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Melgarejo TA, Cespedes MK, Chen LF, Turini T, Lazicki PA, Vinchesi-Vahl A, Gilbertson RL. Unusual outbreaks of curly top disease in processing tomato fields in northern California in 2021 and 2022 were caused by a rare strain of beet curly top virus and facilitated by extreme weather events. Virology 2024; 591:109981. [PMID: 38211381 DOI: 10.1016/j.virol.2024.109981] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 12/06/2023] [Accepted: 01/02/2024] [Indexed: 01/13/2024]
Abstract
In the western United States, curly top disease (CTD) is caused by beet curly top virus (BCTV). In California, CTD causes economic loss to processing tomato production in central and southern areas but, historically, not in the north. Here, we document unusual CTD outbreaks in processing tomato fields in the northern production area in 2021 and 2022, and show that these were caused by the rare spinach curly top strain (BCTV-SpCT). These outbreaks were associated with proximity of fields to foothills and unusually hot, dry, and windy spring weather conditions, possibly by altering migrations of the beet leafhopper (BLH) vector from locations with BCTV-SpCT reservoirs. Support for this hypothesis came from the failure to observe CTD outbreaks and BLH migrations in 2023, when spring weather conditions were cool and wet. Our results show the climate-induced emergence of a rare plant virus strain to cause an economically important disease in a new crop and location.
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Affiliation(s)
- Tomas A Melgarejo
- Department of Plant Pathology, University of California, Davis, One Shield Avenue, Hutchison Hall 273-274, Davis, CA, 95616, United States.
| | - Margaret K Cespedes
- Department of Plant Pathology, University of California, Davis, One Shield Avenue, Hutchison Hall 273-274, Davis, CA, 95616, United States
| | - Li-Fang Chen
- Bayer Crop Science, 37437 CA-16, Woodland, CA, 95695, United States
| | - Thomas Turini
- University of California - Agriculture and Natural Resources, Cooperative Extension Fresno County, 550 E. Shaw Avenue, Suite 210-B, Fresno, CA, 93710, United States
| | - Patricia A Lazicki
- University of California - Agriculture and Natural Resources, Vegetable Crops Advisor, Woodland Administrative Office, 70 Cottonwood Street, Woodland, CA, 95695, United States
| | - Amber Vinchesi-Vahl
- University of New Hampshire, UNH Cooperative Extension Food and Agriculture, 129 Main St., Durham, NH, 03824, United States
| | - Robert L Gilbertson
- Department of Plant Pathology, University of California, Davis, One Shield Avenue, Hutchison Hall 273-274, Davis, CA, 95616, United States
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Kumar A, Rajan LS, Sabarinath PS K, Shete AM, Sahay RR, Patil DY, Ingole N, K K, Padinakarai AC, GB S, Shastri J, Padukone S, Joshi Y, Patil S, Majumdar T, Verma A, Yemul J, Shende N, Kumari V, Vedpathak P, Sathe S, Gawande P, Yadav PD. First detection of Varicella Zoster Virus clade 9 cases in India during mpox surveillance. Ann Med 2023; 55:2253733. [PMID: 37672487 PMCID: PMC10484040 DOI: 10.1080/07853890.2023.2253733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/27/2023] [Revised: 08/01/2023] [Accepted: 08/27/2023] [Indexed: 09/08/2023] Open
Abstract
BACKGROUND The multi-country mpox outbreak across the globe has led to the systematic surveillance of mpox cases in India. During the surveillance of mpox, we encountered cases of Varicella Zoster Virus (VZV) in suspected mpox cases amongst children & adults. This study focused on the genomic characterization of VZV in India. METHODS A total of 331 mpox suspected cases were tested for VZV through real-time PCR, and the positive samples were subjected to next-generation sequencing to retrieve the whole genome of VZV using CLC genomics software. Phylogenetic analysis has been done in MEGA 11.0 software to identify circulating clades. RESULT Of the 331 suspected cases, 28 cases with vesicular rashes were found to be positive for VZV. The maximum genome could be retrieved from the clinical specimens of 16 cases with coverage greater than 98% when mapped with reference strain Dumas (NC 001348). The phylogenetic analyses of these sequences determined the circulation of clades 1, 5, and 9 in India. Further, the sequence analysis demonstrated non-synonymous single nucleotide polymorphism (SNPs) among specific ORF of VZV including ORF 14, ORF 22, ORF 36, ORF 37 and ORF 51. Although clade 1 and 5 has been reported earlier, the circulation of clade 9 of VZV has been determined for the first time in India. CONCLUSION Although the circulation of different clades of VZV was reported from India, the presence of clade 9 was detected for the first time during the mpox surveillance.
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Affiliation(s)
- Abhinendra Kumar
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Lekshmi S. Rajan
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | | | - Anita M. Shete
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Rima R. Sahay
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Deepak Y. Patil
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Nayana Ingole
- Virus Research and Diagnostic Laboratory, Kasturba Hospital for Infectious Diseases, Mumbai, India
| | - Kaveri K
- King Institute of Preventive Medicine and Research, Chennai, India
| | | | - Shantala GB
- Bangalore Medical College and Research Institute, Bengaluru, India
| | - Jayanthi Shastri
- Virus Research and Diagnostic Laboratory, Kasturba Hospital for Infectious Diseases, Mumbai, India
| | | | - Yash Joshi
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Savita Patil
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Triparna Majumdar
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Ajay Verma
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Jyoti Yemul
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Nandini Shende
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Vaishnavi Kumari
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Pratiksha Vedpathak
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Shubhangi Sathe
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Pranita Gawande
- Indian Council of Medical Research-National Institute of Virology, Pune, India
| | - Pragya D. Yadav
- Indian Council of Medical Research-National Institute of Virology, Pune, India
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3
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Guo W, Xie J, Liu J, Chen H, Jung YS. The full-genome characterization and phylogenetic analysis of bovine herpesvirus type 1.2 isolated in China. Front Microbiol 2022; 13:1033008. [PMID: 36386697 PMCID: PMC9664903 DOI: 10.3389/fmicb.2022.1033008] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 09/26/2022] [Indexed: 01/25/2023] Open
Abstract
Bovine herpesvirus type 1 (BHV-1) causes bovine respiratory disease that poses a significant threat to the cattle industry. The prevalence of BHV-1 has recently increased in China. However, the lack of information about the prevalent isolates limits the control of the disease. In this study, a novel strain of BHV-1 was isolated from nasal swabs of Holstein cows in 2020 in China, designated as BHV SHJS. The genome of BHV strain SHJS is 135, 102 bp in length and highly similar to strain SP1777 (KM258883.1) with an identity of 99.64%. Mutations, insertions, or deletions mainly occur in UL27, UL44, and US8, etc., relative to the different genomic coordinates. Phylogenetic tree of UL44 (gC) showed that BHV strain SHJS belongs to BHV-1.2b cluster. The result showed that the strain had a different evolutionary origin from those prevalent in China. This study will enrich our knowledge regarding BHV outbreak strains in China and contribute to the prevention and pathogenic studies of BHV-1.2.
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Affiliation(s)
- Weiqiang Guo
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China
| | - Jia Xie
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Jingyi Liu
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Hongjun Chen
- Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, China
| | - Yong-Sam Jung
- MOE Joint International Research Laboratory of Animal Health and Food Safety, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, Jiangsu, China,*Correspondence: Yong-Sam Jung,
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4
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El-Duah P, Sylverken AA, Owusu M, Amoako YA, Yeboah R, Gorman R, Nyarko-Afriyie E, Schneider J, Jones TC, Bonney J, Adade T, Yeboah ES, Binger T, Corman VM, Drosten C, Phillips RO. Genetic characterization of varicella-zoster and HIV-1 viruses from the cerebrospinal fluid of a co-infected encephalitic patient, Ghana. Virol J 2022; 19:122. [PMID: 35883083 PMCID: PMC9327158 DOI: 10.1186/s12985-022-01854-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2021] [Accepted: 07/15/2022] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Encephalitis is a serious disease of the brain characterized by prodromal and specific neurological symptoms. HIV infections offer opportunistic viruses, such as Varicella-zoster virus (VZV), the chance to cause encephalitis in patients. There is a lack of information on the genetic diversity of VZV in Ghana and other parts of Africa which requires sequencing and characterization studies to address. The active evolution of HIV-1 in West Africa also requires continuous surveillance for the emergence of new genetic forms. CASE PRESENTATION VZV was detected in the CSF sample of an 11-year-old patient presenting with symptoms of encephalitis by real-time PCR diagnostics. To identify possible unknown aetiological pathogens, next-generation sequencing was performed, and revealed an HIV-1 co-infection. Alignments of concatenated HIV-1 genome fragments in the gag, pol, vif, env and nef regions and a near-complete VZV genome were analyzed by Bayesian inference, and phylogenetic trees were generated. The VZV sequence belongs to clade 5 and the HIV-1 sequence is a member of the CRF02_AG predominant circulating recombinant form in Ghana. CONCLUSIONS Diagnostic tests for CSF HIV would be useful where possible in patients presenting with encephalitis due to VZV and other opportunistic viruses in Kumasi to shed light on the role of HIV in encephalitis cases in Ghana. This report reaffirms the role of the CRF02_AG circulating recombinant form in HIV infections in Ghana and also gives a preliminary genetic characterization of VZV in Kumasi, Ghana.
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Affiliation(s)
- Philip El-Duah
- Institute of Virology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Berlin, Germany.
| | - Augustina Angelina Sylverken
- Kumasi Centre for Collaborative Research Into Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Department of Theoretical and Applied Biology, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Michael Owusu
- Kumasi Centre for Collaborative Research Into Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Department of Medical Diagnostics, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Yaw Ampem Amoako
- Kumasi Centre for Collaborative Research Into Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Department of Medicine, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.,Department of Medicine, Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | - Richmond Yeboah
- Kumasi Centre for Collaborative Research Into Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Richmond Gorman
- Kumasi Centre for Collaborative Research Into Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Emmanuella Nyarko-Afriyie
- Kumasi Centre for Collaborative Research Into Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Julia Schneider
- Institute of Virology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Terry C Jones
- Institute of Virology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Berlin, Germany.,Department of Zoology, Centre for Pathogen Evolution, University of Cambridge, Downing St, Cambridge, CB2 3EJ, UK
| | - Joseph Bonney
- Department of Medicine, Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | - Titus Adade
- Department of Medicine, Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | - Eric Smart Yeboah
- Department of Medicine, Komfo Anokye Teaching Hospital, Kumasi, Ghana
| | - Tabea Binger
- Kumasi Centre for Collaborative Research Into Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana
| | - Victor Max Corman
- Institute of Virology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Christian Drosten
- Institute of Virology, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität Zu Berlin, and Berlin Institute of Health, Berlin, Germany.
| | - Richard Odame Phillips
- Kumasi Centre for Collaborative Research Into Tropical Medicine, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana. .,Department of Medicine, College of Health Sciences, Kwame Nkrumah University of Science and Technology, Kumasi, Ghana.
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5
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Palmer WH, Telford M, Navarro A, Santpere G, Norman PJ. Human herpesvirus diversity is altered in HLA class I binding peptides. Proc Natl Acad Sci U S A 2022; 119:e2123248119. [PMID: 35486690 PMCID: PMC9170163 DOI: 10.1073/pnas.2123248119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 03/30/2022] [Indexed: 11/18/2022] Open
Abstract
Herpesviruses are ubiquitous, genetically diverse DNA viruses, with long-term presence in humans associated with infrequent but significant pathology. Human leukocyte antigen (HLA) class I presents intracellularly derived peptide fragments from infected tissue cells to CD8+ T and natural killer cells, thereby directing antiviral immunity. Allotypes of highly polymorphic HLA class I are distinguished by their peptide binding repertoires. Because this HLA class I variation is a major determinant of herpesvirus disease, we examined if sequence diversity of virus proteins reflects evasion of HLA presentation. Using population genomic data from Epstein–Barr virus (EBV), human cytomegalovirus (HCMV), and Varicella–Zoster virus, we tested whether diversity differed between the regions of herpesvirus proteins that can be recognized, or not, by HLA class I. Herpesviruses exhibit lytic and latent infection stages, with the latter better enabling immune evasion. Whereas HLA binding peptides of lytic proteins are conserved, we found that EBV and HCMV proteins expressed during latency have increased peptide sequence diversity. Similarly, latent, but not lytic, herpesvirus proteins have greater population structure in HLA binding than nonbinding peptides. Finally, we found patterns consistent with EBV adaption to the local HLA environment, with less efficient recognition of EBV isolates by high-frequency HLA class I allotypes. Here, the frequency of CD8+ T cell epitopes inversely correlated with the frequency of HLA class I recognition. Previous analyses have shown that pathogen-mediated natural selection maintains exceptional polymorphism in HLA residues that determine peptide recognition. Here, we show that HLA class I peptide recognition impacts diversity of globally widespread pathogens.
