity. In addition to mutations of spike protein, mutations of viral proteins that affect virulence, such as ORF3a, also must be considered. The purpose of this article is to review the current literature on ORF3a, to summarize the molecular actions of SARS-CoV-2 ORF3a, and its role in viral pathogenesis and COVID-19. ORF3a is a polymorphic, multifunctional viral protein that is specific to SARS-CoV/SARS-CoV-2. It was acquired from β-CoV lineage and likely originated from bats through viral evolution. SARS-CoV-2 ORF3a is a viroporin that interferes with ion channel activities in host plasma and endomembranes. It is likely a virion-associated protein that exerts its effect on the viral life cycle during viral entry through endocytosis, endomembrane-associated viral transcription and replication, and viral release through exocytosis. ORF3a induces cellular innate and pro-inflammatory immune responses that can trigger a cytokine storm, especially under hypoxic conditions, by activating NLRP3 inflammasomes, HMGB1, and HIF-1α to promote the production of pro-inflammatory cytokines and chemokines. ORF3a induces cell death through apoptosis, necrosis, and pyroptosis, which leads to tissue damage that affects the severity of COVID-19. ORF3a continues to evolve along with spike and other viral proteins to adapt in the human cellular environment. How the emerging ORF3a mutations alter the function of SARS-CoV-2 ORF3a and its role in viral pathogenesis and COVID-19 is largely unknown. This review provides an in-depth analysis of ORF3a protein's structure, origin, evolution, and mutant variants, and how these characteristics affect its functional role in viral pathogenesis and COVID-19.
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Affiliation(s)
- Jiantao Zhang
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, United States
- Research and Development Service, VA Maryland Health Care System, Baltimore, MD, United States
| | - Amara Ejikemeuwa
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Volodymyr Gerzanich
- Research and Development Service, VA Maryland Health Care System, Baltimore, MD, United States
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Mohamed Nasr
- Drug Development and Clinical Sciences Branch, Division of AIDS, NIAID, NIH, Bethesda, MD, United States
| | - Qiyi Tang
- Department of Microbiology, Howard University College of Medicine, Washington, DC, United States
| | - J. Marc Simard
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, United States
- Research and Development Service, VA Maryland Health Care System, Baltimore, MD, United States
- Department of Neurosurgery, University of Maryland School of Medicine, Baltimore, MD, United States
| | - Richard Y. Zhao
- Department of Pathology, University of Maryland School of Medicine, Baltimore, MD, United States
- Research and Development Service, VA Maryland Health Care System, Baltimore, MD, United States
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, MD, United States
- Institute of Human Virology, University of Maryland School of Medicine, Baltimore, MD, United States
- Institute of Global Health, University of Maryland School of Medicine, Baltimore, MD, United States
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Alam ASMRU, Islam OK, Hasan MS, Islam MR, Mahmud S, Al‐Emran HM, Jahid IK, Crandall KA, Hossain MA. Dominant clade-featured SARS-CoV-2 co-occurring mutations reveal plausible epistasis: An in silico based hypothetical model. J Med Virol 2022; 94:1035-1049. [PMID: 34676891 PMCID: PMC8661685 DOI: 10.1002/jmv.27416] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 10/15/2021] [Accepted: 10/20/2021] [Indexed: 01/18/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved into eight fundamental clades with four of these clades (G, GH, GR, and GV) globally prevalent in 2020. To explain plausible epistatic effects of the signature co-occurring mutations of these circulating clades on viral replication and transmission fitness, we proposed a hypothetical model using in silico approach. Molecular docking and dynamics analyses showed the higher infectiousness of a spike mutant through more favorable binding of G614 with the elastase-2. RdRp mutation p.P323L significantly increased genome-wide mutations (p < 0.0001), allowing for more flexible RdRp (mutated)-NSP8 interaction that may accelerate replication. Superior RNA stability and structural variation at NSP3:C241T might impact protein, RNA interactions, or both. Another silent 5'-UTR:C241T mutation might affect translational efficiency and viral packaging. These four G-clade-featured co-occurring mutations might increase viral replication. Sentinel GH-clade ORF3a:p.Q57H variants constricted the ion-channel through intertransmembrane-domain interaction of cysteine(C81)-histidine(H57). The GR-clade N:p.RG203-204KR would stabilize RNA interaction by a more flexible and hypo-phosphorylated SR-rich region. GV-clade viruses seemingly gained the evolutionary advantage of the confounding factors; nevertheless, N:p.A220V might modulate RNA binding with no phenotypic effect. Our hypothetical model needs further retrospective and prospective studies to understand detailed molecular events and their relationship to the fitness of SARS-CoV-2.
