1
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Cottingham E, Johnstone T, Vaz PK, Hartley CA, Devlin JM. Construction and in vitro characterisation of virus-vectored immunocontraceptive candidates derived from felid alphaherpesvirus 1. Vaccine 2024:S0264-410X(24)00615-7. [PMID: 38824082 DOI: 10.1016/j.vaccine.2024.05.047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2024] [Revised: 05/16/2024] [Accepted: 05/20/2024] [Indexed: 06/03/2024]
Abstract
There is a pressing need for effective feral cat management globally due to overabundant feline populations, disease transmission and their destructive impact on biodiversity. Virus-vectored immunocontraception (VVIC) is an attractive method for cat population management. Virus-vectored immunocontraceptives could be self-disseminating through horizontal transmission of the VVIC in feral cat populations, or they may be modified to act as non-transmissible vaccine-type immunocontraceptives for delivery to individual cats. These later constructs may be particularly attractive for use in owned (pet) cats and stray cats but could also be used for feral cats that are caught, vaccinated, and released. Here, we report the construction of three felid alphaherpesvirus 1 (FHV-1) derived immunocontraceptive candidates containing genes that encode for feline zona pellucida subunit 3 (ZP3) and gonadotropin-releasing hormone (GnRH). Two of the vaccine candidates were engineered to include disruptions to the thymidine kinase viral virulence gene to reduce the ability of the vaccines to be horizontally transmitted. Analysis of in vitro growth characteristics and protein expression are reported, and their potential for use as a population management tool for cats is discussed.
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Affiliation(s)
- Ellen Cottingham
- The Asia Pacific Centre for Animal Health, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Thurid Johnstone
- ARH Essendon Fields, 72 Hargraves Ave, Melbourne (Essendon Fields), VIC 3014, Australia
| | - Paola K Vaz
- The Asia Pacific Centre for Animal Health, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Carol A Hartley
- The Asia Pacific Centre for Animal Health, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Joanne M Devlin
- The Asia Pacific Centre for Animal Health, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
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2
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Shan KJ, Wu C, Tang X, Lu R, Hu Y, Tan W, Lu J. Molecular Evolution of Protein Sequences and Codon Usage in Monkeypox Viruses. GENOMICS, PROTEOMICS & BIOINFORMATICS 2024; 22:qzad003. [PMID: 38862422 DOI: 10.1093/gpbjnl/qzad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 10/06/2023] [Accepted: 10/11/2023] [Indexed: 06/13/2024]
Abstract
The monkeypox virus (mpox virus, MPXV) epidemic in 2022 has posed a significant public health risk. Yet, the evolutionary principles of MPXV remain largely unknown. Here, we examined the evolutionary patterns of protein sequences and codon usage in MPXV. We first demonstrated the signal of positive selection in OPG027, specifically in the Clade I lineage of MPXV. Subsequently, we discovered accelerated protein sequence evolution over time in the variants responsible for the 2022 outbreak. Furthermore, we showed strong epistasis between amino acid substitutions located in different genes. The codon adaptation index (CAI) analysis revealed that MPXV genes tended to use more non-preferred codons compared to human genes, and the CAI decreased over time and diverged between clades, with Clade I > IIa and IIb-A > IIb-B. While the decrease in fatality rate among the three groups aligned with the CAI pattern, it remains unclear whether this correlation was coincidental or if the deoptimization of codon usage in MPXV led to a reduction in fatality rates. This study sheds new light on the mechanisms that govern the evolution of MPXV in human populations.
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Affiliation(s)
- Ke-Jia Shan
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
- Sinovac Biotech Ltd., Beijing 100085, China
| | - Changcheng Wu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Xiaolu Tang
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
| | - Roujian Lu
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Yaling Hu
- Sinovac Biotech Ltd., Beijing 100085, China
| | - Wenjie Tan
- NHC Key Laboratory of Biosafety, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100052, China
| | - Jian Lu
- State Key Laboratory of Protein and Plant Gene Research, Center for Bioinformatics, School of Life Sciences, Peking University, Beijing 100871, China
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Paremskaia AI, Kogan AA, Murashkina A, Naumova DA, Satish A, Abramov IS, Feoktistova SG, Mityaeva ON, Deviatkin AA, Volchkov PY. Codon-optimization in gene therapy: promises, prospects and challenges. Front Bioeng Biotechnol 2024; 12:1371596. [PMID: 38605988 PMCID: PMC11007035 DOI: 10.3389/fbioe.2024.1371596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Accepted: 03/19/2024] [Indexed: 04/13/2024] Open
Abstract
Codon optimization has evolved to enhance protein expression efficiency by exploiting the genetic code's redundancy, allowing for multiple codon options for a single amino acid. Initially observed in E. coli, optimal codon usage correlates with high gene expression, which has propelled applications expanding from basic research to biopharmaceuticals and vaccine development. The method is especially valuable for adjusting immune responses in gene therapies and has the potenial to create tissue-specific therapies. However, challenges persist, such as the risk of unintended effects on protein function and the complexity of evaluating optimization effectiveness. Despite these issues, codon optimization is crucial in advancing gene therapeutics. This study provides a comprehensive review of the current metrics for codon-optimization, and its practical usage in research and clinical applications, in the context of gene therapy.
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Affiliation(s)
- Anastasiia Iu Paremskaia
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, Moscow, Russia
| | - Anna A. Kogan
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, Moscow, Russia
| | - Anastasiia Murashkina
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, Moscow, Russia
| | - Daria A. Naumova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, Moscow, Russia
| | - Anakha Satish
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, Moscow, Russia
| | - Ivan S. Abramov
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, Moscow, Russia
- The MCSC named after A. S. Loginov, Moscow, Russia
| | - Sofya G. Feoktistova
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, Moscow, Russia
| | - Olga N. Mityaeva
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, Moscow, Russia
| | - Andrei A. Deviatkin
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, Moscow, Russia
| | - Pavel Yu Volchkov
- Federal Research Center for Innovator and Emerging Biomedical and Pharmaceutical Technologies, Moscow, Russia
- The MCSC named after A. S. Loginov, Moscow, Russia
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4
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Hsieh WS, Chao CH, Shen CY, Cheng D, Huang SW, Wang YF, Chen CC, Chen SH, Hsu LJ, Wang JR. VP1 codon deoptimization and high-fidelity substitutions in 3D polymerase as potential vaccine strategies for eliciting immune responses against enterovirus A71. J Virol 2024; 98:e0155823. [PMID: 38174926 PMCID: PMC10804986 DOI: 10.1128/jvi.01558-23] [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: 10/05/2023] [Accepted: 11/24/2023] [Indexed: 01/05/2024] Open
Abstract
Enterovirus A71 (EV-A71) can induce severe neurological complications and even fatal encephalitis in children, and it has caused several large outbreaks in Taiwan since 1998. We previously generated VP1 codon-deoptimized (VP1-CD) reverse genetics (rg) EV-A71 viruses (rgEV-A71s) that harbor a high-fidelity (HF) 3D polymerase. These VP1-CD-HF rgEV-A71s showed lower replication kinetics in vitro and decreased virulence in an Institute of Cancer Research (ICR) mouse model of EV-A71 infection, while still retaining their antigenicity in comparison to the wild-type virus. In this study, we aimed to further investigate the humoral and cellular immune responses elicited by VP1-CD-HF rgEV-A71s to assess the potential efficacy of these EV-A71 vaccine candidates. Following intraperitoneal (i.p.) injection of VP1-CD-HF rgEV-A71s in mice, we observed a robust induction of EV-A71-specific neutralizing IgG antibodies in the antisera after 21 days. Splenocytes isolated from VP1-CD-HF rgEV-A71s-immunized mice exhibited enhanced proliferative activities and cytokine production (IL-2, IFN-γ, IL-4, IL-6, and TNF-α) upon re-stimulation with VP1-CD-HF rgEV-A71, as compared to control mice treated with adjuvant only. Importantly, administration of antisera from VP1-CD-HF rgEV-A71s-immunized mice protected against lethal EV-A71 challenge in neonatal mice. These findings highlight that our generated VP1-CD-HF rgEV-A71 viruses are capable of inducing both cellular and humoral immune responses, supporting their potential as next-generation EV-A71 vaccines for combating EV-A71 infection.IMPORTANCEEV-A71 can cause severe neurological diseases and cause death in young children. Here, we report the development of synthetic rgEV-A71s with the combination of codon deoptimization and high-fidelity (HF) substitutions that generate genetically stable reverse genetics (rg) viruses as potential attenuated vaccine candidates. Our work provides insight into the development of low-virulence candidate vaccines through a series of viral genetic editing for maintaining antigenicity and genome stability and suggests a strategy for the development of an innovative next-generation vaccine against EV-A71.
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Affiliation(s)
- Wen-Sheng Hsieh
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chiao-Hsuan Chao
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Chun-Yu Shen
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Dayna Cheng
- The Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Sheng-Wen Huang
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Tainan, Taiwan
| | - Ya-Fang Wang
- National Mosquito-Borne Diseases Control Research Center, National Health Research Institutes, Tainan, Taiwan
| | - Chien-Chin Chen
- Department of Biotechnology and Bioindustry Sciences, College of Bioscience and Biotechnology, National Cheng Kung University, Tainan, Taiwan
- Department of Pathology, Ditmanson Medical Foundation Chia-Yi Christian Hospital, Chiayi, Taiwan
- Department of Cosmetic Science, Chia Nan University of Pharmacy and Science, Tainan, Taiwan
| | - Shun-Hua Chen
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
| | - Li-Jin Hsu
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- The Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
| | - Jen-Ren Wang
- Department of Medical Laboratory Science and Biotechnology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- The Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
- Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan
- National Institute of Infectious Diseases and Vaccinology, National Health Research Institutes, Tainan, Taiwan
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5
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Wu Q, Kinoti WM, Habili N, Tyerman SD, Rinaldo A, Constable FE. Genetic Diversity of Grapevine Virus A in Three Australian Vineyards Using Amplicon High Throughput Sequencing (Amplicon-HTS). Viruses 2023; 16:42. [PMID: 38257742 PMCID: PMC10819895 DOI: 10.3390/v16010042] [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: 11/03/2023] [Revised: 12/18/2023] [Accepted: 12/25/2023] [Indexed: 01/24/2024] Open
Abstract
Shiraz disease (SD) is one of the most destructive viral diseases of grapevines in Australia and is known to cause significant economic loss to local growers. Grapevine virus A (GVA) was reported to be the key pathogen associated with this disease. This study aimed to better understand the diversity of GVA variants both within and between individual SD and grapevine leafroll disease (LRD) affected grapevines located at vineyards in South Australia. Amplicon high throughput sequencing (Amplicon-HTS) combined with median-joining networks (MJNs) was used to analyze the variability in specific gene regions of GVA variants. Several GVAII variant groups contain samples from both vineyards studied, suggesting that these GVAII variants were from a common origin. Variant groups analyzed by MJNs using the overall data set denote that there may be a possible relationship between variant groups of GVA and the geographical location of the grapevines.
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Affiliation(s)
- Qi Wu
- School of Agriculture, Food and Wine, University of Adelaide, Waite Precinct, PMB 1, Glen Osmond, SA 5064, Australia (S.D.T.)
- Australian Wine Research Institute, Wine Innovation Central Building, Hartley Grove crn Paratoo Road, Urrbrae, SA 5064, Australia
| | - Wycliff M. Kinoti
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia
| | - Nuredin Habili
- School of Agriculture, Food and Wine, University of Adelaide, Waite Precinct, PMB 1, Glen Osmond, SA 5064, Australia (S.D.T.)
- Australian Wine Research Institute, Wine Innovation Central Building, Hartley Grove crn Paratoo Road, Urrbrae, SA 5064, Australia
| | - Stephen D. Tyerman
- School of Agriculture, Food and Wine, University of Adelaide, Waite Precinct, PMB 1, Glen Osmond, SA 5064, Australia (S.D.T.)
| | - Amy Rinaldo
- Australian Wine Research Institute, Wine Innovation Central Building, Hartley Grove crn Paratoo Road, Urrbrae, SA 5064, Australia
| | - Fiona E. Constable
- Agriculture Victoria Research, Department of Energy, Environment and Climate Action, AgriBio, Centre for AgriBioscience, 5 Ring Road, Bundoora, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3086, Australia
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6
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Guo F, Yang J, Abd El-Aty AM, Wang R, Ju X. Base composition, adaptation, and evolution of goose astroviruses: codon-based investigation. Poult Sci 2023; 102:103029. [PMID: 37713803 PMCID: PMC10511809 DOI: 10.1016/j.psj.2023.103029] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Revised: 07/24/2023] [Accepted: 08/11/2023] [Indexed: 09/01/2023] Open
Abstract
Goose astroviruses (GoAstVs) are causative agents that account for fatal infection of goslings characterized by visceral urate deposition, resulting in severe economic losses in major goose-producing regions in China since 2017. In this study, we sought to unravel the intrinsic properties associated with adaptation and evolution in the host environment of GoAstVs. Consistent results from phylogenetic analysis and correspondence analysis performed on the codon usage patterns (CUPs) reveal 2 clusters of GoAstVs, namely, GoAstV-1 and GoAstV-2. However, multiple similar compositional characteristics were found, despite the high divergence between GoAstV-1 and GoAstV-2. Studies on the base composition of GoAstVs reveal an A/U bias, indicating a compositional constraint, while natural selection prevailed in determining the CUPs in the virus genome based on our neutrality plot analysis, reflecting high adaptive pressure to fit the host environment. Codon adaptation index (CAI) analysis revealed a higher degree of fitness to the CUPs of the corresponding host for GoAstVs than avian influenza virus and betacoronaviruses, which may be a favorable factor contributing to the high pathogenicity and wide distribution of GoAstVs in goslings. In addition, GoAstVs were less adapted to ducks and chickens, with significantly lower CAI values than to geese, which may be a reason for the different prevalence of GoAstVs among these species. Extensive investigations on dinucleotide distribution revealed a significant suppression of the CpG and UpA motifs in the virus genome, which may facilitate adaptation to the host's innate immune system by evading surveillance. In addition, our study reported the trends of increasing fitness to the host's microenvironment for GoAstVs through increasing adaptation to host CUPs and ongoing reduction of CpG motifs in the virus genome. The present analysis deepens our understanding of the basic biology, pathogenesis, adaptation and evolutionary pattern of GoAstVs, and contributes to the development of novel antiviral strategies.
