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Castellano LA, McNamara RJ, Pallarés HM, Gamarnik AV, Alvarez DE, Bazzini AA. Dengue virus preferentially uses human and mosquito non-optimal codons. Mol Syst Biol 2024:10.1038/s44320-024-00052-7. [PMID: 39039212 DOI: 10.1038/s44320-024-00052-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Revised: 06/25/2024] [Accepted: 06/26/2024] [Indexed: 07/24/2024] Open
Abstract
Codon optimality refers to the effect that codon composition has on messenger RNA (mRNA) stability and translation level and implies that synonymous codons are not silent from a regulatory point of view. Here, we investigated the adaptation of virus genomes to the host optimality code using mosquito-borne dengue virus (DENV) as a model. We demonstrated that codon optimality exists in mosquito cells and showed that DENV preferentially uses nonoptimal (destabilizing) codons and avoids codons that are defined as optimal (stabilizing) in either human or mosquito cells. Human genes enriched in the codons preferentially and frequently used by DENV are upregulated during infection, and so is the tRNA decoding the nonoptimal and DENV preferentially used codon for arginine. We found that adaptation during single-host passaging in human or mosquito cells results in the selection of synonymous mutations towards DENV's preferred nonoptimal codons that increase virus fitness. Finally, our analyses revealed that hundreds of viruses preferentially use nonoptimal codons, with those infecting a single host displaying an even stronger bias, suggesting that host-pathogen interaction shapes virus-synonymous codon choice.
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Affiliation(s)
- Luciana A Castellano
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
| | - Ryan J McNamara
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
| | - Horacio M Pallarés
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires IIBBA-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Andrea V Gamarnik
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires IIBBA-CONICET, Ciudad Autónoma de Buenos Aires, Argentina
| | - Diego E Alvarez
- Instituto de Investigaciones Biotecnológicas, Universidad Nacional de San Martín-CONICET, San Martín B1650, Argentina
| | - Ariel A Bazzini
- Stowers Institute for Medical Research, 1000 E 50th Street, Kansas City, MO, 64110, USA.
- Department of Molecular and Integrative Physiology, University of Kansas Medical Center, 3901 Rainbow Blvd, Kansas City, KS, 66160, USA.
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2
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Manukyan H, Lal M, Zhu C, Singh O, Lin TL, Tritama E, Chumakov K, Lee SM, Laassri M. Application of MPBT Assay for Multiplex Determination of Infectious Titers and for Selection of the Optimal Formulation for the Trivalent Novel Oral Poliovirus Vaccine. Viruses 2024; 16:961. [PMID: 38932253 PMCID: PMC11209357 DOI: 10.3390/v16060961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 06/11/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
Recently, a multiplex PCR-based titration (MPBT) assay was developed for simultaneous determination of infectious titers of all three Sabin strains of the oral poliovirus vaccine (OPV) to replace the conventional CCID50 assay, which is both time-consuming and laborious. The MPBT assay was shown to be reproducible, robust and sensitive. The conventional and MPBT assays showed similar results and sensitivity. The MPBT assay can be completed in two to three days, instead of ten days for the conventional assay. To prevent attenuated vaccine strains of poliovirus from reversion to virulence, a novel, genetically stable OPV (nOPV) was developed by modifying the genomes of conventional Sabin strains used in OPV. In this work, we evaluated the MPBT assay as a rapid screening tool to support trivalent nOPV (tnOPV) formulation development by simultaneous titration of the three nOPV strains to confirm stability as needed, for the selection of the lead tnOPV formulation candidate. We first assessed the ability of the MPBT assay to discriminate a 0.5 log10 titer difference by titrating the two tnOPV samples (undiluted and threefold-diluted) on the same plate. Once the assay was shown to be discriminating, we then tested different formulations of tnOPV drug products (DPs) that were subjected to different exposure times at 37 °C (untreated group and treated groups: 2 and 7 days at 37 °C), and to three freeze and thaw (FT) cycles. Final confirmation of the down selected formulation candidates was achieved by performing the conventional CCID50 assay, comparing the stability of untreated and treated groups and FT stability testing on the top three candidates. The results showed that the MPBT assay generates similar titers as the conventional assay. By testing two trivalent samples in the same plate, the assay can differentiate a 0.5 log10 difference between the titers of the tested nOPV samples. Also, the assay was able to detect the gradual degradation of nOPV viruses with different formulation compositions and under different time/temperature conditions and freeze/thaw cycles. We found that there were three tnOPV formulations which met the stability criteria of less than 0.5 log10 loss after 2 days' exposure to 37 ℃ and after three FT cycles, maintaining the potency of all three serotypes in these formulations. The ability of the MPBT assay to titrate two tnOPV lots (six viruses) in the same plate makes it cheaper and gives it a higher throughput for rapid screening. The assay detected the gradual degradation of the tnOPV and was successful in the selection of optimal formulations for the tnOPV. The results demonstrated that the MPBT method can be used as a stability indicating assay to assess the thermal stability of the nOPV. It can be used for rapid virus titer determination during the vaccine manufacturing process, and in clinical trials. The MPBT assay can be automated and applied for other viruses, including those with no cytopathic effect.
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Affiliation(s)
- Hasmik Manukyan
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA; (H.M.); (O.S.); (T.-L.L.)
| | - Manjari Lal
- Center for Vaccine Innovation and Access, Program for Appropriate Technology in Health (PATH), Seattle, WA 98121, USA; (M.L.); (C.Z.); (S.-M.L.)
| | - Changcheng Zhu
- Center for Vaccine Innovation and Access, Program for Appropriate Technology in Health (PATH), Seattle, WA 98121, USA; (M.L.); (C.Z.); (S.-M.L.)
| | - Olga Singh
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA; (H.M.); (O.S.); (T.-L.L.)
| | - Tsai-Lien Lin
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA; (H.M.); (O.S.); (T.-L.L.)
| | - Erman Tritama
- Research and Development Division, PT Bio Farma, Bandung 40161, Indonesia;
| | - Konstantin Chumakov
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA; (H.M.); (O.S.); (T.-L.L.)
| | - Shwu-Maan Lee
- Center for Vaccine Innovation and Access, Program for Appropriate Technology in Health (PATH), Seattle, WA 98121, USA; (M.L.); (C.Z.); (S.-M.L.)
| | - Majid Laassri
- Center for Biologics Evaluation and Research, US Food and Drug Administration, 10903 New Hampshire Avenue, Silver Spring, MD 20993, USA; (H.M.); (O.S.); (T.-L.L.)
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Tan X, Xie Y, Jiang C, Li H, Lu Y, Shen W, Chen J. Codon usage bias of human papillomavirus type 33 and 58: A comprehensive analysis. J Basic Microbiol 2024; 64:e2300636. [PMID: 38346260 DOI: 10.1002/jobm.202300636] [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: 11/07/2023] [Revised: 01/08/2024] [Accepted: 01/20/2024] [Indexed: 05/03/2024]
Abstract
Cervical cancer is closely linked to specific strains of human papillomavirus (HPV), notably HPV-33 and HPV-58, which exhibit a significant prevalence among women in China. Nevertheless, the codon usage bias in HPV-33 and HPV-58 is not well comprehended. The objective of this research is to analyze the codon usage patterns HPV-33 and HPV-58, pinpoint the primary factors that influence codon preference. The overall preference for codon usage in two HPV genotypes is not significant. Both HPV genotypes exhibit a preference for codons that end with A/U. The GC3 content for HPV-33 is 25.43% ± 0.35%, and for HPV-58, it is 29.44% ± 0.57%. Out of the 26 favored codons in HPV-33 and HPV-58 (relative synonymous codon usage (RSCU) > 1), 25 conclude with A/U. Principal component analysis (PCA) shows a tight clustering of the entire genome sequences of HPV-33 and HPV-58, suggesting a similarity in their RSCU preferences. Moreover, an examination of dinucleotide abundance indicated that translation selection influenced the development of a distinctive dinucleotide usage pattern in HPV-33 and HPV-58. Additionally, a combined analysis involving an effective number of codons plot, parity rule 2, and neutrality analysis demonstrated that, for HPV-33 and HPV-58, the primary determinant influencing codon usage preference is natural selection. HPV-33 and HPV-58 exhibit a restricted set of favored codons in common with humans, potentially mitigating competition for translation resources. Our discoveries could provide valuable perspectives on the evolutionary patterns and codon usage preferences of HPV-33 and HPV-58 viruses, contributing to the development and application of relevant HPV subtype vaccines.
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Affiliation(s)
- Xiaochun Tan
- Department of Laboratory Medicine, The First Hospital of Jiaxing, Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Yucheng Xie
- Department of Laboratory Medicine, The First Hospital of Jiaxing, Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Chaoyue Jiang
- Department of Laboratory Medicine, The First Hospital of Jiaxing, Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Hui Li
- Department of Laboratory Medicine, The First Hospital of Jiaxing, Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Yu Lu
- Department of Laboratory Medicine, The First Hospital of Jiaxing, Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Weifeng Shen
- Department of Laboratory Medicine, The First Hospital of Jiaxing, Affiliated Hospital of Jiaxing University, Jiaxing, China
| | - Jing Chen
- Department of Laboratory Medicine, The First Hospital of Jiaxing, Affiliated Hospital of Jiaxing University, Jiaxing, China
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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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de Andrade KQ, Cirne-Santos CC. Antiviral Activity of Zinc Finger Antiviral Protein (ZAP) in Different Virus Families. Pathogens 2023; 12:1461. [PMID: 38133344 PMCID: PMC10747524 DOI: 10.3390/pathogens12121461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/14/2023] [Accepted: 12/15/2023] [Indexed: 12/23/2023] Open
Abstract
The CCCH-type zinc finger antiviral protein (ZAP) in humans, specifically isoforms ZAP-L and ZAP-S, is a crucial component of the cell's intrinsic immune response. ZAP acts as a post-transcriptional RNA restriction factor, exhibiting its activity during infections caused by retroviruses and alphaviruses. Its function involves binding to CpG (cytosine-phosphate-guanine) dinucleotide sequences present in viral RNA, thereby directing it towards degradation. Since vertebrate cells have a suppressed frequency of CpG dinucleotides, ZAP is capable of distinguishing foreign genetic elements. The expression of ZAP leads to the reduction of viral replication and impedes the assembly of new virus particles. However, the specific mechanisms underlying these effects have yet to be fully understood. Several questions regarding ZAP's mechanism of action remain unanswered, including the impact of CpG dinucleotide quantity on ZAP's activity, whether this sequence is solely required for the binding between ZAP and viral RNA, and whether the recruitment of cofactors is dependent on cell type, among others. This review aims to integrate the findings from studies that elucidate ZAP's antiviral role in various viral infections, discuss gaps that need to be filled through further studies, and shed light on new potential targets for therapeutic intervention.
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Affiliation(s)
- Kívia Queiroz de Andrade
- Laboratory of Immunology of Infectious Disease, Immunology Department, Institute of Biomedical Sciences, University of São Paulo, São Paulo 05508-000, SP, Brazil
| | - Claudio Cesar Cirne-Santos
- Laboratory of Molecular Virology and Marine Biotechnology, Department of Cellular and Molecular Biology, Institute of Biology, Federal Fluminense University, Niterói 24020-150, RJ, Brazil
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6
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Forni D, Pozzoli U, Cagliani R, Clerici M, Sironi M. Dinucleotide biases in RNA viruses that infect vertebrates or invertebrates. Microbiol Spectr 2023; 11:e0252923. [PMID: 37800906 PMCID: PMC10714974 DOI: 10.1128/spectrum.02529-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 08/12/2023] [Indexed: 10/07/2023] Open
Abstract
IMPORTANCE Akin to a molecular signature, dinucleotide composition can be exploited by the zinc-finger antiviral protein (ZAP) to restrict CpG-rich (and UpA-rich) RNA viruses. ZAP evolved in tetrapods, and it is not encoded by invertebrates and fish. Because a systematic analysis is missing, we analyzed the genomes of RNA viruses that infect vertebrates or invertebrates. We show that vertebrate single-stranded (ss) RNA(+) viruses and, to a lesser extent, double-stranded RNA viruses tend to have stronger CpG bias than invertebrate viruses. Conversely, ssRNA(-) viruses have similar dinucleotide composition whether they infect vertebrates or invertebrates. Analysis of ssRNA(+) viruses that infect mammals, reptiles, and fish indicated that ZAP is unlikely to be a major driver of CpG depletion. We also show that, compared to other coronaviruses, the genome of SARS-CoV-2 is not homogeneously CpG-depleted. Our study provides new insights into virus evolution and strategies for recoding RNA virus genomes.
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Affiliation(s)
- Diego Forni
- Bioinformatics Lab, Scientific Institute IRCCS E. MEDEA, Bosisio Parini, Italy
| | - Uberto Pozzoli
- Bioinformatics Lab, Scientific Institute IRCCS E. MEDEA, Bosisio Parini, Italy
| | - Rachele Cagliani
- Bioinformatics Lab, Scientific Institute IRCCS E. MEDEA, Bosisio Parini, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy
- Don C. Gnocchi Foundation ONLUS, IRCCS, Milan, Italy
| | - Manuela Sironi
- Bioinformatics Lab, Scientific Institute IRCCS E. MEDEA, Bosisio Parini, Italy
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Anwar AM, Bayoumi S, Elzalabany S, Magdeldin S, Ahmed AE. parazitCUB: An R package to streamline the process of investigating the adaptations of parasites' codon usage bias. F1000Res 2023; 12:1431. [PMID: 38021405 PMCID: PMC10682597 DOI: 10.12688/f1000research.143223.1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Examining the intricate association between parasites and their hosts, particularly at the codon level, assumes paramount importance in comprehending evolutionary processes and forecasting the characteristics of novel parasites. While diverse metrics and statistical analyses are available to explore codon usage bias (CUB), there presently exists no dedicated tool for examining the co-adaptation of codon usage between parasites and hosts. Therefore, we introduce the parazitCUB R package to address this challenge in a scalable and efficient manner, as it is capable of handling extensive datasets and simultaneously analyzing of multiple parasites with optimized performance. parazitCUB enables the elucidation of parasite-host interactions and the evolutionary patterns of parasites through the implementation of various indices, cluster analysis, multivariate analysis, and data visualization techniques. The tool can be accessed at the following location: https://github.com/AliYoussef96/parazitCUB.