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Affiliation(s)
- William H. Palmer
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Aurora, CO 80045
- Department of Immunology and Microbiology, University of Colorado, Aurora, CO 80045
| | - Marco Telford
- Neurogenomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510
| | - Arcadi Navarro
- Institut de Biologia Evolutiva (Universitat Pompeu Fabra - Consejo Superior de Investigaciones Científicas), Department of Medicine and Life Sciences (MELIS), Barcelona Biomedical Research Park, Universitat Pompeu Fabra, 08003 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats and Universitat Pompeu Fabra, 08010 Barcelona, Spain
- Centre for Genomic Regulation, The Barcelona Institute of Science and Technology, 08003 Barcelona, Spain
- Barcelona Beta Brain Research Center, Pasqual Maragall Foundation, 08005 Barcelona, Spain
| | - Gabriel Santpere
- Neurogenomics Group, Research Programme on Biomedical Informatics (GRIB), Hospital del Mar Medical Research Institute (IMIM), Department of Medicine and Life Sciences (MELIS), Universitat Pompeu Fabra, 08003 Barcelona, Catalonia, Spain
- Department of Neuroscience, Yale University School of Medicine, New Haven, CT 06510
| | - Paul J. Norman
- Division of Biomedical Informatics and Personalized Medicine, University of Colorado, Aurora, CO 80045
- Department of Immunology and Microbiology, University of Colorado, Aurora, CO 80045
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6
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Skripchenko E, Zheleznikova G, Skripchenko N, Alekseeva L, Goleva O, Bessonova T, Zhirkov A. Immunopatological and genetic aspects of pathogenesis of CNS lesions in VZV infection. Zh Nevrol Psikhiatr Im S S Korsakova 2022; 122:46-56. [DOI: 10.17116/jnevro202212210146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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7
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Goldstein RS, Kinchington PR. Varicella Zoster Virus Neuronal Latency and Reactivation Modeled in Vitro. Curr Top Microbiol Immunol 2021; 438:103-134. [PMID: 34904194 DOI: 10.1007/82_2021_244] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Latency and reactivation in neurons are critical aspects of VZV pathogenesis that have historically been difficult to investigate. Viral genomes are retained in many human ganglia after the primary infection, varicella; and about one-third of the naturally infected VZV seropositive population reactivates latent virus, which most often clinically manifests as herpes zoster (HZ or Shingles). HZ is frequently complicated by acute and chronic debilitating pain for which there remains a need for more effective treatment options. Understanding of the latent state is likely to be essential in the design of strategies to reduce reactivation. Experimentally addressing VZV latency has been difficult because of the strict human species specificity of VZV and the fact that until recently, experimental reactivation had not been achieved. We do not yet know the neuron subtypes that harbor latent genomes, whether all can potentially reactivate, what the drivers of VZV reactivation are, and how immunity interplays with the latent state to control reactivation. However, recent advances have enabled a picture of VZV latency to start to emerge. The first is the ability to detect the latent viral genome and its expression in human ganglionic tissues with extraordinary sensitivity. The second, the subject of this chapter, is the development of in vitro human neuron systems permitting the modeling of latent states that can be experimentally reactivated. This review will summarize recent advances of in vitro models of neuronal VZV latency and reactivation, the limitations of the current systems, and discuss outstanding questions and future directions regarding these processes using these and yet to be developed models. Results obtained from the in vitro models to date will also be discussed in light of the recent data gleaned from studies of VZV latency and gene expression learned from human cadaver ganglia, especially the discovery of VZV latency transcripts that seem to parallel the long-studied latency-associated transcripts of other neurotropic alphaherpesviruses.
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Affiliation(s)
| | - Paul R Kinchington
- Department of Ophthalmology, and Department of Molecular Microbiology and Genetics, University of Pittsburgh, EEI 1020, 203 Lothrop Street, Pittsburgh, PA, 156213, USA.
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8
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Latently KSHV-Infected Cells Promote Further Establishment of Latency upon Superinfection with KSHV. Int J Mol Sci 2021; 22:ijms222111994. [PMID: 34769420 PMCID: PMC8584431 DOI: 10.3390/ijms222111994] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 10/27/2021] [Accepted: 11/03/2021] [Indexed: 11/17/2022] Open
Abstract
Kaposi’s sarcoma-associated herpesvirus (KSHV) is a cancer-related virus which engages in two forms of infection: latent and lytic. Latent infection allows the virus to establish long-term persistent infection, whereas the lytic cycle is needed for the maintenance of the viral reservoir and for virus spread. By using recombinant KSHV viruses encoding mNeonGreen and mCherry fluorescent proteins, we show that various cell types that are latently-infected with KSHV can be superinfected, and that the new incoming viruses establish latent infection. Moreover, we show that latency establishment is enhanced in superinfected cells compared to primary infected ones. Further analysis revealed that cells that ectopically express the major latency protein of KSHV, LANA-1, prior to and during infection exhibit enhanced establishment of latency, but not cells expressing LANA-1 fragments. This observation supports the notion that the expression level of LANA-1 following infection determines the efficiency of latency establishment and avoids loss of viral genomes. These findings imply that a host can be infected with more than a single viral genome and that superinfection may support the maintenance of long-term latency.
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9
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Depledge DP, Breuer J. Varicella-Zoster Virus-Genetics, Molecular Evolution and Recombination. Curr Top Microbiol Immunol 2021; 438:1-23. [PMID: 34374828 DOI: 10.1007/82_2021_238] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
This chapter first details the structure, organization and coding content of the VZV genome to provide a foundation on which the molecular evolution of the virus can be projected. We subsequently describe the evolution of molecular profiling approaches from restriction fragment length polymorphisms to single nucleotide polymorphism profiling to modern day high-throughput sequencing approaches. We describe how the application of these methodologies led to our current model of VZV phylogeograpy including the number and structure of geographic clades and the role of recombination in reshaping these.
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Affiliation(s)
- Daniel P Depledge
- Institute of Virology, Hannover Medical School (MHH), Hannover, Germany. .,Department of Microbiology, NYU School of Medicine, New York, USA.
| | - Judith Breuer
- Department of Infection & Immunology, University College London, London, UK
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10
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Metagenomic analysis of a throat swab sample collected in China on a patient infected with Varicella Zoster Virus. Sci Rep 2021; 11:13874. [PMID: 34230529 PMCID: PMC8260771 DOI: 10.1038/s41598-021-93230-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 06/15/2021] [Indexed: 12/26/2022] Open
Abstract
Varicella Zoster Virus (VZV) is endemic worldwide, causing varicella in children and zoster upon reactivation in adults. This study concerned a metagenomic analysis of a throat swab sample collected in China, on a young patient suffering from Systemic Lupus Erythematosus (SLE) and diagnosed with varicella. The complete genome sequence of a VZV strain of clade 2 has been generated. Clade 2 strains are the most prevalent in Asian countries. A comparison of 223 VZV genomes identified 77 clade specific markers, 20 of them specific to clade 2. The metagenomic analysis also identified sequences covering most of the genome of the bacteria Schaalia odontolytica also known as Actinomyces odontolyticus. VZV infection and bacterial infection in the context of SLE is further discussed. Even though the patient presented only mild symptoms, this study is a reminder that vaccination against VZV is critical to avoid severe complications like bacterial superinfection or even death in the case of immunodeficiency.
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11
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Genetic Variation in the Glycoprotein B Sequence of Equid Herpesvirus 5 among Horses of Various Breeds at Polish National Studs. Pathogens 2021; 10:pathogens10030322. [PMID: 33803246 PMCID: PMC7998979 DOI: 10.3390/pathogens10030322] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 03/04/2021] [Accepted: 03/06/2021] [Indexed: 12/16/2022] Open
Abstract
Equid herpesvirus 5 (EHV-5) is one of two γ-herpesviruses that commonly infect horses worldwide. The objective of the study was to estimate the genetic variability within EHV-5 viruses circulating among horses in Poland. Partial glycoprotein B (gB) sequences from 92 Polish horses from 13 studs throughout Poland were compared to each other and to three EHV-5 sequences from other countries. Despite the overall high level of conservation, considerable variability was observed around the putative furin cleavage site. Based on phylogenetic analysis, the viruses clustered within two major lineages (A and B), with further sub-clustering within group A. The clustering of EHV-5 sequences was independent of age or geographical origin of the sampled horses. Recombination was identified as one of the factors contributing to the genomic heterogeneity. Viruses from unweaned foals were more similar to viruses from other foals at the same stud than to viruses form their dams, suggesting the horizontal transfer and/or evolution of EHV-5 within individual hosts. Our data indicate that the gB sequence is not suitable for tracking the source of EHV-5 infection. Further research is needed to elucidate the importance of the sequence variability around the EHV-5 gB furin cleavage site on the biology of the virus.
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12
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Advances and Perspectives in the Management of Varicella-Zoster Virus Infections. Molecules 2021; 26:molecules26041132. [PMID: 33672709 PMCID: PMC7924330 DOI: 10.3390/molecules26041132] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/10/2021] [Accepted: 02/12/2021] [Indexed: 02/06/2023] Open
Abstract
Varicella-zoster virus (VZV), a common and ubiquitous human-restricted pathogen, causes a primary infection (varicella or chickenpox) followed by establishment of latency in sensory ganglia. The virus can reactivate, causing herpes zoster (HZ, shingles) and leading to significant morbidity but rarely mortality, although in immunocompromised hosts, VZV can cause severe disseminated and occasionally fatal disease. We discuss VZV diseases and the decrease in their incidence due to the introduction of live-attenuated vaccines to prevent varicella or HZ. We also focus on acyclovir, valacyclovir, and famciclovir (FDA approved drugs to treat VZV infections), brivudine (used in some European countries) and amenamevir (a helicase-primase inhibitor, approved in Japan) that augur the beginning of a new era of anti-VZV therapy. Valnivudine hydrochloride (FV-100) and valomaciclovir stearate (in advanced stage of development) and several new molecules potentially good as anti-VZV candidates described during the last year are examined. We reflect on the role of antiviral agents in the treatment of VZV-associated diseases, as a large percentage of the at-risk population is not immunized, and on the limitations of currently FDA-approved anti-VZV drugs. Their low efficacy in controlling HZ pain and post-herpetic neuralgia development, and the need of multiple dosing regimens requiring daily dose adaptation for patients with renal failure urges the development of novel anti-VZV drugs.
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13
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Pontremoli C, Forni D, Clerici M, Cagliani R, Sironi M. Possible European Origin of Circulating Varicella Zoster Virus Strains. J Infect Dis 2021; 221:1286-1294. [PMID: 31051029 DOI: 10.1093/infdis/jiz227] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2019] [Accepted: 05/02/2019] [Indexed: 11/13/2022] Open
Abstract
Varicella zoster virus (VZV) is the causative agent of chickenpox and shingles. The geographic distribution of VZV clades was taken as evidence that VZV migrated out of Africa with human populations. We show that extant VZV strains most likely originated in Europe and not in Africa. Europe was also identified as the ancestral location for most internal nodes of the VZV phylogeny, including the ancestor of clade 5 strains. We also show that strains from clades 1, 2, 3, and 5 derived a major proportion of their ancestry from each of 4 ancestral populations. Conversely, viruses from other clades displayed variable levels of admixture. Some low-level admixture was also observed for clade 5 genomes, but only for non-African viruses. This pattern indicates that the clade 5 VZV strains do not represent recent introductions from Africa due to migratory fluxes. These data have also relevance for the definition and classification of VZV clades.
