1
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Samer C, McWilliam HEG, McSharry BP, Burchfield JG, Stanton RJ, Rossjohn J, Villadangos JA, Abendroth A, Slobedman B. Impaired endocytosis and accumulation in early endosomal compartments defines herpes simplex virus-mediated disruption of the non-classical MHC class I-related molecule MR1. J Biol Chem 2024:107748. [PMID: 39260697 DOI: 10.1016/j.jbc.2024.107748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 08/13/2024] [Accepted: 08/21/2024] [Indexed: 09/13/2024] Open
Abstract
Presentation of metabolites by the Major Histocompatibility Complex Class-I-related protein 1 (MR1) molecule to Mucosal-Associated Invariant T (MAIT) cells is impaired during herpes simplex type 1 (HSV-1) and type 2 (HSV-2) infections. This is surprising given these viruses do not directly synthesise MR1 ligands. We have previously identified several HSV proteins responsible for rapidly downregulating the intracellular pool of immature MR1, effectively inhibiting new surface antigen presentation, while pre-existing ligand-bound mature MR1 is surprisingly upregulated by HSV-1. Using flow cytometry, immunoblotting and high throughput fluorescence microscopy we demonstrate that the endocytosis of surface MR1 is impaired during HSV infection, and that internalised molecules accumulate in EEA1-labelled early endosomes, avoiding degradation. We establish that the short MR1 cytoplasmic tail is not required for HSV-1 mediated downregulation of immature molecules, however it may play a role in the retention of mature molecules on the surface and in early endosomes. We also determine that the HSV-1 US3 protein, the shorter US3.5 kinase and the full-length HSV-2 homolog, all predominantly target mature surface rather than total MR1 levels. We propose that the downregulation of intracellular and cell surface MR1 molecules by US3 and other HSV proteins is an immune-evasive countermeasure to minimise the effect of impaired MR1 endocytosis, which might otherwise render infected cells susceptible to MR1-mediated killing by MAIT cells.
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Affiliation(s)
- Carolyn Samer
- Infection, Immunity and Inflammation, School of Medical Sciences, Faculty of Medicine and Health, and the Charles Perkins Centre, The University of Sydney, NSW, Australia
| | - Hamish E G McWilliam
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia
| | - Brian P McSharry
- Infection, Immunity and Inflammation, School of Medical Sciences, Faculty of Medicine and Health, and the Charles Perkins Centre, The University of Sydney, NSW, Australia; School of Dentistry and Medical Sciences, Faculty of Science and Health, Charles Sturt University, Wagga Wagga, NSW, Australia
| | - James G Burchfield
- Charles Perkins Centre, The University of Sydney, Sydney, NSW, Australia; School of Life and Environmental Sciences, University of Sydney, Sydney, NSW, Australia
| | - Richard J Stanton
- Division of Infection & Immunity, School of Medicine, Cardiff University, Cardiff, Wales
| | - Jamie Rossjohn
- Division of Infection & Immunity, School of Medicine, Cardiff University, Cardiff, Wales; Infection and Immunity Program, Department of Biochemistry and Molecular Biology, Biomedicine Discovery Institute, Monash University, VIC, Australia
| | - Jose A Villadangos
- Department of Microbiology and Immunology, Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, VIC, Australia; Department of Biochemistry and Pharmacology, Bio21 Molecular Science and Biotechnology Institute, The University of Melbourne, Parkville, VIC, Australia
| | - Allison Abendroth
- Infection, Immunity and Inflammation, School of Medical Sciences, Faculty of Medicine and Health, and the Charles Perkins Centre, The University of Sydney, NSW, Australia
| | - Barry Slobedman
- Infection, Immunity and Inflammation, School of Medical Sciences, Faculty of Medicine and Health, and the Charles Perkins Centre, The University of Sydney, NSW, Australia.