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Affiliation(s)
- Ali Mostafa Anwar
- Biotechnology and Life Sciences Department, Faculty of Postgraduate Studies for Advanced Sciences, Beni-Suef University, Beni-Suef, Egypt
| | - Salma Bayoumi
- Biochemistry Department, Faculty of Science, Alexandria University, Alexandria, Alexandria Governorate, Egypt
| | - Sagy Elzalabany
- Biomedical Equipment Department, Badr University in Cairo, Badr City, Cairo Governorate, Egypt
| | - Sameh Magdeldin
- Department of Physiology, Faculty of Veterinary Medicine, Suez Canal University, Ismailia, Ismailia Governorate, Egypt
- Basic Research Department, Children’s Cancer Hospital 57357, Cairo, Egypt, Cairo, Egypt
| | - Amr E. Ahmed
- Biotechnology and Life Sciences Department, Faculty of Postgraduate Studies for Advanced Sciences, Beni-Suef University, Beni-Suef, Egypt
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8
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Molteni C, Forni D, Cagliani R, Bravo IG, Sironi M. Evolution and diversity of nucleotide and dinucleotide composition in poxviruses. J Gen Virol 2023; 104. [PMID: 37792576 DOI: 10.1099/jgv.0.001897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/06/2023] Open
Abstract
Poxviruses (family Poxviridae) have long dsDNA genomes and infect a wide range of hosts, including insects, birds, reptiles and mammals. These viruses have substantial incidence, prevalence and disease burden in humans and in other animals. Nucleotide and dinucleotide composition, mostly CpG and TpA, have been largely studied in viral genomes because of their evolutionary and functional implications. We analysed here the nucleotide and dinucleotide composition, as well as codon usage bias, of a set of representative poxvirus genomes, with a very diverse host spectrum. After correcting for overall nucleotide composition, entomopoxviruses displayed low overall GC content, no enrichment in TpA and large variation in CpG enrichment, while chordopoxviruses showed large variation in nucleotide composition, no obvious depletion in CpG and a weak trend for TpA depletion in GC-rich genomes. Overall, intergenome variation in dinucleotide composition in poxviruses is largely accounted for by variation in overall genomic GC levels. Nonetheless, using vaccinia virus as a model, we found that genes expressed at the earliest times in infection are more CpG-depleted than genes expressed at later stages. This observation has parallels in betahepesviruses (also large dsDNA viruses) and suggests an antiviral role for the innate immune system (e.g. via the zinc-finger antiviral protein ZAP) in the early phases of poxvirus infection. We also analysed codon usage bias in poxviruses and we observed that it is mostly determined by genomic GC content, and that stratification after host taxonomy does not contribute to explaining codon usage bias diversity. By analysis of within-species diversity, we show that genomic GC content is the result of mutational biases. Poxvirus genomes that encode a DNA ligase are significantly AT-richer than those that do not, suggesting that DNA repair systems shape mutation biases. Our data shed light on the evolution of poxviruses and inform strategies for their genetic manipulation for therapeutic purposes.
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Affiliation(s)
- Cristian Molteni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Diego Forni
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
| | - Ignacio G Bravo
- Laboratoire MIVEGEC (Univ Montpellier CNRS, IRD), Centre National de la Recherche Scientifique, Montpellier, France
| | - Manuela Sironi
- Scientific Institute IRCCS E. MEDEA, Bioinformatics, Bosisio Parini, Italy
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Yu-Ping Z, Jing L, Teng H, Zhi-Fang Y, Ting Z, Yan-Chun C, Zhi-Mei Z, Yu-Ting F, Jun-Hui T, Qing-Hai Y, Ding-Kai W, Guo-Liang L, Xiao-Lei Y, Li Y, Hong-Bo C, Jian-Feng W, Rui-Ju J, Lei Y, Wei C, Wei Y, Ming-Xue X, Qiong-Zhou Y, Jing P, Li S, Chao H, Yan D, Lu-Kui C, Jian Z, Yu W, Hong-Sen L, Wei H, Zhao-Jun M, Chang-Gui L, Qi-Han L, Jing-Si Y. Evaluation of the immunization effectiveness of bOPV booster immunization and IPV revaccination. NPJ Vaccines 2023; 8:44. [PMID: 36934085 PMCID: PMC10024706 DOI: 10.1038/s41541-023-00642-w] [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: 09/05/2022] [Accepted: 03/07/2023] [Indexed: 03/20/2023] Open
Abstract
To provide a basis for further optimization of the polio sequential immunization schedule, this study evaluated the effectiveness of booster immunization with one dose of bivalent oral poliovirus vaccine (bOPV) at 48 months of age after different primary polio immunization schedules. At 48 months of age, one dose of bOPV was administered, and their poliovirus types 1-3 (PV1, PV2, and PV3, respectively)-specific neutralizing antibody levels were determined. Participants found to be negative for any type of PV-specific neutralizing antibody at 24, 36, or 48 months of age were re-vaccinated with inactivated polio vaccine (IPV). The 439 subjects who received a bOPV booster immunization at the age of 48 months had lower PV2-specific antibody levels compared with those who received IPV. One dose of IPV during basic polio immunization induced the lowest PV2-specific antibody levels. On the basis of our findings, to ensure that no less than 70% of the vaccinated have protection efficiency, we recommend the following: if basic immunization was conducted with 1IPV + 2bOPV (especially Sabin strain-based IPV), a booster immunization with IPV is recommended at 36 months of age, whereas if basic immunization was conducted with 2IPV + 1bOPV, a booster immunization with IPV is recommended at 48 months of age. A sequential immunization schedule of 2IPV + 1bOPV + 1IPV can not only maintain high levels of antibody against PV1 and PV3 but also increases immunity to PV2 and induces early intestinal mucosal immunity, with relatively good safety. Thus, this may be the best sequential immunization schedule for polio in countries or regions at high risk for polio.
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Affiliation(s)
- Zhao Yu-Ping
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China
- National Local Joint Engineering Research Center for Biological Products of Viral Infectious Diseases, Kunming, China
- Kunming Science and Technology Innovation Centre for Research, Development and Industrialization of New Outbreaks and Emerging Highly Pathogenic Pathogens Vaccines, Kunming, China
| | - Li Jing
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China
- National Local Joint Engineering Research Center for Biological Products of Viral Infectious Diseases, Kunming, China
- Kunming Science and Technology Innovation Centre for Research, Development and Industrialization of New Outbreaks and Emerging Highly Pathogenic Pathogens Vaccines, Kunming, China
| | - Huang Teng
- GuangXi Province Center for Disease Prevention and Control, Nanning, China
| | - Ying Zhi-Fang
- National Institutes for Food and Drug Control, Beijing, China
| | - Zhao Ting
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China
- National Local Joint Engineering Research Center for Biological Products of Viral Infectious Diseases, Kunming, China
- Kunming Science and Technology Innovation Centre for Research, Development and Industrialization of New Outbreaks and Emerging Highly Pathogenic Pathogens Vaccines, Kunming, China
| | - Che Yan-Chun
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China
| | - Zhao Zhi-Mei
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China
| | - Fu Yu-Ting
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China
| | - Tao Jun-Hui
- Liujiang District Center for Disease Prevention and Control, Liuzhou, China
| | - Yang Qing-Hai
- Liucheng County Center for Disease Prevention and Control, Liuzhou, China
| | - Wei Ding-Kai
- Rong'an County Center for Disease Prevention and Control, Liuzhou, China
| | - Li Guo-Liang
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China
- National Local Joint Engineering Research Center for Biological Products of Viral Infectious Diseases, Kunming, China
- Kunming Science and Technology Innovation Centre for Research, Development and Industrialization of New Outbreaks and Emerging Highly Pathogenic Pathogens Vaccines, Kunming, China
| | - Yang Xiao-Lei
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China
- National Local Joint Engineering Research Center for Biological Products of Viral Infectious Diseases, Kunming, China
- Kunming Science and Technology Innovation Centre for Research, Development and Industrialization of New Outbreaks and Emerging Highly Pathogenic Pathogens Vaccines, Kunming, China
| | - Yi Li
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China
- National Local Joint Engineering Research Center for Biological Products of Viral Infectious Diseases, Kunming, China
- Kunming Science and Technology Innovation Centre for Research, Development and Industrialization of New Outbreaks and Emerging Highly Pathogenic Pathogens Vaccines, Kunming, China
| | - Chen Hong-Bo
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China
- National Local Joint Engineering Research Center for Biological Products of Viral Infectious Diseases, Kunming, China
| | - Wang Jian-Feng
- National Institutes for Food and Drug Control, Beijing, China
| | - Jiang Rui-Ju
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China
| | - Yu Lei
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China
- National Local Joint Engineering Research Center for Biological Products of Viral Infectious Diseases, Kunming, China
| | - Cai Wei
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China
- National Local Joint Engineering Research Center for Biological Products of Viral Infectious Diseases, Kunming, China
| | - Yang Wei
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China
- National Local Joint Engineering Research Center for Biological Products of Viral Infectious Diseases, Kunming, China
| | - Xie Ming-Xue
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China
- National Local Joint Engineering Research Center for Biological Products of Viral Infectious Diseases, Kunming, China
| | - Yin Qiong-Zhou
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China
| | - Pu Jing
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China
| | - Shi Li
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China
| | - Hong Chao
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China
| | - Deng Yan
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China
- National Local Joint Engineering Research Center for Biological Products of Viral Infectious Diseases, Kunming, China
| | - Cai Lu-Kui
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China
- National Local Joint Engineering Research Center for Biological Products of Viral Infectious Diseases, Kunming, China
- Kunming Science and Technology Innovation Centre for Research, Development and Industrialization of New Outbreaks and Emerging Highly Pathogenic Pathogens Vaccines, Kunming, China
| | - Zhou Jian
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China
| | - Wen Yu
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China
- National Local Joint Engineering Research Center for Biological Products of Viral Infectious Diseases, Kunming, China
| | - Li Hong-Sen
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China
- National Local Joint Engineering Research Center for Biological Products of Viral Infectious Diseases, Kunming, China
- Kunming Science and Technology Innovation Centre for Research, Development and Industrialization of New Outbreaks and Emerging Highly Pathogenic Pathogens Vaccines, Kunming, China
| | - Huang Wei
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China
- National Local Joint Engineering Research Center for Biological Products of Viral Infectious Diseases, Kunming, China
- Kunming Science and Technology Innovation Centre for Research, Development and Industrialization of New Outbreaks and Emerging Highly Pathogenic Pathogens Vaccines, Kunming, China
| | - Mo Zhao-Jun
- GuangXi Province Center for Disease Prevention and Control, Nanning, China.
| | - Li Chang-Gui
- National Institutes for Food and Drug Control, Beijing, China.
| | - Li Qi-Han
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China.
- National Local Joint Engineering Research Center for Biological Products of Viral Infectious Diseases, Kunming, China.
| | - Yang Jing-Si
- Institute of Medical Biology, Chinese Academy of Medical Science & Peking Union Medical College, Kunming, China.
- National Local Joint Engineering Research Center for Biological Products of Viral Infectious Diseases, Kunming, China.
- Kunming Science and Technology Innovation Centre for Research, Development and Industrialization of New Outbreaks and Emerging Highly Pathogenic Pathogens Vaccines, Kunming, China.
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10
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Picard MAL, Leblay F, Cassan C, Willemsen A, Daron J, Bauffe F, Decourcelle M, Demange A, Bravo IG. Transcriptomic, proteomic, and functional consequences of codon usage bias in human cells during heterologous gene expression. Protein Sci 2023; 32:e4576. [PMID: 36692287 PMCID: PMC9926478 DOI: 10.1002/pro.4576] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2022] [Revised: 01/12/2023] [Accepted: 01/14/2023] [Indexed: 01/25/2023]
Abstract
Differences in codon frequency between genomes, genes, or positions along a gene, modulate transcription and translation efficiency, leading to phenotypic and functional differences. Here, we present a multiscale analysis of the effects of synonymous codon recoding during heterologous gene expression in human cells, quantifying the phenotypic consequences of codon usage bias at different molecular and cellular levels, with an emphasis on translation elongation. Six synonymous versions of an antibiotic resistance gene were generated, fused to a fluorescent reporter, and independently expressed in HEK293 cells. Multiscale phenotype was analyzed by means of quantitative transcriptome and proteome assessment, as proxies for gene expression; cellular fluorescence, as a proxy for single-cell level expression; and real-time cell proliferation in absence or presence of antibiotic, as a proxy for the cell fitness. We show that differences in codon usage bias strongly impact the molecular and cellular phenotype: (i) they result in large differences in mRNA levels and protein levels, leading to differences of over 15 times in translation efficiency; (ii) they introduce unpredicted splicing events; (iii) they lead to reproducible phenotypic heterogeneity; and (iv) they lead to a trade-off between the benefit of antibiotic resistance and the burden of heterologous expression. In human cells in culture, codon usage bias modulates gene expression by modifying mRNA availability and suitability for translation, leading to differences in protein levels and eventually eliciting functional phenotypic changes.
