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Yang Y, Wang P, Qaidi SE, Hardwidge PR, Huang J, Zhu G. Loss to gain: pseudogenes in microorganisms, focusing on eubacteria, and their biological significance. Appl Microbiol Biotechnol 2024; 108:328. [PMID: 38717672 PMCID: PMC11078800 DOI: 10.1007/s00253-023-12971-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Revised: 11/26/2023] [Accepted: 12/01/2023] [Indexed: 05/12/2024]
Abstract
Pseudogenes are defined as "non-functional" copies of corresponding parent genes. The cognition of pseudogenes continues to be refreshed through accumulating and updating research findings. Previous studies have predominantly focused on mammals, but pseudogenes have received relatively less attention in the field of microbiology. Given the increasing recognition on the importance of pseudogenes, in this review, we focus on several aspects of microorganism pseudogenes, including their classification and characteristics, their generation and fate, their identification, their abundance and distribution, their impact on virulence, their ability to recombine with functional genes, the extent to which some pseudogenes are transcribed and translated, and the relationship between pseudogenes and viruses. By summarizing and organizing the latest research progress, this review will provide a comprehensive perspective and improved understanding on pseudogenes in microorganisms. KEY POINTS: • Concept, classification and characteristics, identification and databases, content, and distribution of microbial pseudogenes are presented. • How pseudogenization contribute to pathogen virulence is highlighted. • Pseudogenes with potential functions in microorganisms are discussed.
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Affiliation(s)
- Yi Yang
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
- Joint Laboratory of International Cooperation On Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou, 225009, China
| | - Pengzhi Wang
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009, Jiangsu, China
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China
- Joint Laboratory of International Cooperation On Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou, 225009, China
| | - Samir El Qaidi
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Philip R Hardwidge
- College of Veterinary Medicine, Kansas State University, Manhattan, KS, 66506, USA
| | - Jinlin Huang
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
- Jiangsu Key Lab of Zoonosis, Yangzhou University, Yangzhou, 225009, Jiangsu, China.
- College of Bioscience and Biotechnology, Yangzhou University, 12 East Wenhui Road Yangzhou, Jiangsu, 225009, China.
| | - Guoqiang Zhu
- College of Veterinary Medicine, Yangzhou University, 12 East Wenhui Road, Yangzhou, 225009, Jiangsu, China.
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou, 225009, China.
- Joint Laboratory of International Cooperation On Prevention and Control Technology of Important Animal Diseases and Zoonoses of Jiangsu Higher Education Institutions, Yangzhou, 225009, China.
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Wang HY, Valencia SM, Pfeifer SP, Jensen JD, Kowalik TF, Permar SR. Common Polymorphisms in the Glycoproteins of Human Cytomegalovirus and Associated Strain-Specific Immunity. Viruses 2021; 13:v13061106. [PMID: 34207868 PMCID: PMC8227702 DOI: 10.3390/v13061106] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 06/04/2021] [Accepted: 06/07/2021] [Indexed: 12/18/2022] Open
Abstract
Human cytomegalovirus (HCMV), one of the most prevalent viruses across the globe, is a common cause of morbidity and mortality for immunocompromised individuals. Recent clinical observations have demonstrated that mixed strain infections are common and may lead to more severe disease progression. This clinical observation illustrates the complexity of the HCMV genome and emphasizes the importance of taking a population-level view of genotypic evolution. Here we review frequently sampled polymorphisms in the glycoproteins of HCMV, comparing the variable regions, and summarizing their corresponding geographic distributions observed to date. The related strain-specific immunity, including neutralization activity and antigen-specific cellular immunity, is also discussed. Given that these glycoproteins are common targets for vaccine design and anti-viral therapies, this observed genetic variation represents an important resource for future efforts to combat HCMV infections.
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Affiliation(s)
- Hsuan-Yuan Wang
- Department of Pediatrics, Weill Cornell Medicine, New York, NY 10065, USA;
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA;
| | - Sarah M. Valencia
- Duke Human Vaccine Institute, Duke University Medical Center, Durham, NC 27710, USA;
| | - Susanne P. Pfeifer
- Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (S.P.P.); (J.D.J.)
| | - Jeffrey D. Jensen
- Center for Evolution & Medicine, School of Life Sciences, Arizona State University, Tempe, AZ 85281, USA; (S.P.P.); (J.D.J.)
| | - Timothy F. Kowalik
- Department of Microbiology and Physiological Systems, University of Massachusetts Medical School, Worcester, MA 01655, USA;
| | - Sallie R. Permar
- Department of Pediatrics, Weill Cornell Medicine, New York, NY 10065, USA;
- Correspondence: ; Tel.: +1-212-746-4111
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3
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Camiolo S, Suárez NM, Chalka A, Venturini C, Breuer J, Davison AJ. GRACy: A tool for analysing human cytomegalovirus sequence data. Virus Evol 2020; 7:veaa099. [PMID: 33505707 PMCID: PMC7816668 DOI: 10.1093/ve/veaa099] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Modern DNA sequencing has instituted a new era in human cytomegalovirus (HCMV) genomics. A key development has been the ability to determine the genome sequences of HCMV strains directly from clinical material. This involves the application of complex and often non-standardized bioinformatics approaches to analysing data of variable quality in a process that requires substantial manual intervention. To relieve this bottleneck, we have developed GRACy (Genome Reconstruction and Annotation of Cytomegalovirus), an easy-to-use toolkit for analysing HCMV sequence data. GRACy automates and integrates modules for read filtering, genotyping, genome assembly, genome annotation, variant analysis, and data submission. These modules were tested extensively on simulated and experimental data and outperformed generic approaches. GRACy is written in Python and is embedded in a graphical user interface with all required dependencies installed by a single command. It runs on the Linux operating system and is designed to allow the future implementation of a cross-platform version. GRACy is distributed under a GPL 3.0 license and is freely available at https://bioinformatics.cvr.ac.uk/software/ with the manual and a test dataset.