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2
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Primate Simplexviruses Differ in Tropism for Macaque Cells. Microorganisms 2022; 11:microorganisms11010026. [PMID: 36677317 PMCID: PMC9864361 DOI: 10.3390/microorganisms11010026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 12/15/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
Primate simplexviruses are closely related neurotropic herpesviruses, which are largely apathogenic in their respective host species. However, cross-species transmission of Macacine alphaherpesvirus 1 (McHV1, also termed herpes B virus) from rhesus macaques to humans can cause fatal encephalomyelitis. In contrast, closely related viruses, such as Cercopithecine alphaherpesvirus 2 (CeHV2, also termed simian agent 8) or Papiine alphaherpesvirus 2 (PaHV2, also termed herpesvirus papio 2), have not been linked to human disease and are believed to be largely apathogenic in humans. Here, we investigated whether McHV1, PaHV2 and CeHV2 differ in their capacity to infect human and non-human primate (NHP) cells. For comparison, we included the human simplexviruses HSV1 and HSV2 in our analyses. All five viruses replicated efficiently in cell lines of human and African green monkey origin, and McHV1 and PaHV2 also showed robust replication in rhesus macaque cell lines. In contrast, the replication of CeHV2 and particularly HSV1 and HSV2 in cell lines of rhesus macaque origin were reduced or inefficient. Similarly, McHV1, but not CeHV2, efficiently infected rhesus macaque brain organoids. These results point towards the previously unappreciated partial resistance of certain rhesus macaque cells to HSV1/HSV2/CeHV2 infection and reveal similarities between the cell tropism of McHV1 and PaHV2 that might be relevant for risk assessment.
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3
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Mozzi A, Cagliani R, Pontremoli C, Forni D, Saulle I, Saresella M, Pozzoli U, Cappelletti G, Vantaggiato C, Clerici M, Biasin M, Sironi M. Simplexviruses successfully adapt to their host by fine-tuning immune responses. Mol Biol Evol 2022; 39:6613336. [PMID: 35731846 PMCID: PMC9250107 DOI: 10.1093/molbev/msac142] [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] [Indexed: 01/10/2023] Open
Abstract
Primate herpes simplex viruses are species-specific and relatively harmless to their natural hosts. However, cross-species transmission is often associated with severe disease, as exemplified by the virulence of macacine herpesvirus 1 (B virus) in humans. We performed a genome-wide scan for signals of adaptation of simplexviruses to their hominin hosts. Among core genes, we found evidence of episodic positive selection in three glycoproteins, with several selected sites located in antigenic determinants. Positively selected noncore genes were found to be involved in different immune-escape mechanisms. The herpes simplex virus (HSV)-1/HSV-2 encoded product (ICP47) of one of these genes is known to down-modulate major histocompatibility complex class I expression. This feature is not shared with B virus, which instead up-regulates Human Leukocyte Antigen (HLA)-G, an immunomodulatory molecule. By in vitro expression of different ICP47 mutants, we functionally characterized the selection signals. Results indicated that the selected sites do not represent the sole determinants of binding to the transporter associated with antigen processing (TAP). Conversely, the amino acid status at these sites was sufficient to determine HLA-G up-regulation. In fact, both HSV-1 and HSV-2 ICP47 induced HLA-G when mutated to recapitulate residues in B virus, whereas the mutated version of B virus ICP47 failed to determine HLA-G expression. These differences might contribute to the severity of B virus infection in humans. Importantly, they indicate that the evolution of ICP47 in HSV-1/HSV-2 led to the loss of an immunosuppressive effect. Thus, related simplexviruses finely tune the balance between immunosuppressive and immunostimulatory pathways to promote successful co-existence with their primate hosts.
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Affiliation(s)
- Alessandra Mozzi
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, 23842 Bosisio Parini, Italy
| | - Rachele Cagliani
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, 23842 Bosisio Parini, Italy
| | - Chiara Pontremoli
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, 23842 Bosisio Parini, Italy
| | - Diego Forni
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, 23842 Bosisio Parini, Italy
| | - Irma Saulle
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, 20157 Milan, Italy.,Department of Physiopathology and Transplantation, University of Milan, 20090 Milan, Italy
| | - Marina Saresella
- Don C. Gnocchi Foundation ONLUS, IRCCS, Laboratory of Molecular Medicine and Biotechnology, 20148, Milan, Italy
| | - Uberto Pozzoli
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, 23842 Bosisio Parini, Italy
| | - Gioia Cappelletti
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, 20157 Milan, Italy
| | - Chiara Vantaggiato
- Scientific Institute, IRCCS E. MEDEA, Laboratory of Molecular Biology, 23842 Bosisio Parini, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, 20090 Milan, Italy.,Don C. Gnocchi Foundation ONLUS, IRCCS, Laboratory of Molecular Medicine and Biotechnology, 20148, Milan, Italy
| | - Mara Biasin
- Department of Biomedical and Clinical Sciences "L. Sacco", University of Milan, 20157 Milan, Italy
| | - Manuela Sironi
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, 23842 Bosisio Parini, Italy
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4
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Neuronal miR-138 Represses HSV-2 Lytic Infection by Regulating Viral and Host Genes with Mechanistic Differences from HSV-1. J Virol 2022; 96:e0034922. [PMID: 35404085 DOI: 10.1128/jvi.00349-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
HSV-1 and HSV-2 are closely related viruses with major differences. Both viruses establish latency in neurons from which they reactivate to cause disease.
