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Shitrit A, Nisnevich V, Rozenshtein N, Kobo H, Phan HV, Tay S, Szpara M, Weitzman MD, Drayman N, Kobiler O. Shared sequence characteristics identified in non-canonical rearrangements of HSV-1 genomes. J Virol 2023; 97:e0095523. [PMID: 37991369 PMCID: PMC10734421 DOI: 10.1128/jvi.00955-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 10/26/2023] [Indexed: 11/23/2023] Open
Abstract
IMPORTANCE Mutations and genetic rearrangements are the primary driving forces of evolution. Viruses provide valuable model systems for investigating these mechanisms due to their rapid evolutionary rates and vast genetic variability. To investigate genetic rearrangements in the double-stranded DNA genome of herpes simplex virus type 1, the viral population was serially passaged in various cell types. The serial passaging led to formation of defective genomes, resulted from cell-specific non-canonical rearrangements (NCRs). Interestingly, we discovered shared sequence characteristics underlying the formation of these NCRs across all cell types. Moreover, most NCRs identified in clinical samples shared these characteristics. Based on our findings, we propose a model elucidating the formation of NCRs during viral replication within the nucleus of eukaryotic cells.
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Affiliation(s)
- Alina Shitrit
- Department of Clinical Microbiology and Immunology, School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Valerya Nisnevich
- Department of Clinical Microbiology and Immunology, School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Nofar Rozenshtein
- Department of Clinical Microbiology and Immunology, School of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Hila Kobo
- Genomic Research Unit, Faculty of Life Science, Tel Aviv University, Tel Aviv, Israel
| | - Hoang Van Phan
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, USA
| | - Savaş Tay
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, Illinois, USA
- Institute for Genomics and Systems Biology, University of Chicago, Chicago, Illinois, USA
| | - Moriah Szpara
- Department of Biochemistry and Molecular Biology, Department of Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Matthew D. Weitzman
- Division of Protective Immunity, The Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, Pennsylvania, USA
| | - Nir Drayman
- Department of Molecular Biology and Biochemistry, School of Biological Sciences, University of California, Irvine, California, USA
- Center for Virus Research, University of California, Irvine, California, USA
| | - Oren Kobiler
- Department of Clinical Microbiology and Immunology, School of Medicine, Tel Aviv University, Tel Aviv, Israel
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2
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Hayes CK, Villota CK, McEnany FB, Cerón S, Awasthi S, Szpara ML, Friedman HM, Leib DA, Longnecker R, Weitzman MD, Akhtar LN. Herpes Simplex Virus-2 Variation Contributes to Neurovirulence During Neonatal Infection. J Infect Dis 2022; 226:1499-1509. [PMID: 35451492 PMCID: PMC10205897 DOI: 10.1093/infdis/jiac151] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/20/2022] [Indexed: 11/14/2022] Open
Abstract
Herpes simplex virus (HSV) infection of the neonatal brain causes severe encephalitis and permanent neurologic deficits. However, infants infected with HSV at the time of birth follow varied clinical courses, with approximately half of infants experiencing only external infection of the skin rather than invasive neurologic disease. Understanding the cause of these divergent outcomes is essential to developing neuroprotective strategies. To directly assess the contribution of viral variation to neurovirulence, independent of human host factors, we evaluated clinical HSV isolates from neonates with different neurologic outcomes in neurologically relevant in vitro and in vivo models. We found that isolates taken from neonates with encephalitis are more neurovirulent in human neuronal culture and mouse models of HSV encephalitis, as compared to isolates collected from neonates with skin-limited disease. These findings suggest that inherent characteristics of the infecting HSV strain contribute to disease outcome following neonatal infection.