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Affiliation(s)
| | - Nicolás M Suárez
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - Antonia Chalka
- Division of Infection & Immunity, Roslin Institute, R(D)SVM, University of Edinburgh, Edinburgh, UK
| | - Cristina Venturini
- Division of Infection and Immunity, University College London, London, UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
| | - Andrew J Davison
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
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4
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Poole E, Neves TC, Oliveira MT, Sinclair J, da Silva MCC. Human Cytomegalovirus Interleukin 10 Homologs: Facing the Immune System. Front Cell Infect Microbiol 2020; 10:245. [PMID: 32582563 PMCID: PMC7296156 DOI: 10.3389/fcimb.2020.00245] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Accepted: 04/27/2020] [Indexed: 12/12/2022] Open
Abstract
Human Cytomegalovirus (HCMV) can cause a variety of health disorders that can lead to death in immunocompromised individuals and neonates. The HCMV lifecycle comprises both a lytic (productive) and a latent (non-productive) phase. HCMV lytic infection occurs in a wide range of terminally differentiated cell types. HCMV latency has been less well-studied, but one characterized site of latency is in precursor cells of the myeloid lineage. All known viral genes are expressed during a lytic infection and a subset of these are also transcribed during latency. The UL111A gene which encodes the viral IL-10, a homolog of the human IL-10, is one of these genes. During infection, different transcript isoforms of UL111A are generated by alternative splicing. The most studied of the UL111A isoforms are cmvIL-10 (also termed the "A" transcript) and LAcmvIL-10 (also termed the "B" transcript), the latter being a well-characterized latency associated transcript. Both isoforms can downregulate MHC class II, however they differ in a number of other immunomodulatory properties, such as the ability to bind the IL10 receptor and induce signaling through STAT3. There are also a number of other isoforms which have been identified which are expressed by differential splicing during lytic infection termed C, D, E, F, and G, although these have been less extensively studied. HCMV uses the viral IL-10 proteins to manipulate the immune system during lytic and latent phases of infection. In this review, we will discuss the literature on the viral IL-10 transcripts identified to date, their encoded proteins and the structures of these proteins as well as the functional properties of all the different isoforms of viral IL-10.
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Affiliation(s)
- Emma Poole
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Tainan Cerqueira Neves
- Center for Natural and Humanities Sciences, Federal University of ABC (UFABC), São Bernardo do Campo, Brazil
| | - Martha Trindade Oliveira
- Center for Natural and Humanities Sciences, Federal University of ABC (UFABC), São Bernardo do Campo, Brazil
| | - John Sinclair
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
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5
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Suárez NM, Wilkie GS, Hage E, Camiolo S, Holton M, Hughes J, Maabar M, Vattipally SB, Dhingra A, Gompels UA, Wilkinson GWG, Baldanti F, Furione M, Lilleri D, Arossa A, Ganzenmueller T, Gerna G, Hubáček P, Schulz TF, Wolf D, Zavattoni M, Davison AJ. Human Cytomegalovirus Genomes Sequenced Directly From Clinical Material: Variation, Multiple-Strain Infection, Recombination, and Gene Loss. J Infect Dis 2020; 220:781-791. [PMID: 31050742 PMCID: PMC6667795 DOI: 10.1093/infdis/jiz208] [Citation(s) in RCA: 63] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2019] [Accepted: 04/24/2019] [Indexed: 11/29/2022] Open
Abstract
The genomic characteristics of human cytomegalovirus (HCMV) strains sequenced directly from clinical pathology samples were investigated, focusing on variation, multiple-strain infection, recombination, and gene loss. A total of 207 datasets generated in this and previous studies using target enrichment and high-throughput sequencing were analyzed, in the process enabling the determination of genome sequences for 91 strains. Key findings were that (i) it is important to monitor the quality of sequencing libraries in investigating variation; (ii) many recombinant strains have been transmitted during HCMV evolution, and some have apparently survived for thousands of years without further recombination; (iii) mutants with nonfunctional genes (pseudogenes) have been circulating and recombining for long periods and can cause congenital infection and resulting clinical sequelae; and (iv) intrahost variation in single-strain infections is much less than that in multiple-strain infections. Future population-based studies are likely to continue illuminating the evolution, epidemiology, and pathogenesis of HCMV.