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Affiliation(s)
- Fucheng Guo
- Department of Veterinary Medicine, College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, China
| | - Jinjin Yang
- Technology Center of Zhanjiang Customs District, Zhanjiang, 524000, Guangdong, China
| | - A M Abd El-Aty
- Department of Pharmacology, Faculty of Veterinary Medicine, Cairo University, 12211 Giza, Egypt; Department of Medical Pharmacology, Medical Faculty, Ataturk University, Erzurum 25240, Turkey
| | - Ruichen Wang
- Chinese Center for Disease Control and Prevention, National Institute for Viral Disease Control and Prevention, Beijing 102206, China
| | - Xianghong Ju
- Department of Veterinary Medicine, College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang, 524088, China; Marine Medical Research and Development Centre, Shenzhen Institute of Guangdong Ocean University, Shenzhen 518120, China.
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7
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Chin WX, Kong HY, Zhu IXY, Teo ZY, Faruk R, Lee RCH, Ho SX, Aw ZQ, Yi B, Hou XJ, Tan AKY, Yogarajah T, Huber RG, Cai Y, Wan Y, Chu JJH. Flavivirus genome recoding by codon optimisation confers genetically stable in vivo attenuation in both mice and mosquitoes. PLoS Pathog 2023; 19:e1011753. [PMID: 37883598 PMCID: PMC10629665 DOI: 10.1371/journal.ppat.1011753] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 11/07/2023] [Accepted: 10/14/2023] [Indexed: 10/28/2023] Open
Abstract
Virus genome recoding is an attenuation method that confers genetically stable attenuation by rewriting a virus genome with numerous silent mutations. Prior flavivirus genome recoding attempts utilised codon deoptimisation approaches. However, these codon deoptimisation approaches act in a species dependent manner and were unable to confer flavivirus attenuation in mosquito cells or in mosquito animal models. To overcome these limitations, we performed flavivirus genome recoding using the contrary approach of codon optimisation. The genomes of flaviviruses such as dengue virus type 2 (DENV2) and Zika virus (ZIKV) contain functional RNA elements that regulate viral replication. We hypothesised that flavivirus genome recoding by codon optimisation would introduce silent mutations that disrupt these RNA elements, leading to decreased replication efficiency and attenuation. We chose DENV2 and ZIKV as representative flaviviruses and recoded them by codon optimising their genomes for human expression. Our study confirms that this recoding approach of codon optimisation does translate into reduced replication efficiency in mammalian, human, and mosquito cells as well as in vivo attenuation in both mice and mosquitoes. In silico modelling and RNA SHAPE analysis confirmed that DENV2 recoding resulted in the extensive disruption of genomic structural elements. Serial passaging of recoded DENV2 resulted in the emergence of rescue or adaptation mutations, but no reversion mutations. These rescue mutations were unable to rescue the delayed replication kinetics and in vivo attenuation of recoded DENV2, demonstrating that recoding confers genetically stable attenuation. Therefore, our recoding approach is a reliable attenuation method with potential applications for developing flavivirus vaccines.
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Affiliation(s)
- Wei-Xin Chin
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology and Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Hao Yuin Kong
- NUSMed Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Isabelle Xin Yu Zhu
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology and Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Zi Yun Teo
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology and Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Regina Faruk
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology and Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Regina Ching Hua Lee
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology and Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Si Xian Ho
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology and Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Zhen Qin Aw
- NUSMed Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Bowen Yi
- NUSMed Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
| | - Xin Jun Hou
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Antson Kiat Yee Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Thinesshwary Yogarajah
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology and Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
| | - Roland G. Huber
- Bioinformatics Institute, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Yu Cai
- Temasek Life Sciences Laboratory, 1 Research Link, National University of Singapore, Singapore
- Department of Biological Sciences, National University of Singapore, Singapore
| | - Yue Wan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Justin Jang Hann Chu
- Laboratory of Molecular RNA Virology and Antiviral Strategies, Department of Microbiology and Immunology and Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University Health System, National University of Singapore, Singapore
- NUSMed Biosafety Level 3 Core Facility, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A*STAR), Singapore
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8
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Zhou J, Wang X, Zhou Z, Wang S. Insights into the Evolution and Host Adaptation of the Monkeypox Virus from a Codon Usage Perspective: Focus on the Ongoing 2022 Outbreak. Int J Mol Sci 2023; 24:11524. [PMID: 37511283 PMCID: PMC10380431 DOI: 10.3390/ijms241411524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 07/12/2023] [Accepted: 07/13/2023] [Indexed: 07/30/2023] Open
Abstract
The exceptionally widespread outbreak of human monkeypox, an emerging zoonosis caused by the monkeypox virus (MPXV), with more than 69,000 confirmed cases in 100 non-endemic countries since 2022, is a major public health concern. Codon usage patterns reflect genetic variation and adaptation to new hosts and ecological niches. However, detailed analyses of codon usage bias in MPXV based on large-scale genomic data, especially for strains responsible for the 2022 outbreak, are lacking. In this study, we analyzed codon usage in MPXV and its relationship with host adaptation. We confirmed the ongoing outbreak of MPXVs belonging to the West Africa (WA) lineage by principal component analysis based on their codon usage patterns. The 2022 outbreak strains had a relatively low codon usage bias. Codon usage of MPXVs was shaped by mutation and natural selection; however, different from past strains, codon usage in the 2022 outbreak strains was predominantly determined by mutation pressure. Additionally, as revealed by the codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses, the codon usage patterns of MPXVs were also affected by their hosts. In particular, the 2022 outbreak strains showed slightly but significantly greater adaptation to many primates, including humans, and were subjected to stronger selection pressure induced by hosts. Our results suggest that MPXVs contributing to the 2022 outbreak have unique evolutionary features, emphasizing the importance of sustained monitoring of their transmission and evolution.
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Affiliation(s)
- Jianglin Zhou
- Bioinformatics Center of AMMS, Beijing 100850, China
| | - Xuejun Wang
- Bioinformatics Center of AMMS, Beijing 100850, China
| | - Zhe Zhou
- Bioinformatics Center of AMMS, Beijing 100850, China
| | - Shengqi Wang
- Bioinformatics Center of AMMS, Beijing 100850, China
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9
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Noor F, Ashfaq UA, Bakar A, Qasim M, Masoud MS, Alshammari A, Alharbi M, Riaz MS. Identification and characterization of codon usage pattern and influencing factors in HFRS-causing hantaviruses. Front Immunol 2023; 14:1131647. [PMID: 37492567 PMCID: PMC10364125 DOI: 10.3389/fimmu.2023.1131647] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2022] [Accepted: 06/22/2023] [Indexed: 07/27/2023] Open
Abstract
Hemorrhagic fever with renal syndrome (HFRS) is an acute viral zoonosis carried and transmitted by infected rodents through urine, droppings, or saliva. The etiology of HFRS is complex due to the involvement of viral factors and host immune and genetic factors which hinder the development of potential therapeutic solutions for HFRS. Hantaan virus (HTNV), Dobrava-Belgrade virus (DOBV), Seoul virus (SEOV), and Puumala virus (PUUV) are predominantly found in hantaviral species that cause HFRS in patients. Despite ongoing prevention and control efforts, HFRS remains a serious economic burden worldwide. Furthermore, recent studies reported that the hantavirus nucleocapsid protein is a multi-functional protein and plays a major role in the replication cycle of the hantavirus. However, the precise mechanism of the nucleoproteins in viral pathogenesis is not completely understood. In the framework of the current study, various in silico approaches were employed to identify the factors influencing the codon usage pattern of hantaviral nucleoproteins. Based on the relative synonymous codon usage (RSCU) values, a comparative analysis was performed between HFRS-causing hantavirus and their hosts, suggesting that HTNV, DOBV, SEOV, and PUUV, were inclined to evolve their codon usage patterns that were comparable to those of their hosts. The results indicated that most of the overrepresented codons had AU-endings, which revealed that mutational pressure is the major force shaping codon usage patterns. However, the influence of natural selection and geographical factors cannot be ignored on viral codon usage bias. Further analysis also demonstrated that HFRS causing hantaviruses adapted host-specific codon usage patterns to sustain successful replication and transmission chains within hosts. To our knowledge, no study to date reported the factors influencing the codon usage pattern within hantaviral nucleoproteins. Thus, the proposed computational scheme can help in understanding the underlying mechanism of codon usage patterns in HFRS-causing hantaviruses which lend a helping hand in designing effective anti-HFRS treatments in future. This study, although comprehensive, relies on in silico methods and thus necessitates experimental validation for more solid outcomes. Beyond the identified factors influencing viral behavior, there could be other yet undiscovered influences. These potential factors should be targets for further research to improve HFRS therapeutic strategies.
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Affiliation(s)
- Fatima Noor
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Usman Ali Ashfaq
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Abu Bakar
- Centre of Agricultural Biochemistry and Biotechnology (CABB), University of Agriculture, Faisalabad, Pakistan
| | - Muhammad Qasim
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Muhammad Shareef Masoud
- Department of Bioinformatics and Biotechnology, Government College University, Faisalabad, Pakistan
| | - Abdulrahman Alshammari
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Metab Alharbi
- Department of Pharmacology and Toxicology, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
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10
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Medina GN, Spinard E, Azzinaro PA, Rodriguez-Calzada M, Gutkoska J, Kloc A, Rieder EA, Taillon BE, Mueller S, de Los Santos T, Segundo FDS. Deoptimization of FMDV P1 Region Results in Robust Serotype-Independent Viral Attenuation. Viruses 2023; 15:1332. [PMID: 37376631 DOI: 10.3390/v15061332] [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: 04/16/2023] [Revised: 05/23/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
Foot-and-mouth disease (FMD), caused by the FMD virus (FMDV), is a highly contagious disease of cloven-hoofed livestock that can have severe economic impacts. Control and prevention strategies, including the development of improved vaccines, are urgently needed to effectively control FMD outbreaks in endemic settings. Previously, we employed two distinct strategies (codon pair bias deoptimization (CPD) and codon bias deoptimization (CD)) to deoptimize various regions of the FMDV serotype A subtype A12 genome, which resulted in the development of an attenuated virus in vitro and in vivo, inducing varying levels of humoral responses. In the current study, we examined the versatility of the system by using CPD applied to the P1 capsid coding region of FMDV serotype A subtype, A24, and another serotype, Asia1. Viruses carrying recoded P1 (A24-P1Deopt or Asia1-P1Deopt) exhibited different degrees of attenuation (i.e., delayed viral growth kinetics and replication) in cultured cells. Studies in vivo using a mouse model of FMD demonstrated that inoculation with the A24-P1Deopt and Asia1-P1Deopt strains elicited a strong humoral immune response capable of offering protection against challenge with homologous wildtype (WT) viruses. However, different results were obtained in pigs. While clear attenuation was detected for both the A24-P1Deopt and Asia1-P1Deopt strains, only a limited induction of adaptive immunity and protection against challenge was detected, depending on the inoculated dose and serotype deoptimized. Our work demonstrates that while CPD of the P1 coding region attenuates viral strains of multiple FMDV serotypes/subtypes, a thorough assessment of virulence and induction of adaptive immunity in the natural host is required in each case in order to finely adjust the degree of deoptimization required for attenuation without affecting the induction of protective adaptive immune responses.