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Affiliation(s)
- Cooper K Hayes
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Christopher K Villota
- Department of Pediatrics, Division of Infectious Diseases, Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
| | - Fiona B McEnany
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Stacey Cerón
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Sita Awasthi
- Department of Medicine, Division of Infectious Diseases, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Moriah L Szpara
- Departments of Biology, Biochemistry, and Molecular Biology, Center for Infectious Disease Dynamics and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Harvey M Friedman
- Department of Medicine, Division of Infectious Diseases, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - David A Leib
- Department of Microbiology and Immunology, Geisel School of Medicine at Dartmouth, Lebanon, New Hampshire, USA
| | - Richard Longnecker
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Matthew D Weitzman
- Department of Pathology and Laboratory Medicine, Division of Protective Immunity, Children’s Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
- Department of Pathology and Laboratory Medicine, University of Pennsylvania Perelman School of Medicine, Philadelphia, Pennsylvania, USA
| | - Lisa N Akhtar
- Department of Pediatrics, Division of Infectious Diseases, Ann and Robert H. Lurie Children’s Hospital of Chicago, Chicago, Illinois, USA
- Department of Pediatrics, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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3
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Dweikat SN, Renner DW, Bowen CD, Szpara ML. Multi-phenotype analysis for enhanced classification of 11 herpes simplex virus 1 strains. J Gen Virol 2022; 103:001780. [PMID: 36264606 PMCID: PMC10019087 DOI: 10.1099/jgv.0.001780] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Herpes simplex virus 1 (HSV1) is best known for causing oral lesions and mild clinical symptoms, but it can produce a significant range of disease severities and rates of reactivation. To better understand this phenotypic variation, we characterized 11 HSV1 strains that were isolated from individuals with diverse infection outcomes. We provide new data on genomic and in vitro plaque phenotype analysis for these isolates and compare these data to previously reported quantitation of the disease phenotype of each strain in a murine animal model. We show that integration of these three types of data permitted clustering of these HSV1 strains into four groups that were not distinguishable by any single dataset alone, highlighting the benefits of combinatorial multi-parameter phenotyping. Two strains (group 1) produced a partially or largely syncytial plaque phenotype and attenuated disease phenotypes in mice. Three strains of intermediate plaque size, causing severe disease in mice, were genetically clustered to a second group (group 2). Six strains with the smallest average plaque sizes were separated into two subgroups (groups 3 and 4) based on their different genetic clustering and disease severity in mice. Comparative genomics and network graph analysis suggested a separation of HSV1 isolates with attenuated vs. virulent phenotypes. These observations imply that virulence phenotypes of these strains may be traceable to genetic variation within the HSV1 population.
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Affiliation(s)
- Sarah N Dweikat
- Department of Biology, University Park, USA.,Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, USA
| | - Daniel W Renner
- Department of Biology, University Park, USA.,Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, USA
| | - Christopher D Bowen
- Department of Biology, University Park, USA.,Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, USA
| | - Moriah L Szpara
- Department of Biology, University Park, USA.,Center for Infectious Disease Dynamics, Huck Institutes of the Life Sciences, USA.,Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, USA
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4
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Rathbun MM, Shipley MM, Bowen CD, Selke S, Wald A, Johnston C, Szpara ML. Comparison of herpes simplex virus 1 genomic diversity between adult sexual transmission partners with genital infection. PLoS Pathog 2022; 18:e1010437. [PMID: 35587470 PMCID: PMC9119503 DOI: 10.1371/journal.ppat.1010437] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 03/11/2022] [Indexed: 01/15/2023] Open
Abstract
Herpes simplex virus (HSV) causes chronic infection in the human host, characterized by self-limited episodes of mucosal shedding and lesional disease, with latent infection of neuronal ganglia. The epidemiology of genital herpes has undergone a significant transformation over the past two decades, with the emergence of HSV-1 as a leading cause of first-episode genital herpes in many countries. Though dsDNA viruses are not expected to mutate quickly, it is not yet known to what degree the HSV-1 viral population in a natural host adapts over time, or how often viral population variants are transmitted between hosts. This study provides a comparative genomics analysis for 33 temporally-sampled oral and genital HSV-1 genomes derived from five adult sexual transmission pairs. We found that transmission pairs harbored consensus-level viral genomes with near-complete conservation of nucleotide identity. Examination of within-host minor variants in the viral population revealed both shared and unique patterns of genetic diversity between partners, and between anatomical niches. Additionally, genetic drift was detected from spatiotemporally separated samples in as little as three days. These data expand our prior understanding of the complex interaction between HSV-1 genomics and population dynamics after transmission to new infected persons.