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Affiliation(s)
- Nicolás M Suárez
- Medical Research Council-University of Glasgow Centre for Virus Research, United Kingdom
| | - Gavin S Wilkie
- Medical Research Council-University of Glasgow Centre for Virus Research, United Kingdom
| | - Elias Hage
- Institute of Virology, Hannover Medical School, United Kingdom.,German Center for Infection Research, Hannover-Braunschweig site, United Kingdom
| | - Salvatore Camiolo
- Medical Research Council-University of Glasgow Centre for Virus Research, United Kingdom
| | - Marylouisa Holton
- Medical Research Council-University of Glasgow Centre for Virus Research, United Kingdom
| | - Joseph Hughes
- Medical Research Council-University of Glasgow Centre for Virus Research, United Kingdom
| | - Maha Maabar
- Medical Research Council-University of Glasgow Centre for Virus Research, United Kingdom
| | - Sreenu B Vattipally
- Medical Research Council-University of Glasgow Centre for Virus Research, United Kingdom
| | - Akshay Dhingra
- Institute of Virology, Hannover Medical School, United Kingdom
| | - Ursula A Gompels
- Pathogen Molecular Biology Department, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Gavin W G Wilkinson
- Division of Infection and Immunity, School of Medicine, Cardiff University, United Kingdom
| | - Fausto Baldanti
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo, Italy.,Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, University of Pavia, Italy
| | - Milena Furione
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo, Italy
| | - Daniele Lilleri
- Laboratory of Genetics-Transplantology and Cardiovascular Diseases, Italy
| | - Alessia Arossa
- Departments of Obstetrics and Gynecology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Tina Ganzenmueller
- Institute of Virology, Hannover Medical School, United Kingdom.,German Center for Infection Research, Hannover-Braunschweig site, United Kingdom.,Institute for Medical Virology and Epidemiology of Viral Diseases, University Hospital Tuebingen, Germany
| | - Giuseppe Gerna
- Laboratory of Genetics-Transplantology and Cardiovascular Diseases, Italy
| | - Petr Hubáček
- Department of Medical Microbiology, Motol University Hospital, Prague, Czech Republic, Israel
| | - Thomas F Schulz
- Institute of Virology, Hannover Medical School, United Kingdom.,German Center for Infection Research, Hannover-Braunschweig site, United Kingdom
| | - Dana Wolf
- Clinical Virology Unit, Department of Clinical Microbiology and Infectious Diseases, Hadassah University Hospital, Jerusalem, Israel
| | - Maurizio Zavattoni
- Molecular Virology Unit, Microbiology and Virology Department, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico (IRCCS) Policlinico San Matteo, Italy
| | - Andrew J Davison
- Medical Research Council-University of Glasgow Centre for Virus Research, United Kingdom
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6
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Cagliani R, Forni D, Mozzi A, Sironi M. Evolution and Genetic Diversity of Primate Cytomegaloviruses. Microorganisms 2020; 8:E624. [PMID: 32344906 PMCID: PMC7285053 DOI: 10.3390/microorganisms8050624] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2020] [Revised: 04/17/2020] [Accepted: 04/19/2020] [Indexed: 12/30/2022] Open
Abstract
Cytomegaloviruses (CMVs) infect many mammals, including humans and non-human primates (NHPs). Human cytomegalovirus (HCMV) is an important opportunistic pathogen among immunocompromised patients and represents the most common infectious cause of birth defects. HCMV possesses a large genome and very high genetic diversity. NHP-infecting CMVs share with HCMV a similar genomic organization and coding content, as well as the course of viral infection. Recent technological advances have allowed the sequencing of several HCMV strains from clinical samples and provided insight into the diversity of NHP-infecting CMVs. The emerging picture indicates that, with the exclusion of core genes (genes that have orthologs in all herpesviruses), CMV genomes are relatively plastic and diverse in terms of gene content, both at the inter- and at the intra-species level. Such variability most likely underlies the strict species-specificity of these viruses, as well as their ability to persist lifelong and with relatively little damage to their hosts. However, core genes, despite their strong conservation, also represented a target of adaptive evolution and subtle changes in their coding sequence contributed to CMV adaptation to different hosts. Indubitably, important knowledge gaps remain, the most relevant of which concerns the role of viral genetics in HCMV-associated human disease.
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Affiliation(s)
| | | | | | - Manuela Sironi
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, 23842 Bosisio Parini, Italy
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7
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Human Cytomegalovirus Congenital (cCMV) Infection Following Primary and Nonprimary Maternal Infection: Perspectives of Prevention through Vaccine Development. Vaccines (Basel) 2020; 8:vaccines8020194. [PMID: 32340180 PMCID: PMC7349293 DOI: 10.3390/vaccines8020194] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/13/2020] [Accepted: 04/18/2020] [Indexed: 01/26/2023] Open
Abstract
Congenital cytomegalovirus (cCMV) might occur as a result of the human cytomegalovirus (HCMV) primary (PI) or nonprimary infection (NPI) in pregnant women. Immune correlates of protection against cCMV have been partly identified only for PI. Following either PI or NPI, HCMV strains undergo latency. From a diagnostic standpoint, while the serological criteria for the diagnosis of PI are well-established, those for the diagnosis of NPI are still incomplete. Thus far, a recombinant gB subunit vaccine has provided the best results in terms of partial protection. This partial efficacy was hypothetically attributed to the post-fusion instead of the pre-fusion conformation of the gB present in the vaccine. Future efforts should be addressed to verify whether a new recombinant gB pre-fusion vaccine would provide better results in terms of prevention of both PI and NPI. It is still a matter of debate whether human hyperimmune globulin are able to protect from HCMV vertical transmission. In conclusion, the development of an HCMV vaccine that would prevent a significant portion of PI would be a major step forward in the development of a vaccine for both PI and NPI.
