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Prusty BK, Whisnant AW. Revisiting the genomes of herpesviruses. eLife 2020; 9:54037. [PMID: 31944181 PMCID: PMC6964977 DOI: 10.7554/elife.54037] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2020] [Accepted: 01/13/2020] [Indexed: 12/15/2022] Open
Abstract
Combining integrative genomics and systems biology approaches has revealed new and conserved features in the genome of human herpesvirus 6.
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Affiliation(s)
- Bhupesh K Prusty
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
| | - Adam W Whisnant
- Institute for Virology and Immunobiology, Julius-Maximilians-Universität Würzburg, Würzburg, Germany
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Suárez NM, Lau B, Kemble GM, Lee R, Mocarski ES, Wilkinson GWG, Adler SP, McVoy MA, Davison AJ. Genomic analysis of chimeric human cytomegalovirus vaccine candidates derived from strains Towne and Toledo. Virus Genes 2017; 53:650-655. [PMID: 28391502 PMCID: PMC5527331 DOI: 10.1007/s11262-017-1452-0] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 03/30/2017] [Indexed: 12/11/2022]
Abstract
Human cytomegalovirus (HCMV) is an important opportunistic pathogen in immunocompromised patients and a major cause of congenital birth defects when acquired in utero. In the 1990s, four chimeric viruses were constructed by replacing genome segments of the high passage Towne strain with segments of the low passage Toledo strain, with the goal of obtaining live attenuated vaccine candidates that remained safe but were more immunogenic than the overly attenuated Towne vaccine. The chimeras were found to be safe when administered to HCMV-seronegative human volunteers, but to differ significantly in their ability to induce seroconversion. This suggests that chimera-specific genetic differences impacted the ability to replicate or persist in vivo and the consequent ability to induce an antibody response. To identify specific genomic breakpoints between Towne and Toledo sequences and establish whether spontaneous mutations or rearrangements had occurred during construction of the chimeras, complete genome sequences were determined. No major deletions or rearrangements were observed, although a number of unanticipated mutations were identified. However, no clear association emerged between the genetic content of the chimeras and the reported levels of vaccine-induced HCMV-specific humoral or cellular immune responses, suggesting that multiple genetic determinants are likely to impact immunogenicity. In addition to revealing the genome organization of the four vaccine candidates, this study provided an opportunity to probe the genetics of HCMV attenuation in humans. The results may be valuable in the future design of safe live or replication-defective vaccines that optimize immunogenicity and efficacy.
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Affiliation(s)
- Nicolás M Suárez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Betty Lau
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | | | - Ronzo Lee
- Department of Pediatrics, Virginia Commonwealth University, Richmond, VA, USA
| | - Edward S Mocarski
- Department of Microbiology and Immunology, Emory Vaccine Center, Emory University, Atlanta, GA, USA
| | - Gavin W G Wilkinson
- Division of Infection and Immunity, School of Medicine, Cardiff University, Cardiff, UK
| | - Stuart P Adler
- CMV Research Foundation, Virginia Commonwealth University, Richmond, VA, USA
| | - Michael A McVoy
- Department of Pediatrics, Virginia Commonwealth University, Richmond, VA, USA.
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
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Molecular and biological characterization of a new isolate of guinea pig cytomegalovirus. Viruses 2014; 6:448-75. [PMID: 24473341 PMCID: PMC3939465 DOI: 10.3390/v6020448] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2013] [Revised: 01/09/2014] [Accepted: 01/09/2014] [Indexed: 12/28/2022] Open
Abstract
Development of a vaccine against congenital infection with human cytomegalovirus is complicated by the issue of re-infection, with subsequent vertical transmission, in women with pre-conception immunity to the virus. The study of experimental therapeutic prevention of re-infection would ideally be undertaken in a small animal model, such as the guinea pig cytomegalovirus (GPCMV) model, prior to human clinical trials. However, the ability to model re-infection in the GPCMV model has been limited by availability of only one strain of virus, the 22122 strain, isolated in 1957. In this report, we describe the isolation of a new GPCMV strain, the CIDMTR strain. This strain demonstrated morphological characteristics of a typical Herpesvirinae by electron microscopy. Illumina and PacBio sequencing demonstrated a genome of 232,778 nt. Novel open reading frames ORFs not found in reference strain 22122 included an additional MHC Class I homolog near the right genome terminus. The CIDMTR strain was capable of dissemination in immune compromised guinea pigs, and was found to be capable of congenital transmission in GPCMV-immune dams previously infected with salivary gland‑adapted strain 22122 virus. The availability of a new GPCMV strain should facilitate study of re-infection in this small animal model.