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Affiliation(s)
| | - Ovinu Kibria Islam
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - Md. Shazid Hasan
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - Mir Raihanul Islam
- Division of Poverty, Health, and NutritionInternational Food Policy Research InstituteBangladesh
| | - Shafi Mahmud
- Department Genetic Engineering and BiotechnologyUniversity of RajshahiRajshahiBangladesh
| | - Hassan M. Al‐Emran
- Department of Biomedical EngineeringJashore University of Science and TechnologyJashoreBangladesh
| | - Iqbal Kabir Jahid
- Department of MicrobiologyJashore University of Science and TechnologyJashoreBangladesh
| | - Keith A. Crandall
- Department of Biostatistics and Bioinformatics, Computational Biology Institute, Milken Institute School of Public HealthThe George Washington UniversityWashington DCUSA
| | - M. Anwar Hossain
- Office of the Vice ChancellorJashore University of Science and TechnologyJashoreBangladesh
- Department of MicrobiologyUniversity of DhakaDhakaBangladesh
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Tao Y, Yue Y, Qiu G, Ji Z, Spillman M, Gai Z, Chen Q, Bielecki M, Huber M, Trkola A, Wang Q, Cao J, Wang J. Comparison of analytical sensitivity and efficiency for SARS-CoV-2 primer sets by TaqMan-based and SYBR Green-based RT-qPCR. Appl Microbiol Biotechnol 2022; 106:2207-2218. [PMID: 35218386 PMCID: PMC8881549 DOI: 10.1007/s00253-022-11822-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 02/02/2022] [Accepted: 02/04/2022] [Indexed: 12/12/2022]
Abstract
Abstract The pandemic of coronavirus disease 2019 (COVID-19) continues to threaten public health. For developing countries where vaccines are still in shortage, cheaper alternative molecular methods for SARS-CoV-2 identification can be crucial to prevent the next wave. Therefore, 14 primer sets recommended by the World Health Organization (WHO) was evaluated on testing both clinical patient and environmental samples with the gold standard diagnosis method, TaqMan-based RT-qPCR, and a cheaper alternative method, SYBR Green-based RT-qPCR. Using suitable primer sets, such as ORF1ab, 2019_nCoV_N1 and 2019_nCoV_N3, the performance of the SYBR Green approach was comparable or better than the TaqMan approach, even when considering the newly dominating or emerging variants, including Delta, Eta, Kappa, Lambda, Mu, and Omicron. ORF1ab and 2019_nCoV_N3 were the best combination for sensitive and reliable SARS-CoV-2 molecular diagnostics due to their high sensitivity, specificity, and broad accessibility. Key points • With suitable primer sets, the SYBR Green method performs better than the TaqMan one. • With suitable primer sets, both methods should still detect the new variants well. • ORF1ab and 2019_nCoV_N3 were the best combination for SARS-CoV-2 detection. Supplementary Information The online version contains supplementary material available at 10.1007/s00253-022-11822-4.
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Affiliation(s)
- Yile Tao
- Institute of Environmental Engineering, ETH Zurich, 8093, Zurich, Switzerland
- Laboratory for Advanced Analytical Technologies, Empa, Swiss Federal Laboratories for Materials Science and Technology, 8600, Dübendorf, Switzerland
| | - Yang Yue
- Institute of Environmental Engineering, ETH Zurich, 8093, Zurich, Switzerland
- Laboratory for Advanced Analytical Technologies, Empa, Swiss Federal Laboratories for Materials Science and Technology, 8600, Dübendorf, Switzerland
| | - Guangyu Qiu
- Institute of Environmental Engineering, ETH Zurich, 8093, Zurich, Switzerland
- Laboratory for Advanced Analytical Technologies, Empa, Swiss Federal Laboratories for Materials Science and Technology, 8600, Dübendorf, Switzerland
| | - Zheng Ji
- School of Geography and Tourism, Shaanxi Normal University, Xi'an, 710119, China
| | - Martin Spillman
- Institute of Environmental Engineering, ETH Zurich, 8093, Zurich, Switzerland
- Laboratory for Advanced Analytical Technologies, Empa, Swiss Federal Laboratories for Materials Science and Technology, 8600, Dübendorf, Switzerland
| | - Zhibo Gai
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, University of Zurich, 8091, Zurich, Switzerland
| | - Qingfa Chen
- Institute for Tissue Engineering and Regenerative Medicine, Liaocheng University, Liaocheng, 252000, China
| | - Michel Bielecki
- Epidemiology, Biostatistics and Prevention Institute, University of Zurich, 8091, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, 8057, Zurich, Switzerland
| | - Qiyuan Wang
- Key Laboratory of Aerosol Chemistry and Physics, State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, 710061, China
- CAS Center for Excellence in Quaternary Science and Global Change, Xi'an, 710061, China
| | - Junji Cao
- Key Laboratory of Aerosol Chemistry and Physics, State Key Laboratory of Loess and Quaternary Geology, Institute of Earth Environment, Chinese Academy of Sciences, Xi'an, 710061, China
- CAS Center for Excellence in Quaternary Science and Global Change, Xi'an, 710061, China
| | - Jing Wang
- Institute of Environmental Engineering, ETH Zurich, 8093, Zurich, Switzerland.
- Laboratory for Advanced Analytical Technologies, Empa, Swiss Federal Laboratories for Materials Science and Technology, 8600, Dübendorf, Switzerland.
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18
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Analysis of Genomic Characteristics of SARS-CoV-2 in Italy, 29 January to 27 March 2020. Viruses 2022; 14:v14030472. [PMID: 35336879 PMCID: PMC8951147 DOI: 10.3390/v14030472] [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: 06/30/2021] [Revised: 02/01/2022] [Accepted: 02/09/2022] [Indexed: 12/14/2022] Open
Abstract
We performed next-generation sequencing (NGS), phylogenetic analysis, gene flows, and N- and O-glycosylation prediction on SARS-CoV-2 genomes collected from lab-confirmed cases from different Italian regions. To this end, a total of 111 SARS-CoV-2 genomes collected in Italy between 29 January and 27 March 2020 were investigated. The majority of the genomes belonged to lineage B.1, with some descendant lineages. The gene flow analysis showed that the spread occurred mainly from the north to the center and to the south of Italy, as confirmed by epidemiological data. The mean evolutionary rate estimated here was 8.731 × 10−4 (95% highest posterior density, HPD intervals 5.809 × 10−4 to 1.19 × 10−3), in line with values reported by other authors. The dated phylogeny suggested that SARS-CoV-2 lineage B.1 probably entered Italy between the end of January and early February 2020. Continuous molecular surveillance is needed to trace virus circulation and evolution.