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Affiliation(s)
- Gisselle N Medina
- Plum Island Animal Disease Center (PIADC), ARS, USDA, Greenport, NY 11944, USA
- National Bio and Agro-Defense Facility (NBAF), ARS, USDA, Manhattan, KS 66502, USA
| | - Edward Spinard
- Plum Island Animal Disease Center (PIADC), ARS, USDA, Greenport, NY 11944, USA
| | - Paul A Azzinaro
- Plum Island Animal Disease Center (PIADC), ARS, USDA, Greenport, NY 11944, USA
| | - Monica Rodriguez-Calzada
- Plum Island Animal Disease Center (PIADC), ARS, USDA, Greenport, NY 11944, USA
- ORISE-PIADC Research Participation Program, Oak Ridge, TN 37831, USA
| | - Joseph Gutkoska
- Plum Island Animal Disease Center (PIADC), ARS, USDA, Greenport, NY 11944, USA
| | - Anna Kloc
- Department of Biology and Environmental Sciences, University of New Haven, West Haven, CT 06516, USA
| | - Elizabeth A Rieder
- Plum Island Animal Disease Center (PIADC), ARS, USDA, Greenport, NY 11944, USA
| | | | | | | | - Fayna Diaz-San Segundo
- Plum Island Animal Disease Center (PIADC), ARS, USDA, Greenport, NY 11944, USA
- National Institute of Health, NIAID, DMID, OBRRTR, Bethesda, MD 20892, USA
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11
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Khandia R, Khan AA, Karuvantevida N, Gurjar P, Rzhepakovsky IV, Legaz I. Insights into Synonymous Codon Usage Bias in Hepatitis C Virus and Its Adaptation to Hosts. Pathogens 2023; 12:pathogens12020325. [PMID: 36839597 PMCID: PMC9961758 DOI: 10.3390/pathogens12020325] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 01/25/2023] [Accepted: 02/02/2023] [Indexed: 02/17/2023] Open
Abstract
Hepatitis C virus (HCV) is enveloped RNA virus, encoding for a polyprotein that is processed by cellular proteases. The virus is responsible for liver cirrhosis, allograft rejection, and human hepatocellular carcinoma. Based on studies including compositional analysis, odds ratio analysis, parity analysis, skew analysis, relative synonymous codon usage, codon bias, and protein properties, it was evident that codon usage bias in HCV is dependent upon the nucleotide composition. Codon context analysis revealed CTC-CTG as a preferred codon pair. While CGA and CGT codons were rare, none of the codons were rare in HCV-like viruses envisaged in the present study. Many of the preferred codon pairs were valine amino acid-initiated, which possibly infers viral infectivity; hence the role of selection forces appears to act on the HCV genome, which was further validated by neutrality analysis where selection accounted for 87.28%, while mutation accounted for 12.72% force shaping codon usage. Furthermore, codon usage was correlated with the length of the genome. HCV viruses prefer valine-initiated codon pairs, while HCV-like viruses prefer alanine-initiated codon pairs. The HCV host range is very narrow and is confined to only humans and chimpanzees. Based on indices including codon usage correlation analysis, similarity index, and relative codon deoptimization index, it is evident in the study that the chimpanzee is the primary host of the virus. The present study helped elucidate the preferred host for HCV. The information presented in the study paved the way for generating an attenuated vaccine candidate through viral recoding, with finely tuned nucleotide composition and a perfect balance of preferred and rare codons.
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Affiliation(s)
- Rekha Khandia
- Department of Biochemistry and Genetics, Barkatullah University, Bhopal 462026, India
- Correspondence: (R.K.); (I.L.)
| | - Azmat Ali Khan
- Pharmaceutical Biotechnology Laboratory, Department of Pharmaceutical Chemistry, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia
| | - Noushad Karuvantevida
- College of Medicine, Mohammed Bin Rashid University of Medicine and Health Sciences, Dubai P.O. Box 505055, United Arab Emirates
| | - Pankaj Gurjar
- Department of Science and Engineering, Novel Global Community Educational Foundation, Hebersham, NSW 2770, Australia
| | | | - Isabel Legaz
- Department of Legal and Forensic Medicine, Biomedical Research Institute (IMIB), Regional Campus of International Excellence “Campus Mare Nostrum”, Faculty of Medicine, University of Murcia, 30120 Murcia, Spain
- Correspondence: (R.K.); (I.L.)
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12
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Aloke C, Obasi NA, Aja PM, Emelike CU, Egwu CO, Jeje O, Edeogu CO, Onisuru OO, Orji OU, Achilonu I. Combating Lassa Fever in West African Sub-Region: Progress, Challenges, and Future Perspectives. Viruses 2023; 15:146. [PMID: 36680186 PMCID: PMC9864412 DOI: 10.3390/v15010146] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 12/28/2022] [Accepted: 12/28/2022] [Indexed: 01/05/2023] Open
Abstract
Lassa fever (LF) is a rodent-borne disease that threatens human health in the sub-region of West Africa where the zoonotic host of Lassa virus (LASV) is predominant. Currently, treatment options for LF are limited and since no preventive vaccine is approved for its infectivity, there is a high mortality rate in endemic areas. This narrative review explores the transmission, pathogenicity of LASV, advances, and challenges of different treatment options. Our findings indicate that genetic diversity among the different strains of LASV and their ability to circumvent the immune system poses a critical challenge to the development of LASV vaccines/therapeutics. Thus, understanding the biochemistry, physiology and genetic polymorphism of LASV, mechanism of evading host immunity are essential for development of effective LASV vaccines/therapeutics to combat this lethal viral disease. The LASV nucleoprotein (NP) is a novel target for therapeutics as it functions significantly in several aspects of the viral life cycle. Consequently, LASV NP inhibitors could be employed as effective therapeutics as they will potentially inhibit LASV replication. Effective preventive control measures, vaccine development, target validation, and repurposing of existing drugs, such as ribavirin, using activity or in silico-based and computational bioinformatics, would aid in the development of novel drugs for LF management.
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Affiliation(s)
- Chinyere Aloke
- Protein Structure-Function and Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Braamfontein, Johannesburg 2050, South Africa
- Department of Medical Biochemistry, Alex Ekwueme Federal University Ndufu-Alike, Abakaliki PMB 1010, Ebonyi State, Nigeria
| | - Nwogo Ajuka Obasi
- Department of Medical Biochemistry, Alex Ekwueme Federal University Ndufu-Alike, Abakaliki PMB 1010, Ebonyi State, Nigeria
| | - Patrick Maduabuchi Aja
- Department of Biochemistry, Faculty of Biological Sciences, Ebonyi State University, Abakaliki PMB 053, Ebonyi State, Nigeria
- Department of Biochemistry, Faculty of Medicine, Mbarara University of Science and Technology (MUST), Mbarara P.O. Box 1410, Uganda
- Department of Medical Biochemistry, Kampala International University, Bushenyi, Ishaka P.O. Box 71, Uganda
| | - Chinedum Uche Emelike
- Department of Physiology, Alex Ekwueme Federal University Ndufu-Alike, Abakaliki PMB 1010, Ebonyi State, Nigeria
| | - Chinedu Ogbonnia Egwu
- Department of Medical Biochemistry, Alex Ekwueme Federal University Ndufu-Alike, Abakaliki PMB 1010, Ebonyi State, Nigeria
| | - Olamide Jeje
- Protein Structure-Function and Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Braamfontein, Johannesburg 2050, South Africa
| | - Chuks Oswald Edeogu
- Department of Medical Biochemistry, Faculty of Basic Medical Sciences, Ebonyi State University, Abakaliki PMB 053, Ebonyi State, Nigeria
| | - Olalekan Olugbenga Onisuru
- Protein Structure-Function and Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Braamfontein, Johannesburg 2050, South Africa
| | - Obasi Uche Orji
- Department of Biochemistry, Faculty of Biological Sciences, Ebonyi State University, Abakaliki PMB 053, Ebonyi State, Nigeria
| | - Ikechukwu Achilonu
- Protein Structure-Function and Research Unit, School of Molecular and Cell Biology, Faculty of Science, University of the Witwatersrand, Braamfontein, Johannesburg 2050, South Africa
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13
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Desingu PA, Rubeni TP, Sundaresan NR. Evolution of monkeypox virus from 2017 to 2022: In the light of point mutations. Front Microbiol 2022; 13:1037598. [PMID: 36590408 PMCID: PMC9795006 DOI: 10.3389/fmicb.2022.1037598] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2022] [Accepted: 11/24/2022] [Indexed: 12/23/2022] Open
Abstract
Monkeypox virus (MPXV) causing multi-country outbreak-2022 is related to viruses caused outbreak-2017-2018 in West Africa. Still not fully understood which proteins of the MPXV discovered in Nigeria in 2017 have mutated through different lineages to the extent that it could cause a multi-country outbreak in 2022; similarly, codon usage bias, host adaptation indices, and the role of selection or mutation pressure in the mutated genes are also not fully studied. Here we report that according to the available sequence data this monkeypox virus acquires point mutations in multiple proteins in each period, and these point mutations accumulate and become a virus that can root outbreak-2022. Viruses exported from Nigeria to Singapore, Israel, and the United Kingdom in 2018-2019 were developed as evolutionary ancestors to B.1 viruses (MPXVs causing multi-country outbreak-2022) through MPXV/United States/2021/MD virus. Although these exported viruses have different amino acid mutations in different proteins, amino acid mutations in 10 proteins are common among them. The MPXV-United Kingdom-P2 virus evolved with only mutations in these 10 proteins and further evolved into MPXV/United States/2021/MD with amino acid mutations in 26 (including amino acid mutations in 10 proteins of the MPXV-United States-P2) proteins. It is noteworthy that specific amino acid mutations in these 22/26 (presence in MPXV/United States/2021/MD) proteins are present in B.1 viruses. Further, analysis of Relative Synonymous Codon Usage (RSCU), Synonymous Codon Usage Fraction (SCUF), and Effective Number of Codons (ENc) revealed codon usage bias in genes that exhibited nucleotide mutations in lineage B.1. Also, host adaptation indices analyzes such as Codon Adaptation Index (CAI), Expected-CAI (eCAI), Relative Codon Deoptimization Index (RCDI) and Expected value for the RCDI (eRCDI) analyzes reveal that the genes that demonstrated nucleotide mutations in lineage B.1 are favorable for human adaptation. Similarly, ENc-GC3s plot, Neutrality plot, and Parity Rule 2 (PR2)-bias plot analyzes suggest a major role of selection pressure than mutation pressure in the evolution of genes displaying nucleotide mutations in lineage B.1. Overall, from 2017 to 2022, MPXV's mutation and spread suggests that this virus continues to evolve through point mutation in the genes according to the available sequence data.
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Murphy H, Ly H. Understanding Immune Responses to Lassa Virus Infection and to Its Candidate Vaccines. Vaccines (Basel) 2022; 10:1668. [PMID: 36298533 PMCID: PMC9612042 DOI: 10.3390/vaccines10101668] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/27/2022] [Accepted: 09/28/2022] [Indexed: 11/29/2022] Open
Abstract
Lassa fever (LF) is a deadly viral hemorrhagic fever disease that is endemic in several countries in West Africa. It is caused by Lassa virus (LASV), which has been estimated to be responsible for approximately 300,000 infections and 5000 deaths annually. LASV is a highly pathogenic human pathogen without effective therapeutics or FDA-approved vaccines. Here, we aim to provide a literature review of the current understanding of the basic mechanism of immune responses to LASV infection in animal models and patients, as well as to several of its candidate vaccines.
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Affiliation(s)
| | - Hinh Ly
- Comparative & Molecular Biosciences Graduate Program, Department of Veterinary & Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, Twin Cities, St Paul, MN 55108, USA
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15
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Jiang L, Zhang Q, Xiao S, Si F. Deep decoding of codon usage strategies and host adaption preferences of soybean mosaic virus. Int J Biol Macromol 2022; 222:803-817. [PMID: 36167098 DOI: 10.1016/j.ijbiomac.2022.09.179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 09/13/2022] [Accepted: 09/17/2022] [Indexed: 11/05/2022]
Abstract
Soybean mosaic virus (SMV) has threatened the global yield of Leguminosae crops, but the mechanism of its infection, spread, and evolution remains unknown. A systemic analysis of 107 SMV strains was performed to explore the genome-wide codon usage profile and the various factors influencing the codon usage patterns of SMV, which provides insight into its molecular evolution and elucidates its unknown host adaptation pattern. The overall nucleotide composition and correlation analysis revealed that the preferred synonymous codons mostly end with A/U. Clustering by RSCU value of each strain and phylogenetic tree analysis showed that the SMV isolates studied were divided into four clades, with a low overall extent of codon usage bias (CUB) in SMV. According to the ENC, PR2, neutrality plot, and correspondence analysis, natural selection of geographical diversity may play a critical role in the CUB. Higher adaptability was shown in Glycine with SMV and more pressure was received by clade III. These findings could not only provide valuable information about the overall codon usage pattern of the SMV genome, but could also aid in the clarification of the involved mechanisms that dominate the codon usage patterns and genetic evolution of the SMV genome.
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Affiliation(s)
- Li Jiang
- Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Qiang Zhang
- Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, Zhengzhou 450009, China
| | - Shimin Xiao
- Shanwei Marine Industry Institute, Shanwei Institute of Technology, Shanwei 516600, China.
| | - Fusheng Si
- Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Shanghai 201106, China.
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16
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Sophiarani Y, Chakraborty S. Comparison of compositional constraints: Nuclear genome vs plasmid genome of Pseudomonas syringae pv. tomato DC3000. J Biosci 2022. [DOI: 10.1007/s12038-022-00296-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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17
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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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18
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Reverse genetics in virology: A double edged sword. BIOSAFETY AND HEALTH 2022. [DOI: 10.1016/j.bsheal.2022.08.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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19
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Zeng L, Chen M, Wang M, Zhu L, Yan J, Zhang X, Xu J, Zhang S. Enterovirus A Shows Unique Patterns of Codon Usage Bias in Conventional Versus Unconventional Clade. Front Cell Infect Microbiol 2022; 12:941325. [PMID: 35909978 PMCID: PMC9329520 DOI: 10.3389/fcimb.2022.941325] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 06/21/2022] [Indexed: 11/13/2022] Open
Abstract
Enterovirus A (EV-A) species cause hand, foot and mouth disease (HFMD), threatening the health of young children. Understanding the mutual codon usage pattern of the virus and its host(s) has fundamental and applied values. Here, through examining multiple codon usage parameters, we found that the codon usage bias among EV-A strains varies and is clade-specific. EVA76, EVA89, EVA90, EVA91 and EVA92, the unconventional clade of EV-A strains, show unique codon usage pattern relative to the two conventional clades, including EVA71, CVA16, CVA6 and CVA10, etc. Analyses of Effective Number of Codon (ENC), Correspondence Analysis (COA) and Parity Rule 2 (PR2), etc., revealed that the codon usage patterns of EV-A strains are shaped by mutation pressure and natural selection. Based on the neutrality analysis, we determined the dominant role of natural selection in the formation of the codon usage bias of EV-A. In addition, we have determined the codon usage compatibility of potential hosts for EV-A strains using codon adaptation index (CAI), relative codon deoptimization index (RCDI) and similarity index (SiD) analyses, and found that EV-A showed host-specific codon adaptation patterns in different clades. Finally, we confirmed that the unique codon usage pattern of the unconventional clade affected protein expression level in human cell lines. In conclusion, we identified novel characteristics of codon usage bias in distinct EV-A clades associated with their host range, transmission and pathogenicity.