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8
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Dobbins GC, Patki A, Chen D, Tiwari HK, Hendrickson C, Britt WJ, Fowler K, Chen JY, Boppana SB, Ross SA. Association of CMV genomic mutations with symptomatic infection and hearing loss in congenital CMV infection. BMC Infect Dis 2019; 19:1046. [PMID: 31822287 PMCID: PMC6905059 DOI: 10.1186/s12879-019-4681-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 11/29/2019] [Indexed: 12/23/2022] Open
Abstract
Background Congenital cytomegalovirus (cCMV) infection is the most common congenital infection and a leading cause of long-term neurological and sensory sequelae, the most common being sensorineural hearing loss (SNHL). Despite extensive research, clinical or laboratory markers to identify CMV infected children with increased risk for disease have not been identified. This study utilizes viral whole-genome next generation-sequencing (NGS) of specimens from congenitally infected infants to explore viral diversity and specific viral variants that may be associated with symptomatic infection and SNHL. Methods CMV DNA from urine specimens of 30 infants (17 asymptomatic, 13 symptomatic) was target enriched and next generation sequenced resulting in 93% coverage of the CMV genome allowing analysis of viral diversity. Results Variant frequency distribution was compared between children with symptomatic and asymptomatic cCMV and those with (n = 13) and without (n = 17) hearing loss. The CMV genes UL48A, UL88, US19 and US22 were found to have an increase in nucleotide diversity in symptomatic children; while UL57, UL20, UL104, US14, UL115, and UL35 had an increase in diversity in children with hearing loss. An analysis of single variant differences between symptomatic and asymptomatic children found UL55 to have the highest number, while the most variants associated with SNHL were in the RL11 gene family. In asymptomatic infants with SNHL, mutations were observed more frequently in UL33 and UL20. Conclusion CMV genomes from infected newborns can be mapped to 93% of the genome at a depth allowing accurate and reproducible analysis of polymorphisms for variant and gene discovery that may be linked to symptomatic and hearing loss outcomes.
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Affiliation(s)
- G Clement Dobbins
- Department of Pediatrics, The University of Alabama School of Medicine, CHB 116, 1600 6th Avenue South, Birmingham, AL, USA.
| | - Amit Patki
- Department of Biostatistics, The University of Alabama School of Public Health, Birmingham, AL, USA
| | - Dongquan Chen
- Informatics Institute, The University of Alabama at Birmingham, Birmingham, AL, USA.,Department of Medicine, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Hemant K Tiwari
- Department of Biostatistics, The University of Alabama School of Public Health, Birmingham, AL, USA
| | - Curtis Hendrickson
- Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - William J Britt
- Department of Pediatrics, The University of Alabama School of Medicine, CHB 116, 1600 6th Avenue South, Birmingham, AL, USA.,Informatics Institute, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Karen Fowler
- Department of Pediatrics, The University of Alabama School of Medicine, CHB 116, 1600 6th Avenue South, Birmingham, AL, USA
| | - Jake Y Chen
- Informatics Institute, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Suresh B Boppana
- Department of Pediatrics, The University of Alabama School of Medicine, CHB 116, 1600 6th Avenue South, Birmingham, AL, USA.,Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, USA
| | - Shannon A Ross
- Department of Pediatrics, The University of Alabama School of Medicine, CHB 116, 1600 6th Avenue South, Birmingham, AL, USA. .,Department of Microbiology, The University of Alabama at Birmingham, Birmingham, AL, USA.
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9
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Houldcroft CJ. Human Herpesvirus Sequencing in the Genomic Era: The Growing Ranks of the Herpetic Legion. Pathogens 2019; 8:E186. [PMID: 31614759 PMCID: PMC6963362 DOI: 10.3390/pathogens8040186] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 10/10/2019] [Accepted: 10/11/2019] [Indexed: 12/19/2022] Open
Abstract
The nine human herpesviruses are some of the most ubiquitous pathogens worldwide, causing life-long latent infection in a variety of different tissues. Human herpesviruses range from mild childhood infections to known tumour viruses and 'trolls of transplantation'. Epstein-Barr virus was the first human herpesvirus to have its whole genome sequenced; GenBank now includes thousands of herpesvirus genomes. This review will cover some of the recent advances in our understanding of herpesvirus diversity and disease that have come about as a result of new sequencing technologies, such as target enrichment and long-read sequencing. It will also look at the problem of resolving mixed-genotype infections, whether with short or long-read sequencing methods; and conclude with some thoughts on the future of the field as herpesvirus population genomics becomes a reality.
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Affiliation(s)
- Charlotte J Houldcroft
- Department of Medicine, Addenbrooke's Hospital, University of Cambridge, Cambs CB2 0QQ UK.
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambs CB10 1SA, UK.