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Perbolianachis P, Ferla D, Arce R, Ferreiro I, Costábile A, Paz M, Simón D, Moreno P, Cristina J. Phylogenetic analysis of SARS-CoV-2 viruses circulating in the South American region: genetic relations and vaccine strain match. Virus Res 2022; 311:198688. [PMID: 35074431 PMCID: PMC8779862 DOI: 10.1016/j.virusres.2022.198688] [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: 10/27/2021] [Revised: 01/19/2022] [Accepted: 01/20/2022] [Indexed: 01/10/2023]
Abstract
The pandemic of coronavirus disease 2019 (COVID-19) is caused by a novel member of the family Coronaviridae, now known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Recent studies revealed the emergence of virus variants with substitutions in the spike and/or nucleocapsid and RNA-dependent RNA polymerase proteins that are partly responsible for enhanced transmission and reduced or escaped anti-SARS-CoV-2 antibodies that may reduce the efficacy of antibodies and vaccines against the first identified SARS-CoV-2 strains. In order to gain insight into the emergence and evolution of SARS-CoV-2 variants circulating in the South American region, a comprehensive phylogenetic study of SARS-CoV-2 variants circulating in this region was performed. The results of these studies revealed sharp increase in virus effective population size from March to April of 2020. At least 62 different genotypes were found to circulate in this region. Variants of concern (VOCs) Alpha, Beta, Gamma and Delta co-circulate in the region, together with variants of interest (VOIs) Lambda, Mu and Zeta. Most of SARS-CoV-2 variants circulating in the South American region belongs to B.1 genotypes and have substitutions in the spike and/or nucleocapsid and polymerase proteins that confer high transmissibility and/or immune resistance. 148 amino acid positions of the spike protein and 70 positions of the nucleocapsid were found to have substitutions in different variants isolated in the region by comparison with reference strain Wuhan-Hu-1. Significant differences in codon usage among spike genes of SARS-CoV-2 strains circulating in South America was found, which can be linked to SARS-CoV-2 genotypes.
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Affiliation(s)
- Paula Perbolianachis
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Diego Ferla
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Rodrigo Arce
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Irene Ferreiro
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Alicia Costábile
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Mercedes Paz
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Diego Simón
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Pilar Moreno
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay
| | - Juan Cristina
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Iguá 4225, Montevideo 11400, Uruguay.
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20
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Stromberg ZR, Theiler J, Foley BT, Myers Y Gutiérrez A, Hollander A, Courtney SJ, Gans J, Deshpande A, Martinez-Finley EJ, Mitchell J, Mukundan H, Yusim K, Kubicek-Sutherland JZ. Fast Evaluation of Viral Emerging Risks (FEVER): A computational tool for biosurveillance, diagnostics, and mutation typing of emerging viral pathogens. PLOS GLOBAL PUBLIC HEALTH 2022; 2:e0000207. [PMID: 36962401 PMCID: PMC10021650 DOI: 10.1371/journal.pgph.0000207] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 01/23/2022] [Indexed: 12/23/2022]
Abstract
Viral pathogens can rapidly evolve, adapt to novel hosts, and evade human immunity. The early detection of emerging viral pathogens through biosurveillance coupled with rapid and accurate diagnostics are required to mitigate global pandemics. However, RNA viruses can mutate rapidly, hampering biosurveillance and diagnostic efforts. Here, we present a novel computational approach called FEVER (Fast Evaluation of Viral Emerging Risks) to design assays that simultaneously accomplish: 1) broad-coverage biosurveillance of an entire group of viruses, 2) accurate diagnosis of an outbreak strain, and 3) mutation typing to detect variants of public health importance. We demonstrate the application of FEVER to generate assays to simultaneously 1) detect sarbecoviruses for biosurveillance; 2) diagnose infections specifically caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2); and 3) perform rapid mutation typing of the D614G SARS-CoV-2 spike variant associated with increased pathogen transmissibility. These FEVER assays had a high in silico recall (predicted positive) up to 99.7% of 525,708 SARS-CoV-2 sequences analyzed and displayed sensitivities and specificities as high as 92.4% and 100% respectively when validated in 100 clinical samples. The D614G SARS-CoV-2 spike mutation PCR test was able to identify the single nucleotide identity at position 23,403 in the viral genome of 96.6% SARS-CoV-2 positive samples without the need for sequencing. This study demonstrates the utility of FEVER to design assays for biosurveillance, diagnostics, and mutation typing to rapidly detect, track, and mitigate future outbreaks and pandemics caused by emerging viruses.
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Affiliation(s)
- Zachary R Stromberg
- Physical Chemistry and Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - James Theiler
- Space Data Science and Systems, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Brian T Foley
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Adán Myers Y Gutiérrez
- Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Attelia Hollander
- Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Samantha J Courtney
- Physical Chemistry and Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jason Gans
- Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Alina Deshpande
- Biosecurity and Public Health, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | | | - Jason Mitchell
- Presbyterian Healthcare Services, Albuquerque, New Mexico, United States of America
| | - Harshini Mukundan
- Physical Chemistry and Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Karina Yusim
- Theoretical Biology and Biophysics, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
| | - Jessica Z Kubicek-Sutherland
- Physical Chemistry and Applied Spectroscopy, Los Alamos National Laboratory, Los Alamos, New Mexico, United States of America
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21
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Bonacci PG, Bivona DA, Bongiorno D, Stracquadanio S, Massimino M, Bonomo C, Stracuzzi A, Pennisi P, Musso N, Stefani S. Low Represented Mutation Clustering in SARS-CoV-2 B.1.1.7 Sublineage Group with Synonymous Mutations in the E Gene. Diagnostics (Basel) 2021; 11:2286. [PMID: 34943523 PMCID: PMC8700258 DOI: 10.3390/diagnostics11122286] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/28/2021] [Accepted: 12/01/2021] [Indexed: 01/01/2023] Open
Abstract
Starting in 2019, the COVID-19 pandemic is a global threat that is difficult to monitor. SARS-CoV-2 is known to undergo frequent mutations, including SNPs and deletions, which seem to be transmitted together, forming clusters that define specific lineages. Reverse-Transcription quantitative PCR (RT-qPCR) has been used for SARS-CoV-2 diagnosis and is still considered the gold standard method. Our Eukaryotic Host Pathogens Interaction (EHPI) laboratory received six SARS-CoV-2-positive samples from a Sicilian private analysis laboratory, four of which showed a dropout of the E gene. Our sequencing data revealed the presence of a synonymous mutation (c.26415 C > T, TAC > TAT) in the E gene of all four samples showing the dropout in RT-qPCR. Interestingly, these samples also harbored three other mutations (S137L-Orf1ab; N439K-S gene; A156S-N gene), which had a very low diffusion rate worldwide. This combination suggested that these mutations may be linked to each other and more common in a specific area than in the rest of the world. Thus, we decided to analyze the 103 sequences in our internal database in order to confirm or disprove our "mutation cluster hypothesis". Within our database, one sample showed the synonymous mutation (c.26415 C > T, TAC > TAT) in the E gene. This work underlines the importance of territorial epidemiological surveillance by means of NGS and the sequencing of samples with clinical and or technical particularities, e.g., post-vaccine infections or RT-qPCR amplification failures, to allow for the early identification of these SNPs. This approach may be an effective method to detect new mutational clusters and thus to predict new emerging SARS-CoV-2 lineages before they spread globally.