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Affiliation(s)
- Liyan Zeng
- Shanghai Public Health Clinical center AND Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Ming Chen
- Shanghai Public Health Clinical center AND Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Min Wang
- Shanghai Public Health Clinical center AND Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Liuyao Zhu
- Shanghai Public Health Clinical center AND Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Jingjing Yan
- Shanghai Public Health Clinical center AND Institutes of Biomedical Sciences, Fudan University, Shanghai, China
| | - Xiaoyan Zhang
- Shanghai Public Health Clinical center AND Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- *Correspondence: Shuye Zhang, ; Xiaoyan Zhang, ; Jianqing Xu,
| | - Jianqing Xu
- Shanghai Public Health Clinical center AND Institutes of Biomedical Sciences, Fudan University, Shanghai, China
- *Correspondence: Shuye Zhang, ; Xiaoyan Zhang, ; Jianqing Xu,
| | - Shuye Zhang
- Clinical Center for BioTherapy & Institutes of Biomedical Sciences, Zhongshan Hospital, Fudan University, Shanghai, China
- *Correspondence: Shuye Zhang, ; Xiaoyan Zhang, ; Jianqing Xu,
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20
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Multiple Levels of Triggered Factors and the Obligated Requirement of Cell-to-Cell Movement in the Mutation Repair of Cucumber Mosaic Virus with Defects in the tRNA-like Structure. BIOLOGY 2022; 11:biology11071051. [PMID: 36101429 PMCID: PMC9312275 DOI: 10.3390/biology11071051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 11/17/2022]
Abstract
Simple Summary Based on analysis of the tRNA-like structure (TLS) mutation in cucumber mosaic virus (CMV), mutation repair is correlated with several levels of triggered factors, including the dose of inoculation of virus mutants, the quantity effect on corresponding viral RNA, and the quality effect on corresponding viral RNA. All types of TLS mutation in different RNAs of CMV can be repaired at a low dose around the dilution end-point. At a high dose of inoculation, TLS mutations in RNA2 and RNA3, but not RNA1, can be repaired, which correlates with the relative quantity defect of RNA2 or the genome size defect of RNA3. In addition, all the above types of mutation repair necessarily require cell-to-cell movement, which presents the obligated effect of cell-to-cell movement on mutation repair. Abstract Some debilitating mutations in RNA viruses are repairable; however, the triggering factors of mutation repair remain largely unknown. In this study, multiple triggering factors of mutation repair are identified based on genetic damage to the TLS in CMV. TLS mutations in different RNAs distinctively impact viral pathogenicity and present different types of mutation repair. RNA2 relative reduction level or RNA3 sequence change resulting from TLS mutation is correlated with a high rate of mutation repair, and the TLS mutation of RNA1 fails to be repaired at the high inoculum dose. However, the TLS mutation of RNA1 can be repaired at a low dose of inoculation, particularly around the dilution end-point or in the mixed inoculation with RNA2 having a pre-termination mutation of the 2b gene, an RNAi suppressor. Taken together, TLS mutations resulting in quality or quantity defects of the viral genome or TLS mutations at low doses around the dilution end-point are likely to be repaired. Different levels of TLS mutation repair necessarily require cell-to-cell movement, therefore implying its obligated effect on the evolution of low-fitness viruses and providing a new insight into Muller’s ratchet. This study provides important information on virus evolution and the application of mild viral vaccines.
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21
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Wang Q, Lyu X, Cheng J, Fu Y, Lin Y, Abdoulaye AH, Jiang D, Xie J. Codon Usage Provides Insights into the Adaptive Evolution of Mycoviruses in Their Associated Fungi Host. Int J Mol Sci 2022; 23:ijms23137441. [PMID: 35806445 PMCID: PMC9267111 DOI: 10.3390/ijms23137441] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Revised: 06/29/2022] [Accepted: 06/30/2022] [Indexed: 11/16/2022] Open
Abstract
Codon usage bias (CUB) could reflect co-evolutionary changes between viruses and hosts in contrast to plant and animal viruses, and the systematic analysis of codon usage among the mycoviruses that infect plant pathogenic fungi is limited. We performed an extensive analysis of codon usage patterns among 98 characterized RNA mycoviruses from eight phytopathogenic fungi. The GC and GC3s contents of mycoviruses have a wide variation from 29.35% to 64.62% and 24.32% to 97.13%, respectively. Mycoviral CUB is weak, and natural selection plays a major role in the formation of mycoviral codon usage pattern. In this study, we demonstrated that the codon usage of mycoviruses is similar to that of some host genes, especially those involved in RNA biosynthetic process and transcription, suggesting that CUB is a potential evolutionary mechanism that mycoviruses adapt to in their hosts.
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Affiliation(s)
- Qianqian Wang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (X.L.); (J.C.); (A.H.A.); (D.J.)
- The Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Xueliang Lyu
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (X.L.); (J.C.); (A.H.A.); (D.J.)
- The Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
| | - Jiasen Cheng
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (X.L.); (J.C.); (A.H.A.); (D.J.)
- The Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
| | - Yanping Fu
- The Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
| | - Yang Lin
- The Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
| | - Assane Hamidou Abdoulaye
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (X.L.); (J.C.); (A.H.A.); (D.J.)
- The Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
| | - Daohong Jiang
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (X.L.); (J.C.); (A.H.A.); (D.J.)
- The Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
| | - Jiatao Xie
- State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (Q.W.); (X.L.); (J.C.); (A.H.A.); (D.J.)
- The Hubei Key Lab of Plant Pathology, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China; (Y.F.); (Y.L.)
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Correspondence: ; Tel.: +86-185-027-36960
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22
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Li B, Wu H, Miao Z, Hu L, Zhou L, Lu Y. Codon Usage of Hepatitis E Viruses: A Comprehensive Analysis. Front Microbiol 2022; 13:938651. [PMID: 35801104 PMCID: PMC9253588 DOI: 10.3389/fmicb.2022.938651] [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: 05/07/2022] [Accepted: 05/30/2022] [Indexed: 11/25/2022] Open
Abstract
Hepatitis E virus (HEV) is an emerging zoonotic pathogen with multiple species and genotypes, which may be classified into human, animal, and zoonotic HEV. Codon usage bias of HEV remained unclear. This study aims to characterize the codon usage of HEV and elucidate the main drivers influencing the codon usage bias. A total of seven HEV genotypes, HEV-1 (human HEV), HEV-3 and HEV-4 (zoonotic HEV), HEV-8, HEV-B, HEV-C1, and HEV-C2 (emerging animal HEV), were included in the study. Complete coding sequences, ORF1, ORF2, and ORF3, were accordingly obtained in the GenBank. Except for HEV-8, the other six genotypes tended to use codons ending in G/C. Based on the analysis of relatively synonymous codon usage (RSCU) and principal component analysis (PCA), codon usage bias was determined for HEV genotypes. Codon usage bias differed widely across human, zoonotic, and animal HEV genotypes; furthermore, it varied within certain genotypes such as HEV-4, HEV-8, and HEV-C1. In addition, dinucleotide abundance revealed that HEV was affected by translation selection to form a unique dinucleotide usage pattern. Moreover, parity rule 2 analysis (PR2), effective codon number (ENC)-plot, and neutrality analysis were jointly performed. Natural selection played a leading role in forming HEV codon usage bias, which was predominant in HEV-1, HEV-3, HEV-B and HEV-C1, while affected HEV-4, HEV-8, and HEV-C2 in combination with mutation pressure. Our findings may provide insights into HEV evolution and codon usage bias.
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Affiliation(s)
- Bingzhe Li
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
| | - Han Wu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
| | - Ziping Miao
- Institute of Communicable Diseases Prevention and Control, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Linjie Hu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
| | - Lu Zhou
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
| | - Yihan Lu
- Department of Epidemiology, Ministry of Education Key Laboratory of Public Health Safety, School of Public Health, Fudan University, Shanghai, China
- *Correspondence: Yihan Lu,
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23
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Shafat Z, Ahmed A, Parvez MK, Parveen S. Decoding the codon usage patterns in Y-domain region of hepatitis E viruses. J Genet Eng Biotechnol 2022; 20:56. [PMID: 35404024 PMCID: PMC9001762 DOI: 10.1186/s43141-022-00319-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 02/17/2022] [Indexed: 12/17/2022]
Abstract
Background Hepatitis E virus (HEV) is a positive-sense RNA virus belonging to the family Hepeviridae. The genome of HEV is organized into three open-reading frames (ORFs): ORF1, ORF2, and ORF3. The ORF1 non-structural Y-domain region (YDR) has been demonstrated to play an important role in the HEV pathogenesis. The nucleotide composition, synonymous codon usage bias in conjunction with other factors influencing the viral YDR genes of HEV have not been studied. Codon usage represents a significant mechanism in establishing the host-pathogen relationship. The present study for the first time elucidates the detailed codon usage patterns of YDR among HEV and HEV-hosts (Human, Rabbit, Mongoose, Pig, Wild boar, Camel, Monkey). Results The overall nucleotide composition revealed the abundance of C and U nucleotides in YDR genomes. The relative synonymous codon usage (RSCU) analysis indicated biasness towards C and U over A and G ended codons in HEV across all hosts. Codon frequency comparative analyses among HEV-hosts showed both similarities and discrepancies in usage of preferred codons encoding amino acids, which revealed that HEV codon preference neither completely differed nor completely showed similarity with its hosts. Thus, our results clearly indicated that the synonymous codon usage of HEV is a mixture of the two types of codon usage: coincidence and antagonism. Mutation pressure from virus and natural selection from host seems to be accountable for shaping the codon usage patterns in YDR. The study emphasised that the influence of compositional constraints, codon usage biasness, mutational alongside the selective forces were reflected in the occurrence of YDR codon usage patterns. Conclusions Our study is the first in its kind to have reported the analysis of codon usage patterns on a total of seven different natural HEV hosts. Therefore, knowledge of preferred codons obtained from our study will not only augment our understanding towards molecular evolution but is also envisaged to provide insight into the efficient viral expression, viral adaptation, and host effects on the HEV YDR codon usage. Supplementary Information The online version contains supplementary material available at 10.1186/s43141-022-00319-2.
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Affiliation(s)
- Zoya Shafat
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India
| | - Anwar Ahmed
- Centre of Excellence in Biotechnology Research, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Mohammad K Parvez
- Department of Pharmacognosy, College of Pharmacy, King Saud University, Riyadh, Saudi Arabia
| | - Shama Parveen
- Centre for Interdisciplinary Research in Basic Sciences, Jamia Millia Islamia, New Delhi, India.
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24
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Nambou K, Anakpa M, Tong YS. Human genes with codon usage bias similar to that of the nonstructural protein 1 gene of influenza A viruses are conjointly involved in the infectious pathogenesis of influenza A viruses. Genetica 2022; 150:97-115. [PMID: 35396627 PMCID: PMC8992787 DOI: 10.1007/s10709-022-00155-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Accepted: 03/24/2022] [Indexed: 11/27/2022]
Abstract
Molecular mechanisms of the non-structural protein 1 (NS1) in influenza A-induced pathological changes remain ambiguous. This study explored the pathogenesis of human infection by influenza A viruses (IAVs) through identifying human genes with codon usage bias (CUB) similar to NS1 gene of these viruses based on the relative synonymous codon usage (RSCU). CUB of the IAV subtypes H1N1, H3N2, H3N8, H5N1, H5N2, H5N8, H7N9 and H9N2 was analyzed and the correlation of RSCU values of NS1 sequences with those of the human genes was calculated. The CUB of NS1 was uneven and codons ending with A/U were preferred. The ENC-GC3 and neutrality plots suggested natural selection as the main determinant for CUB. The RCDI, CAI and SiD values showed that the viruses had a high degree of adaptability to human. A total of 2155 human genes showed significant RSCU-based correlation (p < 0.05 and r > 0.5) with NS1 coding sequences and was considered as human genes with CUB similar to NS1 gene of IAV subtypes. Differences and similarities in the subtype-specific human protein–protein interaction (PPI) networks and their functions were recorded among IAVs subtypes, indicating that NS1 of each IAV subtype has a specific pathogenic mechanism. Processes and pathways involved in influenza, transcription, immune response and cell cycle were enriched in human gene sets retrieved based on the CUB of NS1 gene of IAV subtypes. The present work may advance our understanding on the mechanism of NS1 in human infections of IAV subtypes and shed light on the therapeutic options.