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Affiliation(s)
- Marion A. L. Picard
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Fiona Leblay
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Cécile Cassan
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Anouk Willemsen
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Josquin Daron
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Frédérique Bauffe
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Mathilde Decourcelle
- BioCampus Montpellier (University of Montpellier, CNRS, INSERM)MontpellierFrance
| | - Antonin Demange
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
| | - Ignacio G. Bravo
- French National Center for Scientific ResearchLaboratory MIVEGEC (CNRS, IRD, University of Montpellier)MontpellierFrance
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11
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Gurjar P, Karuvantevida N, Rzhepakovsky IV, Khan AA, Khandia R. A Synthetic Biology Approach for Vaccine Candidate Design against Delta Strain of SARS-CoV-2 Revealed Disruption of Favored Codon Pair as a Better Strategy over Using Rare Codons. Vaccines (Basel) 2023; 11:vaccines11020487. [PMID: 36851364 PMCID: PMC9967482 DOI: 10.3390/vaccines11020487] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Revised: 02/13/2023] [Accepted: 02/17/2023] [Indexed: 02/22/2023] Open
Abstract
The SARS-CoV-2 delta variant (B.1.617.2) appeared for the first time in December 2020 and later spread worldwide. Currently available vaccines are not so efficacious in curbing the viral pathogenesis of the delta strain of COVID; therefore, the development of a safe and effective vaccine is required. In the present study, we envisaged molecular patterns in the structural genes' spike, nucleoprotein, membrane, and envelope of the SARS-CoV-2 delta variant. The study was based on determining compositional features, dinucleotide odds ratio, synonymous codon usage, positive and negative codon contexts, rare codons, and insight into relatedness between the human host isoacceptor tRNA and preferred codons from the structural genes. We found specific patterns, including a significant abundance of T nucleotide over all other three nucleotides. The underrepresentation of GpA, GpG, CpC, and CpG dinucleotides and the overrepresentation of TpT, ApA, CpT, and TpG were observed. A preference towards ACT- (Thr), AAT- (Asn), TTT- (Phe), and TTG- (Leu) initiated codons and aversion towards CGG (Arg), CCG (Pro), and CAC (His) was present in the structural genes of the delta strain. The interaction between the host tRNA pool and preferred codons of the envisaged structural genes revealed that the virus preferred the codons for those suboptimal numbers of isoacceptor tRNA were present. We see this as a strategy adapted by the virus to keep the translation rate low to facilitate the correct folding of viral proteins. The information generated in the study helps design the attenuated vaccine candidate against the SARS-CoV-2 delta variant using a synthetic biology approach. Three strategies were tested: changing TpT to TpA, introducing rare codons, and disrupting favored codons. It found that disrupting favored codons is a better approach to reducing virus fitness and attenuating SARS-CoV-2 delta strain using structural genes.
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Affiliation(s)
- Pankaj Gurjar
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, NSW 2770, Australia
| | - Noushad Karuvantevida
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai P.O. Box 505055, United Arab Emirates
| | | | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
- Correspondence: (A.A.K.); or (R.K.)
| | - Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah Universty, Bhopal 462026, India
- Correspondence: (A.A.K.); or (R.K.)
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12
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Polio and Its Epidemiology. Infect Dis (Lond) 2023. [DOI: 10.1007/978-1-0716-2463-0_839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/10/2023] Open
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13
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Wang X, Sun J, Lu L, Pu FY, Zhang DR, Xie FQ. Evolutionary dynamics of codon usages for peste des petits ruminants virus. Front Vet Sci 2022; 9:968034. [PMID: 36032280 PMCID: PMC9412750 DOI: 10.3389/fvets.2022.968034] [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: 06/14/2022] [Accepted: 07/25/2022] [Indexed: 11/13/2022] Open
Abstract
Peste des petits ruminants virus (PPRV) is an important agent of contagious, acute and febrile viral diseases in small ruminants, while its evolutionary dynamics related to codon usage are still lacking. Herein, we adopted information entropy, the relative synonymous codon usage values and similarity indexes and codon adaptation index to analyze the viral genetic features for 45 available whole genomes of PPRV. Some universal, lineage-specific, and gene-specific genetic features presented by synonymous codon usages of the six genes of PPRV that encode N, P, M, F, H and L proteins reflected evolutionary plasticity and independence. The high adaptation of PPRV to hosts at codon usages reflected high viral gene expression, but some synonymous codons that are rare in the hosts were selected in high frequencies in the viral genes. Another obvious genetic feature was that the synonymous codons containing CpG dinucleotides had weak tendencies to be selected in viral genes. The synonymous codon usage patterns of PPRV isolated during 2007–2008 and 2013–2014 in China displayed independent evolutionary pathway, although the overall codon usage patterns of these PPRV strains matched the universal codon usage patterns of lineage IV. According to the interplay between nucleotide and synonymous codon usages of the six genes of PPRV, the evolutionary dynamics including mutation pressure and natural selection determined the viral survival and fitness to its host.
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Affiliation(s)
- Xin Wang
- School of Stomatology, Lanzhou University, Lanzhou, China
| | - Jing Sun
- Geriatrics Department, The Second Hospital of Lanzhou University, Lanzhou, China
| | - Lei Lu
- School of Stomatology, Lanzhou University, Lanzhou, China
| | - Fei-yang Pu
- Center for Biomedical Research, Northwest Minzu University, Lanzhou, China
| | - De-rong Zhang
- Center for Biomedical Research, Northwest Minzu University, Lanzhou, China
| | - Fu-qiang Xie
- Maxillofacial Surgery Department, The Second Hospital of Lanzhou University, Lanzhou, China
- *Correspondence: Fu-qiang Xie
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14
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Udenze D, Trus I, Berube N, Karniychuk U. CpG content in the Zika virus genome affects infection phenotypes in the adult brain and fetal lymph nodes. Front Immunol 2022; 13:943481. [PMID: 35983032 PMCID: PMC9379343 DOI: 10.3389/fimmu.2022.943481] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Accepted: 07/11/2022] [Indexed: 11/13/2022] Open
Abstract
Increasing the number of CpG dinucleotides in RNA viral genomes, while preserving the original amino acid composition, leads to impaired infection which does not cause disease. Beneficially, impaired infection evokes antiviral host immune responses providing a cutting-edge vaccine approach. For example, we previously showed that CpG-enriched Zika virus variants cause attenuated infection phenotypes and protect against lethal challenge in mice. While CpG recoding is an emerging and promising vaccine approach, little is known about infection phenotypes caused by recoded viruses in vivo, particularly in non-rodent species. Here, we used well-established mouse and porcine models to study infection phenotypes of the CpG-enriched neurotropic and congenital virus—Zika virus, directly in the target tissues—the brain and placenta. Specifically, we used the uttermost challenge and directly injected mice intracerebrally to compare infection phenotypes caused by wild-type and two CpG-recoded Zika variants and model the scenario where vaccine strains breach the blood-brain barrier. Also, we directly injected porcine fetuses to compare in utero infection phenotypes and model the scenario where recoded vaccine strains breach the placental barrier. While overall infection kinetics were comparable between wild-type and recoded virus variants, we found convergent phenotypical differences characterized by reduced pathology in the mouse brain and reduced replication of CpG-enriched variants in fetal lymph nodes. Next, using next-generation sequencing for the whole virus genome, we compared the stability of de novo introduced CpG dinucleotides during prolonged virus infection in the brain and placenta. Most de novo introduced CpG dinucleotides were preserved in sequences of recoded Zika viruses showing the stability of vaccine variants. Altogether, our study emphasized further directions to fine-tune the CpG recoding vaccine approach for better safety and can inform future immunization strategies.
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Affiliation(s)
- Daniel Udenze
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
- School of Public Health, University of Saskatchewan, Saskatoon, SK, Canada
| | - Ivan Trus
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
- Dioscuri Centre for RNA-Protein Interactions in Human Health and Disease, International Institute of Molecular and Cell Biology, Warsaw, Poland
| | - Nathalie Berube
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
| | - Uladzimir Karniychuk
- Vaccine and Infectious Disease Organization (VIDO), University of Saskatchewan, Saskatoon, SK, Canada
- School of Public Health, University of Saskatchewan, Saskatoon, SK, Canada
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
- *Correspondence: Uladzimir Karniychuk,
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15
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Jaglan A, Satija S, Singh D, Phartyal R, Verma M. Intra-genomic heterogeneity in CpG dinucleotide composition in dengue virus. Acta Trop 2022; 232:106501. [PMID: 35513073 DOI: 10.1016/j.actatropica.2022.106501] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Revised: 04/29/2022] [Accepted: 05/01/2022] [Indexed: 11/01/2022]
Abstract
PURPOSE Dengue virus is a life-threatening virus and cases of dengue infection have been increasing steadily in the past decades causing millions of deaths every year. So far, there is no vaccine that works effectively on all serotypes. Recently, CpG-recoded vaccines have proved to be effective against few viruses. METHODS In this study, evaluation and interpretation of more than 4547 Dengue virus genome sequences were included for analyzing novel CpG dinucleotides rich regions which are shared amid all serotypes. Genomic regions of DENV were synonymously CpG recoded using in silico methods and analyzed for adaptation in both human and Aedes spp. hosts based on CAI scores. RESULTS The analysis mirrored that serotypes 1, 3, and 4 shared CpG islands present in common regions. DENV-2 CpG islands showed no similarity with any of the CpG islands present in other serotypes. While DENV-3 sequences were found to possess the maximum number of conserved CpG islands stretches; DENV-2 was found to possess the lowest number. We found that all serotypes (with an exception of serotype 2) have CpG island in their 3' UTR. In silico CpG recoding of DENV genomic regions resulted in ∼ 3 fold increase of CpG dinucleotide frequency and comparative analysis based on CAI scores showed decreased adaptive fitness of CpG recoded DENV inside human host. CONCLUSION These CG-dinucleotide-enriched RNA sequences can be targeted by ZAP (zinc-finger antiviral protein) which can differentiate between host mRNA and viral mRNA. Our in silico findings can further be exploited for CpG-recoding of DENV genomes which can evoke cellular and humoral immune responses by recruiting ZAP-induced RNA degradation machinery and hence providing a promising approach for vaccine development.
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16
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K.C N, Noatia L, Priyadarshini S, M P, Gali JM, Ali MA, Behera S, Sharma B, Roychoudhury P, Kumar A, Behera P. Recoding anaerobic regulator fnr of Salmonella Typhimurium attenuates it's pathogenicity. Microb Pathog 2022; 168:105591. [DOI: 10.1016/j.micpath.2022.105591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Revised: 05/12/2022] [Accepted: 05/13/2022] [Indexed: 11/28/2022]
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17
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Gaunt ER, Digard P. Compositional biases in RNA viruses: Causes, consequences and applications. WILEY INTERDISCIPLINARY REVIEWS. RNA 2022; 13:e1679. [PMID: 34155814 PMCID: PMC8420353 DOI: 10.1002/wrna.1679] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Revised: 05/29/2021] [Accepted: 05/31/2021] [Indexed: 01/05/2023]
Abstract
If each of the four nucleotides were represented equally in the genomes of viruses and the hosts they infect, each base would occur at a frequency of 25%. However, this is not observed in nature. Similarly, the order of nucleotides is not random (e.g., in the human genome, guanine follows cytosine at a frequency of ~0.0125, or a quarter the number of times predicted by random representation). Codon usage and codon order are also nonrandom. Furthermore, nucleotide and codon biases vary between species. Such biases have various drivers, including cellular proteins that recognize specific patterns in nucleic acids, that once triggered, induce mutations or invoke intrinsic or innate immune responses. In this review we examine the types of compositional biases identified in viral genomes and current understanding of the evolutionary mechanisms underpinning these trends. Finally, we consider the potential for large scale synonymous recoding strategies to engineer RNA virus vaccines, including those with pandemic potential, such as influenza A virus and Severe Acute Respiratory Syndrome Coronavirus Virus 2. This article is categorized under: RNA in Disease and Development > RNA in Disease RNA Evolution and Genomics > Computational Analyses of RNA RNA Interactions with Proteins and Other Molecules > Protein-RNA Recognition.
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Affiliation(s)
- Eleanor R. Gaunt
- Department of Infection and ImmunityThe Roslin Institute, The University of EdinburghEdinburghUK
| | - Paul Digard
- Department of Infection and ImmunityThe Roslin Institute, The University of EdinburghEdinburghUK
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18
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Kumar A, Goyal N, Saranathan N, Dhamija S, Saraswat S, Menon MB, Vivekanandan P. The slowing rate of CpG depletion in SARS-CoV-2 genomes is consistent with adaptations to the human host. Mol Biol Evol 2022; 39:6521032. [PMID: 35134218 PMCID: PMC8892944 DOI: 10.1093/molbev/msac029] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Depletion of CpG dinucleotides in SARS-CoV-2 genomes has been linked to virus evolution, host-switching, virus replication, and innate immune responses. Temporal variations, if any, in the rate of CpG depletion during virus evolution in the host remain poorly understood. Here, we analysed the CpG content of over 1.4 million full-length SARS-CoV-2 genomes representing over 170 million documented infections during the first 17 months of the pandemic. Our findings suggest that the extent of CpG depletion in SARS-CoV-2 genomes is modest. Interestingly, the rate of CpG depletion is highest during early evolution in humans and it gradually tapers off almost reaching an equilibrium; this is consistent with adaptations to the human host. Furthermore, within the coding regions, CpG depletion occurs predominantly at codon positions 2-3 and 3-1. Loss of ZAP-binding motifs in SARS-CoV-2 genomes is primarily driven by the loss of the terminal CpG in the motifs. Nonetheless, majority of the CpG depletion in SARS-CoV-2 genomes occurs outside ZAP-binding motifs. SARS-CoV-2 genomes selectively lose CpGs-motifs from a U-rich context; this may help avoid immune recognition by TLR7. SARS-CoV-2 alpha-, beta- and delta-variants of concern have reduced CpG content compared to sequences from the beginning of the pandemic. In sum, we provide evidence that the rate of CpG depletion in virus genomes is not uniform and it greatly varies over time and during adaptations to the host. This work highlights how temporal variations in selection pressures during virus adaption may impact the rate and the extent of CpG depletion in virus genomes.