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Affiliation(s)
- Paolo Giuseppe Bonacci
- Department of Biomedical and Biotechnological Science (BIOMETEC), University of Catania, Via Santa Sofia 97, 95123 Catania, Italy; (P.G.B.); (D.A.B.); (S.S.); (M.M.); (C.B.); (S.S.)
| | - Dalida Angela Bivona
- Department of Biomedical and Biotechnological Science (BIOMETEC), University of Catania, Via Santa Sofia 97, 95123 Catania, Italy; (P.G.B.); (D.A.B.); (S.S.); (M.M.); (C.B.); (S.S.)
| | - Dafne Bongiorno
- Department of Biomedical and Biotechnological Science (BIOMETEC), University of Catania, Via Santa Sofia 97, 95123 Catania, Italy; (P.G.B.); (D.A.B.); (S.S.); (M.M.); (C.B.); (S.S.)
| | - Stefano Stracquadanio
- Department of Biomedical and Biotechnological Science (BIOMETEC), University of Catania, Via Santa Sofia 97, 95123 Catania, Italy; (P.G.B.); (D.A.B.); (S.S.); (M.M.); (C.B.); (S.S.)
| | - Mariacristina Massimino
- Department of Biomedical and Biotechnological Science (BIOMETEC), University of Catania, Via Santa Sofia 97, 95123 Catania, Italy; (P.G.B.); (D.A.B.); (S.S.); (M.M.); (C.B.); (S.S.)
| | - Carmelo Bonomo
- Department of Biomedical and Biotechnological Science (BIOMETEC), University of Catania, Via Santa Sofia 97, 95123 Catania, Italy; (P.G.B.); (D.A.B.); (S.S.); (M.M.); (C.B.); (S.S.)
| | - Alessia Stracuzzi
- LifeGene Società a Responsabilità Limitata, Via Garibaldi 377, 98121 Messina, Italy; (A.S.); (P.P.)
| | - Paolo Pennisi
- LifeGene Società a Responsabilità Limitata, Via Garibaldi 377, 98121 Messina, Italy; (A.S.); (P.P.)
- Centro Diagnostico Ionia (CDI), Via Cavour 11, Riposto, 95018 Catania, Italy
| | - Nicolò Musso
- Department of Biomedical and Biotechnological Science (BIOMETEC), University of Catania, Via Santa Sofia 97, 95123 Catania, Italy; (P.G.B.); (D.A.B.); (S.S.); (M.M.); (C.B.); (S.S.)
| | - Stefania Stefani
- Department of Biomedical and Biotechnological Science (BIOMETEC), University of Catania, Via Santa Sofia 97, 95123 Catania, Italy; (P.G.B.); (D.A.B.); (S.S.); (M.M.); (C.B.); (S.S.)
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22
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Gupta D, Sharma P, Singh M, Kumar M, Ethayathulla AS, Kaur P. Structural and functional insights into the spike protein mutations of emerging SARS-CoV-2 variants. Cell Mol Life Sci 2021; 78:7967-7989. [PMID: 34731254 PMCID: PMC11073194 DOI: 10.1007/s00018-021-04008-0] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Revised: 10/20/2021] [Accepted: 10/22/2021] [Indexed: 02/07/2023]
Abstract
Since the emergence of the first case of coronavirus disease 2019 (COVID-19), caused by severe acute respiratory syndrome coronavirus (SARS-CoV-2), the viral genome has constantly undergone rapid mutations for better adaptation in the host system. These newer mutations have given rise to several lineages/ variants of the virus that have resulted in high transmission and virulence rates compared to the previously circulating variants. Owing to this, the overall caseload and related mortality have tremendously increased globally to > 233 million infections and > 4.7 million deaths as of Sept. 28th, 2021. SARS-CoV-2, Spike (S) protein binds to host cells by recognizing human angiotensin-converting enzyme 2 (hACE2) receptor. The viral S protein contains S1 and S2 domains that constitute the binding and fusion machinery, respectively. Structural analysis of viral S protein reveals that the virus undergoes conformational flexibility and dynamicity to interact with the hACE2 receptor. The SARS-CoV-2 variants and mutations might be associated with affecting the conformational plasticity of S protein, potentially linked to its altered affinity, infectivity, and immunogenicity. This review focuses on the current circulating variants of SARS-CoV-2 and the structure-function analysis of key S protein mutations linked with increased affinity, higher infectivity, enhanced transmission rates, and immune escape against this infection.
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Affiliation(s)
- Deepali Gupta
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India
| | - Priyanka Sharma
- Department of Microbiology, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India
| | - Mandeep Singh
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India
| | - Mukesh Kumar
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India
| | - A S Ethayathulla
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India
| | - Punit Kaur
- Department of Biophysics, All India Institute of Medical Sciences, New Delhi,, Delhi, 110029, India.