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Affiliation(s)
- Chiara Pontremoli
- Istituto di ricovero e cura a carattere scientifico (IRCCS) E. Medea, Bioinformatics, Bosisio Parini, Milan, Italy
| | - Diego Forni
- Istituto di ricovero e cura a carattere scientifico (IRCCS) E. Medea, Bioinformatics, Bosisio Parini, Milan, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy.,IRCCS Fondazione Don Carlo Gnocchi, Milan, Italy
| | - Rachele Cagliani
- Istituto di ricovero e cura a carattere scientifico (IRCCS) E. Medea, Bioinformatics, Bosisio Parini, Milan, Italy
| | - Manuela Sironi
- Istituto di ricovero e cura a carattere scientifico (IRCCS) E. Medea, Bioinformatics, Bosisio Parini, Milan, Italy
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14
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Analysis of Whole-Genome Sequences of Infectious laryngotracheitis Virus Isolates from Poultry Flocks in Canada: Evidence of Recombination. Viruses 2020; 12:v12111302. [PMID: 33198373 PMCID: PMC7696358 DOI: 10.3390/v12111302] [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: 09/03/2020] [Revised: 10/30/2020] [Accepted: 11/10/2020] [Indexed: 01/09/2023] Open
Abstract
Infectious laryngotracheitis virus (ILTV) is a herpes virus that causes an acute respiratory disease of poultry known as infectious laryngotracheitis (ILT). Chicken embryo origin (CEO) and tissue culture origin (TCO) live attenuated vaccines are routinely used for the control of ILT. However, vaccine virus is known to revert to virulence, and it has been recently shown that ILT field viral strains can undergo recombination with vaccinal ILTV and such recombinant ILT viruses possess greater transmission and pathogenicity potential. Based on complete or partial genes of the ILTV genome, few studies genotyped ILTV strains circulating in Canada, and so far, information is scarce on whole-genome sequencing or the presence of recombination in Canadian ILTV isolates. The objective of this study was to genetically characterize the 14 ILTV isolates that originated from three provinces in Canada (Alberta, British Columbia and Quebec). To this end, a phylogenetic analysis of 50 ILTV complete genome sequences, including 14 sequences of Canadian origin, was carried out. Additional phylogenetic analysis of the unique long, unique short and inverted repeat regions of the ILTV genome was also performed. We observed that 71%, 21% and 7% of the ILTV isolates were categorized as CEO revertant, wild-type and TCO vaccine-related, respectively. The sequences were also analyzed for potential recombination events, which included evidence in the British Columbia ILTV isolate. This event involved two ILTV vaccine (CEO) strains as parental strains. Recombination analysis also identified that one ILTV isolate from Alberta as a potential parental strain for a United States origin ILTV isolate. The positions of the possible recombination breakpoints were identified. These results indicate that the ILTV wild-type strains can recombine with vaccinal strains complicating vaccine-mediated control of ILT. Further studies on the pathogenicity of these ILTV strains, including the recombinant ILTV isolate are currently ongoing.
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15
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Abstract
Alphaherpesviruses, as large double-stranded DNA viruses, were long considered to be genetically stable and to exist in a homogeneous state. Recently, the proliferation of high-throughput sequencing (HTS) and bioinformatics analysis has expanded our understanding of herpesvirus genomes and the variations found therein. Recent data indicate that herpesviruses exist as diverse populations, both in culture and in vivo, in a manner reminiscent of RNA viruses. In this review, we discuss the past, present, and potential future of alphaherpesvirus genomics, including the technical challenges that face the field. We also review how recent data has enabled genome-wide comparisons of sequence diversity, recombination, allele frequency, and selective pressures, including those introduced by cell culture. While we focus on the human alphaherpesviruses, we draw key insights from related veterinary species and from the beta- and gamma-subfamilies of herpesviruses. Promising technologies and potential future directions for herpesvirus genomics are highlighted as well, including the potential to link viral genetic differences to phenotypic and disease outcomes.
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Affiliation(s)
- Chad V. Kuny
- Departments of Biology, and Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
| | - Moriah L. Szpara
- Departments of Biology, and Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, 16802, USA
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16
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Braspenning SE, Sadaoka T, Breuer J, Verjans GMGM, Ouwendijk WJD, Depledge DP. Decoding the Architecture of the Varicella-Zoster Virus Transcriptome. mBio 2020; 11:e01568-20. [PMID: 33024035 PMCID: PMC7542360 DOI: 10.1128/mbio.01568-20] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Accepted: 08/31/2020] [Indexed: 12/14/2022] Open
Abstract
Varicella-zoster virus (VZV), a double-stranded DNA virus, causes varicella, establishes lifelong latency in ganglionic neurons, and reactivates later in life to cause herpes zoster, commonly associated with chronic pain. The VZV genome is densely packed and produces multitudes of overlapping transcripts deriving from both strands. While 71 distinct open reading frames (ORFs) have thus far been experimentally defined, the full coding potential of VZV remains unknown. Here, we integrated multiple short-read RNA sequencing approaches with long-read direct RNA sequencing on RNA isolated from VZV-infected cells to provide a comprehensive reannotation of the lytic VZV transcriptome architecture. Through precise mapping of transcription start sites, splice junctions, and polyadenylation sites, we identified 136 distinct polyadenylated VZV RNAs that encode canonical ORFs, noncanonical ORFs, and ORF fusions, as well as putative noncoding RNAs (ncRNAs). Furthermore, we determined the kinetic class of all VZV transcripts and observed, unexpectedly, that transcripts encoding the ORF62 protein, previously designated Immediate-Early, were expressed with Late kinetics. Our work showcases the complexity of the VZV transcriptome and provides a comprehensive resource that will facilitate future functional studies of coding RNAs, ncRNAs, and the biological mechanisms underlying the regulation of viral transcription and translation during lytic VZV infection.IMPORTANCE Transcription from herpesviral genomes, executed by the host RNA polymerase II and regulated by viral proteins, results in coordinated viral gene expression to efficiently produce infectious progeny. However, the complete coding potential and regulation of viral gene expression remain ill-defined for the human alphaherpesvirus varicella-zoster virus (VZV), causative agent of both varicella and herpes zoster. Here, we present a comprehensive overview of the VZV transcriptome and the kinetic class of all identified viral transcripts, using two virus strains and two biologically relevant cell types. Additionally, our data provide an overview of how VZV diversifies its transcription from one of the smallest herpesviral genomes. Unexpectedly, the transcript encoding the major viral transactivator protein (pORF62) was expressed with Late kinetics, whereas orthologous transcripts in other alphaherpesviruses are typically expressed during the immediate early phase. Therefore, our work both establishes the architecture of the VZV transcriptome and provides insight into regulation of alphaherpesvirus gene expression.
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Affiliation(s)
| | - Tomohiko Sadaoka
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, Kobe, Japan
| | - Judith Breuer
- Department of Infection and Immunity, University College London, London, United Kingdom
| | | | | | - Daniel P Depledge
- Department of Medicine, New York University School of Medicine, New York, New York, USA
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17
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Abstract
Gene drives are genetic modifications designed to propagate in a population with high efficiency. Current gene drive strategies rely on sexual reproduction and are thought to be restricted to sexual organisms. Here, we report on a gene drive system that allows the spread of an engineered trait in populations of DNA viruses and, in particular, herpesviruses. We describe the successful transmission of a gene drive sequence between distinct strains of human cytomegalovirus (human herpesvirus 5) and show that gene drive viruses can efficiently target and replace wildtype populations in cell culture experiments. Moreover, by targeting sequences necessary for viral replication, our results indicate that a viral gene drive can be used as a strategy to suppress a viral infection. Taken together, this work offers a proof of principle for the design of a gene drive in viruses. Current gene drive strategies are restricted to sexually reproducing species. Here the authors develop a gene drive in herpesviruses that allows the spread of an engineered trait through a viral population.
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Affiliation(s)
- Marius Walter
- Buck Institute for Research on Aging, Novato, CA, 94945, USA.
| | - Eric Verdin
- Buck Institute for Research on Aging, Novato, CA, 94945, USA.
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18
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Jensen NJ, Depledge DP, Ng TFF, Leung J, Quinlivan M, Radford KW, Folster J, Tseng HF, LaRussa P, Jacobsen SJ, Breuer J, Schmid DS. Analysis of the reiteration regions (R1 to R5) of varicella-zoster virus. Virology 2020; 546:38-50. [PMID: 32452416 DOI: 10.1016/j.virol.2020.03.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/12/2020] [Accepted: 03/31/2020] [Indexed: 10/24/2022]
Abstract
The varicella-zoster virus (VZV) genome, comprises both unique and repeated regions. The genome also includes reiteration regions, designated R1 to R5, which are tandemly repeating sequences termed elements. These regions represent an understudied feature of the VZV genome. The R4 region is duplicated, with one copy in the internal repeat short (IRs) which we designated R4A and a second copy in the terminal repeat short (TRs) termed R4B. We developed primers to amplify and Sanger sequence these regions, including independent amplification of both R4 regions. Reiteration regions from >80 cases of PCR-confirmed shingles were sequenced and analyzed. Complete genome sequences for the remaining portions of these viruses were determined using Illumina MiSeq. We identified 28 elements not previously reported, including at least one element for each R region. Length heterogeneity was substantial in R3, R4A and R4B. Length heterogeneity between the two copies of R4 was common.
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Affiliation(s)
- Nancy J Jensen
- Division of Viral Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Daniel P Depledge
- Division of Infection and Immunity, University College London, London, United Kingdom; Department of Microbiology, New York University School of Medicine, New York, NY, USA
| | - Terry Fei Fan Ng
- Division of Viral Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jessica Leung
- Division of Viral Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Mark Quinlivan
- Division of Viral Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Kay W Radford
- Division of Viral Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jennifer Folster
- Division of Viral Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Hung-Fu Tseng
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Philip LaRussa
- Department of Pediatrics, College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Steven J Jacobsen
- Department of Research and Evaluation, Kaiser Permanente Southern California, Pasadena, CA, USA
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, United Kingdom
| | - D Scott Schmid
- Division of Viral Diseases, National Center for Immunizations and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
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19
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Harbecke R, Jensen NJ, Depledge DP, Johnson GR, Ashbaugh ME, Schmid DS, Breuer J, Levin MJ, Oxman MN. Recurrent herpes zoster in the Shingles Prevention Study: Are second episodes caused by the same varicella-zoster virus strain? Vaccine 2020; 38:150-157. [PMID: 31679866 DOI: 10.1016/j.vaccine.2019.10.038] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Revised: 10/01/2019] [Accepted: 10/15/2019] [Indexed: 11/17/2022]
Abstract
Herpes zoster (HZ) is caused by reactivation of varicella zoster virus (VZV) that established latency in sensory and autonomic neurons during primary infection. In the Shingles Prevention Study (SPS), a large efficacy trial of live attenuated Oka/Merck zoster vaccine (ZVL), PCR-confirmed second episodes of HZ occurred in two of 660 placebo and one of 321 ZVL recipients with documented HZ during a mean follow-up of 3.13 years. An additional two ZVL recipients experienced a second episode of HZ in the Long-Term Persistence Substudy. All episodes of HZ were caused by wild-type VZV. The first and second episodes of HZ occurred in different dermatomes in each of these five participants, with contralateral recurrences in two. Time between first and second episodes ranged from 12 to 28 months. One of the five participants, who was immunocompetent on study enrollment, was immunocompromised at the onset of his first and second episodes of HZ. VZV DNA isolated from rash lesions from the first and second episodes of HZ was used to sequence the full-length VZV genomes. For the unique-sequence regions of the VZV genome, we employed target enrichment of VZV DNA, followed by deep sequencing. For the reiteration regions, we used PCR amplification and Sanger sequencing. Our analysis and comparison of the VZV genomes from the first and second episodes of HZ in each of the five participants indicate that both episodes were caused by the same VZV strain. This is consistent with the extraordinary stability of VZV during the replication phase of varicella and the subsequent establishment of latency in sensory ganglia throughout the body. Our observations also indicate that VZV is stable during the persistence of latency and the subsequent reactivation and replication that results in HZ.