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Affiliation(s)
- Molly M. Rathbun
- Department of Biochemistry and Molecular Biology, Department of Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Mackenzie M. Shipley
- Department of Biochemistry and Molecular Biology, Department of Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Christopher D. Bowen
- Department of Biochemistry and Molecular Biology, Department of Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
| | - Stacy Selke
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States of America
| | - Anna Wald
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States of America
- Department of Epidemiology, University of Washington, Seattle, Washington, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Christine Johnston
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, United States of America
- Department of Medicine, University of Washington, Seattle, Washington, United States of America
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle, Washington, United States of America
| | - Moriah L. Szpara
- Department of Biochemistry and Molecular Biology, Department of Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, Pennsylvania, United States of America
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5
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Hadi AM, Mohammed Al-Alwany SH, Al-Khafaji ZA, Sharaf M, Mofed D, Khan TU. Molecular diagnosis of Herpes virus type 1 by glycoprotein receptor primers. GENE REPORTS 2022. [DOI: 10.1016/j.genrep.2021.101479] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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Price NB, Wood KE. Distinguishing Features Common to Dual Fatal Herpes Simplex Virus Infections That Occur in Both a Pregnant Woman and Her Newborn Infant. Viruses 2021; 13:v13122542. [PMID: 34960811 PMCID: PMC8705528 DOI: 10.3390/v13122542] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2021] [Revised: 12/14/2021] [Accepted: 12/16/2021] [Indexed: 01/14/2023] Open
Abstract
Deaths from herpes simplex virus type 1 (HSV-1) and herpes simplex virus type 2 (HSV-2) are rare. A major exception is perinatally acquired HSV-1 or HSV-2 infection where the neonatal death rate is substantial. Fatal HSV infection also occurs occasionally in pregnant women. The goal of this review is to enumerate the reports that describe dual deaths of both a pregnant woman and her newborn from a herpesvirus infection. A total of 15 reports were found in the medical literature, of which five described pregnant women with HSV encephalitis and 10 described women with disseminated HSV infection. When the virus was typed, most cases of dual mother/newborn deaths were caused by HSV-2. Of interest, in two situations caused by HSV-1, the pregnant woman probably acquired her primary HSV-1 infection from one of her children and not by sexual transmission. Complete genomic sequencing was performed on one set of HSV-1 isolates collected from mother (blood) and newborn (blood and skin). The mother's strain and the newborn's skin strain were 98.9% identical. When the newborn's two strains were compared, they were 97.4% identical. Only one mother was tested by the HerpeSelect IgG antibody kit. During the nine days of her undiagnosed disseminated infection preceding her death, her serology was negative. In summary, although dual mother/newborn deaths from HSV infection are rare, they continue to be reported as recently as 2017.
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Affiliation(s)
- Nathan B. Price
- Division of Infectious Diseases, Department of Pediatrics, University of Arizona, Tucson, AZ 85719, USA
- Correspondence:
| | - Kelly E. Wood
- Newborn Nursery Service and Hospitalist Service, Division of General Pediatrics and Adolescent Medicine, Stead Family Department of Pediatrics, University of Iowa, Iowa, IA 52242, USA;
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Abstract
Herpes simplex viruses (HSV) cause chronic infection in humans that are characterized by periodic episodes of mucosal shedding and ulcerative disease. HSV causes millions of infections world-wide, with lifelong bouts of viral reactivation from latency in neuronal ganglia. Infected individuals experience different levels of disease severity and frequency of reactivation. There are two distantly related HSV species, with HSV-1 infections historically found most often in the oral niche and HSV-2 infections in the genital niche. Over the last two decades, HSV-1 has emerged as the leading cause of first-episode genital herpes in multiple countries. While HSV-1 has the highest level of genetic diversity among human alpha-herpesviruses, it is not yet known how quickly the HSV-1 viral population in a human host adapts over time, or if there are population bottlenecks associated with viral reactivation and/or transmission. It is also unknown how the ecological environments in which HSV infections occur influence their evolutionary trajectory, or that of co-occurring viruses and microbes. In this review, we explore how HSV accrues genetic diversity within each new infection, and yet maintains its ability to successfully infect most of the human population. A holistic examination of the ecological context of natural human infections can expand our awareness of how HSV adapts as it moves within and between human hosts, and reveal the complexity of these lifelong human-virus interactions. These insights may in turn suggest new areas of exploration for other chronic pathogens that successfully evolve and persist among their hosts.