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23
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Gong Y, Qin S, Dai L, Tian Z. The glycosylation in SARS-CoV-2 and its receptor ACE2. Signal Transduct Target Ther 2021; 6:396. [PMID: 34782609 PMCID: PMC8591162 DOI: 10.1038/s41392-021-00809-8] [Citation(s) in RCA: 96] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2021] [Revised: 10/10/2021] [Accepted: 10/24/2021] [Indexed: 02/05/2023] Open
Abstract
Coronavirus disease 2019 (COVID-19), a highly infectious disease caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), has infected more than 235 million individuals and led to more than 4.8 million deaths worldwide as of October 5 2021. Cryo-electron microscopy and topology show that the SARS-CoV-2 genome encodes lots of highly glycosylated proteins, such as spike (S), envelope (E), membrane (M), and ORF3a proteins, which are responsible for host recognition, penetration, binding, recycling and pathogenesis. Here we reviewed the detections, substrates, biological functions of the glycosylation in SARS-CoV-2 proteins as well as the human receptor ACE2, and also summarized the approved and undergoing SARS-CoV-2 therapeutics associated with glycosylation. This review may not only broad the understanding of viral glycobiology, but also provide key clues for the development of new preventive and therapeutic methodologies against SARS-CoV-2 and its variants.
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Affiliation(s)
- Yanqiu Gong
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China
| | - Suideng Qin
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China
| | - Lunzhi Dai
- National Clinical Research Center for Geriatrics and Department of General Practice, State Key Laboratory of Biotherapy, West China Hospital, Sichuan University, and Collaborative Innovation Center of Biotherapy, 610041, Chengdu, China.
| | - Zhixin Tian
- School of Chemical Science & Engineering, Shanghai Key Laboratory of Chemical Assessment and Sustainability, Tongji University, 200092, Shanghai, China.
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24
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Grosche VR, Santos IA, Ferreira GM, Dutra JVR, Costa LC, Nicolau-Junior N, Queiroz ATL, José DP, Jardim ACG. Insights on the SARS-CoV-2 genome variability: the lesson learned in Brazil and its impacts on the future of pandemics. Microb Genom 2021; 7:000656. [PMID: 34730486 PMCID: PMC8743548 DOI: 10.1099/mgen.0.000656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 07/19/2021] [Indexed: 11/18/2022] Open
Abstract
Since the beginning of the SARS-CoV-2 spread in Brazil, few studies have been published analysing the variability of viral genome. Herein, we described the dynamic of SARS-CoV-2 strains circulating in Brazil from May to September 2020, to better understand viral changes that may affect the ongoing pandemic. Our data demonstrate that some of the mutations identified are currently observed in variants of interest and variants of concern, and emphasize the importance of studying previous periods in order to comprehend the emergence of new variants. From 720 SARS-CoV-2 genome sequences, we found few sites under positive selection pressure, such as the D614G (98.5 %) in the spike, that has replaced the old variant; the V1167F in the spike (41 %), identified in the P.2 variant that emerged from Brazil during the period of analysis; and I292T (39 %) in the N protein. There were a few alterations in the UTRs, which was expected, however, our data suggest that the emergence of new variants was not influenced by mutations in UTR regions, since it maintained its conformational structure in most analysed sequences. In phylogenetic analysis, the spread of SARS-CoV-2 from the large urban centres to the countryside during these months could be explained by the flexibilization of social isolation measures and also could be associated with possible new waves of infection. These results allow a better understanding of SARS-CoV-2 strains that have circulated in Brazil, and thus, with relevant infomation, provide the potential viral changes that may have affected and/or contributed to the current and future scenario of the COVID-19 pandemic.
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Affiliation(s)
- Victória Riquena Grosche
- São Paulo State University, São José do Rio Preto, São Paulo, Brazil
- Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
| | | | | | | | - Larissa Catharina Costa
- Center of Data and Knowledge Integration for Health (CIDACS), Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Bahia, Brazil
| | | | - Artur Trancoso Lopo Queiroz
- Center of Data and Knowledge Integration for Health (CIDACS), Gonçalo Moniz Institute, Oswaldo Cruz Foundation, Salvador, Bahia, Brazil
| | - Diego Pandeló José
- Federal University of Triângulo Mineiro, Campus Universitário Iturama, Iturama, Minas Gerais, Brazil
| | - Ana Carolina Gomes Jardim
- São Paulo State University, São José do Rio Preto, São Paulo, Brazil
- Federal University of Uberlândia, Uberlândia, Minas Gerais, Brazil
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25
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Mohammad T, Choudhury A, Habib I, Asrani P, Mathur Y, Umair M, Anjum F, Shafie A, Yadav DK, Hassan MI. Genomic Variations in the Structural Proteins of SARS-CoV-2 and Their Deleterious Impact on Pathogenesis: A Comparative Genomics Approach. Front Cell Infect Microbiol 2021; 11:765039. [PMID: 34722346 PMCID: PMC8548870 DOI: 10.3389/fcimb.2021.765039] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 09/16/2021] [Indexed: 12/23/2022] Open
Abstract
A continual rise in severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection causing coronavirus disease (COVID-19) has become a global threat. The main problem comes when SARS-CoV-2 gets mutated with the rising infection and becomes more lethal for humankind than ever. Mutations in the structural proteins of SARS-CoV-2, i.e., the spike surface glycoprotein (S), envelope (E), membrane (M) and nucleocapsid (N), and replication machinery enzymes, i.e., main protease (Mpro) and RNA-dependent RNA polymerase (RdRp) creating more complexities towards pathogenesis and the available COVID-19 therapeutic strategies. This study analyzes how a minimal variation in these enzymes, especially in S protein at the genomic/proteomic level, affects pathogenesis. The structural variations are discussed in light of the failure of small molecule development in COVID-19 therapeutic strategies. We have performed in-depth sequence- and structure-based analyses of these proteins to get deeper insights into the mechanism of pathogenesis, structure-function relationships, and development of modern therapeutic approaches. Structural and functional consequences of the selected mutations on these proteins and their association with SARS-CoV-2 virulency and human health are discussed in detail in the light of our comparative genomics analysis.