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Affiliation(s)
- Ruth Harbecke
- Department of Veterans Affairs (VA) San Diego Healthcare System, San Diego, CA, USA; Department of Medicine, University of California San Diego, San Diego, CA, USA.
| | - Nancy J Jensen
- Centers for Disease Control and Prevention, Division of Viral Diseases, Atlanta, GA, USA
| | - Daniel P Depledge
- Division of Infection and Immunity, University College London, London, UK; Department of Medicine, New York University School of Medicine, New York, NY, USA
| | - Gary R Johnson
- Cooperative Studies Program Coordinating Center, Veterans Affairs Connecticut Healthcare System, West Haven, CT, USA
| | - Mark E Ashbaugh
- Department of Veterans Affairs (VA) San Diego Healthcare System, San Diego, CA, USA
| | - D Scott Schmid
- Centers for Disease Control and Prevention, Division of Viral Diseases, Atlanta, GA, USA
| | - Judith Breuer
- Division of Infection and Immunity, University College London, London, UK
| | - Myron J Levin
- Department of Medicine and Department of Pediatrics, University of Colorado, Anschutz Medical Campus, Aurora, CO, USA
| | - Michael N Oxman
- Department of Veterans Affairs (VA) San Diego Healthcare System, San Diego, CA, USA; Department of Medicine, University of California San Diego, San Diego, CA, USA
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20
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Depledge DP, Cudini J, Kundu S, Atkinson C, Brown JR, Haque T, Houldcroft CJ, Koay ES, McGill F, Milne R, Whitfield T, Tang JW, Underhill G, Bergstrom T, Norberg P, Goldstein R, Solomon T, Breuer J. High Viral Diversity and Mixed Infections in Cerebral Spinal Fluid From Cases of Varicella Zoster Virus Encephalitis. J Infect Dis 2019; 218:1592-1601. [PMID: 29986093 PMCID: PMC6173578 DOI: 10.1093/infdis/jiy358] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2018] [Accepted: 06/28/2018] [Indexed: 11/13/2022] Open
Abstract
Background Varicella zoster virus (VZV) may cause encephalitis, both with and without rash. Here we investigate whether viruses recovered from the central nervous system (CNS; encephalitis or meningitis) differ genetically from those recovered from non-CNS samples. Methods Enrichment-based deep sequencing of 45 VZV genomes from cerebral spinal fluid (CSF), plasma, bronchoalveolar lavage (BAL), and vesicles was carried out with samples collected from 34 patients with and without VZV infection of the CNS. Results Viral sequences from multiple sites in the same patient were identical at the consensus level. Virus from vesicle fluid and CSF in cases of meningitis showed low-level diversity. By contrast, plasma, BAL, and encephalitis had higher numbers of variant alleles. Two CSF-encephalitis samples had high genetic diversity, with variant frequency patterns typical of mixed infections with different clades. Conclusions Low viral genetic diversity in vesicle fluid is compatible with previous observations that VZV skin lesions arise from single or low numbers of virions. A similar result was observed in VZV from cases of VZV meningitis, a generally self-limiting infection. CSF from cases of encephalitis had higher diversity with evidence for mixed clade infections in 2 cases. We hypothesize that reactivation from multiple neurons may contribute to the pathogenesis of VZV encephalitis.
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Affiliation(s)
| | - Juliana Cudini
- Division of Infection and Immunity, University College London
| | - Samit Kundu
- School of Human and Life Sciences, Canterbury Christ Church University, University of Kent
| | | | - Julianne R Brown
- Microbiology, Virology and Infection Prevention and Control, Great Ormond Street Hospital NHS Foundation Trust, London
| | | | | | - Evelyn S Koay
- Department of Pathology, National University of Singapore.,Department of Infectious Diseases, Section for Clinical Virology, Institute of Biomedicine, University of Gothenburg, Sweden
| | - Fiona McGill
- Institute of Infection and Global Health, University of Liverpool.,National Institute for Health Research, Health Protection Research Unit in Emerging and Zoonotic Infections, University of Liverpool.,Royal Liverpool University Hospitals
| | - Richard Milne
- Division of Infection and Immunity, University College London
| | - Tom Whitfield
- Institute of Infection and Global Health, University of Liverpool
| | - Julian W Tang
- Clinical Microbiology, University Hospitals of Leicester NHS Trust.,Molecular Diagnosis Centre, National University Hospital, Singapore
| | - Gillian Underhill
- Departments of Clinical Microbiology, Pathology Centre, Queen Alexandra Hospital, Portsmouth
| | - Tomas Bergstrom
- Department of Infectious Diseases, Section for Clinical Virology, Institute of Biomedicine, University of Gothenburg, Sweden
| | - Peter Norberg
- Department of Infectious Diseases, Section for Clinical Virology, Institute of Biomedicine, University of Gothenburg, Sweden
| | | | - Tom Solomon
- Walton Centre NHS Foundation Trust, Liverpool, United Kingdom
| | - Judith Breuer
- Division of Infection and Immunity, University College London
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21
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Breuer J. Molecular Genetic Insights Into Varicella Zoster Virus (VZV), the vOka Vaccine Strain, and the Pathogenesis of Latency and Reactivation. J Infect Dis 2019; 218:S75-S80. [PMID: 30247591 DOI: 10.1093/infdis/jiy279] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Genetic tools for molecular typing of varicella zoster virus (VZV) have been used to understand the spread of virus, to differentiate wild-type and vaccine strains, and to understand the natural history of VZV infection in its cognate host. Molecular genetics has identified 7 clades of VZV (1-6 and 9), with 2 more mooted. Differences between the vOka vaccine strain and wild-type VZVs have been used to distinguish the cause of postimmunization events and to provide insight into the natural history of VZV infections. Importantly molecular genetics has shown that reinfection with establishment of latency by the reinfecting strain is common, that dual infections with different viruses can occur, and that reactivation of the superinfecting genotype can both occur. Whole-genome sequencing of the vOka vaccine has been used to show that vesicles form from a single virion, that latency is established within a few days of inoculation, and that all vaccine strains are capable of establishing latency and reactivating. Novel molecular tools have characterized the transcripts expressed during latent infection in vitro.
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Affiliation(s)
- Judith Breuer
- Division of Infection and Immunity, University College London, United Kingdom
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22
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Harpaz R. Do varicella vaccination programs change the epidemiology of herpes zoster? A comprehensive review, with focus on the United States. Expert Rev Vaccines 2019; 18:793-811. [PMID: 31318605 DOI: 10.1080/14760584.2019.1646129] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Introduction: Policy-makers in many countries have been wary of introducing varicella vaccination programs because of concerns that reduced exposures to varicella-zoster virus could increase herpes zoster (HZ) incidence. The U.S. introduced varicella vaccination in 1996 and has empiric evidence regarding this concern. Areas covered: This comprehensive review provides background emphasizing the epidemiology of varicella and of HZ in the U.S. before and after the introduction of their respective vaccines. The epidemiology is complex, and interpretation is complicated by methodologic challenges, by unexplained increases in age-specific HZ incidence that preceded varicella vaccination, and by introduction of vaccines for prevention of HZ. Nonetheless, observations from studies using different platforms and designs have yielded consistent findings, suggesting they are robust. Expert opinion: There has been no evidence that the U.S. varicella vaccination program increased HZ incidence in the general adult population over baseline trends. Furthermore, HZ incidence in children is declining. The U.S. experience can inform the development of new generations of models to predict HZ trends. More importantly, it provides reassurance for countries considering varicella vaccination that an effective program can reduce varicella morbidity and mortality while reducing the likelihood of HZ among children, and potentially, over time, across the entire population.
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Affiliation(s)
- Rafael Harpaz
- a Division of Viral Diseases, Centers for Disease Control and Prevention , Atlanta , GA , USA
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23
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Marshall EE, Malouli D, Hansen SG, Gilbride RM, Hughes CM, Ventura AB, Ainslie E, Selseth AN, Ford JC, Burke D, Kreklywich CN, Womack J, Legasse AW, Axthelm MK, Kahl C, Streblow D, Edlefsen PT, Picker LJ, Früh K. Enhancing safety of cytomegalovirus-based vaccine vectors by engaging host intrinsic immunity. Sci Transl Med 2019; 11:eaaw2603. [PMID: 31316006 PMCID: PMC6830438 DOI: 10.1126/scitranslmed.aaw2603] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 03/14/2019] [Accepted: 06/13/2019] [Indexed: 12/29/2022]
Abstract
Rhesus cytomegalovirus (RhCMV)-based vaccines maintain effector memory T cell responses (TEM) that protect ~50% of rhesus monkeys (RMs) challenged with simian immunodeficiency virus (SIV). Because human CMV (HCMV) causes disease in immunodeficient subjects, clinical translation will depend upon attenuation strategies that reduce pathogenic potential without sacrificing CMV's unique immunological properties. We demonstrate that "intrinsic" immunity can be used to attenuate strain 68-1 RhCMV vectors without impairment of immunogenicity. The tegument proteins pp71 and UL35 encoded by UL82 and UL35 of HCMV counteract cell-intrinsic restriction via degradation of host transcriptional repressors. When the corresponding RhCMV genes, Rh110 and Rh59, were deleted from 68-1 RhCMV (ΔRh110 and ΔRh59), we observed only a modest growth defect in vitro, but in vivo, these modified vectors manifested little to no amplification at the injection site and dissemination to distant sites, in contrast to parental 68-1 RhCMV. ΔRh110 was not shed at any time after infection and was not transmitted to naïve hosts either by close contact (mother to infant) or by leukocyte transfusion. In contrast, ΔRh59 was both shed and transmitted by leukocyte transfusion, indicating less effective attenuation than pp71 deletion. The T cell immunogenicity of ΔRh110 was essentially identical to 68-1 RhCMV with respect to magnitude, TEM phenotype, epitope targeting, and durability. Thus, pp71 deletion preserves CMV vector immunogenicity while stringently limiting vector spread, making pp71 deletion an attractive attenuation strategy for HCMV vectors.
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Affiliation(s)
- Emily E Marshall
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Daniel Malouli
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Scott G Hansen
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Roxanne M Gilbride
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Colette M Hughes
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Abigail B Ventura
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Emily Ainslie
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Andrea N Selseth
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Julia C Ford
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - David Burke
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Craig N Kreklywich
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Jennie Womack
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Alfred W Legasse
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Michael K Axthelm
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Christoph Kahl
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Daniel Streblow
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Paul T Edlefsen
- Statistical Center for HIV/AIDS Research and Prevention, Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Louis J Picker
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA.
| | - Klaus Früh
- Vaccine and Gene Therapy Institute and Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA.
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24
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Wegner F, Lassalle F, Depledge DP, Balloux F, Breuer J. Co-evolution of sites under immune selection shapes Epstein-Barr Virus population structure. Mol Biol Evol 2019; 36:2512-2521. [PMID: 31273385 PMCID: PMC6805225 DOI: 10.1093/molbev/msz152] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 06/03/2019] [Accepted: 06/19/2019] [Indexed: 12/13/2022] Open
Abstract
Epstein–Barr virus (EBV) is one of the most common viral infections in humans and persists within its host for life. EBV therefore represents an extremely successful virus that has evolved complex strategies to evade the host’s innate and adaptive immune response during both initial and persistent stages of infection. Here, we conducted a comparative genomics analysis on 223 whole genome sequences of worldwide EBV strains. We recover extensive genome-wide linkage disequilibrium (LD) despite pervasive genetic recombination. This pattern is explained by the global EBV population being subdivided into three main subpopulations, one primarily found in East Asia, one in Southeast Asia and Oceania, and the third including most of the other globally distributed genomes we analyzed. Additionally, sites in LD were overrepresented in immunogenic genes. Taken together, our results suggest that host immune selection and local adaptation to different human host populations has shaped the genome-wide patterns of genetic diversity in EBV.
