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Wang XF, Lin YZ, Li Q, Liu Q, Zhao WW, Du C, Chen J, Wang X, Zhou JH. Genetic Evolution during the development of an attenuated EIAV vaccine. Retrovirology 2016; 13:9. [PMID: 26842878 PMCID: PMC4738788 DOI: 10.1186/s12977-016-0240-6] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2015] [Accepted: 01/18/2016] [Indexed: 08/30/2023] Open
Abstract
Background The equine infectious anemia virus (EIAV) vaccine is the only attenuated lentiviral vaccine applied on a large scale that has been shown to be effective in controlling the prevalence of EIA in China. This vaccine was developed by successive passaging of a field-isolated virulent strain in different hosts and cultivated cells. To explore the molecular basis for the phenotype alteration of this vaccine strain, we systematically analyzed its genomic evolution during vaccine development. Results Sequence analysis revealed that the genetic distance between the wild-type strain and six representative strains isolated from key development stages gradually increased with the number of passages. Env gene, but not gag and pol, showed a clear evolutionary flow similar to that of the whole genomes of different generations during the attenuation. Stable mutations were identified in multiple regions of multiple genes along with virus passaging. The adaption of the virus to the growth environment of cultured cells with accumulated genomic and genetic variations was positively correlated with the reduction in pathogenicity and rise of immunogenicity. Statistical analyses revealed significant differences in the frequency of the most stable mutations between in vivo and ex vivo-adapted strains and between virulent and attenuated strains. Conclusions These data indicate that EIAV evolution during vaccine development generated an accumulation of mutations under the selective drive force, which helps to better understand the molecular basis of lentivirus pathogenicity and immunogenicity. Electronic supplementary material The online version of this article (doi:10.1186/s12977-016-0240-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xue-Feng Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China. .,Department of Preventive Veterinary Medicine, College of Veterinary Medicine, Northeast Agricultural University, Harbin, China.
| | - Yue-Zhi Lin
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China.
| | - Qiang Li
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China. .,Harbin Weike Biotechnology Development Company, Harbin, China.
| | - Qiang Liu
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China.
| | - Wei-Wei Zhao
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China.
| | - Cheng Du
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China.
| | - Jie Chen
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China.
| | - Xiaojun Wang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China.
| | - Jian-Hua Zhou
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, 150001, China. .,Harbin Pharmaceutical Group Biovaccine Co., Harbin, 150069, China.
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Ma J, Jiang C, Lin Y, Wang X, Zhao L, Xiang W, Shao Y, Shen R, Kong X, Zhou J. In vivo evolution of the gp90 gene and consistently low plasma viral load during transient immune suppression demonstrate the safety of an attenuated equine infectious anemia virus (EIAV) vaccine. Arch Virol 2009; 154:867-73. [PMID: 19363668 DOI: 10.1007/s00705-009-0378-9] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2008] [Accepted: 03/30/2009] [Indexed: 10/20/2022]
Abstract
To study the in vivo evolution of the attenuated Chinese equine infectious anemia virus (EIAV) vaccine, viral gp90 gene variation and virus replication in immunosuppressed hosts were investigated. The results showed that after vaccination, the gp90 gene followed an evolutionary trend of declining diversity. The trend coincided with the maturation of immunity to EIAV, and eventually, the gp90 gene became highly homologous. The sequences of these predominant quasispecies were consistently detected up to 18 months after vaccination. Furthermore, after transient immune suppression with dexamethasone, the plasma viral RNA copy number of the vaccine strain in three vaccinated ponies remained consistently below the "pathogenic threshold" level, while the viral load increased by 25,000-fold in the positive control of an inapparent carrier of the parental virulent strain. This study is the first to provide evidence for the safety of an attenuated lentiviral vaccine with decreased genomic diversity and consistently low viral replication under suppressed immunity.
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Affiliation(s)
- Jian Ma
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, China
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Liang H, He X, Shen RX, Shen T, Tong X, Ma Y, Xiang WH, Zhang XY, Shao YM. Combined amino acid mutations occurring in the envelope closely correlate with pathogenicity of EIAV. Arch Virol 2006; 151:1387-403. [PMID: 16502285 DOI: 10.1007/s00705-005-0718-3] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2005] [Accepted: 11/29/2005] [Indexed: 11/26/2022]
Abstract
The Chinese equine infectious anemia virus (EIAV) donkey-leukocyte attenuated vaccine (DLV) provides a unique natural model system to study the attenuation mechanism and immunological control of lentivirus replication. Critical consensus mutations were identified between virulent Chinese EIAV strains and vaccine strains. Based on a full-length infectious clone of EIAV vaccine strain pLGFD3, two molecular clones, mFD5-4-7 and mFD7-2-11, were successfully constructed, in which 4 and 6 critical consensus mutations in the env gene of the vaccine strain were point-mutated to the wild-type sequence, respectively by an overlap PCR mutagenesis strategy. The infectivity, virulence, and pathogenesis of the constructed clones were investigated in vitro using a reverse transcriptase assay, an indirect immunofluorescence assay, observation of cytopathogenic effect, and virion observation as well as in vivo by inoculation of animals with the resulting infectious clones. The pathogenic symptoms in horses inoculated with mFD7-2-11 were more severe than those inoculated with mFD5-4-7, whereas no pathogenic symptoms were detected in animals inoculated with their parental clone pLGFD3 strain. The results indicate that the consensus mutation residues of the env region involved in this study play significant roles in the virulence and pathogenicity of EIAV. This will contribute to the elucidation of the attenuating and protective mechanisms of the Chinese EIAV vaccine.