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5
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López-Muñoz AD, Rastrojo A, Martín R, Alcamí A. Herpes simplex virus 2 (HSV-2) evolves faster in cell culture than HSV-1 by generating greater genetic diversity. PLoS Pathog 2021; 17:e1009541. [PMID: 34437654 PMCID: PMC8389525 DOI: 10.1371/journal.ppat.1009541] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 07/15/2021] [Indexed: 12/11/2022] Open
Abstract
Herpes simplex virus type 1 and 2 (HSV-1 and HSV-2, respectively) are prevalent human pathogens of clinical relevance that establish long-life latency in the nervous system. They have been considered, along with the Herpesviridae family, to exhibit a low level of genetic diversity during viral replication. However, the high ability shown by these viruses to rapidly evolve under different selective pressures does not correlates with that presumed genetic stability. High-throughput sequencing has revealed that heterogeneous or plaque-purified populations of both serotypes contain a broad range of genetic diversity, in terms of number and frequency of minor genetic variants, both in vivo and in vitro. This is reminiscent of the quasispecies phenomenon traditionally associated with RNA viruses. Here, by plaque-purification of two selected viral clones of each viral subtype, we reduced the high level of genetic variability found in the original viral stocks, to more genetically homogeneous populations. After having deeply characterized the genetic diversity present in the purified viral clones as a high confidence baseline, we examined the generation of de novo genetic diversity under culture conditions. We found that both serotypes gradually increased the number of de novo minor variants, as well as their frequency, in two different cell types after just five and ten passages. Remarkably, HSV-2 populations displayed a much higher raise of nonconservative de novo minor variants than the HSV-1 counterparts. Most of these minor variants exhibited a very low frequency in the population, increasing their frequency over sequential passages. These new appeared minor variants largely impacted the coding diversity of HSV-2, and we found some genes more prone to harbor higher variability. These data show that herpesviruses generate de novo genetic diversity differentially under equal in vitro culture conditions. This might have contributed to the evolutionary divergence of HSV-1 and HSV-2 adapting to different anatomical niche, boosted by selective pressures found at each epithelial and neuronal tissue. Herpesviruses are highly human pathogens that establish latency in neurons of the peripheral nervous system. Colonization of nerve endings is required for herpes simplex virus (HSV) persistence and pathogenesis. HSV-1 global prevalence is much higher than HSV-2, in addition to their preferential tendency to infect the oronasal and genital areas, respectively. How these closely related viruses have been adapting and evolving to replicate and colonize these two different anatomical areas remains unclear. Herpesviruses were presumed to mutate much less than viruses with RNA genomes, due to the higher fidelity of the DNA polymerase and proofreading mechanisms when replicating. However, the worldwide accessibility and development of high-throughput sequencing technologies have revealed the heterogenicity and high diversity present in viral populations clinically isolated. Here we show that HSV-2 mutates much faster than HSV-1, when compared under similar and controlled cell culture conditions. This high mutation rate is translated into an increase in coding diversity, since the great majority of these new mutations lead to nonconservative changes in viral proteins. Understanding how herpesviruses differentially mutate under similar selective pressures is critical to prevent resistance to anti-viral drugs.