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Affiliation(s)
- Fanny Wegner
- Division of Infection & Immunity, University College London, London, UK.,Microbial Evolutionary Genomics, Institut Pasteur, Paris, France
| | - Florent Lassalle
- UCL Genetic Institute, University College London, London, UK.,MRC Centre for Outbreak Analysis and Modelling, Imperial College, London, UK
| | - Daniel P Depledge
- Division of Infection & Immunity, University College London, London, UK
| | | | - Judith Breuer
- Division of Infection & Immunity, University College London, London, UK
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d'Offay JM, Fulton RW, Fishbein M, Eberle R, Dubovi EJ. Isolation of a naturally occurring vaccine/wild-type recombinant bovine herpesvirus type 1 (BoHV-1) from an aborted bovine fetus. Vaccine 2019; 37:4518-4524. [PMID: 31266667 DOI: 10.1016/j.vaccine.2019.06.059] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2019] [Revised: 06/17/2019] [Accepted: 06/18/2019] [Indexed: 01/17/2023]
Abstract
Bovine herpesvirus type 1 (BoHV-1) causes various disease syndromes in cattle including respiratory disease and abortions. During an investigation into the potential role of BoHV-1 modified-live vaccines (MLV) causing diseases in cattle, we performed whole genome sequencing on six BoHV-1 field strains isolated at Cornell Animal Health Diagnostic Center in the late 1970s. Three isolates (two respiratory and a fetal) were identified as vaccine-derived isolates, having SNP patterns identical to that of a previously sequenced MLV virus that exhibited a deleted US2 and truncated US1.67 genes. Two other isolates (a respiratory and a fetal) were categorized as wild-type (WT) viruses based on their unique SNP pattern that is distinct from MLV viruses. The sixth isolate from an aborted fetus was a recombinant virus with 62% of its genome exhibiting SNPs identical to one of the above-mentioned WT viruses also recovered from an aborted fetus. The remaining 38% consisted of two blocks of sequences derived from the MLV virus. The first block replaced the UL9-UL19 region, and the second vaccine-derived sequence block encompassed all the genes within the unique short region and the internal/terminal repeats containing the regulatory genes BICP4 and BICP22. This is confirmatory evidence that recombination between BoHV-1 MLV and WT viruses can occur under natural conditions and cause disease. It is important in that it underscores the potential for the glycoprotein E negative (gE-) marker vaccine used to eradicate BoHV-1 in some countries, to recombine with virulent field strains allowing them to capture the gE- marker, thereby endangering the control and eradication programs.
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Affiliation(s)
- Jean M d'Offay
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA.
| | - Robert W Fulton
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA
| | - Mark Fishbein
- Department of Plant Biology, Ecology & Evolution, Oklahoma State University, 301 Physical Sciences, Stillwater, OK 74078, USA
| | - R Eberle
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA
| | - Edward J Dubovi
- Animal Health Diagnostic Center, Cornell University, Ithaca, NY 14852, USA
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Abstract
Varicella is a common vaccine-preventable disease that usually presents as a mild disorder but can lead to severe complications. Before the implementation of universal varicella vaccination (UVV) in some European countries, the burden of varicella disease was broadly similar across the region. Despite this, countries adopted heterogeneous varicella vaccination strategies. UVV is currently recommended in 12 European countries. Known barriers to UVV implementation in Europe include (1) a perceived low disease burden and low public health priority; (2) cost-effectiveness and funding availability; (3) concerns related to a shift in varicella disease and incidence of herpes zoster and (4) safety concerns related to measles, mumps, rubella and varicella-associated febrile seizures after the first dose. Countries that implemented UVV experienced decreases in varicella incidence, hospitalizations and complications, showing overall beneficial impact. Alternative strategies targeting susceptible individuals at higher risk of complications have been less effective. This article discusses ways to overcome the barriers to move varicella forward as a truly vaccine preventable disease.
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González I, Molina-Ortega A, Pérez-Romero P, Echevarría JE, He L, Tarragó D. Varicella-zoster virus clades circulating in Spain over two decades. J Clin Virol 2018; 110:17-21. [PMID: 30517902 DOI: 10.1016/j.jcv.2018.11.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Revised: 08/30/2018] [Accepted: 11/26/2018] [Indexed: 11/28/2022]
Abstract
BACKGROUND Despite childhood universal VZV immunization was introduced in 2015, there are no data on VZV clade distribution in Spain. OBJECTIVES To characterize the varicella-zoster virus strains circulating in Spain between 1997 and 2016. STUDY DESIGN In this retrospective study, we determined the VZV clades in 294 patients with different pathologies (mainly encephalitis, zoster and varicella) by sequencing three fragments within ORF 22, ORF 21 and ORF 50 and, subsequently analyzing 7 relevant SNPs. RESULTS Among these 294 patients, 132(44.9%) patients were infected by clade 1, 42(14.3%) patients by clade 3, 19(6.5%) by clade 5, 29(9.9%) by clade VI and 3(1%) by clade 4. Four patients (1.4%) were infected by clade 2 vOKA strains, who received one dose of live-attenuated varicella vaccine. Putative recombinant clade 1/3 was identified in 6 cases (2.0%). Results obtained from partial sequences were assigned to clade 1 or 3 in 56(19%) patients and clade 5 or VI in 3(1.0%) patients. In the multivariate analysis, encephalitis was independently associated with clades 1 and 3 and age >14y.o. (P = 0.035 and P = 0.021, respectively). Additionally, Madrid had significant fewer cases of encephalitis compared with the rest of regions analyzed (P = 0.001). CONCLUSIONS Higher prevalence of clades 1 and 3 and their relation with encephalitis and age >14y.o. suggest earlier introduction of this clades in Spain. Putative interclade 1 and 3 recombinants are circulating in patients with encephalitis, herpes zoster and varicella. Several cases were related to vOKA vaccination but vaccine strains do not seem to circulate in the general population.
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Affiliation(s)
- Irene González
- Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III, Majadahonda, Spain
| | - Alejandro Molina-Ortega
- Instituto de Biomedicina de Sevilla (IBIS)/CSIC/University of Sevilla, University Hospital Virgen del Rocío. Sevilla, Spain
| | - Pilar Pérez-Romero
- Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III, Majadahonda, Spain
| | - Juan E Echevarría
- Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III, Majadahonda, Spain; CIBER de Epidemiología y Salud Pública (CIBERESP), Madrid, Spain
| | - Lante He
- Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III, Majadahonda, Spain
| | - David Tarragó
- Centro Nacional de Microbiología (CNM), Instituto de Salud Carlos III, Majadahonda, Spain.
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28
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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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Berenstein AJ, Lorenzetti MA, Preciado MV. Recombination rates along the entire Epstein Barr virus genome display a highly heterogeneous landscape. INFECTION GENETICS AND EVOLUTION 2018; 65:96-103. [PMID: 30031929 DOI: 10.1016/j.meegid.2018.07.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2018] [Revised: 07/10/2018] [Accepted: 07/18/2018] [Indexed: 12/30/2022]
Abstract
Epstein Barr virus (EBV) has a large DNA genome assumed to be stable, but also subject to mutational processes such as nucleotide substitution and recombination, the latter explored to a lesser extent. Moreover, differences in the extent of recombination events across herpes sub-families were recently reported. Given the relevance of recombination in viral evolution and its possible impact in pathogenesis, we aimed to fully characterize and quantify its extension in all available EBV complete genome by assessing global and local recombination rate values (⍴/bp). Our results provide the first EBV recombination map based on recombination rates assessment, both at a global and gene by gene level, where the mean value for the entire genome was 0.035 (HPDI 0.020-0.062) ⍴/bp. We quantified how this evolutionary process changes along the EBV genome, and proved it to be non-homogeneous, since regulatory regions depicted the lowest recombination rate values while repetitive regions the highest signal. Moreover, GC content rich regions seem not to be linked to high recombination rates as previously reported. At an intragenic level, four genes (EBNA3C, EBNA3B, BRRF2 and BBLF2-BBLF3) presented a recombination rate above genome average. We specifically quantified the signal strength among different recombination-initiators previously described features and concluded that those which elicited the greatest amount of changes in ⍴/bp, TGGAG and CCCAG, were two well characterized recombination inducing motifs in eukaryotic cells. Strikingly, although TGGAG was not the most frequently detected DNA motif across the EBV genome (697 hits), it still induced a significantly greater proportion of initiation events (0.025 events/hits) than other more represented motifs, p-value = 0.04; one tailed proportion test. Present results support the idea that diversity and evolution of herpesviruses are impacted by mechanisms, such as recombination, which extends beyond the usual consideration of point mutations.
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Affiliation(s)
- Ariel José Berenstein
- Instituto Multidisciplinario de Investigaciones en Patologías Pediátricas (IMIPP), CONICET-GCBA, Laboratorio de Biología Molecular, División Patología, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - Mario Alejandro Lorenzetti
- Instituto Multidisciplinario de Investigaciones en Patologías Pediátricas (IMIPP), CONICET-GCBA, Laboratorio de Biología Molecular, División Patología, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina
| | - María Victoria Preciado
- Instituto Multidisciplinario de Investigaciones en Patologías Pediátricas (IMIPP), CONICET-GCBA, Laboratorio de Biología Molecular, División Patología, Hospital de Niños Ricardo Gutiérrez, Buenos Aires, Argentina.
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30
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Depledge DP, Sadaoka T, Ouwendijk WJD. Molecular Aspects of Varicella-Zoster Virus Latency. Viruses 2018; 10:v10070349. [PMID: 29958408 PMCID: PMC6070824 DOI: 10.3390/v10070349] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 06/19/2018] [Accepted: 06/27/2018] [Indexed: 02/07/2023] Open
Abstract
Primary varicella-zoster virus (VZV) infection causes varicella (chickenpox) and the establishment of a lifelong latent infection in ganglionic neurons. VZV reactivates in about one-third of infected individuals to cause herpes zoster, often accompanied by neurological complications. The restricted host range of VZV and, until recently, a lack of suitable in vitro models have seriously hampered molecular studies of VZV latency. Nevertheless, recent technological advances facilitated a series of exciting studies that resulted in the discovery of a VZV latency-associated transcript (VLT) and provide novel insights into our understanding of VZV latency and factors that may initiate reactivation. Deducing the function(s) of VLT and the molecular mechanisms involved should now be considered a priority to improve our understanding of factors that govern VZV latency and reactivation. In this review, we summarize the implications of recent discoveries in the VZV latency field from both a virus and host perspective and provide a roadmap for future studies.
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Affiliation(s)
- Daniel P Depledge
- Department of Microbiology, New York University School of Medicine, New York, NY 10016, USA.
| | - Tomohiko Sadaoka
- Division of Clinical Virology, Center for Infectious Diseases, Kobe University Graduate School of Medicine, 7-5-1 Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan.
| | - Werner J D Ouwendijk
- Department of Viroscience, Erasmus Medical Centre, 3015 CN Rotterdam, The Netherlands.
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31
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He L, Li J, Zhang Y, Luo J, Cao Y, Xue C. Phylogenetic and molecular epidemiological studies reveal evidence of recombination among Marek's disease viruses. Virology 2018; 516:202-209. [PMID: 29407378 DOI: 10.1016/j.virol.2018.01.019] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/24/2018] [Accepted: 01/25/2018] [Indexed: 01/09/2023]
Abstract
Marek's disease has brought enormous loss in chicken production worldwide and the increasing virulence of Marek's disease virus (MDV) became a severe problem. To better understand the genetic basis underlying, a Chinese MDV strain HNGS101 isolated from immunized chickens was sequenced. Phylogenetic analysis implied that HNGS101 showed more relatedness to Eurasian strains than GaHV-2 circulating in North America. Recombination networks analysis showed the evidence of recombination among MDV strains, and several recombination events in the UL and US region were found. Further analysis indicated that the HNGS101 strain seemed to be generated by the recombination of the earliest Eurasian strains and North American strains in the US region, which may be responsible for the MD outbreaks in China. In summary, this study demonstrates recombination events among MDV strains [corrected], which may shed light on the mechanism of virulence enhancement.
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Affiliation(s)
- Liangliang He
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jie Li
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China; School of Biology and Food Engineering, Changshu Institute of Technology, Changshu 215500, China
| | - Yun Zhang
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Jun Luo
- Key Laboratory of Animal Immunology of the Ministry of Agriculture, Henan Provincial Key Laboratory of Animal Immunology, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China; College of Animal Science and Technology, Henan University of Science and Technology, Luoyang 471003, China
| | - Yongchang Cao
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China
| | - Chunyi Xue
- State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510006, China.