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Affiliation(s)
- Komi Nambou
- Shenzhen Nambou1 Biotech Company Limited, 998 Wisdom Valley, No. 38-56 Zhenming Road, Guangming District, Shenzhen, 518106, China.
| | - Manawa Anakpa
- Centre d'Informatique et de Calcul, Université de Lomé, Boulevard Gnassingbé Eyadema, 01 B.P. 1515, Lomé, Togo
| | - Yin Selina Tong
- Shenzhen Nambou1 Biotech Company Limited, 998 Wisdom Valley, No. 38-56 Zhenming Road, Guangming District, Shenzhen, 518106, China
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25
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Codon Usage for Genetic Diversity, and Evolutionary Dynamics of Novel Porcine Parvoviruses 2 through 7 (PPV2–PPV7). Viruses 2022; 14:v14020170. [PMID: 35215764 PMCID: PMC8876854 DOI: 10.3390/v14020170] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 01/13/2022] [Accepted: 01/14/2022] [Indexed: 02/06/2023] Open
Abstract
Porcine parvovirus (PPV) is the main pathogen of reproductive disorders. In recent years, a new type of porcine parvovirus has been discovered and named porcine parvovirus 2 to 7 (PPV2–PPV7), and it is associated with porcine circovirus type 2 in pigs. Codon usage patterns and their effects on the evolution and host adaptation of different PPV sub-types are still largely unknown. Here, we define six main sub-types based on the Bayesian method of structural proteins of each sub-type of PPV, including PPV2, PPV3, PPV4, PPV5, PPV6, and PPV7, which show different degrees of codon usage preferences. The effective number of codons (ENC) indicates that all PPV sub-types have low codon bias. According to the codon adaptation index (CAI), PPV3 and PPV7 have the highest similarity with the host, which is related to the main popular tendency of the host in the field; according to the frequency of optimal codons (FOP), PPV7 has the highest frequency of optimal codons, indicating the most frequently used codons in its genes; and according to the relative codon deoptimization index (RCDI), PPV3 has a higher degree. Therefore, it is determined that mutational stress has a certain impact on the codon usage preference of PPV genes, and natural selection plays a very decisive and dominant role in the codon usage pattern. Our research provides a new perspective on the evolution of porcine parvovirus (PPV) and may help provide a new method for future research on the origin, evolutionary model, and host adaptation of PPV.
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26
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Sa-nguanmoo N, Namdee K, Khongkow M, Ruktanonchai U, Zhao Y, Liang XJ. Review: Development of SARS-CoV-2 immuno-enhanced COVID-19 vaccines with nano-platform. NANO RESEARCH 2022; 15:2196-2225. [PMID: 34659650 PMCID: PMC8501370 DOI: 10.1007/s12274-021-3832-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 08/19/2021] [Accepted: 08/19/2021] [Indexed: 05/04/2023]
Abstract
Vaccination is the most effective way to prevent coronavirus disease 2019 (COVID-19). Vaccine development approaches consist of viral vector vaccines, DNA vaccine, RNA vaccine, live attenuated virus, and recombinant proteins, which elicit a specific immune response. The use of nanoparticles displaying antigen is one of the alternative approaches to conventional vaccines. This is due to the fact that nano-based vaccines are stable, able to target, form images, and offer an opportunity to enhance the immune responses. The diameters of ultrafine nanoparticles are in the range of 1-100 nm. The application of nanotechnology on vaccine design provides precise fabrication of nanomaterials with desirable properties and ability to eliminate undesirable features. To be successful, nanomaterials must be uptaken into the cell, especially into the target and able to modulate cellular functions at the subcellular levels. The advantages of nano-based vaccines are the ability to protect a cargo such as RNA, DNA, protein, or synthesis substance and have enhanced stability in a broad range of pH, ambient temperatures, and humidity for long-term storage. Moreover, nano-based vaccines can be engineered to overcome biological barriers such as nonspecific distribution in order to elicit functions in antigen presenting cells. In this review, we will summarize on the developing COVID-19 vaccine strategies and how the nanotechnology can enhance antigen presentation and strong immunogenicity using advanced technology in nanocarrier to deliver antigens. The discussion about their safe, effective, and affordable vaccines to immunize against COVID-19 will be highlighted.
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Affiliation(s)
- Nawamin Sa-nguanmoo
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, Beijing, 100190 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
| | - Katawut Namdee
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani, 12120 Thailand
| | - Mattaka Khongkow
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani, 12120 Thailand
| | - Uracha Ruktanonchai
- National Nanotechnology Center (NANOTEC), National Science and Technology Development Agency, Pathum Thani, 12120 Thailand
| | - YongXiang Zhao
- National Center for International Research of Biotargeting Theranostics, Guangxi Key Laboratory of Biotargeting Theranostics, Collaborative Innovation Center for Targeting Tumour Theranostics and Therapy, Guangxi Medical University, Nanning, 530021 China
| | - Xing-Jie Liang
- CAS Center for Excellence in Nanoscience, CAS Key Laboratory for Biomedical Effects of Nanomaterials and Nanosafety, National Center for Nanoscience and Technology of China, Beijing, 100190 China
- University of Chinese Academy of Sciences, Beijing, 100049 China
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27
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Chen JW, Yang L, Santos C, Hassan SA, Collins PL, Buchholz UJ, Le Nouën C. Reversion mutations in phosphoprotein P of a codon-pair-deoptimized human respiratory syncytial virus confer increased transcription, immunogenicity, and genetic stability without loss of attenuation. PLoS Pathog 2021; 17:e1010191. [PMID: 34965283 PMCID: PMC8751989 DOI: 10.1371/journal.ppat.1010191] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 01/11/2022] [Accepted: 12/09/2021] [Indexed: 11/18/2022] Open
Abstract
Recoding viral genomes by introducing numerous synonymous nucleotide substitutions that create suboptimal codon pairs provides new live-attenuated vaccine candidates. Because recoding typically involves a large number of nucleotide substitutions, the risk of de-attenuation is presumed to be low. However, this has not been thoroughly studied. We previously generated human respiratory syncytial virus (RSV) in which the NS1, NS2, N, P, M and SH ORFs were codon-pair deoptimized (CPD) by 695 synonymous nucleotide changes (Min A virus). Min A exhibited a global reduction in transcription and protein synthesis, was restricted for replication in vitro and in vivo, and exhibited moderate temperature sensitivity. Here, we show that under selective pressure by serial passage at progressively increasing temperatures, Min A regained replication fitness and lost its temperature sensitivity. Whole-genome deep sequencing identified numerous missense mutations in several genes, in particular ones accumulating between codons 25 and 34 of the phosphoprotein (P), a polymerase cofactor and chaperone. When re-introduced into Min A, these P mutations restored viral transcription to wt level, resulting in increased protein expression and RNA replication. Molecular dynamic simulations suggested that these P mutations increased the flexibility of the N-terminal domain of P, which might facilitate its interaction with the nucleoprotein N, and increase the functional efficiency of the RSV transcription/replication complex. Finally, we evaluated the effect of the P mutations on Min A replication and immunogenicity in hamsters. Mutation P[F28V] paradoxically reduced Min A replication but not its immunogenicity. The further addition of one missense mutation each in M and L generated a version of Min A with increased genetic stability. Thus, this study provides further insight into the adaptability of large-scale recoded RNA viruses under selective pressure and identified an improved CPD RSV vaccine candidate. Synonymous recoding of viral genomes by codon-pair deoptimization (CPD) generates live-attenuated vaccines presumed to be genetically stable due to the high number of nucleotide substitutions. However, their actual genetic stability under selective pressure was largely unknown. In a recoded human respiratory syncytial virus (RSV) mutant called Min A, six of 11 ORFs were CPD, reducing protein expression and inducing moderate temperature sensitivity and attenuation. When passaged in vitro under selective pressure, Min A lost its temperature-sensitive phenotype and regained fitness by the acquisition of numerous mutations, in particular missense mutations in the viral phosphoprotein (P), a polymerase cofactor and a chaperone for soluble nucleoprotein. These P mutations increased RSV gene transcription globally, thereby increasing RSV protein expression, RNA replication, and virus particle production. Thus, the P mutations increased the efficiency of the RSV transcription/replication complex, compensating for the reduced protein expression due to CPD. In addition, introduction of the P mutations into Min A generated a live-attenuated vaccine candidate with increased genetic stability. Surprisingly, this vaccine candidate exhibited increased attenuation and, paradoxically, exhibited increased immunogenicity per plaque-forming unit in hamsters. This study provides insights into the adaptability of large-scale recoded RNA viruses and identified an improved CPD RSV vaccine candidate.
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Affiliation(s)
- Jessica W. Chen
- RNA Viruses Section, Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Lijuan Yang
- RNA Viruses Section, Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Celia Santos
- RNA Viruses Section, Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Sergio A. Hassan
- Bioinformatics and Computational Biosciences Branch, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Peter L. Collins
- RNA Viruses Section, Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Ursula J. Buchholz
- RNA Viruses Section, Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, Maryland, United States of America
| | - Cyril Le Nouën
- RNA Viruses Section, Laboratory of Infectious Diseases, NIAID, NIH, Bethesda, Maryland, United States of America
- * E-mail:
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28
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Zhang Z, Guo F, Roy A, Yang J, Luo W, Shen X, Irwin DM, Chen RA, Shen Y. Evolutionary perspectives and adaptation dynamics of human seasonal influenza viruses from 2009 to 2019: An insight from codon usage. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2021; 96:105067. [PMID: 34487866 DOI: 10.1016/j.meegid.2021.105067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/21/2021] [Revised: 08/28/2021] [Accepted: 09/01/2021] [Indexed: 06/13/2023]
Abstract
The annually recurrent seasonal influenza viruses, namely, influenza A viruses (H1N1/pdm2009 and H3N2) and influenza B viruses, contribute substantially to human disease burden. Elucidation of host adaptation, population dynamics and evolutionary patterns of these viruses contribute to better control of current epidemic situation and bolster efforts towards pandemic preparedness. Present study has been addressed at unraveling the signatures of codon usage and dinucleotide distribution of these seasonal influenza viruses associating with their fitness and ongoing adaptive evolution in human population. Thorough analysis of codon usage adaptation revealed that H3N2 has been exhibited best adapted to human cellular system, which correlate with its highest epidemic intensity as compared with the other seasonal influenza viruses. CpG dinucleotide was found to be strongly avoided among the seasonal influenza viruses with more restraint among influenza B viruses than influenza A viruses, and might be accounted to the strategy of the viral pathogens in evading human immune signals. Dynamic scenes of ongoing evolution in codon usage and elimination of CpG motif among the viruses, which correlate with their distinct host adaption state, signifying the marked impact of selective force operational on the viral genomes, aimed at proficient circulation, enhanced fitness and successful infective manifestations in humans.
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Affiliation(s)
- Zhipeng Zhang
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Fucheng Guo
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China
| | - Ayan Roy
- Department of Biotechnology, Lovely Professional University, Punjab, India
| | - Jinjin Yang
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Wen Luo
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Xuejuan Shen
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto M5S 1A8, Canada; Banting and Best Diabetes Centre, University of Toronto, Toronto M5S 1A8, Canada
| | - Rui-Ai Chen
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Zhaoqing Institute of Biotechnology, Zhaoqing 526238, China.
| | - Yongyi Shen
- Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing 526238, China; Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou 510642, China; Zhaoqing Institute of Biotechnology, Zhaoqing 526238, China; Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou 510642, China.
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29
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Si F, Jiang L, Yu R, Wei W, Li Z. Study on the Characteristic Codon Usage Pattern in Porcine Epidemic Diarrhea Virus Genomes and Its Host Adaptation Phenotype. Front Microbiol 2021; 12:738082. [PMID: 34733253 PMCID: PMC8558211 DOI: 10.3389/fmicb.2021.738082] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2021] [Accepted: 09/20/2021] [Indexed: 11/29/2022] Open
Abstract
Porcine epidemic diarrhea virus (PEDV), which classified in the genus Alphacoronavirus, family Coronaviridae, is one of the most important pathogens that cause heavy economic losses in pig industry. Although intensive mutation and recombination analysis of PEDV strains were provided, systematic genome analysis were needed to elucidate the evolution mechanism and codon usage adaptation profiles of the pathogen. Here, a comprehensive investigation was carried out to reveal the systematic evolutionary processes of synonymous codon usage and host-adapted evolution phenotype of PEDV genome. We found a low codon usage bias (CUB) in PEDV genome and that nucleotide compositions, natural selection, mutation pressure and geographical diversity shapes the codon usage patterns of PEDV, with natural selection dominated the overall codon usage bias in PEDV than the others. By using the relative codon deoptimization index (RCDI) and similarity index (SiD) analysis, we observed that genotype II PEDV strains showed the highest level of adaptation phenotype to Sus scrofa than another divergent clade. To the best of our knowledge, this is the first comprehensive report elaborating the codon usage and host adaptation of PEDV. The findings offer an insight into our understanding of factors involved in PEDV evolution, adaptation and fitness toward their hosts.