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Affiliation(s)
- Akhil Kumar
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Nishank Goyal
- Department of Chemical Engineering, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Nandhini Saranathan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Sonam Dhamija
- CSIR-Institute of Genomics and Integrative Biology, New Delhi-110025, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad- 201002, India
| | - Saurabh Saraswat
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Manoj B Menon
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi-110016, India
| | - Perumal Vivekanandan
- Kusuma School of Biological Sciences, Indian Institute of Technology Delhi, New Delhi-110016, India
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19
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Trus I, Udenze D, Karniychuk U. Generation of CpG-Recoded Zika Virus Vaccine Candidates. Methods Mol Biol 2022; 2410:289-302. [PMID: 34914053 DOI: 10.1007/978-1-0716-1884-4_14] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Experimental increase of cytosine-phosphate-guanine (CpG) dinucleotides in an RNA virus genome impairs infection. Beneficially, this weak infection may lead to robust antiviral host immunity providing a cutting-edge approach for vaccines. For example, we have recently demonstrated that recoded Zika virus variants with the increased CpG content showed considerable attenuated infection phenotypes and protection against lethal challenge in mice. Here, we describe the workflow for the design and generation of CpG-recoded Zika virus vaccine candidates. The workflow can be adapted for other viruses.
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Affiliation(s)
- Ivan Trus
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada
| | - Daniel Udenze
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada
| | - Uladzimir Karniychuk
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada.
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20
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Pintó RM, Burns CC, Moratorio G. Editorial: Codon Usage and Dinucleotide Composition of Virus Genomes: From the Virus-Host Interaction to the Development of Vaccines. Front Microbiol 2021; 12:791750. [PMID: 34917065 PMCID: PMC8671033 DOI: 10.3389/fmicb.2021.791750] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 11/02/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Rosa M Pintó
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, University of Barcelona, Barcelona, Spain
| | - Cara C Burns
- Division of Viral Disease, Molecular Epidemiology and Surveillance, Centers for Disease Control and Prevention (CDC), Atlanta, GA, United States
| | - Gonzalo Moratorio
- Molecular Virology Laboratory, Experimental Evolution Laboratory, Nuclear Research Centre, School of Sciences, University of la República, Institute Pasteur, Montevideo, Uruguay
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21
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Daron J, Bravo IG. Variability in Codon Usage in Coronaviruses Is Mainly Driven by Mutational Bias and Selective Constraints on CpG Dinucleotide. Viruses 2021; 13:v13091800. [PMID: 34578381 PMCID: PMC8473333 DOI: 10.3390/v13091800] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/30/2021] [Accepted: 08/31/2021] [Indexed: 12/18/2022] Open
Abstract
The Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the third human-emerged virus of the 21st century from the Coronaviridae family, causing the ongoing coronavirus disease 2019 (COVID-19) pandemic. Due to the high zoonotic potential of coronaviruses, it is critical to unravel their evolutionary history of host species breadth, host-switch potential, adaptation and emergence, to identify viruses posing a pandemic risk in humans. We present here a comprehensive analysis of the composition and codon usage bias of the 82 Orthocoronavirinae members, infecting 47 different avian and mammalian hosts. Our results clearly establish that synonymous codon usage varies widely among viruses, is only weakly dependent on their primary host, and is dominated by mutational bias towards AU-enrichment and by CpG avoidance. Indeed, variation in GC3 explains around 34%, while variation in CpG frequency explains around 14% of total variation in codon usage bias. Further insight on the mutational equilibrium within Orthocoronavirinae revealed that most coronavirus genomes are close to their neutral equilibrium, the exception being the three recently infecting human coronaviruses, which lie further away from the mutational equilibrium than their endemic human coronavirus counterparts. Finally, our results suggest that, while replicating in humans, SARS-CoV-2 is slowly becoming AU-richer, likely until attaining a new mutational equilibrium.
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Affiliation(s)
- Josquin Daron
- Laboratoire MIVEGEC (CNRS, IRD, Université de Montpellier), 34394 Montpellier, France;
- Correspondence:
| | - Ignacio G. Bravo
- Laboratoire MIVEGEC (CNRS, IRD, Université de Montpellier), 34394 Montpellier, France;
- Center for Research on the Ecology and Evolution of Diseases (CREES), 34394 Montpellier, France
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22
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Wahid R, Mercer L, Macadam A, Carlyle S, Stephens L, Martin J, Chumakov K, Laassri M, Petrovskaya S, Smits SL, Stittelaar KJ, Gast C, Weldon WC, Konopka-Anstadt JL, Steven Oberste M, Van Damme P, De Coster I, Rüttimann R, Bandyopadhyay A, Konz J. Assessment of genetic changes and neurovirulence of shed Sabin and novel type 2 oral polio vaccine viruses. NPJ Vaccines 2021; 6:94. [PMID: 34326330 PMCID: PMC8322168 DOI: 10.1038/s41541-021-00355-y] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 07/06/2021] [Indexed: 11/09/2022] Open
Abstract
Sabin-strain oral polio vaccines (OPV) can, in rare instances, cause disease in recipients and susceptible contacts or evolve to become circulating vaccine-derived strains with the potential to cause outbreaks. Two novel type 2 OPV (nOPV2) candidates were designed to stabilize the genome against the rapid reversion that is observed following vaccination with Sabin OPV type 2 (mOPV2). Next-generation sequencing and a modified transgenic mouse neurovirulence test were applied to shed nOPV2 viruses from phase 1 and 2 studies and shed mOPV2 from a phase 4 study. The shed mOPV2 rapidly reverted in the primary attenuation site (domain V) and increased in virulence. In contrast, the shed nOPV2 viruses showed no evidence of reversion in domain V and limited or no increase in neurovirulence in mice. Based on these results and prior published data on safety, immunogenicity, and shedding, the nOPV2 viruses are promising alternatives to mOPV2 for outbreak responses.
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Affiliation(s)
- Rahnuma Wahid
- Center for Vaccine Innovation and Access, PATH, Seattle, WA, USA.
| | - Laina Mercer
- Center for Vaccine Innovation and Access, PATH, Seattle, WA, USA
| | - Andrew Macadam
- National Institute for Biological Standards and Control (NIBSC), Hertfordshire, UK
| | - Sarah Carlyle
- National Institute for Biological Standards and Control (NIBSC), Hertfordshire, UK
| | - Laura Stephens
- National Institute for Biological Standards and Control (NIBSC), Hertfordshire, UK
| | - Javier Martin
- National Institute for Biological Standards and Control (NIBSC), Hertfordshire, UK
| | - Konstantin Chumakov
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
- Global Virus Network Center of Excellence, Baltimore, MD, USA
| | - Majid Laassri
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Svetlana Petrovskaya
- Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA
| | - Saskia L Smits
- Viroclinics Biosciences B.V., Rotterdam, the Netherlands
| | - Koert J Stittelaar
- Viroclinics Xplore, Viroclinics Biosciences B.V., Rotterdam, the Netherlands
| | - Chris Gast
- Center for Vaccine Innovation and Access, PATH, Seattle, WA, USA
| | - William C Weldon
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - M Steven Oberste
- Division of Viral Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Pierre Van Damme
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Ilse De Coster
- Centre for the Evaluation of Vaccination, Vaccine and Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - Ricardo Rüttimann
- Fighting Infectious Diseases in Emerging Countries (FIDEC), Miami, FL, USA
| | | | - John Konz
- Center for Vaccine Innovation and Access, PATH, Seattle, WA, USA
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23
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Jia F, Li L, Liu H, Lv P, Shi X, Wu Y, Ling C, Xu F. Development of a rabies virus-based retrograde tracer with high trans-monosynaptic efficiency by reshuffling glycoprotein. Mol Brain 2021; 14:109. [PMID: 34238335 PMCID: PMC8265122 DOI: 10.1186/s13041-021-00821-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 07/04/2021] [Indexed: 11/12/2022] Open
Abstract
Rabies virus (RV) is the most widely used vector for mapping neural circuits. Previous studies have shown that the RV glycoprotein can be a target to improve the retrograde transsynaptic tracing efficiency. However, the current versions still label only a small portion of all presynaptic neurons. Here, we reshuffled the oG sequence, a chimeric glycoprotein, with positive codon pair bias score (CPBS) based on bioinformatic analysis of mouse codon pair bias, generating ooG, a further optimized glycoprotein. Our experimental data reveal that the ooG has a higher expression level than the oG in vivo, which significantly increases the tracing efficiency by up to 12.6 and 62.1-fold compared to oG and B19G, respectively. The new tool can be used for labeling neural circuits Therefore, the approach reported here provides a convenient, efficient and universal strategy to improve protein expression for various application scenarios such as trans-synaptic tracing efficiency, cell engineering, and vaccine and oncolytic virus designs.
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Affiliation(s)
- Fan Jia
- Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Key Laboratory of Brain Connectome and Manipulation, The Brain Cognition and Brain Disease Institute (BCBDI), Translational Research Center for the Nervous System (TRCNS), Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, 518055, China.
- NMPA Key Laboratory for Research and Evaluation of Viral Vector Technology in Cell and Gene Therapy Medicinal Products, Key Laboratory of Quality Control Technology for Virus-Based Therapeutics, Guangdong Provincial Medical Products Administration, Shenzhen Key Laboratory of Viral Vectors for Biomedicine, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Li Li
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems,, Wuhan Center for Magnetic Resonance, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Haizhou Liu
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Pei Lv
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems,, Wuhan Center for Magnetic Resonance, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Xiangwei Shi
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems,, Wuhan Center for Magnetic Resonance, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yang Wu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems,, Wuhan Center for Magnetic Resonance, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China
| | - Chen Ling
- Division of Molecular and Cellular Therapy, Department of Pediatrics, College of Medicine, University of Florida, Gainesville, FL, USA
| | - Fuqiang Xu
- Guangdong Provincial Key Laboratory of Brain Connectome and Behavior, CAS Key Laboratory of Brain Connectome and Manipulation, The Brain Cognition and Brain Disease Institute (BCBDI), Translational Research Center for the Nervous System (TRCNS), Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen, 518055, China.
- NMPA Key Laboratory for Research and Evaluation of Viral Vector Technology in Cell and Gene Therapy Medicinal Products, Key Laboratory of Quality Control Technology for Virus-Based Therapeutics, Guangdong Provincial Medical Products Administration, Shenzhen Key Laboratory of Viral Vectors for Biomedicine, Shenzhen Institute of Advanced Technology, Chinese Academy of Sciences, Shenzhen, 518055, China.
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Key Laboratory of Magnetic Resonance in Biological Systems,, Wuhan Center for Magnetic Resonance, Innovation Academy for Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, 430071, China.
- Wuhan National Laboratory for Optoelectronics, Huazhong University of Science and Technology, Wuhan, 430074, China.
- Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, 430071, China.
- Center for Excellence in Brain Science and Intelligence Technology, Chinese Academy of Sciences, Shanghai, 200031, China.
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24
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Pereira-Gómez M, Carrau L, Fajardo Á, Moreno P, Moratorio G. Altering Compositional Properties of Viral Genomes to Design Live-Attenuated Vaccines. Front Microbiol 2021; 12:676582. [PMID: 34276608 PMCID: PMC8278477 DOI: 10.3389/fmicb.2021.676582] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Accepted: 06/01/2021] [Indexed: 12/11/2022] Open
Abstract
Live-attenuated vaccines have been historically used to successfully prevent numerous diseases caused by a broad variety of RNA viruses due to their ability to elicit strong and perdurable immune-protective responses. In recent years, various strategies have been explored to achieve viral attenuation by rational genetic design rather than using classic and empirical approaches, based on successive passages in cell culture. A deeper understanding of evolutionary implications of distinct viral genomic compositional aspects, as well as substantial advances in synthetic biology technologies, have provided a framework to achieve new viral attenuation strategies. Herein, we will discuss different approaches that are currently applied to modify compositional features of viruses in order to develop novel live-attenuated vaccines.
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Affiliation(s)
- Marianoel Pereira-Gómez
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Lucía Carrau
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY, United States
| | - Álvaro Fajardo
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Pilar Moreno
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo, Uruguay
| | - Gonzalo Moratorio
- Laboratorio de Virología Molecular, Centro de Investigaciones Nucleares, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
- Laboratorio de Evolución Experimental de Virus, Institut Pasteur de Montevideo, Montevideo, Uruguay
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25
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Zuber PLF, Gruber M, Kaslow DC, Chen RT, Giersing BK, Friede MH. Evolving pharmacovigilance requirements with novel vaccines and vaccine components. BMJ Glob Health 2021; 6:bmjgh-2020-003403. [PMID: 34011500 PMCID: PMC8137242 DOI: 10.1136/bmjgh-2020-003403] [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: 07/09/2020] [Revised: 08/04/2020] [Accepted: 08/09/2020] [Indexed: 01/08/2023] Open
Abstract
This paper explores the pipeline of new and upcoming vaccines as it relates to monitoring their safety. Compared with most currently available vaccines, that are constituted of live attenuated organisms or inactive products, future vaccines will also be based on new technologies. Several products that include such technologies are either already licensed or at an advanced stage of clinical development. Those include viral vectors, genetically attenuated live organisms, nucleic acid vaccines, novel adjuvants, increased number of antigens present in a single vaccine, novel mode of vaccine administration and thermostabilisation. The Global Advisory Committee on Vaccine Safety (GACVS) monitors novel vaccines, from the time they become available for large scale use. GACVS maintains their safety profile as evidence emerges from post-licensure surveillance and observational studies. Vaccines and vaccine formulations produced with novel technologies will have different safety profiles that will require adapting pharmacovigilance approaches. For example, GACVS now considers viral vector templates developed on the model proposed by Brighton Collaboration. The characteristics of those novel products will also have implications for the risk management plans (RMPs). Questions related to the duration of active monitoring for genetic material, presence of adventitious agents more easily detected with enhanced biological screening, or physiological mechanisms of novel adjuvants are all considerations that will belong to the preparation of RMPs. In addition to assessing those novel products and advising experts, GACVS will also consider how to more broadly communicate about risk assessment, so vaccine users can also benefit from the committee’s advice.