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32
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Law GA, Herr AE, Cwick JP, Taylor MP. A New Approach to Assessing HSV-1 Recombination during Intercellular Spread. Viruses 2018; 10:v10050220. [PMID: 29693602 PMCID: PMC5977213 DOI: 10.3390/v10050220] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2018] [Revised: 04/17/2018] [Accepted: 04/20/2018] [Indexed: 12/16/2022] Open
Abstract
The neuroinvasive Herpes simplex virus type 1 (HSV-1) utilizes intergenomic recombination in order to diversify viral populations. Research efforts to assess HSV-1 recombination are often complicated by the use of attenuating mutations, which differentiate viral progeny but unduly influence the replication and spread. In this work, we generated viruses with markers that allowed for classification of viral progeny with limited attenuation of viral replication. We isolated viruses, harboring either a cyan (C) or yellow (Y) fluorescent protein (FP) expression cassette inserted in two different locations within the viral genome, in order to visually quantify the recombinant progeny based on plaque fluorescence. We found that the FP marked genomes had a limited negative affect on the viral replication and production of progeny virions. A co-infection of the two viruses resulted in recombinant progeny that was dependent on the multiplicity of infection and independent of the time post infection, at a rate that was similar to previous reports. The sequential passage of mixed viral populations revealed a limited change in the distribution of the parental and recombinant progeny. Interestingly, the neuroinvasive spread within neuronal cultures and an in vivo mouse model, revealed large, random shifts in the parental and recombinant distributions in viral populations. In conclusion, our approach highlights the utility of FP expressing viruses in order to provide new insights into mechanisms of HSV-1 recombination.
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Affiliation(s)
- Gabrielle A Law
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT 59717, USA.
| | - Alix E Herr
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT 59717, USA.
| | - James P Cwick
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT 59717, USA.
| | - Matthew P Taylor
- Department of Microbiology & Immunology, Montana State University, Bozeman, MT 59717, USA.
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Genomic, Recombinational and Phylogenetic Characterization of Global Feline Herpesvirus 1 Isolates. Virology 2018; 518:385-397. [PMID: 29605685 DOI: 10.1016/j.virol.2018.03.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 03/20/2018] [Accepted: 03/21/2018] [Indexed: 11/23/2022]
Abstract
Feline herpes virus type 1 (FHV-1) is widely considered to be the leading cause of ocular disease in cats and has been implicated in upper respiratory tract infections. Little, however is known about interstrain phylogenetic relationships, and details of the genomic structure. For the present study, twenty-six FHV-1 isolates from different cats in animal shelters were collected from eight separate locations in the USA, and the genomes sequenced. Genomic characterization of these isolates includied short sequence repeat (SSR) detection, with fewer SSRs detected, compared to herpes simplex viruses type 1 and 2. For phylogenetic and recombination analysis, 27 previously sequenced isolates of FHV-1 were combined with the 26 strains sequenced for the present study. The overall genomic interstrain genetic distance between all available isolates was 0.093%. Phylogenetic analysis identified four main FHV-1 clades primarily corresponding to geographical collection site. Recombination analysis suggested that interclade recombination has occurred.
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34
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Morrison CL, Iwanowicz L, Work TM, Fahsbender E, Breitbart M, Adams C, Iwanowicz D, Sanders L, Ackermann M, Cornman RS. Genomic evolution, recombination, and inter-strain diversity of chelonid alphaherpesvirus 5 from Florida and Hawaii green sea turtles with fibropapillomatosis. PeerJ 2018; 6:e4386. [PMID: 29479497 PMCID: PMC5824677 DOI: 10.7717/peerj.4386] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 01/29/2018] [Indexed: 12/18/2022] Open
Abstract
Chelonid alphaherpesvirus 5 (ChHV5) is a herpesvirus associated with fibropapillomatosis (FP) in sea turtles worldwide. Single-locus typing has previously shown differentiation between Atlantic and Pacific strains of this virus, with low variation within each geographic clade. However, a lack of multi-locus genomic sequence data hinders understanding of the rate and mechanisms of ChHV5 evolutionary divergence, as well as how these genomic changes may contribute to differences in disease manifestation. To assess genomic variation in ChHV5 among five Hawaii and three Florida green sea turtles, we used high-throughput short-read sequencing of long-range PCR products amplified from tumor tissue using primers designed from the single available ChHV5 reference genome from a Hawaii green sea turtle. This strategy recovered sequence data from both geographic regions for approximately 75% of the predicted ChHV5 coding sequences. The average nucleotide divergence between geographic populations was 1.5%; most of the substitutions were fixed differences between regions. Protein divergence was generally low (average 0.08%), and ranged between 0 and 5.3%. Several atypical genes originally identified and annotated in the reference genome were confirmed in ChHV5 genomes from both geographic locations. Unambiguous recombination events between geographic regions were identified, and clustering of private alleles suggests the prevalence of recombination in the evolutionary history of ChHV5. This study significantly increased the amount of sequence data available from ChHV5 strains, enabling informed selection of loci for future population genetic and natural history studies, and suggesting the (possibly latent) co-infection of individuals by well-differentiated geographic variants.
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Affiliation(s)
- Cheryl L Morrison
- National Fish Health Research Laboratory, Leetown Science Center, US Geological Survey, Kearneysville, WV, United States of America
| | - Luke Iwanowicz
- National Fish Health Research Laboratory, Leetown Science Center, US Geological Survey, Kearneysville, WV, United States of America
| | - Thierry M Work
- National Wildlife Health Center, Honolulu Field Station, US Geological Survey, Honolulu, HI, United States of America
| | - Elizabeth Fahsbender
- College of Marine Science, University of South Florida, St. Petersburg, FL, United States of America
| | - Mya Breitbart
- College of Marine Science, University of South Florida, St. Petersburg, FL, United States of America
| | - Cynthia Adams
- National Fish Health Research Laboratory, Leetown Science Center, US Geological Survey, Kearneysville, WV, United States of America
| | - Deb Iwanowicz
- National Fish Health Research Laboratory, Leetown Science Center, US Geological Survey, Kearneysville, WV, United States of America
| | - Lakyn Sanders
- National Fish Health Research Laboratory, Leetown Science Center, US Geological Survey, Kearneysville, WV, United States of America
| | | | - Robert S Cornman
- Fort Collins Science Center, US Geological Survey, Fort Collins, CO, United States of America
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35
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Bryant NA, Wilkie GS, Russell CA, Compston L, Grafham D, Clissold L, McLay K, Medcalf L, Newton R, Davison AJ, Elton DM. Genetic diversity of equine herpesvirus 1 isolated from neurological, abortigenic and respiratory disease outbreaks. Transbound Emerg Dis 2018; 65:817-832. [PMID: 29423949 PMCID: PMC5947664 DOI: 10.1111/tbed.12809] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2017] [Indexed: 12/14/2022]
Abstract
Equine herpesvirus 1 (EHV‐1) causes respiratory disease, abortion, neonatal death and neurological disease in equines and is endemic in most countries. The viral factors that influence EHV‐1 disease severity are poorly understood, and this has hampered vaccine development. However, the N752D substitution in the viral DNA polymerase catalytic subunit has been shown statistically to be associated with neurological disease. This has given rise to the term “neuropathic strain,” even though strains lacking the polymorphism have been recovered from cases of neurological disease. To broaden understanding of EHV‐1 diversity in the field, 78 EHV‐1 strains isolated over a period of 35 years were sequenced. The great majority of isolates originated from the United Kingdom and included in the collection were low passage isolates from respiratory, abortigenic and neurological outbreaks. Phylogenetic analysis of regions spanning 80% of the genome showed that up to 13 viral clades have been circulating in the United Kingdom and that most of these are continuing to circulate. Abortion isolates grouped into nine clades, and neurological isolates grouped into five. Most neurological isolates had the N752D substitution, whereas most abortion isolates did not, although three of the neurological isolates from linked outbreaks had a different polymorphism. Finally, bioinformatic analysis suggested that recombination has occurred between EHV‐1 clades, between EHV‐1 and equine herpesvirus 4, and between EHV‐1 and equine herpesvirus 8.
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Affiliation(s)
- N A Bryant
- Animal Health Trust, Kentford, Newmarket, Suffolk, UK
| | - G S Wilkie
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - C A Russell
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - L Compston
- Animal Health Trust, Kentford, Newmarket, Suffolk, UK
| | - D Grafham
- Sheffield Children's NHS Foundation Trust, Sheffield, South Yorkshire, UK
| | - L Clissold
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, UK
| | - K McLay
- Earlham Institute, Norwich Research Park, Norwich, Norfolk, UK
| | - L Medcalf
- Animal Health Trust, Kentford, Newmarket, Suffolk, UK
| | - R Newton
- Animal Health Trust, Kentford, Newmarket, Suffolk, UK
| | - A J Davison
- MRC-University of Glasgow Centre for Virus Research, Glasgow, UK
| | - D M Elton
- Animal Health Trust, Kentford, Newmarket, Suffolk, UK
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Impacts of Genome-Wide Analyses on Our Understanding of Human Herpesvirus Diversity and Evolution. J Virol 2017; 92:JVI.00908-17. [PMID: 29046445 PMCID: PMC5730764 DOI: 10.1128/jvi.00908-17] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Until fairly recently, genome-wide evolutionary dynamics and within-host diversity were more commonly examined in the context of small viruses than in the context of large double-stranded DNA viruses such as herpesviruses. The high mutation rates and more compact genomes of RNA viruses have inspired the investigation of population dynamics for these species, and recent data now suggest that herpesviruses might also be considered candidates for population modeling. High-throughput sequencing (HTS) and bioinformatics have expanded our understanding of herpesviruses through genome-wide comparisons of sequence diversity, recombination, allele frequency, and selective pressures. Here we discuss recent data on the mechanisms that generate herpesvirus genomic diversity and underlie the evolution of these virus families. We focus on human herpesviruses, with key insights drawn from veterinary herpesviruses and other large DNA virus families. We consider the impacts of cell culture on herpesvirus genomes and how to accurately describe the viral populations under study. The need for a strong foundation of high-quality genomes is also discussed, since it underlies all secondary genomic analyses such as RNA sequencing (RNA-Seq), chromatin immunoprecipitation, and ribosome profiling. Areas where we foresee future progress, such as the linking of viral genetic differences to phenotypic or clinical outcomes, are highlighted as well.
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37
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Kolb AW, Lewin AC, Moeller Trane R, McLellan GJ, Brandt CR. Phylogenetic and recombination analysis of the herpesvirus genus varicellovirus. BMC Genomics 2017; 18:887. [PMID: 29157201 PMCID: PMC5697016 DOI: 10.1186/s12864-017-4283-4] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 11/07/2017] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND The varicelloviruses comprise a genus within the alphaherpesvirus subfamily, and infect both humans and other mammals. Recently, next-generation sequencing has been used to generate genomic sequences of several members of the Varicellovirus genus. Here, currently available varicellovirus genomic sequences were used for phylogenetic, recombination, and genetic distance analysis. RESULTS A phylogenetic network including genomic sequences of individual species, was generated and suggested a potential restriction between the ungulate and non-ungulate viruses. Intraspecies genetic distances were higher in the ungulate viruses (pseudorabies virus (SuHV-1) 1.65%, bovine herpes virus type 1 (BHV-1) 0.81%, equine herpes virus type 1 (EHV-1) 0.79%, equine herpes virus type 4 (EHV-4) 0.16%) than non-ungulate viruses (feline herpes virus type 1 (FHV-1) 0.0089%, canine herpes virus type 1 (CHV-1) 0.005%, varicella-zoster virus (VZV) 0.136%). The G + C content of the ungulate viruses was also higher (SuHV-1 73.6%, BHV-1 72.6%, EHV-1 56.6%, EHV-4 50.5%) compared to the non-ungulate viruses (FHV-1 45.8%, CHV-1 31.6%, VZV 45.8%), which suggests a possible link between G + C content and intraspecies genetic diversity. Varicellovirus clade nomenclature is variable across different species, and we propose a standardization based on genomic genetic distance. A recent study reported no recombination between sequenced FHV-1 strains, however in the present study, both splitstree, bootscan, and PHI analysis indicated recombination. We also found that the recently sequenced Brazilian CHV-1 strain BTU-1 may contain a genetic signal in the UL50 gene from an unknown varicellovirus. CONCLUSION Together, the data contribute to a greater understanding of varicellovirus genomics, and we also suggest a new clade nomenclature scheme based on genetic distances.