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10
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Martí-Carreras J, Maes P. Human cytomegalovirus genomics and transcriptomics through the lens of next-generation sequencing: revision and future challenges. Virus Genes 2019; 55:138-164. [PMID: 30604286 PMCID: PMC6458973 DOI: 10.1007/s11262-018-1627-3] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/14/2018] [Indexed: 12/13/2022]
Abstract
The human cytomegalovirus (HCMV) genome was sequenced by hierarchical shotgun almost 30 years ago. Over these years, low and high passaged strains have been sequenced, improving, albeit still far from complete, the understanding of the coding potential, expression dynamics and diversity of wild-type HCMV strains. Next-generation sequencing (NGS) platforms have enabled a huge advancement, facilitating the comparison of differentially passaged strains, challenging diagnostics and research based on a single or reduced gene set genotyping. In addition, it allowed to link genetic features to different viral phenotypes as for example, correlating large genomic re-arrangements to viral attenuation or different mutations to antiviral resistance and cell tropism. NGS platforms provided the first high-resolution experiments to HCMV dynamics, allowing the study of intra-host viral population structures and the description of rare transcriptional events. Long-read sequencing has recently become available, helping to identify new genomic re-arrangements, partially accounting for the genetic variability displayed in clinical isolates, as well as, in changing the understanding of the HCMV transcriptome. Better knowledge of the transcriptome resulted in a vast number of new splicing events and alternative transcripts, although most of them still need additional validation. This review summarizes the sequencing efforts reached so far, discussing its approaches and providing a revision and new nuances on HCMV sequence variability in the sequencing field.
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Affiliation(s)
- Joan Martí-Carreras
- Zoonotic Infectious Diseases Unit, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, Box 1040, 3000, Leuven, Belgium
| | - Piet Maes
- Zoonotic Infectious Diseases Unit, Department of Microbiology and Immunology, Rega Institute, KU Leuven, Herestraat 49, Box 1040, 3000, Leuven, Belgium.
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11
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Sallah N, Palser AL, Watson SJ, Labo N, Asiki G, Marshall V, Newton R, Whitby D, Kellam P, Barroso I. Genome-Wide Sequence Analysis of Kaposi Sarcoma-Associated Herpesvirus Shows Diversification Driven by Recombination. J Infect Dis 2018; 218:1700-1710. [PMID: 30010810 PMCID: PMC6195662 DOI: 10.1093/infdis/jiy427] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2018] [Accepted: 07/11/2018] [Indexed: 12/29/2022] Open
Abstract
Background Kaposi sarcoma-associated herpesvirus (KSHV) establishes lifelong infection in the human host and has been associated with a variety of malignancies. KSHV displays striking geographic variation in prevalence, which is highest in sub-Saharan Africa. The current KSHV genome sequences available are all tumor cell line-derived or primary tumor-associated viruses, which have provided valuable insights into KSHV genetic diversity. Methods Here, we sequenced 45 KSHV genomes from a Ugandan population cohort in which KSHV is endemic; these are the only genome sequences obtained from nondiseased individuals and of KSHV DNA isolated from saliva. Results Population structure analysis, along with the 25 published genome sequences from other parts of the world, showed whole-genome variation, separating sequences and variation within the central genome contributing to clustering of genomes by geography. We reveal new evidence for the presence of intragenic recombination and multiple recombination events contributing to the divergence of genomes into at least 5 distinct types. Discussion This study shows that large-scale genome-wide sequencing from clinical and epidemiological samples is necessary to capture the full extent of genetic diversity of KSHV, including recombination, and provides evidence to suggest a revision of KSHV genotype nomenclature.
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Affiliation(s)
- Neneh Sallah
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge
| | | | | | - Nazzarena Labo
- AIDS and Cancer Virus Program, Viral Oncology Section, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Maryland
| | - Gershim Asiki
- Medical Research Council/Uganda Virus Research Institute, Uganda Research Unit, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Vickie Marshall
- AIDS and Cancer Virus Program, Viral Oncology Section, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Maryland
| | - Robert Newton
- Medical Research Council/Uganda Virus Research Institute, Uganda Research Unit, London School of Hygiene and Tropical Medicine, United Kingdom
| | - Denise Whitby
- AIDS and Cancer Virus Program, Viral Oncology Section, Leidos Biomedical Research, Frederick National Laboratory for Cancer Research, Maryland
| | - Paul Kellam
- Kymab Ltd, Babraham Research Complex, Cambridge
- Department of Medicine, Imperial College London, United Kingdom
| | - Inês Barroso
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge
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12
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Karamitros T, van Wilgenburg B, Wills M, Klenerman P, Magiorkinis G. Nanopore sequencing and full genome de novo assembly of human cytomegalovirus TB40/E reveals clonal diversity and structural variations. BMC Genomics 2018; 19:577. [PMID: 30068288 PMCID: PMC6090854 DOI: 10.1186/s12864-018-4949-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2018] [Accepted: 07/19/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Human cytomegalovirus (HCMV) has a double-stranded DNA genome of approximately 235 Kbp that is structurally complex including extended GC-rich repeated regions. Genomic recombination events are frequent in HCMV cultures but have also been observed in vivo. Thus, the assembly of HCMV whole genomes from technologies producing shorter than 500 bp sequences is technically challenging. Here we improved the reconstruction of HCMV full genomes by means of a hybrid, de novo genome-assembly bioinformatics pipeline upon data generated from the recently released MinION MkI B sequencer from Oxford Nanopore Technologies. RESULTS The MinION run of the HCMV (strain TB40/E) library resulted in ~ 47,000 reads from a single R9 flowcell and in ~ 100× average read depth across the virus genome. We developed a novel, self-correcting bioinformatics algorithm to assemble the pooled HCMV genomes in three stages. In the first stage of the bioinformatics algorithm, long contigs (N50 = 21,892) of lower accuracy were reconstructed. In the second stage, short contigs (N50 = 5686) of higher accuracy were assembled, while in the final stage the high quality contigs served as template for the correction of the longer contigs resulting in a high-accuracy, full genome assembly (N50 = 41,056). We were able to reconstruct a single representative haplotype without employing any scaffolding steps. The majority (98.8%) of the genomic features from the reference strain were accurately annotated on this full genome construct. Our method also allowed the detection of multiple alternative sub-genomic fragments and non-canonical structures suggesting rearrangement events between the unique (UL /US) and the repeated (T/IRL/S) genomic regions. CONCLUSIONS Third generation high-throughput sequencing technologies can accurately reconstruct full-length HCMV genomes including their low-complexity and highly repetitive regions. Full-length HCMV genomes could prove crucial in understanding the genetic determinants and viral evolution underpinning drug resistance, virulence and pathogenesis.