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Affiliation(s)
- Patrick L F Zuber
- Access to Medicines and Health Products Division, World Health Organization, Geneva, Switzerland
| | - Marion Gruber
- Center for Biologics Evaluation and Research, Food and Drugs Administration, Silver Spring, Massachusetts, USA
| | | | - Robert T Chen
- Brighton Collaboration, Task Force for Global Health, Decatur, Georgia, USA
| | - Brigitte K Giersing
- Immunization, Vaccines and Biologicals Department, World Health Organization, Geneva, Switzerland
| | - Martin H Friede
- Immunization, Vaccines and Biologicals Department, World Health Organization, Geneva, Switzerland
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26
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The Evolution of Severe Acute Respiratory Syndrome Coronavirus-2 during Pandemic and Adaptation to the Host. J Mol Evol 2021; 89:341-356. [PMID: 33993372 PMCID: PMC8123100 DOI: 10.1007/s00239-021-10008-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 03/25/2021] [Indexed: 12/02/2022]
Abstract
Severe Acute Respiratory Syndrome Coronavirus-2 is a zoonotic virus with a possible origin in bats and potential transmission to humans through an intermediate host. When zoonotic viruses jump to a new host, they undergo both mutational and natural selective pressures that result in non-synonymous and synonymous adaptive changes, necessary for efficient replication and rapid spread of diseases in new host species. The nucleotide composition and codon usage pattern of SARS-CoV-2 indicate the presence of a highly conserved, gene-specific codon usage bias. The codon usage pattern of SARS-CoV-2 is mostly antagonistic to human and bat codon usage. SARS-CoV-2 codon usage bias is mainly shaped by the natural selection, while mutational pressure plays a minor role. The time-series analysis of SARS-CoV-2 genome indicates that the virus is slowly evolving. Virus isolates from later stages of the outbreak have more biased codon usage and nucleotide composition than virus isolates from early stages of the outbreak.
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27
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Wang G, Zheng C. Zinc finger proteins in the host-virus interplay: multifaceted functions based on their nucleic acid-binding property. FEMS Microbiol Rev 2021; 45:fuaa059. [PMID: 33175962 DOI: 10.1093/femsre/fuaa059] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2020] [Accepted: 11/07/2020] [Indexed: 12/14/2022] Open
Abstract
Zinc finger proteins (ZFPs) are a huge family comprised of massive, structurally diverse proteins characterized by zinc ion coordinating. They engage in the host-virus interplay in-depth and occupy a significant portion of the host antiviral arsenal. Nucleic acid-binding is the basic property of certain ZFPs, which draws increasing attention due to their immense influence on viral infections. ZFPs exert multiple roles on the viral replications and host cell transcription profiles by recognizing viral genomes and host mRNAs. Their roles could be either antiviral or proviral and were separately discussed. Our review covers the recent research progress and provides a comprehensive understanding of ZFPs in antiviral immunity based on their DNA/RNA binding property.
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Affiliation(s)
- Guanming Wang
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, No.1 Xue Yuan Road, University Town, FuZhou Fujian, 350108, China
| | - Chunfu Zheng
- Department of Immunology, School of Basic Medical Sciences, Fujian Medical University, No.1 Xue Yuan Road, University Town, FuZhou Fujian, 350108, China
- Department of Microbiology, Immunology and Infectious Diseases, University of Calgary, 3330 Hospital Dr NW, Calgary, Alberta, Canada, AB T2N 4N1
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28
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Callens M, Pradier L, Finnegan M, Rose C, Bedhomme S. Read between the lines: Diversity of non-translational selection pressures on local codon usage. Genome Biol Evol 2021; 13:6263832. [PMID: 33944930 PMCID: PMC8410138 DOI: 10.1093/gbe/evab097] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/28/2021] [Indexed: 12/14/2022] Open
Abstract
Protein coding genes can contain specific motifs within their nucleotide sequence that function as a signal for various biological pathways. The presence of such sequence motifs within a gene can have beneficial or detrimental effects on the phenotype and fitness of an organism, and this can lead to the enrichment or avoidance of this sequence motif. The degeneracy of the genetic code allows for the existence of alternative synonymous sequences that exclude or include these motifs, while keeping the encoded amino acid sequence intact. This implies that locally, there can be a selective pressure for preferentially using a codon over its synonymous alternative in order to avoid or enrich a specific sequence motif. This selective pressure could -in addition to mutation, drift and selection for translation efficiency and accuracy- contribute to shape the codon usage bias. In this review, we discuss patterns of avoidance of (or enrichment for) the various biological signals contained in specific nucleotide sequence motifs: transcription and translation initiation and termination signals, mRNA maturation signals, and antiviral immune system targets. Experimental data on the phenotypic or fitness effects of synonymous mutations in these sequence motifs confirm that they can be targets of local selection pressures on codon usage. We also formulate the hypothesis that transposable elements could have a similar impact on codon usage through their preferred integration sequences. Overall, selection on codon usage appears to be a combination of a global selection pressure imposed by the translation machinery, and a patchwork of local selection pressures related to biological signals contained in specific sequence motifs.
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Affiliation(s)
- Martijn Callens
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche pour le Développement, 34000 Montpellier, France
| | - Léa Pradier
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche pour le Développement, 34000 Montpellier, France
| | - Michael Finnegan
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche pour le Développement, 34000 Montpellier, France
| | - Caroline Rose
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche pour le Développement, 34000 Montpellier, France
| | - Stéphanie Bedhomme
- Centre d'Ecologie Fonctionnelle et Evolutive, CNRS, Université de Montpellier, Université Paul Valéry Montpellier 3, Ecole Pratique des Hautes Etudes, Institut de Recherche pour le Développement, 34000 Montpellier, France
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29
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Goswami P, Bartas M, Lexa M, Bohálová N, Volná A, Červeň J, Červeňová V, Pečinka P, Špunda V, Fojta M, Brázda V. SARS-CoV-2 hot-spot mutations are significantly enriched within inverted repeats and CpG island loci. Brief Bioinform 2021; 22:1338-1345. [PMID: 33341900 PMCID: PMC7799342 DOI: 10.1093/bib/bbaa385] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Revised: 11/16/2020] [Accepted: 11/27/2020] [Indexed: 12/18/2022] Open
Abstract
SARS-CoV-2 is an intensively investigated virus from the order Nidovirales (Coronaviridae family) that causes COVID-19 disease in humans. Through enormous scientific effort, thousands of viral strains have been sequenced to date, thereby creating a strong background for deep bioinformatics studies of the SARS-CoV-2 genome. In this study, we inspected high-frequency mutations of SARS-CoV-2 and carried out systematic analyses of their overlay with inverted repeat (IR) loci and CpG islands. The main conclusion of our study is that SARS-CoV-2 hot-spot mutations are significantly enriched within both IRs and CpG island loci. This points to their role in genomic instability and may predict further mutational drive of the SARS-CoV-2 genome. Moreover, CpG islands are strongly enriched upstream from viral ORFs and thus could play important roles in transcription and the viral life cycle. We hypothesize that hypermethylation of these loci will decrease the transcription of viral ORFs and could therefore limit the progression of the disease.
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Affiliation(s)
- Pratik Goswami
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.,National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Martin Bartas
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Matej Lexa
- Faculty of Informatics, Masaryk University, Brno, Czech Republic
| | - Natália Bohálová
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic.,Department of Experimental Biology, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Adriana Volná
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Jiří Červeň
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Veronika Červeňová
- Department of Mathematics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Petr Pečinka
- Department of Biology and Ecology, Faculty of Science, University of Ostrava, Ostrava, Czech Republic
| | - Vladimír Špunda
- Department of Physics, Faculty of Science, University of Ostrava, Ostrava, Czech Republic.,Global Change Research Institute of the Czech Academy of Sciences, Brno, Czech Republic
| | - Miroslav Fojta
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
| | - Václav Brázda
- Department of Biophysical Chemistry and Molecular Oncology, Institute of Biophysics of the Czech Academy of Sciences, Brno, Czech Republic
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30
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Jordan-Paiz A, Franco S, Martínez MA. Impact of Synonymous Genome Recoding on the HIV Life Cycle. Front Microbiol 2021; 12:606087. [PMID: 33796084 PMCID: PMC8007914 DOI: 10.3389/fmicb.2021.606087] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 02/25/2021] [Indexed: 12/19/2022] Open
Abstract
Synonymous mutations within protein coding regions introduce changes in DNA or messenger (m) RNA, without mutating the encoded proteins. Synonymous recoding of virus genomes has facilitated the identification of previously unknown virus biological features. Moreover, large-scale synonymous recoding of the genome of human immunodeficiency virus type 1 (HIV-1) has elucidated new antiviral mechanisms within the innate immune response, and has improved our knowledge of new functional virus genome structures, the relevance of codon usage for the temporal regulation of viral gene expression, and HIV-1 mutational robustness and adaptability. Continuous improvements in our understanding of the impacts of synonymous substitutions on virus phenotype - coupled with the decreased cost of chemically synthesizing DNA and improved methods for assembling DNA fragments - have enhanced our ability to identify potential HIV-1 and host factors and other aspects involved in the infection process. In this review, we address how silent mutagenesis impacts HIV-1 phenotype and replication capacity. We also discuss the general potential of synonymous recoding of the HIV-1 genome to elucidate unknown aspects of the virus life cycle, and to identify new therapeutic targets.
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Affiliation(s)
- Ana Jordan-Paiz
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Badalona, Spain
| | - Sandra Franco
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Badalona, Spain
| | - Miguel Angel Martínez
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Badalona, Spain
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31
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Strumillo ST, Kartavykh D, de Carvalho FF, Cruz NC, de Souza Teodoro AC, Sobhie Diaz R, Curcio MF. Host-virus interaction and viral evasion. Cell Biol Int 2021; 45:1124-1147. [PMID: 33533523 PMCID: PMC8014853 DOI: 10.1002/cbin.11565] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 01/24/2021] [Indexed: 12/12/2022]
Abstract
With each infectious pandemic or outbreak, the medical community feels the need to revisit basic concepts of immunology to understand and overcome the difficult times brought about by these infections. Regarding viruses, they have historically been responsible for many deaths, and such a peculiarity occurs because they are known to be obligate intracellular parasites that depend upon the host's cell machinery for their replication. Successful infection with the production of essential viral components requires constant viral evolution as a strategy to manipulate the cellular environment, including host internal factors, the host's nonspecific and adaptive immune responses to viruses, the metabolic and energetic state of the infected cell, and changes in the intracellular redox environment during the viral infection cycle. Based on this knowledge, it is fundamental to develop new therapeutic strategies for controlling viral dissemination, by means of antiviral therapies, vaccines, or antioxidants, or by targeting the inhibition or activation of cell signaling pathways or metabolic pathways that are altered during infection. The rapid recovery of altered cellular homeostasis during viral infection is still a major challenge. Here, we review the strategies by which viruses evade the host's immune response and potential tools used to develop more specific antiviral therapies to cure, control, or prevent viral diseases.
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Affiliation(s)
- Scheilla T Strumillo
- Department of Biochemistry, Laboratory of Cell Signaling, Federal University of São Paulo, São Paulo, Brazil
| | - Denis Kartavykh
- Department of Medicine, Laboratory of Retrovirology, Federal University of São Paulo, São Paulo, Brazil
| | - Fábio F de Carvalho
- Departament of Educational Development, Getulio Vargas Foundation, São Paulo, Brazil
| | - Nicolly C Cruz
- Department of Medicine, Laboratory of Retrovirology, Federal University of São Paulo, São Paulo, Brazil
| | - Ana C de Souza Teodoro
- Department of Biochemistry, Laboratory of Cell Signaling, Federal University of São Paulo, São Paulo, Brazil
| | - Ricardo Sobhie Diaz
- Department of Medicine, Laboratory of Retrovirology, Federal University of São Paulo, São Paulo, Brazil
| | - Marli F Curcio
- Department of Medicine, Laboratory of Retrovirology, Federal University of São Paulo, São Paulo, Brazil
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32
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Giménez-Roig J, Núñez-Manchón E, Alemany R, Villanueva E, Fillat C. Codon Usage and Adenovirus Fitness: Implications for Vaccine Development. Front Microbiol 2021; 12:633946. [PMID: 33643266 PMCID: PMC7902882 DOI: 10.3389/fmicb.2021.633946] [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: 11/26/2020] [Accepted: 01/20/2021] [Indexed: 02/03/2023] Open
Abstract
Vaccination is the most effective method to date to prevent viral diseases. It intends to mimic a naturally occurring infection while avoiding the disease, exposing our bodies to viral antigens to trigger an immune response that will protect us from future infections. Among different strategies for vaccine development, recombinant vaccines are one of the most efficient ones. Recombinant vaccines use safe viral vectors as vehicles and incorporate a transgenic antigen of the pathogen against which we intend to generate an immune response. These vaccines can be based on replication-deficient viruses or replication-competent viruses. While the most effective strategy involves replication-competent viruses, they must be attenuated to prevent any health hazard while guaranteeing a strong humoral and cellular immune response. Several attenuation strategies for adenoviral-based vaccine development have been contemplated over time. In this paper, we will review them and discuss novel approaches based on the principle that protein synthesis from individual genes can be modulated by codon usage bias manipulation. We will summarize vaccine approaches that consider recoding of viral proteins to produce adenoviral attenuation and recoding of the transgene antigens for both viral attenuation and efficient viral epitope expression.