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Affiliation(s)
- Aaron W Kolb
- Department of Ophthalmology and Visual Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, 550 Bardeen Laboratories, 1300 University Ave., Madison, WI, 53706, USA
| | - Andrew C Lewin
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
| | - Ralph Moeller Trane
- Department of Ophthalmology and Visual Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, 550 Bardeen Laboratories, 1300 University Ave., Madison, WI, 53706, USA
| | - Gillian J McLellan
- Department of Ophthalmology and Visual Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, 550 Bardeen Laboratories, 1300 University Ave., Madison, WI, 53706, USA
- Department of Surgical Sciences, School of Veterinary Medicine, University of Wisconsin-Madison, Madison, WI, USA
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, USA
| | - Curtis R Brandt
- Department of Ophthalmology and Visual Sciences, School of Medicine and Public Health, University of Wisconsin-Madison, 550 Bardeen Laboratories, 1300 University Ave., Madison, WI, 53706, USA.
- McPherson Eye Research Institute, University of Wisconsin-Madison, Madison, WI, USA.
- Medical Microbiology and Immunology, School of Medicine and Public Health, University of Wisconsin-Madison, Madison, WI, USA.
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Johnston C, Magaret A, Roychoudhury P, Greninger AL, Cheng A, Diem K, Fitzgibbon MP, Huang ML, Selke S, Lingappa JR, Celum C, Jerome KR, Wald A, Koelle DM. Highly conserved intragenic HSV-2 sequences: Results from next-generation sequencing of HSV-2 U L and U S regions from genital swabs collected from 3 continents. Virology 2017; 510:90-98. [PMID: 28711653 PMCID: PMC5565707 DOI: 10.1016/j.virol.2017.06.031] [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: 04/28/2017] [Revised: 06/24/2017] [Accepted: 06/27/2017] [Indexed: 12/21/2022]
Abstract
INTRODUCTION Understanding the variability in circulating herpes simplex virus type 2 (HSV-2) genomic sequences is critical to the development of HSV-2 vaccines. METHODS Genital lesion swabs containing ≥ 107log10 copies HSV DNA collected from Africa, the USA, and South America underwent next-generation sequencing, followed by K-mer based filtering and de novo genomic assembly. Sites of heterogeneity within coding regions in unique long and unique short (UL_US) regions were identified. Phylogenetic trees were created using maximum likelihood reconstruction. RESULTS Among 46 samples from 38 persons, 1468 intragenic base-pair substitutions were identified. The maximum nucleotide distance between strains for concatenated UL_US segments was 0.4%. Phylogeny did not reveal geographic clustering. The most variable proteins had non-synonymous mutations in < 3% of amino acids. CONCLUSIONS Unenriched HSV-2 DNA can undergo next-generation sequencing to identify intragenic variability. The use of clinical swabs for sequencing expands the information that can be gathered directly from these specimens.
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Affiliation(s)
- Christine Johnston
- Department of Medicine, University of Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, USA.
| | - Amalia Magaret
- Department of Laboratory Medicine, University of Washington, USA; Department of Biostatistics, University of Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, USA
| | | | | | - Anqi Cheng
- Department of Biostatistics, University of Washington, USA
| | - Kurt Diem
- Department of Laboratory Medicine, University of Washington, USA
| | - Matthew P Fitzgibbon
- Genomics and Bioinformatics Resource, Fred Hutchinson Cancer Research Center, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine, University of Washington, USA
| | - Stacy Selke
- Department of Laboratory Medicine, University of Washington, USA
| | - Jairam R Lingappa
- Department of Medicine, University of Washington, USA; Department of Global Health, University of Washington, USA; Department of Pediatrics, University of Washington, USA
| | - Connie Celum
- Department of Medicine, University of Washington, USA; Department of Epidemiology, University of Washington, USA; Department of Global Health, University of Washington, USA
| | - Keith R Jerome
- Department of Laboratory Medicine, University of Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, USA
| | - Anna Wald
- Department of Medicine, University of Washington, USA; Department of Laboratory Medicine, University of Washington, USA; Department of Epidemiology, University of Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, USA
| | - David M Koelle
- Department of Medicine, University of Washington, USA; Department of Laboratory Medicine, University of Washington, USA; Department of Global Health, University of Washington, USA; Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, USA; Benaroya Research Institute, Seattle, WA, USA
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Targeted Genome Sequencing Reveals Varicella-Zoster Virus Open Reading Frame 12 Deletion. J Virol 2017; 91:JVI.01141-17. [PMID: 28747504 DOI: 10.1128/jvi.01141-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 07/21/2017] [Indexed: 12/19/2022] Open
Abstract
The neurotropic herpesvirus varicella-zoster virus (VZV) establishes a lifelong latent infection in humans following primary infection. The low abundance of VZV nucleic acids in human neurons has hindered an understanding of the mechanisms that regulate viral gene transcription during latency. To overcome this critical barrier, we optimized a targeted capture protocol to enrich VZV DNA and cDNA prior to whole-genome/transcriptome sequence analysis. Since the VZV genome is remarkably stable, it was surprising to detect that VZV32, a VZV laboratory strain with no discernible growth defect in tissue culture, contained a 2,158-bp deletion in open reading frame (ORF) 12. Consequently, ORF 12 and 13 protein expression was abolished and Akt phosphorylation was inhibited. The discovery of the ORF 12 deletion, revealed through targeted genome sequencing analysis, points to the need to authenticate the VZV genome when the virus is propagated in tissue culture.IMPORTANCE Viruses isolated from clinical samples often undergo genetic modifications when cultured in the laboratory. Historically, VZV is among the most genetically stable herpesviruses, a notion supported by more than 60 complete genome sequences from multiple isolates and following multiple in vitro passages. However, application of enrichment protocols to targeted genome sequencing revealed the unexpected deletion of a significant portion of VZV ORF 12 following propagation in cultured human fibroblast cells. While the enrichment protocol did not introduce bias in either the virus genome or transcriptome, the findings indicate the need for authentication of VZV by sequencing when the virus is propagated in tissue culture.
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40
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Characterization and phylogenetic analysis of Varicella-zoster virus strains isolated from Korean patients. J Microbiol 2017; 55:665-672. [PMID: 28752294 DOI: 10.1007/s12275-017-7171-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2017] [Revised: 06/15/2017] [Accepted: 06/22/2017] [Indexed: 12/24/2022]
Abstract
Varicella-zoster virus (VZV) is a causative agent of chickenpox in primary infection and shingles after its reactivation from latency. Complete or almost-complete genomic DNA sequences for various VZV strains have been reported. Recently, clinical VZV strains were isolated from Korean patients whose genome was sequenced using high-throughput sequencing technology. In this study, we analyzed single nucleotide polymorphism (SNP) of VZV strains to genetically characterize Korean clinical isolates. Phylogenetic analyses revealed that three Korean strains, YC01, YC02, and YC03, were linked to clade 2. Comprehensive SNP analysis identified 86 sites specific for the 5 VZV clades. VZV strains isolated from Korea did not form a phylogenetic cluster. Rather, YC02 and YC03 clustered strongly with Chinese strain 84-7 within clade 2, more specifically cluster 2a. Signature sequences for the cluster 2a were identified and found to play an important role in the separation of cluster 2a strains from other clade 2 strains, as shown in substitution studies. Further genetic analysis with additional strains isolated from Japan, China, and other Asian countries would provide a novel insight into the significance of two distinct subclades within clade 2.
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41
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Herr AE, Hain KS, Taylor MP. Limitations on the Multiplicity of Cellular Infection During Human Alphaherpesvirus Disease. CURRENT CLINICAL MICROBIOLOGY REPORTS 2017. [DOI: 10.1007/s40588-017-0071-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
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42
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Jensen NJ, Rivailler P, Tseng HF, Quinlivan ML, Radford K, Folster J, Harpaz R, LaRussa P, Jacobsen S, Scott Schmid D. Revisiting the genotyping scheme for varicella-zoster viruses based on whole-genome comparisons. J Gen Virol 2017; 98:1434-1438. [PMID: 28613146 DOI: 10.1099/jgv.0.000772] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
We report whole-genome sequences (WGSs) for four varicella-zoster virus (VZV) samples from a shingles study conducted by Kaiser Permanente of Southern California. Comparative genomics and phylogenetic analysis of all published VZV WGSs revealed that strain KY037798 is in clade IX, which shall henceforth be designated clade 9. Previously published single nucleotide polymorphisms (SNP)-based genotyping schemes fail to discriminate between clades 6 and VIII and employ positions that are not clade-specific. We provide an updated list of clade-specific positions that supersedes the list determined at the 2008 VZV nomenclature meeting. Finally, we propose a new targeted genotyping scheme that will discriminate the circulating VZV clades with at least a twofold redundancy. Genotyping strategies using a limited set of targeted SNPs will continue to provide an efficient 'first pass' method for VZV strain surveillance as vaccination programmes for varicella and zoster influence the dynamics of VZV transmission.
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Affiliation(s)
- Nancy J Jensen
- Centers for Disease Control and Prevention, National Center for Immunizations and Respiratory Diseases, Division of Viral Diseases, Atlanta, GA, USA
| | - Pierre Rivailler
- Centers for Disease Control and Prevention, National Center for Immunizations and Respiratory Diseases, Division of Viral Diseases, Atlanta, GA, USA
| | - Hung Fu Tseng
- Kaiser Permanente of Southern California, Department of Research and Evaluation, Pasadena, CA, USA
| | - Mark L Quinlivan
- Centers for Disease Control and Prevention, National Center for Immunizations and Respiratory Diseases, Division of Viral Diseases, Atlanta, GA, USA.,Present address: Labtech International Ltd, Uckfield, East Sussex, UK
| | - Kay Radford
- Centers for Disease Control and Prevention, National Center for Immunizations and Respiratory Diseases, Division of Viral Diseases, Atlanta, GA, USA
| | - Jennifer Folster
- Centers for Disease Control and Prevention, National Center for Immunizations and Respiratory Diseases, Division of Viral Diseases, Atlanta, GA, USA
| | - Rafael Harpaz
- Centers for Disease Control and Prevention, National Center for Immunizations and Respiratory Diseases, Division of Viral Diseases, Atlanta, GA, USA
| | - Philip LaRussa
- Department of Pediatrics, Columbia University, College of Physicians and Surgeons,, New York, NY, USA
| | - Steven Jacobsen
- Kaiser Permanente of Southern California, Department of Research and Evaluation, Pasadena, CA, USA
| | - D Scott Schmid
- Centers for Disease Control and Prevention, National Center for Immunizations and Respiratory Diseases, Division of Viral Diseases, Atlanta, GA, USA
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43
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Natural recombination in alphaherpesviruses: Insights into viral evolution through full genome sequencing and sequence analysis. INFECTION GENETICS AND EVOLUTION 2017; 49:174-185. [DOI: 10.1016/j.meegid.2016.12.022] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Revised: 12/20/2016] [Accepted: 12/21/2016] [Indexed: 01/05/2023]
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44
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Development and application of a TaqMan single nucleotide polymorphism genotyping assay to study infectious laryngotracheitis virus recombination in the natural host. PLoS One 2017; 12:e0174590. [PMID: 28350819 PMCID: PMC5370143 DOI: 10.1371/journal.pone.0174590] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Accepted: 03/10/2017] [Indexed: 12/25/2022] Open
Abstract
To date, recombination between different strains of the avian alphaherpesvirus infectious laryngotracheitis virus (ILTV) has only been detected in field samples using full genome sequencing and sequence analysis. These previous studies have revealed that natural recombination is widespread in ILTV and have demonstrated that recombination between two attenuated ILTV vaccine strains generated highly virulent viruses that produced widespread disease within poultry flocks in Australia. In order to better understand ILTV recombination, this study developed a TaqMan single nucleotide polymorphism (SNP) genotyping assay to detect recombination between two field strains of ILTV (CSW-1 and V1-99 ILTV) under experimental conditions. Following in vivo co-inoculation of these two ILTV strains in specific pathogen free (SPF) chickens, recovered viruses were plaque purified and subjected to the SNP genotyping assay. This assay revealed ILTV recombinants in all co-inoculated chickens. In total 64/87 (74%) of the recovered viruses were recombinants and 23 different recombination patterns were detected, with some of them occurring more frequently than others. The results from this study demonstrate that the TaqMan SNP genotyping assay is a useful tool to study recombination in ILTV and also show that recombination occurs frequently during experimental co-infection with ILTV in SPF chickens. This tool, when used to assess ILTV recombination in the natural host, has the potential to greatly contribute to our understanding of alphaherpesvirus recombination.