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Affiliation(s)
- Taj Mohammad
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Arunabh Choudhury
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Insan Habib
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Purva Asrani
- Department of Microbiology, University of Delhi, New Delhi, India
| | - Yash Mathur
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Mohd Umair
- Department of Computer Science, Jamia Millia Islamia, New Delhi, India
| | - Farah Anjum
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Alaa Shafie
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, Saudi Arabia
| | - Dharmendra Kumar Yadav
- Department of Pharmacy and Gachon Institute of Pharmaceutical Science, College of Pharmacy, Gachon University, Incheon, South Korea
| | - Md. Imtaiyaz Hassan
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
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26
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Rachiglio AM, De Sabato L, Roma C, Cennamo M, Fiorenza M, Terracciano D, Pasquale R, Bergantino F, Cavalcanti E, Botti G, Vaccari G, Portella G, Normanno N. SARS-CoV-2 complete genome sequencing from the Italian Campania region using a highly automated next generation sequencing system. J Transl Med 2021; 19:246. [PMID: 34090468 PMCID: PMC8179693 DOI: 10.1186/s12967-021-02912-4] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 05/25/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Since the first complete genome sequencing of SARS-CoV-2 in December 2019, more than 550,000 genomes have been submitted into the GISAID database. Sequencing of the SARS-CoV-2 genome might allow identification of variants with increased contagiousness, different clinical patterns and/or different response to vaccines. A highly automated next generation sequencing (NGS)-based method might facilitate an active genomic surveillance of the virus. METHODS RNA was extracted from 27 nasopharyngeal swabs obtained from citizens of the Italian Campania region in March-April 2020 who tested positive for SARS-CoV-2. Following viral RNA quantification, sequencing was performed using the Ion AmpliSeq SARS-CoV-2 Research Panel on the Genexus Integrated Sequencer, an automated technology for library preparation and sequencing. The SARS-CoV-2 complete genomes were built using the pipeline SARS-CoV-2 RECoVERY (REconstruction of COronaVirus gEnomes & Rapid analYsis) and analysed by IQ-TREE software. RESULTS The complete genome (100%) of SARS-CoV-2 was successfully obtained for 21/27 samples. In particular, the complete genome was fully sequenced for all 15 samples with high viral titer (> 200 copies/µl), for the two samples with a viral genome copy number < 200 but greater than 20, and for 4/10 samples with a viral load < 20 viral copies. The complete genome sequences classified into the B.1 and B.1.1 SARS-CoV-2 lineages. In comparison to the reference strain Wuhan-Hu-1, 48 total nucleotide variants were observed with 26 non-synonymous substitutions, 18 synonymous and 4 reported in untranslated regions (UTRs). Ten of the 26 non-synonymous variants were observed in ORF1ab, 7 in S, 1 in ORF3a, 2 in M and 6 in N genes. CONCLUSIONS The Genexus system resulted successful for SARS-CoV-2 complete genome sequencing, also in cases with low viral copies. The use of this highly automated system might facilitate the standardization of SARS-CoV-2 sequencing protocols and make faster the identification of novel variants during the pandemic.
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Affiliation(s)
- Anna Maria Rachiglio
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione Giovanni Pascale", IRCCS, Via Mariano Semmola, 80131, Napoli, Italy
| | - Luca De Sabato
- ISS-Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Cristin Roma
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione Giovanni Pascale", IRCCS, Via Mariano Semmola, 80131, Napoli, Italy
| | - Michele Cennamo
- Dipartimento Scienze Mediche Traslazionali, Università di Napoli "Federico II", 80131, Napoli, Italy
| | - Mariano Fiorenza
- Dipartimento Scienze Mediche Traslazionali, Università di Napoli "Federico II", 80131, Napoli, Italy
| | - Daniela Terracciano
- Dipartimento Scienze Mediche Traslazionali, Università di Napoli "Federico II", 80131, Napoli, Italy
| | - Raffaella Pasquale
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione Giovanni Pascale", IRCCS, Via Mariano Semmola, 80131, Napoli, Italy
| | - Francesca Bergantino
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione Giovanni Pascale", IRCCS, Via Mariano Semmola, 80131, Napoli, Italy
| | - Ernesta Cavalcanti
- Laboratory Medicine Unit, Istituto Nazionale Tumori-IRCCS "Fondazione G. Pascale", 80131, Napoli, Italy
| | - Gerardo Botti
- Scientific Direction, Istituto Nazionale Tumori-Irccs-Fondazione G. Pascale, 80131, Napoli, Italy
| | - Gabriele Vaccari
- ISS-Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161, Rome, Italy
| | - Giuseppe Portella
- Dipartimento Scienze Mediche Traslazionali, Università di Napoli "Federico II", 80131, Napoli, Italy
| | - Nicola Normanno
- Cell Biology and Biotherapy Unit, Istituto Nazionale Tumori "Fondazione Giovanni Pascale", IRCCS, Via Mariano Semmola, 80131, Napoli, Italy.