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Affiliation(s)
- Timokratis Karamitros
- Department of Zoology, University of Oxford, Oxford, United Kingdom. .,Public Health Laboratories, Department of Microbiology, Hellenic Pasteur Institute, 127 Vas Sofias Ave, 11527, Athens, Greece.
| | - Bonnie van Wilgenburg
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Mark Wills
- Department of Medicine, University of Cambridge, Cambridge, United Kingdom
| | - Paul Klenerman
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom.,NIHR Biomedical Research Centre, Oxford, United Kingdom
| | - Gkikas Magiorkinis
- Department of Zoology, University of Oxford, Oxford, United Kingdom. .,Department of Hygiene, Epidemiology and Medical Statistics, Medical School, National and Kapodistrian University of Athens, M. Asias 75 str., 11527, Athens, Greece.
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13
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Lewandowska DW, Zagordi O, Geissberger FD, Kufner V, Schmutz S, Böni J, Metzner KJ, Trkola A, Huber M. Optimization and validation of sample preparation for metagenomic sequencing of viruses in clinical samples. MICROBIOME 2017; 5:94. [PMID: 28789678 PMCID: PMC5549297 DOI: 10.1186/s40168-017-0317-z] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/07/2017] [Accepted: 07/25/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Sequence-specific PCR is the most common approach for virus identification in diagnostic laboratories. However, as specific PCR only detects pre-defined targets, novel virus strains or viruses not included in routine test panels will be missed. Recently, advances in high-throughput sequencing allow for virus-sequence-independent identification of entire virus populations in clinical samples, yet standardized protocols are needed to allow broad application in clinical diagnostics. Here, we describe a comprehensive sample preparation protocol for high-throughput metagenomic virus sequencing using random amplification of total nucleic acids from clinical samples. RESULTS In order to optimize metagenomic sequencing for application in virus diagnostics, we tested different enrichment and amplification procedures on plasma samples spiked with RNA and DNA viruses. A protocol including filtration, nuclease digestion, and random amplification of RNA and DNA in separate reactions provided the best results, allowing reliable recovery of viral genomes and a good correlation of the relative number of sequencing reads with the virus input. We further validated our method by sequencing a multiplexed viral pathogen reagent containing a range of human viruses from different virus families. Our method proved successful in detecting the majority of the included viruses with high read numbers and compared well to other protocols in the field validated against the same reference reagent. Our sequencing protocol does work not only with plasma but also with other clinical samples such as urine and throat swabs. CONCLUSIONS The workflow for virus metagenomic sequencing that we established proved successful in detecting a variety of viruses in different clinical samples. Our protocol supplements existing virus-specific detection strategies providing opportunities to identify atypical and novel viruses commonly not accounted for in routine diagnostic panels.
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Affiliation(s)
- Dagmara W Lewandowska
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Osvaldo Zagordi
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | | | - Verena Kufner
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Stefan Schmutz
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Jürg Böni
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Karin J Metzner
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
- Department of Infectious Diseases and Hospital Epidemiology, University Hospital Zurich, Rämistrasse 100, 8091, Zurich, Switzerland
| | - Alexandra Trkola
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland
| | - Michael Huber
- Institute of Medical Virology, University of Zurich, Winterthurerstrasse 190, 8057, Zurich, Switzerland.
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14
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Affiliation(s)
- Philip E Pellett
- Department of Microbiology, Immunology, and Biochemistry, Wayne State University School of Medicine, Detroit, Michigan
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15
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Young VP, Mariano MC, Tu CC, Allaire KM, Avdic S, Slobedman B, Spencer JV. Modulation of the Host Environment by Human Cytomegalovirus with Viral Interleukin 10 in Peripheral Blood. J Infect Dis 2017; 215:874-882. [PMID: 28453840 PMCID: PMC5853888 DOI: 10.1093/infdis/jix043] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2016] [Accepted: 01/17/2017] [Indexed: 12/23/2022] Open
Abstract
Background Human cytomegalovirus (HCMV) is a herpesvirus with both lytic and latent life cycles. Human cytomegalovirus encodes 2 viral cytokines that are orthologs of human cellular interleukin 10 (cIL-10). Both cytomegalovirus interleukin 10 (cmvIL-10) and Latency-associated cytomegalovirus interleukin 10 (LAcmvIL-10) (collectively vIL-10) are expressed during lytic infection and cause immunosuppressive effects that impede virus clearance. LAcmvIL-10 is also expressed during latent infection of myeloid progenitor cells and monocytes and facilitates persistence. Here, we investigated whether vIL-10 could be detected during natural infection. Methods Plasma from healthy blood donors was tested by enzyme-linked immunosorbent assay for anti-HCMV immunoglobulin G and immunoglobulin M and for cIL-10 and vIL-10 levels using a novel vIL-10 assay that detects cmvIL-10 and LAcmvIL-10, with no cross-reactivity to cIL-10. Results vIL-10 was evident in HCMV+ donors (n = 19 of 26), at levels ranging 31-547 pg/mL. By comparison, cIL-10 was detected at lower levels ranging 3-69 pg/mL. There was a strong correlation between vIL-10 and cIL-10 levels (P = .01). Antibodies against vIL-10 were also detected and neutralized vIL-10 activity. Conclusions vIL-10 was detected in peripheral blood of healthy blood donors. These findings suggest that vIL-10 may play a key role in sensing or modifying the host environment during latency and, therefore, may be a potential target for intervention strategies.