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Affiliation(s)
- Fusheng Si
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Li Jiang
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, China
| | - Ruisong Yu
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai, China
| | - Wenqiang Wei
- Department of Microbiology, School of Basic Medical Sciences, Henan University, Kaifeng, China
| | - Zhen Li
- Shanghai Key Laboratory of Agricultural Genetics and Breeding, Shanghai Engineering Research Center of Breeding Pig, Institute of Animal Science and Veterinary Medicine, Shanghai Academy of Agricultural Sciences, Shanghai, China
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30
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Ramos-González PL, Pons T, Chabi-Jesus C, Arena GD, Freitas-Astua J. Poorly Conserved P15 Proteins of Cileviruses Retain Elements of Common Ancestry and Putative Functionality: A Theoretical Assessment on the Evolution of Cilevirus Genomes. FRONTIERS IN PLANT SCIENCE 2021; 12:771983. [PMID: 34804105 PMCID: PMC8602818 DOI: 10.3389/fpls.2021.771983] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 10/18/2021] [Indexed: 06/13/2023]
Abstract
The genus Cilevirus groups enveloped single-stranded (+) RNA virus members of the family Kitaviridae, order Martellivirales. Proteins P15, scarcely conserved polypeptides encoded by cileviruses, have no apparent homologs in public databases. Accordingly, the open reading frames (ORFs) p15, located at the 5'-end of the viral RNA2 molecules, are considered orphan genes (ORFans). In this study, we have delved into ORFs p15 and the relatively poorly understood biochemical properties of the proteins P15 to posit their importance for viruses across the genus and theorize on their origin. We detected that the ORFs p15 are under purifying selection and that, in some viral strains, the use of synonymous codons is biased, which might be a sign of adaptation to their plant hosts. Despite the high amino acid sequence divergence, proteins P15 show the conserved motif [FY]-L-x(3)-[FL]-H-x-x-[LIV]-S-C-x-C-x(2)-C-x-G-x-C, which occurs exclusively in members of this protein family. Proteins P15 also show a common predicted 3D structure that resembles the helical scaffold of the protein ORF49 encoded by radinoviruses and the phosphoprotein C-terminal domain of mononegavirids. Based on the 3D structural similarities of P15, we suggest elements of common ancestry, conserved functionality, and relevant amino acid residues. We conclude by postulating a plausible evolutionary trajectory of ORFans p15 and the 5'-end of the RNA2 of cileviruses considering both protein fold superpositions and comparative genomic analyses with the closest kitaviruses, negeviruses, nege/kita-like viruses, and unrelated viruses that share the ecological niches of cileviruses.
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Affiliation(s)
- Pedro L. Ramos-González
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico de São Paulo, São Paulo, Brazil
| | - Tirso Pons
- National Centre for Biotechnology (CNB-CSIC), Madrid, Spain
| | - Camila Chabi-Jesus
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico de São Paulo, São Paulo, Brazil
- Escola Superior de Agricultura Luiz de Queiroz (ESALQ), Universidade de São Paulo, Piracicaba, Brazil
| | - Gabriella Dias Arena
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico de São Paulo, São Paulo, Brazil
| | - Juliana Freitas-Astua
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico de São Paulo, São Paulo, Brazil
- Embrapa Mandioca e Fruticultura, Cruz das Almas, Brazil
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31
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Household Clusters of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Infection in Suzhou, China. BIOMED RESEARCH INTERNATIONAL 2021; 2021:5565549. [PMID: 34664026 PMCID: PMC8520496 DOI: 10.1155/2021/5565549] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 05/27/2021] [Accepted: 09/12/2021] [Indexed: 01/08/2023]
Abstract
Objectives The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an emerging virus causing substantial morbidity and mortality worldwide. We performed a cross-sectional investigation of SARS-CoV-2 clusters in Suzhou to determine the transmissibility of the virus among close contacts and to assess the demographic and clinical characteristics between index and secondary cases. Methods We review the clustered patients with SARS-CoV-2 infections in Suzhou between 22 January and 29 February 2020. The demographic and clinical characteristics were compared between index and secondary cases. We calculated the basic reproduction number (R0) among close contacts with SLI model. Results By 22 February, 87 patients with SARS-CoV-2 infection were reported, including 50 sporadic and 37 clustered cases, who were generated from 13 clusters. On admission, 5 (20.8%) out of 24 secondary cases were asymptomatic. The male ratio of index cases was significantly higher than that of secondary cases. Additionally, the index cases were more likely to have fever and increased CRP levels than the secondary cases. The R0 values of clusters displayed a significantly declining trend over time for all clusters. The relative risk of infection in blood-related contacts of cases versus unrelated contacts was 1.60 for SARS-CoV-2 (95% CI: 0.42-2.95). Conclusions In conclusion, SARS-CoV-2 has great person-to-person transmission capability among close contacts. The secondary cases are more prone to have mild symptoms than index cases. There is no increased RR of secondary infection in blood relatives versus unrelated contacts. The high rate of asymptomatic SARS-CoV-2 infections highlights the urgent need to enhance active case finding strategy for early detection of infectious patients.
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Abstract
Background: The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) had led to a global pandemic since December 2019. SARS-CoV-2 is a single-stranded RNA virus, which mutates at a higher rate. Multiple studies had been done to identify and study nonsynonymous mutations, which change amino acid residues of SARS-CoV-2 proteins. On the other hand, there is little study on the effects of SARS-CoV-2 synonymous mutations. Although these mutations do not alter amino acids, some studies suggest that they may affect viral fitness. This study aims to predict the effect of synonymous mutations on the SARS-CoV-2 genome. Methods: A total of 30,229 SARS-CoV-2 genomic sequences were retrieved from Global Initiative on Sharing all Influenza Data (GISAID) database and aligned using MAFFT. Then, the mutations and their respective frequency were identified. A prediction of RNA secondary structures and their base pair probabilities was performed to study the effect of synonymous mutations on RNA structure and stability. Relative synonymous codon usage (RSCU) analysis was also performed to measure the codon usage bias (CUB) of SARS-CoV-2. Results: A total of 150 synonymous mutations were identified. The synonymous mutation identified with the highest frequency is C3037U mutation in the nsp3 of ORF1a, followed by C313U and C9286U mutation in nsp1 and nsp4 of ORF1a, respectively. Conclusion: Among the synonymous mutations identified, C913U mutation in ORF1a and C26735U in membrane (M) protein may affect RNA secondary structure, reducing the stability of RNA folding and possibly resulting in a higher translation rate. However, lab experiments are required to validate the results obtained from prediction analysis.
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Hansen CA, Barrett ADT. The Present and Future of Yellow Fever Vaccines. Pharmaceuticals (Basel) 2021; 14:ph14090891. [PMID: 34577591 PMCID: PMC8468696 DOI: 10.3390/ph14090891] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2021] [Revised: 08/26/2021] [Accepted: 08/27/2021] [Indexed: 12/05/2022] Open
Abstract
The disease yellow fever (YF) is prevented by a live-attenuated vaccine, termed 17D, which has been in use since the 1930s. One dose of the vaccine is thought to give lifelong (35+ years) protective immunity, and neutralizing antibodies are the correlate of protection. Despite being a vaccine-preventable disease, YF remains a major public health burden, causing an estimated 109,000 severe infections and 51,000 deaths annually. There are issues of supply and demand for the vaccine, and outbreaks in 2016 and 2018 resulted in fractional dosing of the vaccine to meet demand. The World Health Organization (WHO) has established the “Eliminate Yellow Fever Epidemics” (EYE) initiative to reduce the burden of YF over the next 10 years. As with most vaccines, the WHO has recommendations to assure the quality, safety, and efficacy of the YF vaccine. These require the use of live 17D vaccine only produced in embryonated chicken eggs, and safety evaluated in non-human primates only. Thus, any second-generation vaccines would require modification of WHO recommendations if they were to be used in endemic countries. There are multiple second-generation YF vaccine candidates in various stages of development that must be shown to be non-inferior to the current 17D vaccine in terms of safety and immunogenicity to progress through clinical trials to potential licensing. The historic 17D vaccine continues to shape the global vaccine landscape in its use in the generation of multiple licensed recombinant chimeric live vaccines and vaccine candidates, in which its structural protein genes are replaced with those of other viruses, such as dengue and Japanese encephalitis. There is no doubt that the YF 17D live-attenuated vaccine will continue to play a role in the development of new vaccines for YF, as well as potentially for many other pathogens.
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Affiliation(s)
- Clairissa A. Hansen
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555-4036, USA;
| | - Alan D. T. Barrett
- Department of Pathology, University of Texas Medical Branch, Galveston, TX 77555-4036, USA;
- Sealy Institute for Vaccine Sciences, University of Texas Medical Branch, Galveston, TX 77555-4036, USA
- Correspondence:
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Hoxie I, Dennehy JJ. Rotavirus A Genome Segments Show Distinct Segregation and Codon Usage Patterns. Viruses 2021; 13:v13081460. [PMID: 34452326 PMCID: PMC8402926 DOI: 10.3390/v13081460] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 07/05/2021] [Accepted: 07/07/2021] [Indexed: 12/29/2022] Open
Abstract
Reassortment of the Rotavirus A (RVA) 11-segment dsRNA genome may generate new genome constellations that allow RVA to expand its host range or evade immune responses. Reassortment may also produce phylogenetic incongruities and weakly linked evolutionary histories across the 11 segments, obscuring reassortment-specific epistasis and changes in substitution rates. To determine the co-segregation patterns of RVA segments, we generated time-scaled phylogenetic trees for each of the 11 segments of 789 complete RVA genomes isolated from mammalian hosts and compared the segments’ geodesic distances. We found that segments 4 (VP4) and 9 (VP7) occupied significantly different tree spaces from each other and from the rest of the genome. By contrast, segments 10 and 11 (NSP4 and NSP5/6) occupied nearly indistinguishable tree spaces, suggesting strong co-segregation. Host-species barriers appeared to vary by segment, with segment 9 (VP7) presenting the weakest association with host species. Bayesian Skyride plots were generated for each segment to compare relative genetic diversity among segments over time. All segments showed a dramatic decrease in diversity around 2007 coinciding with the introduction of RVA vaccines. To assess selection pressures, codon adaptation indices and relative codon deoptimization indices were calculated with respect to different host genomes. Codon usage varied by segment with segment 11 (NSP5) exhibiting significantly higher adaptation to host genomes. Furthermore, RVA codon usage patterns appeared optimized for expression in humans and birds relative to the other hosts examined, suggesting that translational efficiency is not a barrier in RVA zoonosis.
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Affiliation(s)
- Irene Hoxie
- Biology Department, The Graduate Center, The City University of New York, New York, NY 10016, USA;
- Biology Department, Queens College, The City University of New York, Flushing, New York, NY 11367, USA
- Correspondence:
| | - John J. Dennehy
- Biology Department, The Graduate Center, The City University of New York, New York, NY 10016, USA;
- Biology Department, Queens College, The City University of New York, Flushing, New York, NY 11367, USA
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Abstract
Atypical porcine pestivirus (APPV) has been identified as the main causative agent for congenital tremor (CT) type A-II in piglets, which is threatening the health of the global swine herd. However, the evolution of APPV remains largely unknown. In this study, phylogenetic analysis showed that APPV could be divided into three phylogroups (I, II, and III). Phylogroups I and II included viral strains from China, while phylogroup III contained strains from Europe, North America, and Asia. Phylogroups I and II are tentatively thought to be of Chinese origin. Next, compositional property analysis revealed that a high frequency of nucleotide A and A-end codons was used in the APPV genome. Intriguingly, the analysis of preferred codons revealed that the AGA[Arg] and AGG[Arg] were overrepresented. Dinucleotide CC was found to be overrepresented, and dinucleotide CG was underrepresented. Furthermore, it was found that the weak codon usage bias of APPV was mainly dominated by selection pressures versus mutational forces. The codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses showed that the codon usage patterns of phylogroup II and III were more similar to the one of a pig than phylogroup I, suggesting that phylogroup II and III may be more adaptive to pigs. Overall, this study provides insights into APPV evolution through phylogeny and codon usage pattern analysis.
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Affiliation(s)
- Shuonan Pan
- College of Veterinary Medicine, Yangzhou University , Yangzhou, Jiangsu, People's Republic of China
| | - Chunxiao Mou
- College of Veterinary Medicine, Yangzhou University , Yangzhou, Jiangsu, People's Republic of China.,Institute of Comparative Medicine, Yangzhou University , Yangzhou, Jiangsu, People's Republic of China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University , Yangzhou, Jiangsu, People's Republic of China
| | - Huiguang Wu
- College of Veterinary Medicine, Yangzhou University , Yangzhou, Jiangsu, People's Republic of China.,Institute of Comparative Medicine, Yangzhou University , Yangzhou, Jiangsu, People's Republic of China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University , Yangzhou, Jiangsu, People's Republic of China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University , Yangzhou, Jiangsu, People's Republic of China
| | - Zhenhai Chen
- College of Veterinary Medicine, Yangzhou University , Yangzhou, Jiangsu, People's Republic of China.,Institute of Comparative Medicine, Yangzhou University , Yangzhou, Jiangsu, People's Republic of China.,Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University , Yangzhou, Jiangsu, People's Republic of China.,Joint International Research Laboratory of Agriculture and Agri-Product Safety, the Ministry of Education of China, Yangzhou University , Yangzhou, Jiangsu, People's Republic of China
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36
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Ata G, Wang H, Bai H, Yao X, Tao S. Edging on Mutational Bias, Induced Natural Selection From Host and Natural Reservoirs Predominates Codon Usage Evolution in Hantaan Virus. Front Microbiol 2021; 12:699788. [PMID: 34276633 PMCID: PMC8283416 DOI: 10.3389/fmicb.2021.699788] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2021] [Accepted: 06/07/2021] [Indexed: 12/14/2022] Open
Abstract
The molecular evolutionary dynamics that shape hantaviruses’ evolution are poorly understood even now, besides the contribution of virus-host interaction to their evolution remains an open question. Our study aimed to investigate these two aspects in Hantaan virus (HTNV)—the prototype of hantaviruses and an emerging zoonotic pathogen that infects humans, causing hemorrhagic fever with renal syndrome (HFRS): endemic in Far East Russia, China, and South Korea—via a comprehensive, phylogenetic-dependent codon usage analysis. We found that host- and natural reservoir-induced natural selection is the primary determinant of its biased codon choices, exceeding the mutational bias effect. The phylogenetic analysis of HTNV strains resulted in three distinct clades: South Korean, Russian, and Chinese. An effective number of codon (ENC) analysis showed a slightly biased codon usage in HTNV genomes. Nucleotide composition and RSCU analyses revealed a significant bias toward A/U nucleotides and A/U-ended codons, indicating the potential influence of mutational bias on the codon usage patterns of HTNV. Via ENC-plot, Parity Rule 2 (PR2), and neutrality plot analyses, we would conclude the presence of both mutation pressure and natural selection effect in shaping the codon usage patterns of HTNV; however, natural selection is the dominant factor influencing its codon usage bias. Codon adaptation index (CAI), Relative codon deoptimization index (RCDI), and Similarity Index (SiD) analyses uncovered the intense selection pressure from the host (Human) and natural reservoirs (Striped field mouse and Chinese white-bellied rat) in shaping HTNV biased codon choices. Our study clearly revealed the evolutionary processes in HTNV and the role of virus-host interaction in its evolution. Moreover, it opens the door for a more comprehensive codon usage analysis for all hantaviruses species to determine their molecular evolutionary dynamics and adaptability to several hosts and environments. We believe that our research will help in a better and deep understanding of HTNV evolution that will serve its future basic research and aid live attenuated vaccines design.