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Affiliation(s)
- Judit Giménez-Roig
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Estela Núñez-Manchón
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Ramon Alemany
- Procure Program, Institut Català d’Oncologia- Oncobell Program, IDIBELL, L’Hospitalet de Llobregat, Barcelona, Spain
| | - Eneko Villanueva
- Cambridge Centre for Proteomics, Department of Biochemistry, University of Cambridge, Cambridge, United Kingdom
| | - Cristina Fillat
- Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
- Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Barcelona, Spain
- Facultat de Medicina i Ciències de la Salut, Universitat de Barcelona (UB), Barcelona, Spain
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33
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Abstract
RNA viruses are responsible for some of the worst pandemics known to mankind, including outbreaks of Influenza, Ebola, and COVID-19. One major challenge in tackling RNA viruses is the fact they are extremely genetically diverse. Nevertheless, they share common features that include their dependence on host cells for replication, and high mutation rates. We set out to search for shared evolutionary characteristics that may aid in gaining a broader understanding of RNA virus evolution, and constructed a phylogeny-based data set spanning thousands of sequences from diverse single-stranded RNA viruses of animals. Strikingly, we found that the vast majority of these viruses have a skewed nucleotide composition, manifested as adenine rich (A-rich) coding sequences. In order to test whether A-richness is driven by selection or by biased mutation processes, we harnessed the effects of incomplete purifying selection at the tips of virus phylogenies. Our results revealed consistent mutational biases toward U rather than A in genomes of all viruses. In +ssRNA viruses, we found that this bias is compensated by selection against U and selection for A, which leads to A-rich genomes. In -ssRNA viruses, the genomic mutational bias toward U on the negative strand manifests as A-rich coding sequences, on the positive strand. We investigated possible reasons for the advantage of A-rich sequences including weakened RNA secondary structures, codon usage bias, and selection for a particular amino acid composition, and conclude that host immune pressures may have led to similar biases in coding sequence composition across very divergent RNA viruses.
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Affiliation(s)
- Talia Kustin
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel
| | - Adi Stern
- The Shmunis School of Biomedicine and Cancer Research, Tel Aviv University, Tel Aviv, Israel.,Edmond J. Safra Center for Bioinformatics, Tel Aviv University, Tel Aviv, Israel
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34
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Kalkowska DA, Pallansch MA, Wilkinson A, Bandyopadhyay AS, Konopka-Anstadt JL, Burns CC, Oberste MS, Wassilak SGF, Badizadegan K, Thompson KM. Updated Characterization of Outbreak Response Strategies for 2019-2029: Impacts of Using a Novel Type 2 Oral Poliovirus Vaccine Strain. RISK ANALYSIS : AN OFFICIAL PUBLICATION OF THE SOCIETY FOR RISK ANALYSIS 2021; 41:329-348. [PMID: 33174263 PMCID: PMC7887065 DOI: 10.1111/risa.13622] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 10/08/2020] [Accepted: 10/16/2020] [Indexed: 05/06/2023]
Abstract
Delays in achieving the global eradication of wild poliovirus transmission continue to postpone subsequent cessation of all oral poliovirus vaccine (OPV) use. Countries must stop OPV use to end all cases of poliomyelitis, including vaccine-associated paralytic polio (VAPP) and cases caused by vaccine-derived polioviruses (VDPVs). The Global Polio Eradication Initiative (GPEI) coordinated global cessation of all type 2 OPV (OPV2) use in routine immunization in 2016 but did not successfully end the transmission of type 2 VDPVs (VDPV2s), and consequently continues to use type 2 OPV (OPV2) for outbreak response activities. Using an updated global poliovirus transmission and OPV evolution model, we characterize outbreak response options for 2019-2029 related to responding to VDPV2 outbreaks with a genetically stabilized novel OPV (nOPV2) strain or with the currently licensed monovalent OPV2 (mOPV2). Given uncertainties about the properties of nOPV2, we model different assumptions that appear consistent with the evidence on nOPV2 to date. Using nOPV2 to respond to detected cases may reduce the expected VDPV and VAPP cases and the risk of needing to restart OPV2 use in routine immunization compared to mOPV2 use for outbreak response. The actual properties, availability, and use of nOPV2 will determine its effects on type 2 poliovirus transmission in populations. Even with optimal nOPV2 performance, countries and the GPEI would still likely need to restart OPV2 use in routine immunization in OPV-using countries if operational improvements in outbreak response to stop the transmission of cVDPV2s are not implemented effectively.
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Affiliation(s)
| | - Mark A. Pallansch
- National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Amanda Wilkinson
- Global Immunization Division, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Jennifer L. Konopka-Anstadt
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Cara C. Burns
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - M. Steven Oberste
- Division of Viral Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Steven G. F. Wassilak
- Global Immunization Division, Center for Global Health, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | | | - Kimberly M. Thompson
- Kid Risk, Inc., Orlando, FL, USA
- Correspondence to: Kimberly Thompson, Kid Risk, Inc., 7512 Dr. Phillips Blvd. #50-523, Orlando, FL 32819, USA,
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35
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Diaz-San Segundo F, Medina GN, Spinard E, Kloc A, Ramirez-Medina E, Azzinaro P, Mueller S, Rieder E, de Los Santos T. Use of Synonymous Deoptimization to Derive Modified Live Attenuated Strains of Foot and Mouth Disease Virus. Front Microbiol 2021; 11:610286. [PMID: 33552021 PMCID: PMC7861043 DOI: 10.3389/fmicb.2020.610286] [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: 09/25/2020] [Accepted: 12/23/2020] [Indexed: 12/12/2022] Open
Abstract
Foot-and-mouth disease (FMD) is one of the most economically important viral diseases that can affect livestock. In the last 70 years, use of an inactivated whole antigen vaccine has contributed to the eradication of disease from many developed nations. However, recent outbreaks in Europe and Eastern Asia demonstrated that infection can spread as wildfire causing economic and social devastation. Therefore, it is essential to develop new control strategies that could confer early protection and rapidly stop disease spread. Live attenuated vaccines (LAV) are one of the best choices to obtain a strong early and long-lasting protection against viral diseases. In proof of concept studies, we previously demonstrated that “synonymous codon deoptimization” could be applied to the P1 capsid coding region of the viral genome to derive attenuated FMDV serotype A12 strains. Here, we demonstrate that a similar approach can be extended to the highly conserved non-structural P2 and P3 coding regions, providing a backbone for multiple serotype FMDV LAV development. Engineered codon deoptimized P2, P3 or P2, and P3 combined regions were included into the A24Cruzeiro infectious clone optimized for vaccine production, resulting in viable progeny that exhibited different degrees of attenuation in cell culture, in mice, and in the natural host (swine). Derived strains were thoroughly characterized in vitro and in vivo. Our work demonstrates that overall, the entire FMDV genome tolerates codon deoptimization, highlighting the potential of using this technology to derive novel improved LAV candidates.
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Affiliation(s)
- Fayna Diaz-San Segundo
- Plum Island Animal Disease Center (PIADC), Agricultural Research Service, United States Department of Agriculture, Greenport, NY, United States
| | - Gisselle N Medina
- Plum Island Animal Disease Center (PIADC), Agricultural Research Service, United States Department of Agriculture, Greenport, NY, United States.,Kansas State University College of Veterinary Medicine, Manhattan, KS, United States
| | - Edward Spinard
- Plum Island Animal Disease Center (PIADC), Agricultural Research Service, United States Department of Agriculture, Greenport, NY, United States.,PIADC Research Participation Program, Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States
| | - Anna Kloc
- Plum Island Animal Disease Center (PIADC), Agricultural Research Service, United States Department of Agriculture, Greenport, NY, United States.,PIADC Research Participation Program, Oak Ridge Institute for Science and Education, Oak Ridge, TN, United States
| | - Elizabeth Ramirez-Medina
- Plum Island Animal Disease Center (PIADC), Agricultural Research Service, United States Department of Agriculture, Greenport, NY, United States.,Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, CT, United States
| | - Paul Azzinaro
- Plum Island Animal Disease Center (PIADC), Agricultural Research Service, United States Department of Agriculture, Greenport, NY, United States
| | | | - Elizabeth Rieder
- Plum Island Animal Disease Center (PIADC), Agricultural Research Service, United States Department of Agriculture, Greenport, NY, United States
| | - Teresa de Los Santos
- Plum Island Animal Disease Center (PIADC), Agricultural Research Service, United States Department of Agriculture, Greenport, NY, United States
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36
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Wei Y, Silke JR, Aris P, Xia X. Coronavirus genomes carry the signatures of their habitats. PLoS One 2020; 15:e0244025. [PMID: 33351847 PMCID: PMC7755226 DOI: 10.1371/journal.pone.0244025] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2020] [Accepted: 12/01/2020] [Indexed: 12/15/2022] Open
Abstract
Coronaviruses such as SARS-CoV-2 regularly infect host tissues that express antiviral proteins (AVPs) in abundance. Understanding how they evolve to adapt or evade host immune responses is important in the effort to control the spread of infection. Two AVPs that may shape viral genomes are the zinc finger antiviral protein (ZAP) and the apolipoprotein B mRNA editing enzyme-catalytic polypeptide-like 3 (APOBEC3). The former binds to CpG dinucleotides to facilitate the degradation of viral transcripts while the latter frequently deaminates C into U residues which could generate notable viral sequence variations. We tested the hypothesis that both APOBEC3 and ZAP impose selective pressures that shape the genome of an infecting coronavirus. Our investigation considered a comprehensive number of publicly available genomes for seven coronaviruses (SARS-CoV-2, SARS-CoV, and MERS infecting Homo sapiens, Bovine CoV infecting Bos taurus, MHV infecting Mus musculus, HEV infecting Sus scrofa, and CRCoV infecting Canis lupus familiaris). We show that coronaviruses that regularly infect tissues with abundant AVPs have CpG-deficient and U-rich genomes; whereas those that do not infect tissues with abundant AVPs do not share these sequence hallmarks. Among the coronaviruses surveyed herein, CpG is most deficient in SARS-CoV-2 and a temporal analysis showed a marked increase in C to U mutations over four months of SARS-CoV-2 genome evolution. Furthermore, the preferred motifs in which these C to U mutations occur are the same as those subjected to APOBEC3 editing in HIV-1. These results suggest that both ZAP and APOBEC3 shape the SARS-CoV-2 genome: ZAP imposes a strong CpG avoidance, and APOBEC3 constantly edits C to U. Evolutionary pressures exerted by host immune systems onto viral genomes may motivate novel strategies for SARS-CoV-2 vaccine development.
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Affiliation(s)
- Yulong Wei
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Jordan R. Silke
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Parisa Aris
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
| | - Xuhua Xia
- Department of Biology, University of Ottawa, Ottawa, Ontario, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, Ontario, Canada
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37
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Loew L, Goonawardane N, Ratcliff J, Nguyen D, Simmonds P. Use of a small DNA virus model to investigate mechanisms of CpG dinucleotide-induced attenuation of virus replication. J Gen Virol 2020; 101:1202-1218. [PMID: 32783803 PMCID: PMC7879557 DOI: 10.1099/jgv.0.001477] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 07/10/2020] [Indexed: 01/19/2023] Open
Abstract
Suppression of the CpG dinucleotide is widespread in RNA viruses infecting vertebrates and plants, and in the genomes of retroviruses and small mammalian DNA viruses. The functional basis for CpG suppression in the latter was investigated through the construction of mutants of the parvovirus, minute virus of mice (MVM) with increased CpG or TpA dinucleotides in the VP gene. CpG-high mutants displayed extraordinary attenuation in A9 cells compared to wild-type MVM (>six logs), while TpA elevation showed no replication effect. Attenuation was independent of Toll-like receptor 9 and STING-mediated DNA recognition pathways and unrelated to effects on translation efficiency. While translation from codon-optimized VP RNA was enhanced in a cell-free assay, MVM containing this sequence was highly attenuated. Further mutational analysis indicated that this arose through its increased numbers of CpG dinucleotides (7→70) and separately from its increased G+C content (42.3→57.4 %), which independently attenuated replication. CpG-high viruses showed impaired NS mRNA expression by qPCR and reduced NS and particularly VP protein expression detected by immunofluorescence and replication in A549 cells, effects reversed in zinc antiviral protein (ZAP) knockout cells, even though nuclear relocalization of VP remained defective. The demonstrated functional basis for CpG suppression in MVM and potentially other small DNA viruses and the observed intolerance of CpGs in coding sequences, even after codon optimization, has implications for the use of small DNA virus vectors in gene therapy and immunization.
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Affiliation(s)
- Lisa Loew
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
- Present address: Clinical Biomanufacturing Facility, University of Oxford, Old Road, Headington, Oxford OX3 7BN, UK
| | - Niluka Goonawardane
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
| | - Jeremy Ratcliff
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
| | - Dung Nguyen
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
| | - Peter Simmonds
- Nuffield Department of Medicine, Peter Medawar Building for Pathogen Research, University of Oxford, Oxford OX1 3SY, UK
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38
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Van Leuven JT, Ederer MM, Burleigh K, Scott L, Hughes RA, Codrea V, Ellington AD, Wichman HA, Miller CR. ΦX174 Attenuation by Whole-Genome Codon Deoptimization. Genome Biol Evol 2020; 13:5921183. [PMID: 33045052 PMCID: PMC7881332 DOI: 10.1093/gbe/evaa214] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/07/2020] [Indexed: 12/11/2022] Open
Abstract
Natural selection acting on synonymous mutations in protein-coding genes influences genome composition and evolution. In viruses, introducing synonymous mutations in genes encoding structural proteins can drastically reduce viral growth, providing a means to generate potent, live-attenuated vaccine candidates. However, an improved understanding of what compositional features are under selection and how combinations of synonymous mutations affect viral growth is needed to predictably attenuate viruses and make them resistant to reversion. We systematically recoded all nonoverlapping genes of the bacteriophage ΦX174 with codons rarely used in its Escherichia coli host. The fitness of recombinant viruses decreases as additional deoptimizing mutations are made to the genome, although not always linearly, and not consistently across genes. Combining deoptimizing mutations may reduce viral fitness more or less than expected from the effect size of the constituent mutations and we point out difficulties in untangling correlated compositional features. We test our model by optimizing the same genes and find that the relationship between codon usage and fitness does not hold for optimization, suggesting that wild-type ΦX174 is at a fitness optimum. This work highlights the need to better understand how selection acts on patterns of synonymous codon usage across the genome and provides a convenient system to investigate the genetic determinants of virulence.