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Affiliation(s)
- Vivian P Young
- Department of Biology, University of San Francisco, California, USA
| | | | - Carolyn C Tu
- Department of Biology, University of San Francisco, California, USA
| | | | - Selmir Avdic
- Discipline of Infectious Diseases and Immunology, University of Sydney, New South Wales, Australia
| | - Barry Slobedman
- Discipline of Infectious Diseases and Immunology, University of Sydney, New South Wales, Australia
| | - Juliet V Spencer
- Department of Biology, University of San Francisco, California, USA
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16
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Genome Sequences of Diverse Human Cytomegalovirus Strains with Utility in Drug Screening and Vaccine Evaluation. GENOME ANNOUNCEMENTS 2017; 5:5/3/e01433-16. [PMID: 28104650 PMCID: PMC5255926 DOI: 10.1128/genomea.01433-16] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Abstract
Cytomegalovirus displays genetic heterogeneity, which has implications for antiviral and vaccine development. Many studies have focused on laboratory isolates that have been extensively adapted for growth on fibroblasts. Here, we report whole-genome sequences for 10 human cytomegalovirus (HCMV) strains that readily grow on ARPE-19 human retinal pigment epithelial cells.
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17
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Kaminski H, Fishman JA. The Cell Biology of Cytomegalovirus: Implications for Transplantation. Am J Transplant 2016; 16:2254-69. [PMID: 26991039 DOI: 10.1111/ajt.13791] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 02/17/2016] [Accepted: 03/07/2016] [Indexed: 01/25/2023]
Abstract
Interpretation of clinical data regarding the impact of cytomegalovirus (CMV) infection on allograft function is complicated by the diversity of viral strains and substantial variability of cellular receptors and viral gene expression in different tissues. Variation also exists in nonspecific (monocytes and dendritic cells) and specific (NK cells, antibodies) responses that augment T cell antiviral activities. Innate immune signaling pathways and expanded pools of memory NK cells and γδ T cells also serve to amplify host responses to infection. The clinical impact of specific memory T cell anti-CMV responses that cross-react with graft antigens and alloantigens is uncertain but appears to contribute to graft injury and to the abrogation of allograft tolerance. These responses are modified by diverse immunosuppressive regimens and by underlying host immune deficits. The impact of CMV infection on the transplant recipient reflects cellular changes and corresponding host responses, the convergence of which has been termed the "indirect effects" of CMV infection. Future studies will clarify interactions between CMV infection and allograft injury and will guide interventions that may enhance clinical outcomes in transplantation.
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Affiliation(s)
- H Kaminski
- Kidney Transplant Unit, CHU Bordeaux Pellegrin, Place Raba Léon, Bordeaux, France
| | - J A Fishman
- Transplant Infectious Disease and Immunocompromised Host Program and MGH Transplant Center, Massachusetts General Hospital, Boston, MA
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18
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Construction of recombinant pseudorabies viruses by using PRV BACs deficient in IE180 or pac sequences: Application of vBAC90D recombinant virus to production of PRV amplicons. Virus Res 2016; 213:274-282. [PMID: 26756577 DOI: 10.1016/j.virusres.2015.11.028] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2015] [Revised: 11/26/2015] [Accepted: 11/27/2015] [Indexed: 11/21/2022]
Abstract
We describe a simple and efficient method to obtain recombinant pseudorabies virus (PRV) in mammalian cells by using the PRV BACs, PBAC80 deficient in pac sequences and PBAC90 deficient in the IE180 gene. These essential viral sequences were used as targets to obtain viable recombinant viruses. PBAC80 was constructed, confirmed to encode a copy of the IE180 gene regulated by the inducible Ptet promoter, and used to obtain recombinant attenuated PRV viruses that express the EGFP protein (PRV-BT80GF virus). PBAC90 was used to obtain the vBAC90D virus, deficient in IE180 and free of replication-competent revertants, and which can be used as a helper in the production of PRV amplicons.
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19
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Datta S, Budhauliya R, Das B, Chatterjee S, Vanlalhmuaka, Veer V. Next-generation sequencing in clinical virology: Discovery of new viruses. World J Virol 2015; 4:265-276. [PMID: 26279987 PMCID: PMC4534817 DOI: 10.5501/wjv.v4.i3.265] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/24/2015] [Revised: 03/23/2015] [Accepted: 05/08/2015] [Indexed: 02/05/2023] Open
Abstract
Viruses are a cause of significant health problem worldwide, especially in the developing nations. Due to different anthropological activities, human populations are exposed to different viral pathogens, many of which emerge as outbreaks. In such situations, discovery of novel viruses is utmost important for deciding prevention and treatment strategies. Since last century, a number of different virus discovery methods, based on cell culture inoculation, sequence-independent PCR have been used for identification of a variety of viruses. However, the recent emergence and commercial availability of next-generation sequencers (NGS) has entirely changed the field of virus discovery. These massively parallel sequencing platforms can sequence a mixture of genetic materials from a very heterogeneous mix, with high sensitivity. Moreover, these platforms work in a sequence-independent manner, making them ideal tools for virus discovery. However, for their application in clinics, sample preparation or enrichment is necessary to detect low abundance virus populations. A number of techniques have also been developed for enrichment or viral nucleic acids. In this manuscript, we review the evolution of sequencing; NGS technologies available today as well as widely used virus enrichment technologies. We also discuss the challenges associated with their applications in the clinical virus discovery.