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27
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Potdar V, Vipat V, Ramdasi A, Jadhav S, Pawar-Patil J, Walimbe A, Patil SS, Choudhury ML, Shastri J, Agrawal S, Pawar S, Lole K, Abraham P, Cherian S. Phylogenetic classification of the whole-genome sequences of SARS-CoV-2 from India & evolutionary trends. Indian J Med Res 2021; 153:166-174. [PMID: 33818474 PMCID: PMC8184080 DOI: 10.4103/ijmr.ijmr_3418_20] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND & OBJECTIVES Several phylogenetic classification systems have been devised to trace the viral lineages of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). However, inconsistency in the nomenclature limits uniformity in its epidemiological understanding. This study provides an integration of existing classifications and describes evolutionary trends of the SARS-CoV-2 strains circulating in India. METHODS The whole genomes of 330 SARS-CoV-2 samples were sequenced using next-generation sequencing (NGS). Phylogenetic and sequence analysis of a total of 3014 Indian SARS-CoV-2 sequences from 20 different States/Union Territories (January to September 2020) from the Global Initiative on Sharing All Influenza Data (GISAID) database was performed to observe the clustering of Nextstrain and Phylogenetic Assignment of Named Global Outbreak LINeages (Pangolin) lineages with the GISAID clades. The identification of mutational sites under selection pressure was performed using Mixed Effects Model of Evolution and Single-Likelihood Ancestor Counting methods available in the Datamonkey server. RESULTS Temporal data of the Indian SARS-CoV-2 genomes revealed that except for Uttarakhand, West Bengal and Haryana that showed the circulation of GISAID clade O even after July 2020, the rest of the States showed a complete switch to GR/GH clades. Pangolin lineages B.1.1.8 and B.1.113 identified within GR and GH clades, respectively, were noted to be indigenous evolutions. Sites identified to be under positive selection pressure within these clades were found to occur majorly in the non-structural proteins coded by ORF1a and ORF1b. INTERPRETATION & CONCLUSIONS This study interpreted the geographical and temporal dominance of SARS-CoV-2 strains in India over a period of nine months based on the GISAID classification. An integration of the GISAID, Nextstrain and Pangolin classifications is also provided. The emergence of new lineages B.1.1.8 and B.1.113 was indicative of host-specific evolution of the SARS-CoV-2 strains in India. The hotspot mutations such as those driven by positive selection need to be further characterized.
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Affiliation(s)
- Varsha Potdar
- Influenza Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Veena Vipat
- Influenza Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Ashwini Ramdasi
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Santosh Jadhav
- Bioinformatics & Data Management Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | | | - Atul Walimbe
- Bioinformatics & Data Management Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Sucheta S. Patil
- Bioinformatics & Data Management Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | | | - Jayanthi Shastri
- Department of Microbiology, Topiwala National Medical College & B.Y.L. Nair Charitable Hospital, Mumbai, Maharashtra, India
| | - Sachee Agrawal
- Department of Microbiology, Topiwala National Medical College & B.Y.L. Nair Charitable Hospital, Mumbai, Maharashtra, India
| | - Shailesh Pawar
- ICMR-National Institute of Virology, Mumbai Unit, Mumbai, Maharashtra, India
| | - Kavita Lole
- Hepatitis Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Priya Abraham
- ICMR-National Institute of Virology, Pune, Maharashtra, India
| | - Sarah Cherian
- Bioinformatics & Data Management Group, ICMR-National Institute of Virology, Pune, Maharashtra, India
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Tramuto F, Reale S, Lo Presti A, Vitale F, Pulvirenti C, Rezza G, Vitale F, Purpari G, Maida CM, Zichichi S, Scibetta S, Mazzucco W, Stefanelli P. Genomic Analysis and Lineage Identification of SARS-CoV-2 Strains in Migrants Accessing Europe Through the Libyan Route. Front Public Health 2021; 9:632645. [PMID: 33937168 PMCID: PMC8082074 DOI: 10.3389/fpubh.2021.632645] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2020] [Accepted: 02/15/2021] [Indexed: 12/03/2022] Open
Abstract
Many African countries, representing the origin of the majority of refugees, asylum-seekers, and other migrants, toward regions bordering on the Mediterranean area, are experiencing sustained local transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Sicily is one of the main entry gates of migrants crossing into Europe. We conducted a pilot study, based on the full-genome sequencing of SARS-CoV-2 strains isolated from migrants coming to Sicily by crossing the Mediterranean Sea, with the aim to investigate the viral genome polymorphism and to describe their genetic variations and the phylogenetic relationships. On June 21, a nongovernmental organization vessel rescued 210 migrants crossing the Mediterranean Sea from Libya to Sicily. Of them, 13.4% tested positive for SARS-CoV-2. Eighteen whole genome sequences were obtained to explore viral genetic variability. All but one of the sequences clustered with other viral African strains within the lineage A, whereas only one intermixed among B.1 lineage genomes. Our findings documented that most of the investigated migrants acquired SARS-CoV-2 infection before landing in Sicily. However, SARS-CoV-2 transmission during travel or in overcrowded Libyan immigrant camps and/or illegal transport boats could not be ruled out. SARS-CoV-2 molecular surveillance on migrants arriving in Europe through the Sicilian gate may improve the knowledge of global SARS-CoV-2 transmission dynamic also in light of the emergence of new variants.