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MESH Headings
- Amino Acid Sequence
- Amino Acid Substitution
- Animals
- Body Temperature
- Cell Line
- Cytopathogenic Effect, Viral
- Disease Models, Animal
- Equidae
- Equine Infectious Anemia/physiopathology
- Equine Infectious Anemia/virology
- Fluorescent Antibody Technique, Direct
- Gene Products, env/chemistry
- Gene Products, env/genetics
- Genes, env
- Horses
- Infectious Anemia Virus, Equine/genetics
- Infectious Anemia Virus, Equine/pathogenicity
- Microscopy, Electron, Transmission
- Molecular Sequence Data
- Platelet Count
- Point Mutation
- Sequence Alignment
- Vaccines, Attenuated/genetics
- Viral Vaccines/genetics
- Virulence/genetics
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Affiliation(s)
- H Liang
- State Key Laboratory for Infectious Disease Prevention and Control, National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, PR China
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Costantini S, Colonna G, Facchiano AM. Amino acid propensities for secondary structures are influenced by the protein structural class. Biochem Biophys Res Commun 2006; 342:441-51. [PMID: 16487481 DOI: 10.1016/j.bbrc.2006.01.159] [Citation(s) in RCA: 97] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2006] [Accepted: 01/31/2006] [Indexed: 11/15/2022]
Abstract
Amino acid propensities for secondary structures were used since the 1970s, when Chou and Fasman evaluated them within datasets of few tens of proteins and developed a method to predict secondary structure of proteins, still in use despite prediction methods having evolved to very different approaches and higher reliability. Propensity for secondary structures represents an intrinsic property of amino acid, and it is used for generating new algorithms and prediction methods, therefore our work has been aimed to investigate what is the best protein dataset to evaluate the amino acid propensities, either larger but not homogeneous or smaller but homogeneous sets, i.e., all-alpha, all-beta, alpha-beta proteins. As a first analysis, we evaluated amino acid propensities for helix, beta-strand, and coil in more than 2000 proteins from the PDBselect dataset. With these propensities, secondary structure predictions performed with a method very similar to that of Chou and Fasman gave us results better than the original one, based on propensities derived from the few tens of X-ray protein structures available in the 1970s. In a refined analysis, we subdivided the PDBselect dataset of proteins in three secondary structural classes, i.e., all-alpha, all-beta, and alpha-beta proteins. For each class, the amino acid propensities for helix, beta-strand, and coil have been calculated and used to predict secondary structure elements for proteins belonging to the same class by using resubstitution and jackknife tests. This second round of predictions further improved the results of the first round. Therefore, amino acid propensities for secondary structures became more reliable depending on the degree of homogeneity of the protein dataset used to evaluate them. Indeed, our results indicate also that all algorithms using propensities for secondary structure can be still improved to obtain better predictive results.
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Affiliation(s)
- Susan Costantini
- Laboratorio di Bioinformatica e Biologia Computazionale, Istituto di Scienze dell'Alimentazione, CNR, Avellino, Italy
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Shen T, Liang H, Tong X, Fan X, He X, Ma Y, Xiang W, Shen R, Zhang X, Shao Y. Amino acid mutations of the infectious clone from Chinese EIAV attenuated vaccine resulted in reversion of virulence. Vaccine 2005; 24:738-49. [PMID: 16202485 DOI: 10.1016/j.vaccine.2005.08.084] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2005] [Accepted: 08/16/2005] [Indexed: 11/21/2022]
Abstract
The Chinese equine infectious anemia virus (EIAV) donkey-leukocyte attenuated vaccine (DLV) provides a unique natural model system by which attenuated mechanism and immunological control of lentivirus replication may be studied. We analyzed the critical consensus mutations that occurred during the viral passages in vitro and in vivo for vaccine's preparation. Based on the full-length infectious clone pLGFD3 (EIAV vaccine background) and according to mutations displayed during viral attenuation, we successfully constructed an infectious clones pLG5-3-l in which gag and env genes were point-mutated by overlap PCR mutagenesis strategy. pLG5-3-l was proved to have the ability of effective replication in vitro cells culture systems by Reverse Transcriptase Assay and virion observation under electron microscopy. Results of the in vivo experiments indicated that marked differences occurred between the mutated virus and their parental virus in clinical manifestation and plasma viral replication during 6-month observation period. In contrast to asymptom of animals infected with pLGFD3-V, the mutated virus (pLG5-3-l-V) developed typical clinical progression in the corresponding experimentally infected animals. The results of the distinct differences in clinical profiles and viral dynamics before and after mutation of EIAV infectious clone will help to understand the protective mechanism of Chinese EIAV vaccine and shed light on novel HIV vaccine design.
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Affiliation(s)
- Tao Shen
- National Center for AIDS/STD Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 100050, China
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