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Affiliation(s)
- James T Van Leuven
- Department of Biological Science, University of Idaho.,Institute for Modeling Collaboration and Innovation, University of Idaho
| | | | - Katelyn Burleigh
- Department of Biological Science, University of Idaho.,Present address: Seattle Children's Research Institute, Seattle, WA
| | - LuAnn Scott
- Department of Biological Science, University of Idaho
| | - Randall A Hughes
- Applied Research Laboratories, University of Texas, Austin.,Present address: Biotechnology Branch, CCDC US Army Research Laboratory, Adelphi, MD
| | - Vlad Codrea
- Institute for Cellular and Molecular Biology, University of Texas, Austin
| | - Andrew D Ellington
- Applied Research Laboratories, University of Texas, Austin.,Institute for Cellular and Molecular Biology, University of Texas, Austin
| | - Holly A Wichman
- Department of Biological Science, University of Idaho.,Institute for Modeling Collaboration and Innovation, University of Idaho
| | - Craig R Miller
- Department of Biological Science, University of Idaho.,Institute for Modeling Collaboration and Innovation, University of Idaho
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39
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Abstract
Wild mammalian species, including bats, constitute the natural reservoir of betacoronavirus (including SARS, MERS, and the deadly SARS-CoV-2). Different hosts or host tissues provide different cellular environments, especially different antiviral and RNA modification activities that can alter RNA modification signatures observed in the viral RNA genome. The zinc finger antiviral protein (ZAP) binds specifically to CpG dinucleotides and recruits other proteins to degrade a variety of viral RNA genomes. Many mammalian RNA viruses have evolved CpG deficiency. Increasing CpG dinucleotides in these low-CpG viral genomes in the presence of ZAP consistently leads to decreased viral replication and virulence. Because ZAP exhibits tissue-specific expression, viruses infecting different tissues are expected to have different CpG signatures, suggesting a means to identify viral tissue-switching events. The author shows that SARS-CoV-2 has the most extreme CpG deficiency in all known betacoronavirus genomes. This suggests that SARS-CoV-2 may have evolved in a new host (or new host tissue) with high ZAP expression. A survey of CpG deficiency in viral genomes identified a virulent canine coronavirus (alphacoronavirus) as possessing the most extreme CpG deficiency, comparable with that observed in SARS-CoV-2. This suggests that the canine tissue infected by the canine coronavirus may provide a cellular environment strongly selecting against CpG. Thus, viral surveys focused on decreasing CpG in viral RNA genomes may provide important clues about the selective environments and viral defenses in the original hosts.
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Affiliation(s)
- Xuhua Xia
- Department of Biology, University of Ottawa, Ottawa, ON, Canada
- Ottawa Institute of Systems Biology, University of Ottawa, Ottawa, ON, Canada
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40
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Digard P, Lee HM, Sharp C, Grey F, Gaunt E. Intra-genome variability in the dinucleotide composition of SARS-CoV-2. Virus Evol 2020; 6:veaa057. [PMID: 33029383 PMCID: PMC7454914 DOI: 10.1093/ve/veaa057] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
CpG dinucleotides are under-represented in the genomes of single-stranded RNA viruses, and SARS-CoV-2 is no exception to this. Artificial modification of CpG frequency is a valid approach for live attenuated vaccine development; if this is to be applied to SARS-CoV-2, we must first understand the role CpG motifs play in regulating SARS-CoV-2 replication. Accordingly, the CpG composition of the SARS-CoV-2 genome was characterised. CpG suppression among coronaviruses does not differ between virus genera but does vary with host species and primary replication site (a proxy for tissue tropism), supporting the hypothesis that viral CpG content may influence cross-species transmission. Although SARS-CoV-2 exhibits overall strong CpG suppression, this varies considerably across the genome, and the Envelope (E) open reading frame (ORF) and ORF10 demonstrate an absence of CpG suppression. Across the Coronaviridae, E genes display remarkably high variation in CpG composition, with those of SARS and SARS-CoV-2 having much higher CpG content than other coronaviruses isolated from humans. This is an ancestrally derived trait reflecting their bat origins. Conservation of CpG motifs in these regions suggests that they have a functionality which over-rides the need to suppress CpG; an observation relevant to future strategies towards a rationally attenuated SARS-CoV-2 vaccine.
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Affiliation(s)
- Paul Digard
- Department of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Hui Min Lee
- Department of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Colin Sharp
- Department of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Finn Grey
- Department of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
| | - Eleanor Gaunt
- Department of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Easter Bush Campus, Midlothian, EH25 9RG, UK
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41
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Khodary SM, Anwar AM. Insights into The Codon Usage Bias of 13 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Isolates from Different Geo-locations. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2020:2020.04.01.019463. [PMID: 34013275 PMCID: PMC8132235 DOI: 10.1101/2020.04.01.019463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 06/12/2023]
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of Coronavirus disease 2019 (COVID-19) which is an infectious disease that spread throughout the world and was declared as a pandemic by the World Health Organization (WHO). In this study, we performed a genome-wide analysis on the codon usage bias (CUB) of 13 SARS-CoV-2 isolates from different geo-locations (countries) in an attempt to characterize it, unravel the main force shaping its pattern, and understand its adaptation to Homo sapiens . Overall results revealed that, SARS-CoV-2 codon usage is slightly biased similarly to other RNA viruses. Nucleotide and dinucleotide compositions displayed a bias toward A/U content in all codon positions and CpU-ended codons preference, respectively. Eight common putative preferred codons were identified, and all of them were A/U-ended (U-ended: 7, A-ended: 1). In addition, natural selection was found to be the main force structuring the codon usage pattern of SARS-CoV-2. However, mutation pressure and other factors such as compositional constraints and hydrophobicity had an undeniable contribution. Two adaptation indices were utilized and indicated that SARS-CoV-2 is moderately adapted to Homo sapiens compared to other human viruses. The outcome of this study may help in understanding the underlying factors involved in the evolution of SARS-CoV-2 and may aid in vaccine design strategies.
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42
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Sun J, Ren C, Huang Y, Chao W, Xie F. The effects of synonymous codon usages on genotypic formation of open reading frames in hepatitis E virus. INFECTION GENETICS AND EVOLUTION 2020; 85:104450. [PMID: 32629045 DOI: 10.1016/j.meegid.2020.104450] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 06/08/2020] [Accepted: 06/27/2020] [Indexed: 12/27/2022]
Abstract
Hepatitis E virus (HEV) infection has emerged as an important public health issue. As a zoonotic RNA virus, new strains are continuously discovered from human or various animal species. However, the capability of cross-species infection varies largely among different strains. Because the classical nucleotide-based genotyping system provides little functional insight, this study aimed to comprehensively investigate codon usage of the HEV coding regions for better understanding the evolutional orientation, virus-host interaction and cross-species transmission. We observed significant differences of the four nucleotide usages in the three open reading frames, indicating that the evolutional tendency of HEV caused by mutation pressure is modified by the evolutional dynamic related to positive selection. Furthermore, significant differences of nucleotide usages were found among HEV isolated from different host species, suggesting an important role of natural selection related to the host. Analysis of effective number of codons revealed distinct degrees of biased codon usage caused by mutation pressure or the host. Finally, we have mapped the similarity levels of the overall codon usage between the virus and the host to assess the potential of cross-species infection. Thus, this study has provided a novel aspect for better understanding the HEV genetic orientation and the zoonotic nature.
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Affiliation(s)
- Jing Sun
- Geriatrics Department, The Second Hospital of Lanzhou University, Lanzhou University, No. 82 Cuiying Men, Chengguan District, Lanzhou City, Gansu Province 730000, China
| | - Caiqin Ren
- Geriatrics Department, The Second Hospital of Lanzhou University, Lanzhou University, No. 82 Cuiying Men, Chengguan District, Lanzhou City, Gansu Province 730000, China
| | - Ying Huang
- Maxillofacial Surgery Department, The Second Hospital of Lanzhou University, Lanzhou University, No. 82 Cuiying Men, Chengguan District, Lanzhou City, Gansu Province 730000, China
| | - Wenhan Chao
- Geriatrics Department, The Second Hospital of Lanzhou University, Lanzhou University, No. 82 Cuiying Men, Chengguan District, Lanzhou City, Gansu Province 730000, China
| | - Fuqiang Xie
- Maxillofacial Surgery Department, The Second Hospital of Lanzhou University, Lanzhou University, No. 82 Cuiying Men, Chengguan District, Lanzhou City, Gansu Province 730000, China.
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43
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Martínez MA, Jordan-Paiz A, Franco S, Nevot M. Synonymous genome recoding: a tool to explore microbial biology and new therapeutic strategies. Nucleic Acids Res 2020; 47:10506-10519. [PMID: 31584076 PMCID: PMC6846928 DOI: 10.1093/nar/gkz831] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 09/12/2019] [Accepted: 09/30/2019] [Indexed: 12/18/2022] Open
Abstract
Synthetic genome recoding is a new means of generating designed organisms with altered phenotypes. Synonymous mutations introduced into the protein coding region tolerate modifications in DNA or mRNA without modifying the encoded proteins. Synonymous genome-wide recoding has allowed the synthetic generation of different small-genome viruses with modified phenotypes and biological properties. Recently, a decreased cost of chemically synthesizing DNA and improved methods for assembling DNA fragments (e.g. lambda red recombination and CRISPR-based editing) have enabled the construction of an Escherichia coli variant with a 4-Mb synthetic synonymously recoded genome with a reduced number of sense codons (n = 59) encoding the 20 canonical amino acids. Synonymous genome recoding is increasing our knowledge of microbial interactions with innate immune responses, identifying functional genome structures, and strategically ameliorating cis-inhibitory signaling sequences related to splicing, replication (in eukaryotes), and complex microbe functions, unraveling the relevance of codon usage for the temporal regulation of gene expression and the microbe mutant spectrum and adaptability. New biotechnological and therapeutic applications of this methodology can easily be envisaged. In this review, we discuss how synonymous genome recoding may impact our knowledge of microbial biology and the development of new and better therapeutic methodologies.
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Affiliation(s)
- Miguel Angel Martínez
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Badalona, Spain
| | - Ana Jordan-Paiz
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Badalona, Spain
| | - Sandra Franco
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Badalona, Spain
| | - Maria Nevot
- IrsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona (UAB), Badalona, Spain
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44
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Nchioua R, Bosso M, Kmiec D, Kirchhoff F. Cellular Factors Targeting HIV-1 Transcription and Viral RNA Transcripts. Viruses 2020; 12:v12050495. [PMID: 32365692 PMCID: PMC7290996 DOI: 10.3390/v12050495] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Revised: 04/24/2020] [Accepted: 04/27/2020] [Indexed: 02/06/2023] Open
Abstract
Restriction factors are structurally and functionally diverse cellular proteins that constitute a first line of defense against viral pathogens. Exceptions exist, but typically these proteins are upregulated by interferons (IFNs), target viral components, and are rapidly evolving due to the continuous virus–host arms race. Restriction factors may target HIV replication at essentially each step of the retroviral replication cycle, and the suppression of viral transcription and the degradation of viral RNA transcripts are emerging as major innate immune defense mechanisms. Recent data show that some antiviral factors, such as the tripartite motif-containing protein 22 (TRIM22) and the γ-IFN-inducible protein 16 (IFI16), do not target HIV-1 itself but limit the availability of the cellular transcription factor specificity protein 1 (Sp1), which is critical for effective viral gene expression. In addition, several RNA-interacting cellular factors including RNAse L, the NEDD4-binding protein 1 (N4BP1), and the zinc finger antiviral protein (ZAP) have been identified as important immune effectors against HIV-1 that may be involved in the maintenance of the latent viral reservoirs, representing the major obstacle against viral elimination and cure. Here, we review recent findings on specific cellular antiviral factors targeting HIV-1 transcription or viral RNA transcripts and discuss their potential role in viral latency.
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Affiliation(s)
- Rayhane Nchioua
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (R.N.); (M.B.)
| | - Matteo Bosso
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (R.N.); (M.B.)
| | - Dorota Kmiec
- Department of Infectious Diseases, King’s College London, Guy’s Hospital, London SE1 9RT, UK;
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, 89081 Ulm, Germany; (R.N.); (M.B.)
- Correspondence: ; Tel.: +49-731-5006-5150
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45
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Caudill VR, Qin S, Winstead R, Kaur J, Tisthammer K, Pineda EG, Solis C, Cobey S, Bedford T, Carja O, Eggo RM, Koelle K, Lythgoe K, Regoes R, Roy S, Allen N, Aviles M, Baker BA, Bauer W, Bermudez S, Carlson C, Castellanos E, Catalan FL, Chemel AK, Elliot J, Evans D, Fiutek N, Fryer E, Goodfellow SM, Hecht M, Hopp K, Hopson ED, Jaberi A, Kinney C, Lao D, Le A, Lo J, Lopez AG, López A, Lorenzo FG, Luu GT, Mahoney AR, Melton RL, Nascimento GD, Pradhananga A, Rodrigues NS, Shieh A, Sims J, Singh R, Sulaeman H, Thu R, Tran K, Tran L, Winters EJ, Wong A, Pennings PS. CpG-creating mutations are costly in many human viruses. Evol Ecol 2020; 34:339-359. [PMID: 32508375 PMCID: PMC7245597 DOI: 10.1007/s10682-020-10039-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 03/11/2020] [Indexed: 01/26/2023]
Abstract
Mutations can occur throughout the virus genome and may be beneficial, neutral or deleterious. We are interested in mutations that yield a C next to a G, producing CpG sites. CpG sites are rare in eukaryotic and viral genomes. For the eukaryotes, it is thought that CpG sites are rare because they are prone to mutation when methylated. In viruses, we know less about why CpG sites are rare. A previous study in HIV suggested that CpG-creating transition mutations are more costly than similar non-CpG-creating mutations. To determine if this is the case in other viruses, we analyzed the allele frequencies of CpG-creating and non-CpG-creating mutations across various strains, subtypes, and genes of viruses using existing data obtained from Genbank, HIV Databases, and Virus Pathogen Resource. Our results suggest that CpG sites are indeed costly for most viruses. By understanding the cost of CpG sites, we can obtain further insights into the evolution and adaptation of viruses.