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Affiliation(s)
- Fabio Tramuto
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D'Alessandro”, University of Palermo, Palermo, Italy
- Regional Reference Laboratory of Western Sicily for the Emergency of COVID-19, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, Palermo, Italy
| | - Stefano Reale
- Molecular Biology Area, Zoo-prophilactic Experimental Institute of Sicily “A. Mirri”, Palermo, Italy
| | | | - Francesco Vitale
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D'Alessandro”, University of Palermo, Palermo, Italy
- Regional Reference Laboratory of Western Sicily for the Emergency of COVID-19, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, Palermo, Italy
| | - Claudio Pulvirenti
- Uffici di sanità marittima, aerea e di frontiera (USMAF) – Servizi Assistenza Sanitaria Naviganti (SASN) Sicily, Ministry of Health, Directorate-General for Health Prevention, Rome, Italy
| | - Giovanni Rezza
- Directorate-General for Health Prevention, Ministry of Health, Rome, Italy
| | - Fabrizio Vitale
- Molecular Biology Area, Zoo-prophilactic Experimental Institute of Sicily “A. Mirri”, Palermo, Italy
| | - Giuseppa Purpari
- Virological Diagnostic Area, Zoo-prophilactic Experimental Institute of Sicily “A. Mirri”, Palermo, Italy
| | - Carmelo Massimo Maida
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D'Alessandro”, University of Palermo, Palermo, Italy
- Regional Reference Laboratory of Western Sicily for the Emergency of COVID-19, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, Palermo, Italy
| | - Salvatore Zichichi
- Uffici di sanità marittima, aerea e di frontiera (USMAF) – Servizi Assistenza Sanitaria Naviganti (SASN) Sicily, Ministry of Health, Directorate-General for Health Prevention, Rome, Italy
| | - Silvia Scibetta
- Molecular Biology Area, Zoo-prophilactic Experimental Institute of Sicily “A. Mirri”, Palermo, Italy
| | - Walter Mazzucco
- Department of Health Promotion, Mother and Child Care, Internal Medicine and Medical Specialties “G. D'Alessandro”, University of Palermo, Palermo, Italy
- Regional Reference Laboratory of Western Sicily for the Emergency of COVID-19, Clinical Epidemiology Unit, University Hospital “Paolo Giaccone”, Palermo, Italy
- Division of Biostatistics and Epidemiology, Cincinnati Children's Hospital Medical Centre, Cincinnati, OH, United States
| | - Paola Stefanelli
- Department of Infectious Diseases, National Health Institute, Rome, Italy
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29
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Elaswad A, Fawzy M. Mutations in Animal SARS-CoV-2 Induce Mismatches with the Diagnostic PCR Assays. Pathogens 2021; 10:371. [PMID: 33808783 PMCID: PMC8003424 DOI: 10.3390/pathogens10030371] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2021] [Revised: 03/15/2021] [Accepted: 03/16/2021] [Indexed: 02/06/2023] Open
Abstract
Recently, the severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) was detected in several animal species. After transmission to animals, the virus accumulates mutations in its genome as adaptation to the new animal host progresses. Therefore, we investigated whether these mutations result in mismatches with the diagnostic PCR assays and suggested proper modifications to the oligo sequences accordingly. A comprehensive bioinformatic analysis was conducted using 28 diagnostic PCR assays and 793 publicly available SARS-CoV-2 genomes isolated from animals. Sixteen out of the investigated 28 PCR assays displayed at least one mismatch with their targets at the 0.5% threshold. Mismatches were detected in seven, two, two, and six assays targeting the ORF1ab, spike, envelope, and nucleocapsid genes, respectively. Several of these mismatches, such as the deletions and mismatches at the 3' end of the primer or probe, are expected to negatively affect the diagnostic PCR assays resulting in false-negative results. The modifications to the oligo sequences should result in stronger template binding by the oligos, better sensitivity of the assays, and higher confidence in the result. It is necessary to monitor the targets of diagnostic PCR assays for any future mutations that may occur as the virus continues to evolve in animals.
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Affiliation(s)
- Ahmed Elaswad
- Department of Animal Wealth Development, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
| | - Mohamed Fawzy
- Department of Virology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia 41522, Egypt
- Middle East for Vaccines (ME VAC®), Sharquia 44813, Egypt
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30
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Sarkar R, Mitra S, Chandra P, Saha P, Banerjee A, Dutta S, Chawla-Sarkar M. Comprehensive analysis of genomic diversity of SARS-CoV-2 in different geographic regions of India: an endeavour to classify Indian SARS-CoV-2 strains on the basis of co-existing mutations. Arch Virol 2021; 166:801-812. [PMID: 33464421 PMCID: PMC7814186 DOI: 10.1007/s00705-020-04911-0] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 10/21/2020] [Indexed: 01/24/2023]
Abstract
Accumulation of mutations within the genome is the primary driving force in viral evolution within an endemic setting. This inherent feature often leads to altered virulence, infectivity and transmissibility, and antigenic shifts to escape host immunity, which might compromise the efficacy of vaccines and antiviral drugs. Therefore, we carried out a genome-wide analysis of circulating SARS-CoV-2 strains to detect the emergence of novel co-existing mutations and trace their geographical distribution within India. Comprehensive analysis of whole genome sequences of 837 Indian SARS-CoV-2 strains revealed the occurrence of 33 different mutations, 18 of which were unique to India. Novel mutations were observed in the S glycoprotein (6/33), NSP3 (5/33), RdRp/NSP12 (4/33), NSP2 (2/33), and N (1/33). Non-synonymous mutations were found to be 3.07 times more prevalent than synonymous mutations. We classified the Indian isolates into 22 groups based on their co-existing mutations. Phylogenetic analysis revealed that the representative strains of each group were divided into various sub-clades within their respective clades, based on the presence of unique co-existing mutations. The A2a clade was found to be dominant in India (71.34%), followed by A3 (23.29%) and B (5.36%), but a heterogeneous distribution was observed among various geographical regions. The A2a clade was highly predominant in East India, Western India, and Central India, whereas the A2a and A3 clades were nearly equal in prevalence in South and North India. This study highlights the divergent evolution of SARS-CoV-2 strains and co-circulation of multiple clades in India. Monitoring of the emerging mutations will pave the way for vaccine formulation and the design of antiviral drugs.
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Affiliation(s)
- Rakesh Sarkar
- grid.419566.90000 0004 0507 4551Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010 India
| | - Suvrotoa Mitra
- grid.419566.90000 0004 0507 4551Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010 India
| | - Pritam Chandra
- grid.419566.90000 0004 0507 4551Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010 India
| | - Priyanka Saha
- grid.419566.90000 0004 0507 4551Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010 India
| | - Anindita Banerjee
- grid.419566.90000 0004 0507 4551Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010 India
| | - Shanta Dutta
- grid.419566.90000 0004 0507 4551Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010 India
| | - Mamta Chawla-Sarkar
- grid.419566.90000 0004 0507 4551Division of Virology, National Institute of Cholera and Enteric Diseases, P-33, C.I.T. Road, Scheme-XM, Beliaghata, Kolkata, West Bengal 700010 India
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