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20
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High-throughput analysis of human cytomegalovirus genome diversity highlights the widespread occurrence of gene-disrupting mutations and pervasive recombination. J Virol 2015; 89:7673-7695. [PMID: 25972543 DOI: 10.1128/jvi.00578-15] [Citation(s) in RCA: 121] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Human cytomegalovirus is a widespread pathogen of major medical importance. It causes significant morbidity and mortality in the immunocompromised and congenital infections can result in severe disabilities or stillbirth. Development of a vaccine is prioritized, but no candidate is close to release. Although correlations of viral genetic variability with pathogenicity are suspected, knowledge about strain diversity of the 235kb genome is still limited. In this study, 96 full-length human cytomegalovirus genomes from clinical isolates were characterized, quadrupling the available information for full-genome analysis. These data provide the first high-resolution map of human cytomegalovirus interhost diversity and evolution. We show that cytomegalovirus is significantly more divergent than all other human herpesviruses and highlight hotspots of diversity in the genome. Importantly, 75% of strains are not genetically intact, but contain disruptive mutations in a diverse set of 26 genes, including immunomodulative genes UL40 and UL111A. These mutants are independent from culture passaging artifacts and circulate in natural populations. Pervasive recombination, which is linked to the widespread occurrence of multiple infections, was found throughout the genome. Recombination density was significantly higher than in other human herpesviruses and correlated with strain diversity. While the overall effects of strong purifying selection on virus evolution are apparent, evidence of diversifying selection was found in several genes encoding proteins that interact with the host immune system, including UL18, UL40, UL142 and UL147. These residues may present phylogenetic signatures of past and ongoing virus-host interactions. IMPORTANCE Human cytomegalovirus has the largest genome of all viruses that infect humans. Currently, there is a great interest in establishing associations between genetic variants and strain pathogenicity of this herpesvirus. Since the number of publicly available full-genome sequences is limited, knowledge about strain diversity is highly fragmented and biased towards a small set of loci. Combined with our previous work, we have now contributed 101 complete genome sequences. We have used these data to conduct the first high-resolution analysis of interhost genome diversity, providing an unbiased and comprehensive overview of cytomegalovirus variability. These data are of major value to the development of novel antivirals and a vaccine and to identify potential targets for genotype-phenotype experiments. Furthermore, they have enabled a thorough study of the evolutionary processes that have shaped cytomegalovirus diversity.
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Abstract
In celebrating the 60th anniversary of the first isolation of human cytomegalovirus (HCMV), we reflect on the merits and limitations of the viral strains currently being used to develop urgently needed treatments. HCMV research has been dependent for decades on the high-passage strains AD169 and Towne, heavily exploiting their capacity to replicate efficiently in fibroblasts. However, the genetic integrity of these strains is so severely compromised that great caution needs to be exercised when considering their past and future use. It is now evident that wild-type HCMV strains are not readily propagated in vitro. HCMV mutants are rapidly selected during isolation in fibroblasts, reproducibly affecting gene RL13, the UL128 locus (which includes genes UL128, UL130 and UL131A) and often the UL/b′ region. As a result, the virus becomes less cell associated, altered in tropism and less pathogenic. This problem is not restricted to high-passage strains, as even low-passage strains can harbour biologically significant mutations. Cloning and manipulation of the HCMV genome as a bacterial artificial chromosome (BAC) offers a means of working with stable, genetically defined strains. To this end, the low-passage strain Merlin genome was cloned as a BAC and sequentially repaired to match the viral sequence in the original clinical sample from which Merlin was derived. Restoration of UL128L to wild type was detrimental to growth in fibroblasts, whereas restoration of RL13 impaired growth in all cell types tested. Stable propagation of phenotypically wild-type virus could be achieved only by placing both regions under conditional expression. In addition to the development of these tools, the Merlin transcriptome and proteome have been characterized in unparalleled detail. Although Merlin may be representative of the clinical agent, high-throughput whole-genome deep sequencing studies have highlighted the remarkable high level of interstrain variation present in circulating virus. There is a need to develop systems capable of addressing the significance of this diversity, free from the confounding effects of genetic changes associated with in vitro adaptation. The generation of a set of BAC clones, each containing the genome of a different HCMV strain repaired to match the sequence in the clinical sample, would provide a pathway to address the biological and clinical effects of natural variation in wild-type HCMV.
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Abstract
Equid herpesvirus 3 (EHV-3) is a member of the subfamily Alphaherpesvirinae that causes equine coital exanthema. Here, we report the first complete genome sequence of EHV-3. The 151,601-nt genome encodes 76 distinct genes like other equine alphaherpesviruses, but genetically, EHV-3 is significantly more divergent.
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