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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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9
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Lassalle F, Beale MA, Bharucha T, Williams CA, Williams RJ, Cudini J, Goldstein R, Haque T, Depledge DP, Breuer J. Whole genome sequencing of Herpes Simplex Virus 1 directly from human cerebrospinal fluid reveals selective constraints in neurotropic viruses. Virus Evol 2020; 6:veaa012. [PMID: 32099667 PMCID: PMC7031915 DOI: 10.1093/ve/veaa012] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Herpes Simplex Virus type 1 (HSV-1) chronically infects over 70 per cent of the global population. Clinical manifestations are largely restricted to recurrent epidermal vesicles. However, HSV-1 also leads to encephalitis, the infection of the brain parenchyma, with high associated rates of mortality and morbidity. In this study, we performed target enrichment followed by direct sequencing of HSV-1 genomes, using target enrichment methods on the cerebrospinal fluid (CSF) of clinical encephalitis patients and from skin swabs of epidermal vesicles on non-encephalopathic patients. Phylogenetic analysis revealed high inter-host diversity and little population structure. In contrast, samples from different lesions in the same patient clustered with similar patterns of allelic variants. Comparison of consensus genome sequences shows HSV-1 has been freely recombining, except for distinct islands of linkage disequilibrium (LD). This suggests functional constraints prevent recombination between certain genes, notably those encoding pairs of interacting proteins. Distinct LD patterns characterised subsets of viruses recovered from CSF and skin lesions, which may reflect different evolutionary constraints in different body compartments. Functions of genes under differential constraint related to immunity or tropism and provide new hypotheses on tissue-specific mechanisms of viral infection and latency.
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Affiliation(s)
- Florent Lassalle
- Department of Infectious Disease Epidemiology, Imperial College London, St-Mary's Hospital campus, Praed Street, London W2 1NY, UK
- MRC Centre for Global Infectious Disease Analysis, Imperial College London, St-Mary's Hospital campus, Praed Street, London W2 1NY, UK
| | - Mathew A Beale
- Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Saffron Walden CB10 1SA, UK
| | - Tehmina Bharucha
- Department of Virology, Royal Free Hospital, 10 Pond Street, Hampstead, London NW3 2PS, UK
| | - Charlotte A Williams
- Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK
| | - Rachel J Williams
- Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK
| | - Juliana Cudini
- Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK
- Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Saffron Walden CB10 1SA, UK
| | - Richard Goldstein
- Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK
| | - Tanzina Haque
- Department of Virology, Royal Free Hospital, 10 Pond Street, Hampstead, London NW3 2PS, UK
| | - Daniel P Depledge
- Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK
| | - Judith Breuer
- Division of Infection and Immunity, University College London, Gower Street, London WC1E 6BT, UK
- Great Ormond Street Hospital for Children NHS Foundation Trust, Great Ormond Street, London WC1N 3JH
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Akhtar LN, Szpara ML. Viral genetic diversity and its potential contributions to the development and progression of neonatal herpes simplex virus (HSV) disease. CURRENT CLINICAL MICROBIOLOGY REPORTS 2019; 6:249-256. [PMID: 32944492 PMCID: PMC7491914 DOI: 10.1007/s40588-019-00131-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
PURPOSE OF REVIEW Neonatal infection by herpes simplex virus (HSV) 1 or 2 presents a devastating burden to new parents, due to the unpredictability of severe clinical outcomes, as well as the potential for lifelong reactivation. While just under half of neonatal HSV infections have mild clinical impacts akin to those observed in adults, the other half experience viral spread throughout the body (disseminated infection) and/or the brain (central nervous system infection). SUMMARY Here we summarize current data on clinical diagnostic measures, antiviral therapy, and known factors of human host biology that contribute to the distinct neonatal outcomes of HSV infection. RECENT FINDINGS We then explore recent new data on how viral genetic diversity between infections may impact clinical outcomes. Further research will be critical to build upon these early findings and to provide statistical power to our ability to discern and/or predict the potential clinical path of a given neonatal infection.
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Affiliation(s)
- Lisa N. Akhtar
- Department of Pediatrics, Division of Infectious Diseases, Children’s Hospital of Philadelphia, and University of Pennsylvania Perelman School of Medicine, Philadelphia, PA
| | - Moriah L. Szpara
- Department of Biochemistry and Molecular Biology, Center for Infectious Disease Dynamics, and the Huck Institutes of the Life Sciences, Pennsylvania State University, University Park, PA
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