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45
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Koelle DM, Norberg P, Fitzgibbon MP, Russell RM, Greninger AL, Huang ML, Stensland L, Jing L, Magaret AS, Diem K, Selke S, Xie H, Celum C, Lingappa JR, Jerome KR, Wald A, Johnston C. Worldwide circulation of HSV-2 × HSV-1 recombinant strains. Sci Rep 2017; 7:44084. [PMID: 28287142 PMCID: PMC5347006 DOI: 10.1038/srep44084] [Citation(s) in RCA: 69] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2016] [Accepted: 02/02/2017] [Indexed: 12/18/2022] Open
Abstract
Homo sapiens harbor two distinct, medically significant species of simplexviruses, herpes simplex virus (HSV)-1 and HSV-2, with estimated divergence 6-8 million years ago (MYA). Unexpectedly, we found that circulating HSV-2 strains can contain HSV-1 DNA segments in three distinct genes. Using over 150 genital swabs from North and South America and Africa, we detected recombinants worldwide. Common, widely distributed gene UL39 genotypes are parsimoniously explained by an initial >457 basepair (bp) HSV-1 × HSV-2 crossover followed by back-recombination to HSV-2. Blocks of >244 and >539 bp of HSV-1 DNA within genes UL29 and UL30, respectively, have reached near fixation, with a minority of strains retaining sequences we posit as ancestral HSV-2. Our data add to previous in vitro and animal work, implying that in vivo cellular co-infection with HSV-1 and HSV-2 yields viable interspecies recombinants in the natural human host.
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Affiliation(s)
- David M. Koelle
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Benaroya Research Institute, Seattle, WA 98102, USA
| | - Peter Norberg
- Department of Infectious Diseases, University of Gothenburg, Guldhedsgatan 10B, 41346, Gothenburg, Sweden
| | | | - Ronnie M. Russell
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Alex L. Greninger
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Meei-Li Huang
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Larry Stensland
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Lichen Jing
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Amalia S. Magaret
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Biostatistics, University of Washington, Seattle, WA 98195, USA
| | - Kurt Diem
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Stacy Selke
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Hong Xie
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
| | - Connie Celum
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Jairam R. Lingappa
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Global Health, University of Washington, Seattle, WA 98195, USA
- Department of Pediatrics, University of Washington, Seattle, WA 98195, USA
| | - Keith R. Jerome
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Anna Wald
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Department of Laboratory Medicine, University of Washington, Seattle, WA 98195, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
- Department of Epidemiology, University of Washington, Seattle, WA 98195, USA
| | - Christine Johnston
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
- Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
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Halling GC, Grose C. Focal herpes zoster encephalitis without a rash: diagnostic confusion between astrogliosis and low-grade glioma. Expert Rev Anti Infect Ther 2016; 14:1109-1111. [PMID: 27748148 DOI: 10.1080/14787210.2016.1248944] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
| | - Charles Grose
- b Virology Laboratory, Children's Hospital , University of Iowa , Iowa City , IA , USA
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Abdelgawad A, Damiani A, Ho SYW, Strauss G, Szentiks CA, East ML, Osterrieder N, Greenwood AD. Zebra Alphaherpesviruses (EHV-1 and EHV-9): Genetic Diversity, Latency and Co-Infections. Viruses 2016; 8:v8090262. [PMID: 27657113 PMCID: PMC5035975 DOI: 10.3390/v8090262] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2016] [Revised: 09/12/2016] [Accepted: 09/14/2016] [Indexed: 12/18/2022] Open
Abstract
Alphaherpesviruses are highly prevalent in equine populations and co-infections with more than one of these viruses’ strains frequently diagnosed. Lytic replication and latency with subsequent reactivation, along with new episodes of disease, can be influenced by genetic diversity generated by spontaneous mutation and recombination. Latency enhances virus survival by providing an epidemiological strategy for long-term maintenance of divergent strains in animal populations. The alphaherpesviruses equine herpesvirus 1 (EHV-1) and 9 (EHV-9) have recently been shown to cross species barriers, including a recombinant EHV-1 observed in fatal infections of a polar bear and Asian rhinoceros. Little is known about the latency and genetic diversity of EHV-1 and EHV-9, especially among zoo and wild equids. Here, we report evidence of limited genetic diversity in EHV-9 in zebras, whereas there is substantial genetic variability in EHV-1. We demonstrate that zebras can be lytically and latently infected with both viruses concurrently. Such a co-occurrence of infection in zebras suggests that even relatively slow-evolving viruses such as equine herpesviruses have the potential to diversify rapidly by recombination. This has potential consequences for the diagnosis of these viruses and their management in wild and captive equid populations.
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Affiliation(s)
- Azza Abdelgawad
- Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Strasse 17, Berlin 10315, Germany.
| | - Armando Damiani
- Institut für Virologie, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, Berlin 14163, Germany.
| | - Simon Y W Ho
- School of Life and Environmental Sciences, University of Sydney, Sydney, NSW 2006, Australia.
| | - Günter Strauss
- Tierpark Berlin-Friedrichsfelde, Am Tierpark 125, Berlin 10307, Germany.
| | - Claudia A Szentiks
- Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Strasse 17, Berlin 10315, Germany.
| | - Marion L East
- Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Strasse 17, Berlin 10315, Germany.
| | - Nikolaus Osterrieder
- Institut für Virologie, Freie Universität Berlin, Robert-von-Ostertag-Str. 7-13, Berlin 14163, Germany.
| | - Alex D Greenwood
- Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Strasse 17, Berlin 10315, Germany.
- Department of Veterinary Medicine, Freie Universität Berlin, Oertzenweg 19, Berlin 14163, Germany.
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48
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Wu H, Padhi A, Xu J, Gong X, Tien P. Evidence for Within-Host Genetic Recombination among the Human Pegiviral Strains in HIV Infected Subjects. PLoS One 2016; 11:e0161880. [PMID: 27560699 PMCID: PMC4999292 DOI: 10.1371/journal.pone.0161880] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2016] [Accepted: 08/12/2016] [Indexed: 12/19/2022] Open
Abstract
The non-pathogenic Human Pegivirus (HPgV, formerly GBV-C/HGV), the most prevalent RNA virus worldwide, is known to be associated with reduced morbidity and mortality in HIV-infected individuals. Although previous studies documented its ubiquity and important role in HIV-infected individuals, little is known about the underlying genetic mechanisms that maintain high genetic diversity of HPgV within the HIV-infected individuals. To assess the within-host genetic diversity of HPgV and forces that maintain such diversity within the co-infected hosts, we performed phylogenetic analyses taking into account 229 HPgV partial E1-E2 clonal sequences representing 15 male and 8 female co-infected HIV patients from Hubei province of central China. Our results revealed the presence of eleven strongly supported clades. While nine clades belonged to genotype 3, two clades belonged to genotype 2. Additionally, four clades that belonged to genotype 3 exhibited inter-clade recombination events. The presence of clonal sequences representing multiple clades within the HIV-infected individual provided the evidence of co-circulation of HPgV strains across the region. Of the 23 patients, six patients (i.e., five males and one female) were detected to have HPgV recombinant sequences. Our results also revealed that while male patients shared the viral strains with other patients, viral strains from the female patients had restricted dispersal. Taken together, the present study revealed that multiple infections with divergent HPgV viral strains may have caused within-host genetic recombination, predominantly in male patients, and therefore, could be the major driver in shaping genetic diversity of HPgV.
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Affiliation(s)
- Haoming Wu
- College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, China
| | - Abinash Padhi
- Department of Animal and Avian Sciences, University of Maryland, College Park, 20742, MD, United States of America
| | - Junqiang Xu
- Hubei Provincial Centers for Disease Control and Prevention, Wuhan 430072, Hubei, China
| | - Xiaoyan Gong
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, Hubei, China
- * E-mail: (PT); (XG)
| | - Po Tien
- College of Life Sciences, Wuhan University, Wuhan 430072, Hubei, China
- Institute of Microbiology, Chinese Academy of Sciences, Beijing 100101, China
- * E-mail: (PT); (XG)
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49
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Jeon JS, Won YH, Kim IK, Ahn JH, Shin OS, Kim JH, Lee CH. Analysis of single nucleotide polymorphism among Varicella-Zoster Virus and identification of vaccine-specific sites. Virology 2016; 496:277-286. [PMID: 27376245 DOI: 10.1016/j.virol.2016.06.017] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2016] [Revised: 06/11/2016] [Accepted: 06/21/2016] [Indexed: 12/30/2022]
Abstract
Varicella-zoster virus (VZV) is a causative agent for chickenpox and zoster. Live attenuated vaccines have been developed based on Oka and MAV/06 strains. In order to understand the molecular mechanisms of attenuation, complete genome sequences of vaccine and wild-type strains were compared and single nucleotide polymorphism (SNP) was analyzed. ORF22 and ORF62 contained the highest number of SNPs. The detailed analysis of the SNPs suggested 24 potential vaccine-specific sites. All the mutational events found in vaccine-specific sites were transitional, and most of them were substitution of AT to GC pair. Interestingly, 18 of the vaccine-specific sites of the vaccine strains appeared to be genetically heterogeneous. The probability of a single genome of vaccine strain to contain all 24 vaccine-type sequences was calculated to be less than 4%. The average codon adaptation index (CAI) value of the vaccine strains was significantly lower than the CAI value of the clinical strains.
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Affiliation(s)
- Jeong Seon Jeon
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea
| | - Youn Hee Won
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea
| | - In Kyo Kim
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea
| | - Jin Hyun Ahn
- Department of Molecular Cell Biology, Sungkyunkwan University School of Medicine, Suwon, South Korea
| | - Ok Sarah Shin
- Department of Biomedical Sciences, College of Medicine, Korea University, Seoul, South Korea
| | - Jung Hwan Kim
- Mogam Biotechnology Research Institute, Yongin, South Korea
| | - Chan Hee Lee
- Department of Microbiology, Chungbuk National University, Cheongju, South Korea.
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Devlin JM, Vaz PK, Coppo MJ, Browning GF. Impacts of poultry vaccination on viruses of wild bird. Curr Opin Virol 2016; 19:23-9. [PMID: 27359320 DOI: 10.1016/j.coviro.2016.06.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2016] [Revised: 05/31/2016] [Accepted: 06/13/2016] [Indexed: 12/11/2022]
Abstract
Spillover of viruses from farmed poultry into wild birds is a relatively new area of study at the livestock-wildlife interface. These transmission events can threaten the health of wild birds. There is growing evidence of transmission of vaccine viruses from poultry to wild birds, including attenuated vaccine strains of Newcastle disease virus and infectious bronchitis virus, and also spread of virulent viruses that may have evolved under the pressure of vaccine use, such as Marek's disease virus. Viral contaminants of poultry vaccines, including reticuloendotheliosis virus, may also be transmitted to wild birds and result in disease. New, vectored vaccines are less likely to directly spread to wild birds but this risk may rise as a result of recombination.
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Affiliation(s)
- Joanne M Devlin
- Asia Pacific Centre for Animal Health, The Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia.
| | - Paola K Vaz
- Asia Pacific Centre for Animal Health, The Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Mauricio Jc Coppo
- Asia Pacific Centre for Animal Health, The Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Glenn F Browning
- Asia Pacific Centre for Animal Health, The Faculty of Veterinary and Agricultural Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
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