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Affiliation(s)
- Victoria R. Caudill
- Department of Biology, San Francisco State University, San Francisco, CA USA
- Department of Biology, University of Oregon, Eugene, OR USA
| | - Sarina Qin
- Department of Biology, San Francisco State University, San Francisco, CA USA
- Quantitative Systems Biology, Univeristy of California, Merced, CA USA
| | - Ryan Winstead
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Jasmeen Kaur
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Kaho Tisthammer
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - E. Geo Pineda
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Caroline Solis
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Sarah Cobey
- Department of Ecology and Evolution, University of Chicago, Chicago, IL USA
| | - Trevor Bedford
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA USA
| | - Oana Carja
- Department of Computational Biology, School of Computer Science, Carnegie Mellon University, Pittsburgh, USA
| | - Rosalind M. Eggo
- Department of Infectious Disease Epidemiology, London School of Hygiene & Tropical Medicine, London, UK
| | - Katia Koelle
- Department of Biology, Emory University, Atlanta, GA USA
| | | | - Roland Regoes
- Department of Environmental Systems Science, ETH Zurich, Zurich, Switzerland
| | - Scott Roy
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Nicole Allen
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Milo Aviles
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Brittany A. Baker
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - William Bauer
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Shannel Bermudez
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Corey Carlson
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Edgar Castellanos
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Francisca L. Catalan
- Department of Biology, San Francisco State University, San Francisco, CA USA
- Department of Neurological Surgery, University of California, San Francisco, CA USA
| | | | - Jacob Elliot
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Dwayne Evans
- Department of Biology, San Francisco State University, San Francisco, CA USA
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA USA
| | - Natalie Fiutek
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Emily Fryer
- Department of Biology, San Francisco State University, San Francisco, CA USA
- Department of Plant Biology, Carnegie Institution for Science, Stanford, CA USA
| | - Samuel Melvin Goodfellow
- Department of Biology, San Francisco State University, San Francisco, CA USA
- Health Sciences Center, University of New Mexico, Albuquerque, NM USA
| | - Mordecai Hecht
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Kellen Hopp
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - E. Deshawn Hopson
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Amirhossein Jaberi
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Christen Kinney
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Derek Lao
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Adrienne Le
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Jacky Lo
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Alejandro G. Lopez
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Andrea López
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Fernando G. Lorenzo
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Gordon T. Luu
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Andrew R. Mahoney
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Rebecca L. Melton
- Department of Biology, San Francisco State University, San Francisco, CA USA
- UCSD Biomed Sciences PhD Program, University of California, San Diego, CA USA
| | | | - Anjani Pradhananga
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Nicole S. Rodrigues
- Department of Biology, San Francisco State University, San Francisco, CA USA
- Biochemistry, Molecular, Cellular and Developmental Biology Graduate Group, University of California, Davis, CA USA
| | - Annie Shieh
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Jasmine Sims
- Department of Biology, San Francisco State University, San Francisco, CA USA
- UCSF Tetrad Graduate Program, University of California, San Francisco, CA USA
| | - Rima Singh
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Hasan Sulaeman
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Ricky Thu
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Krystal Tran
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Livia Tran
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | | | - Albert Wong
- Department of Biology, San Francisco State University, San Francisco, CA USA
| | - Pleuni S. Pennings
- Department of Biology, San Francisco State University, San Francisco, CA USA
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46
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Groenke N, Trimpert J, Merz S, Conradie AM, Wyler E, Zhang H, Hazapis OG, Rausch S, Landthaler M, Osterrieder N, Kunec D. Mechanism of Virus Attenuation by Codon Pair Deoptimization. Cell Rep 2020; 31:107586. [DOI: 10.1016/j.celrep.2020.107586] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2019] [Revised: 03/06/2020] [Accepted: 04/08/2020] [Indexed: 12/17/2022] Open
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47
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Development of a new oral poliovirus vaccine for the eradication end game using codon deoptimization. NPJ Vaccines 2020; 5:26. [PMID: 32218998 PMCID: PMC7083942 DOI: 10.1038/s41541-020-0176-7] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2019] [Accepted: 02/14/2020] [Indexed: 11/30/2022] Open
Abstract
Enormous progress has been made in global efforts to eradicate poliovirus, using live-attenuated Sabin oral poliovirus vaccine (OPV). However, as the incidence of disease due to wild poliovirus has declined, vaccine-derived poliovirus (VDPV) has emerged in areas of low-vaccine coverage. Coordinated global cessation of routine, type 2 Sabin OPV (OPV2) use has not resulted in fewer VDPV outbreaks, and continued OPV use in outbreak-response campaigns has seeded new emergences in low-coverage areas. The limitations of existing vaccines and current eradication challenges warranted development of more genetically stable OPV strains, most urgently for OPV2. Here, we report using codon deoptimization to further attenuate Sabin OPV2 by changing preferred codons across the capsid to non-preferred, synonymous codons. Additional modifications to the 5′ untranslated region stabilized known virulence determinants. Testing of this codon-deoptimized new OPV2 candidate (nOPV2-CD) in cell and animal models demonstrated that nOPV2-CD is highly attenuated, grows sufficiently for vaccine manufacture, is antigenically indistinguishable from Sabin OPV2, induces neutralizing antibodies as effectively as Sabin OPV2, and unlike Sabin OPV2 is genetically stable and maintains an attenuation phenotype. In-human clinical trials of nOPV2-CD are ongoing, with potential for nOPV strains to serve as critical vaccine tools for achieving and maintaining polio eradication.
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48
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Ficarelli M, Antzin-Anduetza I, Hugh-White R, Firth AE, Sertkaya H, Wilson H, Neil SJD, Schulz R, Swanson CM. CpG Dinucleotides Inhibit HIV-1 Replication through Zinc Finger Antiviral Protein (ZAP)-Dependent and -Independent Mechanisms. J Virol 2020; 94:e01337-19. [PMID: 31748389 PMCID: PMC7158733 DOI: 10.1128/jvi.01337-19] [Citation(s) in RCA: 46] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2019] [Accepted: 11/06/2019] [Indexed: 02/07/2023] Open
Abstract
CpG dinucleotides are suppressed in the genomes of many vertebrate RNA viruses, including HIV-1. The cellular antiviral protein ZAP (zinc finger antiviral protein) binds CpGs and inhibits HIV-1 replication when CpGs are introduced into the viral genome. However, it is not known if ZAP-mediated restriction is the only mechanism driving CpG suppression. To determine how CpG dinucleotides affect HIV-1 replication, we increased their abundance in multiple regions of the viral genome and analyzed the effect on RNA expression, protein abundance, and infectious-virus production. We found that the antiviral effect of CpGs was not correlated with their abundance. Interestingly, CpGs inserted into some regions of the genome sensitize the virus to ZAP antiviral activity more efficiently than insertions into other regions, and this sensitivity can be modulated by interferon treatment or ZAP overexpression. Furthermore, the sensitivity of the virus to endogenous ZAP was correlated with its sensitivity to the ZAP cofactor KHNYN. Finally, we show that CpGs in some contexts can also inhibit HIV-1 replication by ZAP-independent mechanisms, and one of these is the activation of a cryptic splice site at the expense of a canonical splice site. Overall, we show that the location and sequence context of the CpG in the viral genome determines its antiviral activity.IMPORTANCE Some RNA virus genomes are suppressed in the nucleotide combination of a cytosine followed by a guanosine (CpG), indicating that they are detrimental to the virus. The antiviral protein ZAP binds viral RNA containing CpGs and prevents the virus from multiplying. However, it remains unknown how the number and position of CpGs in viral genomes affect restriction by ZAP and whether CpGs have other antiviral mechanisms. Importantly, manipulating the CpG content in viral genomes could help create new vaccines. HIV-1 shows marked CpG suppression, and by introducing CpGs into its genome, we show that ZAP efficiently targets a specific region of the viral genome, that the number of CpGs does not predict the magnitude of antiviral activity, and that CpGs can inhibit HIV-1 gene expression through a ZAP-independent mechanism. Overall, the position of CpGs in the HIV-1 genome determines the magnitude and mechanism through which they inhibit the virus.
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Affiliation(s)
- Mattia Ficarelli
- Department of Infectious Diseases, King's College London, London, United Kingdom
| | | | - Rupert Hugh-White
- Department of Medical and Molecular Genetics, King's College London, London, United Kingdom
| | - Andrew E Firth
- Division of Virology, University of Cambridge, Cambridge, United Kingdom
| | - Helin Sertkaya
- Department of Infectious Diseases, King's College London, London, United Kingdom
| | - Harry Wilson
- Department of Infectious Diseases, King's College London, London, United Kingdom
| | - Stuart J D Neil
- Department of Infectious Diseases, King's College London, London, United Kingdom
| | - Reiner Schulz
- Department of Medical and Molecular Genetics, King's College London, London, United Kingdom
| | - Chad M Swanson
- Department of Infectious Diseases, King's College London, London, United Kingdom
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49
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Trus I, Udenze D, Berube N, Wheler C, Martel MJ, Gerdts V, Karniychuk U. CpG-Recoding in Zika Virus Genome Causes Host-Age-Dependent Attenuation of Infection With Protection Against Lethal Heterologous Challenge in Mice. Front Immunol 2020; 10:3077. [PMID: 32038625 PMCID: PMC6993062 DOI: 10.3389/fimmu.2019.03077] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 12/17/2019] [Indexed: 12/12/2022] Open
Abstract
Experimental increase of CpG dinucleotides in an RNA virus genome impairs infection providing a promising approach for vaccine development. While CpG recoding is an emerging and promising vaccine approach, little is known about infection phenotypes caused by recoded viruses in vivo. For example, infection phenotypes, immunogenicity, and protective efficacy induced by CpG-recoded viruses in different age groups were not studied yet. This is important, because attenuation of infection phenotypes caused by recoded viruses may depend on the population-based expression of cellular components targeting viral CpG dinucleotides. In the present study, we generated several Zika virus (ZIKV) variants with the increasing CpG content and compared infection in neonatal and adult mice. Increasing the CpG content caused host-age-dependent attenuation of infection with considerable attenuation in neonates and high attenuation in adults. Expression of the zinc-finger antiviral protein (ZAP)—the host protein targeting viral CpG dinucleotides—was also age-dependent. Similar to the wild-type virus, ZIKV variants with the increased CpG content evoked robust cellular and humoral immune responses and protection against lethal challenge. Collectively, the host age should be accounted for in future studies on mechanisms targeting viral CpG dinucleotides, development of safe dinucleotide recoding strategies, and applications of CpG-recoded vaccines.
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Affiliation(s)
- Ivan Trus
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada
| | - Daniel Udenze
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada.,School of Public Health, University of Saskatchewan, Saskatoon, SK, Canada
| | - Nathalie Berube
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada
| | - Colette Wheler
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada
| | - Marie-Jocelyne Martel
- Department of Obstetrics and Gynecology, College of Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Volker Gerdts
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada.,Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
| | - Uladzimir Karniychuk
- Vaccine and Infectious Disease Organization-International Vaccine Centre (VIDO-InterVac), University of Saskatchewan, Saskatoon, SK, Canada.,School of Public Health, University of Saskatchewan, Saskatoon, SK, Canada.,Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK, Canada
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50
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Kmiec D, Nchioua R, Sherrill-Mix S, Stürzel CM, Heusinger E, Braun E, Gondim MVP, Hotter D, Sparrer KMJ, Hahn BH, Sauter D, Kirchhoff F. CpG Frequency in the 5' Third of the env Gene Determines Sensitivity of Primary HIV-1 Strains to the Zinc-Finger Antiviral Protein. mBio 2020; 11:e02903-19. [PMID: 31937644 PMCID: PMC6960287 DOI: 10.1128/mbio.02903-19] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 11/27/2019] [Indexed: 02/07/2023] Open
Abstract
CpG dinucleotide suppression has been reported to allow HIV-1 to evade inhibition by the zinc-finger antiviral protein (ZAP). Here, we show that primate lentiviruses display marked differences in CpG frequencies across their genome, ranging from 0.44% in simian immunodeficiency virus SIVwrc from Western red colobus to 2.3% in SIVmon infecting mona monkeys. Moreover, functional analyses of a large panel of human and simian immunodeficiency viruses revealed that the magnitude of CpG suppression does not correlate with their susceptibility to ZAP. However, we found that the number of CpG dinucleotides within a region of ∼700 bases at the 5' end of the env gene determines ZAP sensitivity of primary HIV-1 strains but not of HIV-2. Increased numbers of CpGs in this region were associated with reduced env mRNA expression and viral protein production. ZAP sensitivity profiles of chimeric simian-human immunodeficiency viruses (SHIVs) expressing different HIV-1 env genes were highly similar to those of the corresponding HIV-1 strains. The frequency of CpGs in the identified env region correlated with differences in clinical progression rates. Thus, the CpG frequency in a specific part of env, rather than the overall genomic CpG content, governs the susceptibility of HIV-1 to ZAP and might affect viral pathogenicity in vivoIMPORTANCE Evasion of the zinc-finger antiviral protein (ZAP) may drive CpG dinucleotide suppression in HIV-1 and many other viral pathogens but the viral determinants of ZAP sensitivity are poorly defined. Here, we examined CpG suppression and ZAP sensitivity in a large number of primate lentiviruses and demonstrate that their genomic frequency of CpGs varies substantially and does not correlate with ZAP sensitivity. We further show that the number of CpG residues in a defined region at the 5' end of the env gene together with structural features plays a key role in HIV-1 susceptibility to ZAP and correlates with differences in clinical progression rates in HIV-1-infected individuals. Our identification of a specific part of env as a major determinant of HIV-1 susceptibility to ZAP restriction provides a basis for future studies of the underlying inhibitory mechanisms and their potential relevance in the pathogenesis of AIDS.
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Affiliation(s)
- Dorota Kmiec
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Rayhane Nchioua
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Scott Sherrill-Mix
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Christina M Stürzel
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Elena Heusinger
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Elisabeth Braun
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Marcos V P Gondim
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Dominik Hotter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | | | - Beatrice H Hahn
- Department of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania, USA
- Department of Microbiology, University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Daniel Sauter
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
| | - Frank Kirchhoff
- Institute of Molecular Virology, Ulm University Medical Center, Ulm, Germany
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