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The DNA Sequence of the RK Strain of Human Herpesvirus 7 by A. George

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The DNA Sequence of the RK Strain of Human Herpesvirus 7 by A. George The DNA sequence of the RK strain of human herpesvirus 7 by A. George Megaw A Thesis presented for the Degree of Doctor of Philosophy in The Faculty of Science at the University of Glasgow Institute of Virology December 1997 Church Street Glasgow ProQuest Num ber: 13818610 All rights reserved INFORMATION TO ALL USERS The quality of this reproduction is dependent upon the quality of the copy submitted. In the unlikely event that the author did not send a com plete manuscript and there are missing pages, these will be noted. Also, if material had to be removed, a note will indicate the deletion. uest ProQuest 13818610 Published by ProQuest LLC(2018). Copyright of the Dissertation is held by the Author. All rights reserved. This work is protected against unauthorized copying under Title 17, United States C ode Microform Edition © ProQuest LLC. ProQuest LLC. 789 East Eisenhower Parkway P.O. Box 1346 Ann Arbor, Ml 48106- 1346 GLASGOWUtyVERSITY LIBRARY lU W7 (cof^ \) ACKNOWLEDGEMENTS I would like to thank the following people who have contributed to the completion of this thesis. Prof. D.J. McGeoch, Professor J.B. Clements, Dr. H. Marsden and Professor J.H. Subak- Sharpe, for the provision of the facilities in the Institute of Virology. Dr. A.J. Davison for his support, wisdom and advice (especially in the technical aspects of splicing) throughout the course of this work and also for his thorough criticism of this manuscript; your patience is a virtue. Professor N. Frenkel and Dr. D. Rapaportfor provision of HHV-7 strain RK genomic DNA. The washroom and media staff for provision of glassware and general solutions used in this project. Katherine, I owe a debt of understanding that I shall never be able to repay - 1 love you. Aoife, who appeared not to notice, your newborn giggles and smiles were like watching the snow fall. Everyone else who helped a little bit every day (Charles, Robin, Wendy, Ali, Moira, Steve and the others) - thank you. During the course of this study, the author was in receipt of a Medical Research Council studentship and, unless otherwise stated, all results were obtained by the author's own efforts. SUMMARY Human herpesvirus 7 (HHV-7) was first isolated by Frenkel and colleagues in 1989 from CD4+ T- cells, during experiments concerning propagation of HHV-6. Uninfected cells underwent spontaneous cytopathic effect following conditions promoting T-cell activation. A new herpesvirus was isolated which was related to but distinct from human herpesvirus 6 (HHV-6) This virus was designated HHV-7 (RK). HHV-7 is ubiquitous in the human population - probably more than 85% of people are infected. It is likely that HHV-7 is transmitted through saliva, with primary infection occurring before three years of age. The virus has no proven involvement in any disease. HHV-7 is a member of the Betaherpesvirinae and is more closely related to HHV-6 than to human cytomegalovirus (HCMV). The genome is approximately 145 kbp in length and has an overall structure like that of HHV-6, consisting of a long unique region (U) flanked by a direct repeat (DR). Since 1984, the complete sequences of fourteen herpesvirus genomes have been published and at least four more have been completed. This has allowed comparative studies of individual genes and permitted extensive and detailed understanding of the relationships between the herpesviruses. In addition, recent reports based on molecular sequence analysis, have provided a detailed phylogeny and allowed an evolutionary timescale to be derived. The aims of this project were to determine the complete DNA sequence of HHV-7 and to analyse the coding potential of the sequence. The work was initiated in collaboration with Professor N. Frenkel (Tel-Aviv University, Israel), who provided genomic DNA from the RK strain. During the course of this work the complete DNA sequences of HHV-6 strain U1102 and HHV-7 strain Jl were published by other groups. Therefore, the HHV-7 strain RK sequence was compared with these two sequences in order to appraise evolutionary divergence and to re­ evaluate the genetic contents of HHV-6 and HHV-7. The HHV-7 RK genome was sequenced by direct shotgun cloning of random DNA fragments into an M13 vector. Approximately 7,000 fragments were sequenced and compiled into a database with the aid of a computer. The genetic content of the sequence was interpreted using a suite of computer programs. This analysis was then extended to reassess the sequence of HHV-6. Special attention was paid to potential splicing. The HHV-7 RK genome sequence obtained is 153,080 bp in length and comprises U (133,012 bp) flanked on each side by a copy of DR (10,034 bp). Four different reiterated sequences are present in the genome, two in U and two in DR. the latter comprise arrays of a human telomere­ like element. Complexity and size resulted in one of these arrays being particularly challenging to resolve, and an unsatisfactory solution in this region is reflected in the likelihood that the sequence obtained is approximately 3 kbp longer than the actual genome. Analysis of the differences between HHV-7 RK and Jl indicated that the lineages resulting in the two strains diverged from a common ancestor of the order of 10,000 years ago. It was concluded on the basis of various analytical criteria that the HHV-7 genome contains 84 genes, only one of which has no direct counterpart in HHV-6. However, the latter is related to an adjacent gene which has an HHV-6 homologue. By the same criteria, HHV-6 contains 85 genes, two of which lack counterparts in HHV-7. One encodes a putative membrane glycoprotein and the other is a homologue of the adeno-associated virus type 2 rep gene. Furthermore, sequence comparisons between HHV-7 and HHV-6 also allowed the identification of putative splice sites in eleven genes. One of these genes is predicted to encode a previously unrecognised membrane glycoprotein. This study lays the foundation for continuing experimental investigation of gene expression in HHV-7, particularly in regard to splicing. CONTENTS 1.0. INTRODUCTION 1.0. FOREWORD................................................................................................................1 1.1. THE HERPESVIRIDAE..............................................................................................1 1.1.1. Overview....................................................................................................................... 1 1.1.2. Clinical manifestations ....................................................................................................3 1.1.2.1. General ....................................................................................................... 3 1.1.2.2. Human herpesviruses .................................................................................. 3 1.1.3. Life cycle........................................................................................................................6 1.1.3.1. The lytic cycle...............................................................................................6 1.1.3.2. The latent cycle ............................................................................................7 1.1.4. Herpesvirus genes ......................................................................................................... 7 1.1.5. Herpesvirus classification ...............................................................................................8 1.1.5.1. Formal classification ..................................................................................... 8 1.1.5.2. Genetic classification ...................................................................................10 1.1.6. Genetic content ............................................................................................................ 11 1.1.6.1. Genome sequences ....................................................................................11 1.1.6.2. Gene conservation ......................................................................................12 1.1.7. Genome evolution .........................................................................................................13 1.1.7.1. Mechanisms ............................................................................................... 13 1.1.7.2. Phylogeny ...................................................................................................15 1.1.7.3. Evolutionary timescale ................................................................................16 1.2. HUMAN CYTOMEGALOVIRUS............................................................................. 18 1.2.1. Basic characteristics.....................................................................................................18 1.2.2. Epidemiology ......................................:........................................................................18 1.2.3. Cellular tropism ............................................................................................................ 18 1.2.4. Growth properties .........................................................................................................19 1.2.5. Disease and therapy .....................................................................................................20 1.2.6. The HCMV genome ..................................................................................................... 21 1.2.6.1. Size and structure ...................................................................................... 21 1.2.6.2.
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