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Affiliation(s)
- Galal Ata
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Xianyang, China
| | - Hao Wang
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Xianyang, China
| | - Haoxiang Bai
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Xianyang, China
| | - Xiaoting Yao
- College of Veterinary Medicine, Northwest A&F University, Xianyang, China
| | - Shiheng Tao
- State Key Laboratory of Crop Stress Biology in Arid Areas, College of Life Sciences, Northwest A&F University, Xianyang, China
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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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Liu W, Li J, Du H, Ou Z. Mutation Profiles, Glycosylation Site Distribution and Codon Usage Bias of Human Papillomavirus Type 16. Viruses 2021; 13:v13071281. [PMID: 34209097 PMCID: PMC8310365 DOI: 10.3390/v13071281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2021] [Revised: 06/13/2021] [Accepted: 06/21/2021] [Indexed: 11/29/2022] Open
Abstract
Human papillomavirus type 16 (HPV16) is the most prevalent HPV type causing cervical cancers. Herein, using 1597 full genomes, we systemically investigated the mutation profiles, surface protein glycosylation sites and the codon usage bias (CUB) of HPV16 from different lineages and sublineages. Multiple lineage- or sublineage-conserved mutation sites were identified. Glycosylation analysis showed that HPV16 lineage D contained the highest number of different glycosylation sites from lineage A in both L1 and L2 capsid proteins, which might lead to their antigenic distances between the two lineages. CUB analysis showed that the HPV16 open reading frames (ORFs) preferred codons ending with A/T. The CUB of HPV16 ORFs was mainly affected by natural selection except for E1, E5 and L2. HPV16 only shared some of the preferred codons with humans, which might help reduce competition in translational resources. These findings increase our understanding of the heterogeneity between HPV16 lineages and sublineages, and the adaptation mechanism of HPV in human cells. In summary, this study might facilitate HPV classification and improve vaccine development and application.
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Affiliation(s)
- Wei Liu
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510000, China; (W.L.); (J.L.); (H.D.)
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Junhua Li
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510000, China; (W.L.); (J.L.); (H.D.)
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
| | - Hongli Du
- School of Biology and Biological Engineering, South China University of Technology, Guangzhou 510000, China; (W.L.); (J.L.); (H.D.)
| | - Zhihua Ou
- BGI-Shenzhen, Shenzhen 518083, China
- Shenzhen Key Laboratory of Unknown Pathogen Identification, BGI-Shenzhen, Shenzhen 518083, China
- Correspondence: ; Tel.: +86-134-3428-7879
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Guo F, Roy A, Wang R, Yang J, Zhang Z, Luo W, Shen X, Chen RA, Irwin DM, Shen Y. Host Adaptive Evolution of Avian-Origin H3N2 Canine Influenza Virus. Front Microbiol 2021; 12:655228. [PMID: 34194404 PMCID: PMC8236823 DOI: 10.3389/fmicb.2021.655228] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 05/11/2021] [Indexed: 11/13/2022] Open
Abstract
Since its first isolation in around 2007, the avian-origin H3N2 canine influenza virus (CIV) has become established and continues to circulate in dog populations. This virus serves as a useful model for deciphering the complex evolutionary process of interspecies transmission of influenza A virus (IAV) from one species to its subsequent circulation in another mammalian host. The present investigation is a comprehensive effort to identify and characterize genetic changes that accumulated in the avian-origin H3N2 CIV during its circulation in the dog. We revealed that H3N2 CIV experiences greater selection pressure with extremely high global non-synonymous to synonymous substitution ratios per codon (dN/dS ratio) for each gene compared to the avian reservoir viruses. A total of 54 amino acid substitutions were observed to have accumulated and become fixed in the H3N2 CIV population based on our comprehensive codon-based frequency diagram analysis. Of these substitutions, 11 sites also display high prevalence in H3N8 CIV, indicating that convergent evolution has occurred on different lineages of CIV. Notably, six substitutions, including HA-G146S, M1-V15I, NS1-E227K, PA-C241Y, PB2-K251R, and PB2-G590S, have been reported to play imperative roles in facilitating the transmission and spillover of IAVs across species barriers. Most of these substitutions were found to have become fixed in around 2015, which might have been a favorable factor that facilitating the spread of these CIV lineages from South Asia to North America and subsequent further circulation in these areas. We also detected 12 sites in six viral genes with evidence for positive selection by comparing the rates of non-synonymous and synonymous substitutions at each site. Besides, our study reports trends of enhanced ongoing adaptation of H3N2 CIV to their respective host cellular systems, based on the codon adaptation index analysis, which points toward increasing fitness for efficient viral replication. In addition, a reduction in the abundance of the CpG motif, as evident from an analysis of relative dinucleotide abundance, may contribute to the successful evasion of host immune recognition. The present study provides key insights into the adaptive changes that have accumulated in the avian-origin H3N2 viral genomes during its establishment and circulation into dog populations.
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Affiliation(s)
- Fucheng Guo
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Ayan Roy
- Department of Biotechnology, Lovely Professional University, Phagwara, India
| | - Ruichen Wang
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jinjin Yang
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Zhipeng Zhang
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Wen Luo
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Xuejuan Shen
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing, China
| | - Rui-Ai Chen
- Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing, China
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Banting and Best Diabetes Centre, University of Toronto, Toronto, ON, Canada
| | - Yongyi Shen
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,Center for Emerging and Zoonotic Diseases, College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Zhaoqing Branch Center of Guangdong Laboratory for Lingnan Modern Agricultural Science and Technology, Zhaoqing, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
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40
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Wang L, Li Y, Guo Z, Yi Y, Zhang H, Shangguan H, Huang C, Ge J. Genetic changes and evolutionary analysis of canine circovirus. Arch Virol 2021; 166:2235-2247. [PMID: 34104994 DOI: 10.1007/s00705-021-05125-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 04/15/2021] [Indexed: 11/28/2022]
Abstract
Canine circovirus (canineCV) has been found to be associated with vasculitis, hemorrhage, hemorrhagic enteritis, and diarrhea of canines. CanineCV, like other circoviruses, may also be associated with lymphoid depletion and immunosuppression. This circovirus has been detected worldwide in different countries and species. Recombination and mutation events in the canineCV genome have been described, indicating that the virus is continuing to evolve. However, the origin, codon usage patterns, and host adaptation of canineCV remain to be studied. Here, the coding sequences of 93 canineCV sequences available in the GenBank database were used for analysis. The results showed that canineCV sequences could be classified into five genotypes, as confirmed by phylogenetic and principal component analysis (PCA). Maximum clade credibility (MCC) and maximum-likelihood (ML) trees suggested that canineCV originated from bat circovirus. G/T and A/C nucleotide biases were observed in ORF1 and ORF2, respectively, and a low codon usage bias (CUB) was found in canineCV using an effective number of codon (ENC) analysis. Correlation analysis, ENC plot analysis and neutrality plot analysis indicated that the codon usage pattern was mainly shaped by natural selection. Codon adaptation index (CAI) analysis, relative codon deoptimization index (RCDI) analysis, and similarity index (SiD) analysis revealed a better adaption to Vulpes vulpes than to Canis familiaris. Furthermore, a cross-species transmission hypothesis that canineCV may have evolved from bats (origin analysis) and subsequently adapted to wolves, arctic foxes, dogs, and red foxes, was proposed. This study contributes to our understanding of the factors related to canineCV evolution and host adaption.
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Affiliation(s)
- Lin Wang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Yifan Li
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Zhiyuan Guo
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Ying Yi
- College of Animal Science and Technology, Northeast Agricultural University, Harbin, 150030, China
| | - Han Zhang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Haikun Shangguan
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Chengshi Huang
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China
| | - Junwei Ge
- College of Veterinary Medicine, Northeast Agricultural University, Harbin, 150030, China. .,Northeastern Science Inspection Station, China Ministry of Agriculture Key Laboratory of Animal Pathogen Biology, Harbin, 150030, China.
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Evolutionary Patterns of Codon Usage in Major Lineages of Porcine Reproductive and Respiratory Syndrome Virus in China. Viruses 2021; 13:v13061044. [PMID: 34072978 PMCID: PMC8228872 DOI: 10.3390/v13061044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2021] [Revised: 05/16/2021] [Accepted: 05/25/2021] [Indexed: 11/17/2022] Open
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) is economically important and characterized by its extensive variation. The codon usage patterns and their influence on viral evolution and host adaptation among different PRRSV strains remain largely unknown. Here, the codon usage of ORF5 genes from lineages 1, 3, 5, and 8, and MLV strains of type 2 PRRSV in China was analyzed. A compositional property analysis of ORF5 genes revealed that nucleotide C is most frequently used at the third position of codons, accompanied by rich GC3s. The effective number of codon (ENC) and codon pair bias (CPB) values indicate that all ORF5 genes have low codon bias and the differences in CPB scores among four lineages are almost not significant. When compared with host codon usage patterns, lineage 1 strains show higher CAI and SiD values, with a high similarity to pig, which might relate to its predominant epidemic propensity in the field. The CAI, RCDI, and SiD values of ORF5 genes from different passages of MLV JXA1R indicate no relation between attenuation and CPB or codon adaptation decrease during serial passage on non-host cells. These findings provide a novel way of understanding the PRRSV's evolution, related to viral survival, host adaptation, and virulence.
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42
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Das JK, Chakraborty S, Roy S. A scheme for inferring viral-host associations based on codon usage patterns identifies the most affected signaling pathways during COVID-19. J Biomed Inform 2021; 118:103801. [PMID: 33965637 PMCID: PMC8102073 DOI: 10.1016/j.jbi.2021.103801] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Revised: 05/02/2021] [Accepted: 05/03/2021] [Indexed: 12/16/2022]
Abstract
Understanding the molecular mechanism of COVID-19 pathogenesis helps in the rapid therapeutic target identification. Usually, viral protein targets host proteins in an organized fashion. The expression of any viral gene depends mostly on the host translational machinery. Recent studies report the great significance of codon usage biases in establishing host-viral protein–protein interactions (PPI). Exploring the codon usage patterns between a pair of co-evolved host and viral proteins may present novel insight into the host-viral protein interactomes during disease pathogenesis. Leveraging the similarity in codon usage patterns, we propose a computational scheme to recreate the host-viral protein–protein interaction network. We use host proteins from seventeen (17) essential signaling pathways for our current work towards understanding the possible targeting mechanism of SARS-CoV-2 proteins. We infer both negatively and positively interacting edges in the network. Further, extensive analysis is performed to understand the host PPI network topologically and the attacking behavior of the viral proteins. Our study reveals that viral proteins mostly utilize codons, rare in the targeted host proteins (negatively correlated interaction). Among them, non-structural proteins, NSP3 and structural protein, Spike (S), are the most influential proteins in interacting with multiple host proteins. While ranking the most affected pathways, MAPK pathways observe to be the worst affected during the SARS-CoV-2 infection. Several proteins participating in multiple pathways are highly central in host PPI and mostly targeted by multiple viral proteins. We observe many potential targets (host proteins) from the affected pathways associated with the various drug molecules, including Arsenic trioxide, Dexamethasone, Hydroxychloroquine, Ritonavir, and Interferon beta, which are either under clinical trial or in use during COVID-19.
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Affiliation(s)
- Jayanta Kumar Das
- Department of Pediatrics, Johns Hopkins University, School of Medicine, MD, USA
| | | | - Swarup Roy
- Network Reconstruction & Analysis (NetRA) Lab, Department of Computer Applications, Sikkim University, Gangtok, India.
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Pintó RM, Bosch A. The codon usage code for co-translational folding of viral capsids. Genome Biol Evol 2021; 13:6259148. [PMID: 33914886 PMCID: PMC8410136 DOI: 10.1093/gbe/evab089] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2021] [Indexed: 12/25/2022] Open
Abstract
Codon bias is common to all organisms and is the result of mutation, drift, and selection. Selection for the efficiency and accuracy of translation is well recognized as a factor shaping the codon usage. In contrast, fewer studies report the control of the rate of translation as an additional selective pressure influencing the codon usage of an organism. Experimental molecular evolution using RNA virus populations is a powerful tool for the identification of mechanisms underlying the codon bias. Indeed, the role of deoptimized codons on the cotranslational folding has been proven in the capsids of two fecal-orally transmitted picornaviruses, poliovirus, and the hepatitis A virus, emphasizing the role of the frequency of codons in determining the phenotype. However, most studies on virus codon usage rely only on computational analyses, and experimental studies should be encouraged to clearly define the role of selection on codon evolution.