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Cunningham C, Gatherer D, Hilfrich B, Baluchova K, Dargan DJ, Thomson M, Griffiths PD, Wilkinson GWG, Schulz TF, Davison AJ. Sequences of complete human cytomegalovirus genomes from infected cell cultures and clinical specimens. J Gen Virol 2010; 91:605-15. [PMID: 19906940 PMCID: PMC2885759 DOI: 10.1099/vir.0.015891-0] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2009] [Accepted: 11/09/2009] [Indexed: 12/14/2022] Open
Abstract
We have assessed two approaches to sequencing complete human cytomegalovirus (HCMV) genomes (236 kbp) in DNA extracted from infected cell cultures (strains 3157, HAN13, HAN20 and HAN38) or clinical specimens (strains JP and 3301). The first approach involved amplifying genomes from the DNA samples as overlapping PCR products, sequencing these by the Sanger method, acquiring reads from a capillary instrument and assembling these using the Staden programs. The second approach involved generating sequence data from the DNA samples by using an Illumina Genome Analyzer (IGA), processing the filtered reads by reference-independent (de novo) assembly, utilizing the resulting sequence to direct reference-dependent assembly of the same data and finishing by limited PCR sequencing. Both approaches were successful. In particular, the investigation demonstrated the utility of IGA data for efficiently sequencing genomes from clinical samples containing as little as 3 % HCMV DNA. Analysis of the genome sequences obtained showed that each of the strains grown in cell culture was a mutant. Certain of the mutations were shared among strains from independent clinical sources, thus suggesting that they may have arisen in a common ancestor during natural infection. Moreover, one of the strains (JP) sequenced directly from a clinical specimen was mutated in two genes, one of which encodes a proposed immune-evasion function, viral interleukin-10. These observations imply that HCMV mutants exist in human infections.
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Affiliation(s)
- Charles Cunningham
- MRC Virology Unit, Institute of Virology, University of Glasgow, Church Street, Glasgow G11 5JR, UK
| | - Derek Gatherer
- MRC Virology Unit, Institute of Virology, University of Glasgow, Church Street, Glasgow G11 5JR, UK
| | - Birgitta Hilfrich
- Institute of Virology, Hannover Medical School, Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany
| | - Katarina Baluchova
- MRC Virology Unit, Institute of Virology, University of Glasgow, Church Street, Glasgow G11 5JR, UK
| | - Derrick J. Dargan
- MRC Virology Unit, Institute of Virology, University of Glasgow, Church Street, Glasgow G11 5JR, UK
| | - Marian Thomson
- The GenePool, Ashworth Laboratories, King's Buildings, University of Edinburgh, Edinburgh EH9 3JT, UK
| | - Paul D. Griffiths
- Centre for Virology, University College Medical School, Royal Free Campus, Rowland Hill Street, Hampstead, London NW3 2QG, UK
| | - Gavin W. G. Wilkinson
- Department of Medical Microbiology, Tenovus Building, School of Medicine, Cardiff University, Heath Park, Cardiff CF14 4XX, UK
| | - Thomas F. Schulz
- Institute of Virology, Hannover Medical School, Carl-Neuberg-Strasse 1, D-30625 Hannover, Germany
| | - Andrew J. Davison
- MRC Virology Unit, Institute of Virology, University of Glasgow, Church Street, Glasgow G11 5JR, UK
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Expression of human cytomegalovirus pp150 gene in transgenic Vicia faba L. and immunogenicity of pp150 protein in mice. Biologicals 2010; 38:265-72. [DOI: 10.1016/j.biologicals.2009.11.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2009] [Revised: 09/03/2009] [Accepted: 11/09/2009] [Indexed: 11/21/2022] Open
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Dulal K, Zhang Z, Zhu H. Development of a gene capture method to rescue a large deletion mutant of human cytomegalovirus. J Virol Methods 2009; 157:180-7. [PMID: 19162076 DOI: 10.1016/j.jviromet.2008.12.021] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Revised: 12/13/2008] [Accepted: 12/17/2008] [Indexed: 11/17/2022]
Abstract
Human cytomegalovirus (HCMV) is an opportunistic human pathogen that causes serious clinical illness in immunocompromised individuals. A major breakthrough in the progression of HCMV genetics studies is the development of bacterial artificial chromosome (BAC) clones of the viral genome. Recently, a luciferase reporter gene was inserted in the BAC clone (BAC(luc)) which facilitates monitoring of the virus growth both in vitro and in vivo. The virus made from the BAC(luc) grew with the similar kinetics as the wild-type strain indicating that the luciferase gene insertion does not interfere with the virus growth. Although the construction of the BAC clone has eased genetic studies of herpesviruses tremendously, there are still difficulties in cloning large DNA fragments of the virus to rescue mutations with large deletions. This paper describes a novel method termed "gene capture", which allows easier cloning of large pieces of DNA. As an application of this method, a 15-kb fragment that was deleted from the HCMV genome was rescued back into the viral genome. A mutant HCMV clone with the 15-kb region deletion was generated first using the lambda prophage recombination system in E. coli. Utilizing the new rescue method, the deleted fragment was then rescued in two steps: the 15-kb region was captured into a vector by homologous recombination; and the captured DNA fragment from the vector was inserted back into its native site in the mutant viral BAC by second homologous recombination. This method will be useful particularly for cloning large DNA fragments from any genome without introducing undesired mutations by traditional PCR-based approaches.
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Affiliation(s)
- Kalpana Dulal
- Department of Microbiology and Molecular Genetics, UMDNJ-New Jersey Medical School, Newark, 07101, USA
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