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Affiliation(s)
- Rosa M Pintó
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Section of Microbiology, Virology and Biotechnology, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Barcelona, Spain
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44
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Pintó RM, Pérez-Rodríguez FJ, Costafreda MI, Chavarria-Miró G, Guix S, Ribes E, Bosch A. Pathogenicity and virulence of hepatitis A virus. Virulence 2021; 12:1174-1185. [PMID: 33843464 PMCID: PMC8043188 DOI: 10.1080/21505594.2021.1910442] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Hepatitis A is an acute infection of the liver, which is mostly asymptomatic in children and increases the severity with age. Although in most patients the infection resolves completely, in a few of them it may follow a prolonged or relapsed course or even a fulminant form. The reason for these different outcomes is unknown, but it is generally accepted that host factors such as the immunological status, age and the occurrence of underlaying hepatic diseases are the main determinants of the severity. However, it cannot be ruled out that some virus traits may also contribute to the severe clinical outcomes. In this review, we will analyze which genetic determinants of the virus may determine virulence, in the context of a paradigmatic virus in terms of its genomic, molecular, replicative, and evolutionary features.
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Affiliation(s)
- Rosa M Pintó
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Barcelona, Spain
| | - Francisco-Javier Pérez-Rodríguez
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Barcelona, Spain.,Present Address: Division of Infectious Diseases, Laboratory of Virology, University of Geneva Hospitals, Geneva, Switzerland
| | - Maria-Isabel Costafreda
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Barcelona, Spain
| | - Gemma Chavarria-Miró
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Barcelona, Spain
| | - Susana Guix
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Barcelona, Spain
| | - Enric Ribes
- Enteric Virus Laboratory, Department of Cell Biology, Physiology and Immunology, University of Barcelona, Barcelona, Spain
| | - Albert Bosch
- Enteric Virus Laboratory, Department of Genetics, Microbiology and Statistics, School of Biology, and Institute of Nutrition and Safety, University of Barcelona, Barcelona, Spain
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Roy A, Guo F, Singh B, Gupta S, Paul K, Chen X, Sharma NR, Jaishee N, Irwin DM, Shen Y. Base Composition and Host Adaptation of the SARS-CoV-2: Insight From the Codon Usage Perspective. Front Microbiol 2021; 12:548275. [PMID: 33889134 PMCID: PMC8057303 DOI: 10.3389/fmicb.2021.548275] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2020] [Accepted: 03/12/2021] [Indexed: 12/12/2022] Open
Abstract
The novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has been spreading rapidly all over the world and has raised grave concern globally. The present research aims to conduct a robust base compositional analysis of SARS-CoV-2 to reveal adaptive intricacies to the human host. Multivariate statistical analysis revealed a complex interplay of various factors including compositional constraint, natural selection, length of viral coding sequences, hydropathicity, and aromaticity of the viral gene products that are operational to codon usage patterns, with compositional bias being the most crucial determinant. UpG and CpA dinucleotides were found to be highly preferred whereas, CpG dinucleotide was mostly avoided in SARS-CoV-2, a pattern consistent with the human host. Strict avoidance of the CpG dinucleotide might be attributed to a strategy for evading a human immune response. A lower degree of adaptation of SARS-CoV-2 to the human host, compared to Middle East respiratory syndrome (MERS) coronavirus and SARS-CoV, might be indicative of its milder clinical severity and progression contrasted to SARS and MERS. Similar patterns of enhanced adaptation between viral isolates from intermediate and human hosts, contrasted with those isolated from the natural bat reservoir, signifies an indispensable role of the intermediate host in transmission dynamics and spillover events of the virus to human populations. The information regarding avoided codon pairs in SARS-CoV-2, as conferred by the present analysis, promises to be useful for the design of vaccines employing codon pair deoptimization based synthetic attenuated virus engineering.
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Affiliation(s)
- Ayan Roy
- Department of Biotechnology, Lovely Professional University, Phagwara, India
| | - Fucheng Guo
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Bhupender Singh
- Department of Biotechnology, Lovely Professional University, Phagwara, India
| | - Shelly Gupta
- Department of Biotechnology, Lovely Professional University, Phagwara, India
| | - Karan Paul
- Department of Biochemistry, DAV University, Jalandhar, India
| | - Xiaoyuan Chen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Neeta Raj Sharma
- Department of Biotechnology, Lovely Professional University, Phagwara, India
| | - Nishika Jaishee
- Department of Botany, St Joseph's College, Darjeeling, India
| | - David M Irwin
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Banting and Best Diabetes Centre, University of Toronto, Toronto, ON, Canada
| | - Yongyi Shen
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China.,Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China.,Key Laboratory of Zoonosis Prevention and Control of Guangdong Province, Guangzhou, China
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Rescue of codon-pair deoptimized respiratory syncytial virus by the emergence of genomes with very large internal deletions that complemented replication. Proc Natl Acad Sci U S A 2021; 118:2020969118. [PMID: 33753491 DOI: 10.1073/pnas.2020969118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Recoding viral genomes by introducing numerous synonymous but suboptimal codon pairs-called codon-pair deoptimization (CPD)-provides new types of live-attenuated vaccine candidates. The large number of nucleotide changes resulting from CPD should provide genetic stability to the attenuating phenotype, but this has not been rigorously tested. Human respiratory syncytial virus in which the G and F surface glycoprotein ORFs were CPD (called Min B) was temperature-sensitive and highly restricted in vitro. When subjected to selective pressure by serial passage at increasing temperatures, Min B substantially regained expression of F and replication fitness. Whole-genome deep sequencing showed many point mutations scattered across the genome, including one combination of six linked point mutations. However, their reintroduction into Min B provided minimal rescue. Further analysis revealed viral genomes bearing very large internal deletions (LD genomes) that accumulated after only a few passages. The deletions relocated the CPD F gene to the first or second promoter-proximal gene position. LD genomes amplified de novo in Min B-infected cells were encapsidated, expressed high levels of F, and complemented Min B replication in trans This study provides insight on a variation of the adaptability of a debilitated negative-strand RNA virus, namely the generation of defective minihelper viruses to overcome its restriction. This is in contrast to the common "defective interfering particles" that interfere with the replication of the virus from which they originated. To our knowledge, defective genomes that promote rather than inhibit replication have not been reported before in RNA viruses.
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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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Lee MHP, Tan CW, Tee HK, Ong KC, Sam IC, Chan YF. Vaccine candidates generated by codon and codon pair deoptimization of enterovirus A71 protect against lethal challenge in mice. Vaccine 2021; 39:1708-1720. [PMID: 33640144 DOI: 10.1016/j.vaccine.2021.02.024] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Revised: 02/01/2021] [Accepted: 02/10/2021] [Indexed: 11/25/2022]
Abstract
Enterovirus A71 (EV-A71) causes hand, foot and mouth disease (HFMD) in young children. It is associated with severe neurological complications and death. This study aims to develop a live-attenuated vaccine by codon deoptimization (CD) and codon-pair deoptimization (CPD) of EV-A71. CD is generated by introducing the least preferred codons for amino acids while CPD increases the presence of underrepresented codon pairs in the specific genes. CD and CPD chimeras were generated by synonymous mutations at the VP2, VP3, VP1 and 2A gene regions, designated as XYZ. All twelve deoptimized viruses were viable with similar replication kinetics, but the plaque sizes were inversely proportional to the level of deoptimization. All the deoptimized viruses showed attenuated growth in vitro with reduced viral protein expression at 48 h and lower viral RNA at 39 °C. Six-week-old ICR mice were immunized intraperitoneally with selected CD and CPD X and XY vaccine candidates covering the VP2-VP3 and VP2-VP3-VP1 genes, respectively. All vaccine candidates elicited high anti-EV-A71 IgG levels similar to wild-type (WT) EV-A71. The CD X and CPD X vaccines produced robust neutralizing antibodies but not the CD XY and CPD XY. On lethal challenge, offspring of mice immunized with WT, CD X and CPD X were fully protected, but the CD XY- and CPD XY-vaccinated mice had delayed symptoms and eventually died. Similarly, active immunization of 1-day-old suckling mice with CD X, CPD X and CD XY vaccine candidates provided complete immune protection but CPD XY only protected 40% of the challenged mice. Histology of the muscles from CD X- and CPD X-vaccinated mice showed minimal pathology compared to extensive inflammation in the post-challenged mock-vaccinated mice. Overall, we demonstrated that the CD X and CPD X elicited good neutralizing antibodies, conferred immune protection and are promising live-attenuated vaccine candidates for EV-A71.
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Affiliation(s)
- Michelle Hui Pheng Lee
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Chee Wah Tan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Han Kang Tee
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Kien Chai Ong
- Department of Biomedical Science, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - I-Ching Sam
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Yoke Fun Chan
- Department of Medical Microbiology, Faculty of Medicine, University of Malaya, 50603 Kuala Lumpur, Malaysia.
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49
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Maldonado LL, Bertelli AM, Kamenetzky L. Molecular features similarities between SARS-CoV-2, SARS, MERS and key human genes could favour the viral infections and trigger collateral effects. Sci Rep 2021; 11:4108. [PMID: 33602998 PMCID: PMC7893037 DOI: 10.1038/s41598-021-83595-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 01/26/2021] [Indexed: 01/31/2023] Open
Abstract
In December 2019, rising pneumonia cases caused by a novel β-coronavirus (SARS-CoV-2) occurred in Wuhan, China, which has rapidly spread worldwide, causing thousands of deaths. The WHO declared the SARS-CoV-2 outbreak as a public health emergency of international concern, since then several scientists are dedicated to its study. It has been observed that many human viruses have codon usage biases that match highly expressed proteins in the tissues they infect and depend on the host cell machinery for the replication and co-evolution. In this work, we analysed 91 molecular features and codon usage patterns for 339 viral genes and 463 human genes that consisted of 677,873 codon positions. Hereby, we selected the highly expressed genes from human lung tissue to perform computational studies that permit to compare their molecular features with those of SARS, SARS-CoV-2 and MERS genes. The integrated analysis of all the features revealed that certain viral genes and overexpressed human genes have similar codon usage patterns. The main pattern was the A/T bias that together with other features could propitiate the viral infection, enhanced by a host dependant specialization of the translation machinery of only some of the overexpressed genes. The envelope protein E, the membrane glycoprotein M and ORF7 could be further benefited. This could be the key for a facilitated translation and viral replication conducting to different comorbidities depending on the genetic variability of population due to the host translation machinery. This is the first codon usage approach that reveals which human genes could be potentially deregulated due to the codon usage similarities between the host and the viral genes when the virus is already inside the human cells of the lung tissues. Our work leaded to the identification of additional highly expressed human genes which are not the usual suspects but might play a role in the viral infection and settle the basis for further research in the field of human genetics associated with new viral infections. To identify the genes that could be deregulated under a viral infection is important to predict the collateral effects and determine which individuals would be more susceptible based on their genetic features and comorbidities associated.
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Affiliation(s)
- Lucas L Maldonado
- IMPaM, CONICET, Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina.
| | | | - Laura Kamenetzky
- IMPaM, CONICET, Facultad de Medicina, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
- iB3 | Instituto de Biociencias, Biotecnología y Biología traslacional, Departamento de Fisiologia y Biologia Molecular y Celular, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Autónoma de Buenos Aires, Argentina
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50
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Tan X, Letendre JH, Collins JJ, Wong WW. Synthetic biology in the clinic: engineering vaccines, diagnostics, and therapeutics. Cell 2021; 184:881-898. [PMID: 33571426 PMCID: PMC7897318 DOI: 10.1016/j.cell.2021.01.017] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 01/12/2021] [Accepted: 01/13/2021] [Indexed: 12/17/2022]
Abstract
Synthetic biology is a design-driven discipline centered on engineering novel biological functions through the discovery, characterization, and repurposing of molecular parts. Several synthetic biological solutions to critical biomedical problems are on the verge of widespread adoption and demonstrate the burgeoning maturation of the field. Here, we highlight applications of synthetic biology in vaccine development, molecular diagnostics, and cell-based therapeutics, emphasizing technologies approved for clinical use or in active clinical trials. We conclude by drawing attention to recent innovations in synthetic biology that are likely to have a significant impact on future applications in biomedicine.
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Affiliation(s)
- Xiao Tan
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Division of Gastroenterology, Massachusetts General Hospital, 55 Fruit Street, Boston, MA 02114, USA; Harvard Medical School, 25 Shattuck St., Boston, MA 02115, USA; Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA
| | - Justin H Letendre
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Biological Design Center, Boston University, Boston, MA 02215, USA
| | - James J Collins
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA 02115, USA; Institute for Medical Engineering and Science, MIT, Cambridge, MA 02139, USA; Department of Biological Engineering, MIT, Cambridge, MA 02139, USA; Synthetic Biology Center, MIT, 77 Massachusetts Ave., Cambridge, MA 02139, USA; Harvard-MIT Program in Health Sciences and Technology, Cambridge, MA 02139, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02139, USA.
| | - Wilson W Wong
- Department of Biomedical Engineering, Boston University, Boston, MA 02215, USA; Biological Design Center, Boston University, Boston, MA 02215, USA.
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