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Affiliation(s)
- Alberto Domingo López-Muñoz
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), Madrid, Spain
| | - Alberto Rastrojo
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), Madrid, Spain
| | - Rocío Martín
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), Madrid, Spain
| | - Antonio Alcamí
- Centro de Biología Molecular Severo Ochoa (Consejo Superior de Investigaciones Científicas and Universidad Autónoma de Madrid), Madrid, Spain
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6
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Shohael AM, Moin AT, Chowdhury MAB, Riana SH, Ullah MA, Araf Y, Sarkar B. An Updated Overview of Herpes Simplex Virus-1 Infection: Insights from Origin to Mitigation Measures. ELECTRONIC JOURNAL OF GENERAL MEDICINE 2021. [DOI: 10.29333/ejgm/10869] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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7
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Forni D, Pontremoli C, Clerici M, Pozzoli U, Cagliani R, Sironi M. Recent Out-of-Africa Migration of Human Herpes Simplex Viruses. Mol Biol Evol 2021; 37:1259-1271. [PMID: 31917410 DOI: 10.1093/molbev/msaa001] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Herpes simplex virus types 1 and 2 (HSV-1 and HSV-2) are ubiquitous human pathogens. Both viruses evolved from simplex viruses infecting African primates and they are thus thought to have left Africa during early human migrations. We analyzed the population structure of HSV-1 and HSV-2 circulating strains. Results indicated that HSV-1 populations have limited geographic structure and the most evident clustering by geography is likely due to recent bottlenecks. For HSV-2, the only level of population structure is accounted for by the so-called "worldwide" and "African" lineages. Analysis of ancestry components and nucleotide diversity, however, did not support the view that the worldwide lineage followed early humans during out-of-Africa dispersal. Although phylogeographic analysis confirmed an African origin for both viruses, molecular dating with a method that corrects for the time-dependent rate phenomenon indicated that HSV-1 and HSV-2 migrated from Africa in relatively recent times. In particular, we estimated that the HSV-2 worldwide lineage left the continent in the 18th century, which corresponds to the height of the transatlantic slave trade, possibly explaining the high prevalence of HSV-2 in the Americas (second highest after Africa). The limited geographic clustering of HSV-1 makes it difficult to date its exit from Africa. The split between the basal clade, containing mostly African sequences, and all other strains was dated at ∼5,000 years ago. Our data do not imply that herpes simplex viruses did not infect early humans but show that the worldwide distribution of circulating strains is the result of relatively recent events.
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Affiliation(s)
- Diego Forni
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, Lecco, Italy
| | | | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan, Italy.,IRCCS Fondazione Don Carlo Gnocchi, Milan, Italy
| | - Uberto Pozzoli
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, Lecco, Italy
| | - Rachele Cagliani
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, Lecco, Italy
| | - Manuela Sironi
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, Lecco, Italy
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8
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Wertheim JO, Hostager R, Ryu D, Merkel K, Angedakin S, Arandjelovic M, Ayimisin EA, Babweteera F, Bessone M, Brun-Jeffery KJ, Dieguez P, Eckardt W, Fruth B, Herbinger I, Jones S, Kuehl H, Langergraber KE, Lee K, Madinda NF, Metzger S, Ormsby LJ, Robbins MM, Sommer V, Stoinski T, Wessling EG, Wittig RM, Yuh YG, Leendertz FH, Calvignac-Spencer S. Discovery of Novel Herpes Simplexviruses in Wild Gorillas, Bonobos, and Chimpanzees Supports Zoonotic Origin of HSV-2. Mol Biol Evol 2021; 38:2818-2830. [PMID: 33720357 PMCID: PMC8233514 DOI: 10.1093/molbev/msab072] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Viruses closely related to human pathogens can reveal the origins of human infectious diseases. Human herpes simplexvirus type 1 (HSV-1) and type 2 (HSV-2) are hypothesized to have arisen via host-virus codivergence and cross-species transmission. We report the discovery of novel herpes simplexviruses during a large-scale screening of fecal samples from wild gorillas, bonobos, and chimpanzees. Phylogenetic analysis indicates that, contrary to expectation, simplexviruses from these African apes are all more closely related to HSV-2 than to HSV-1. Molecular clock-based hypothesis testing suggests the divergence between HSV-1 and the African great ape simplexviruses likely represents a codivergence event between humans and gorillas. The simplexviruses infecting African great apes subsequently experienced multiple cross-species transmission events over the past 3 My, the most recent of which occurred between humans and bonobos around 1 Ma. These findings revise our understanding of the origins of human herpes simplexviruses and suggest that HSV-2 is one of the earliest zoonotic pathogens.
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Affiliation(s)
- Joel O Wertheim
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Reilly Hostager
- Department of Medicine, University of California San Diego, San Diego, CA, USA
| | - Diane Ryu
- Viral Evolution, Robert Koch Institute, Berlin, Germany.,Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Kevin Merkel
- Viral Evolution, Robert Koch Institute, Berlin, Germany.,Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Samuel Angedakin
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Mimi Arandjelovic
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | | | - Mattia Bessone
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,School of Biological & Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom
| | | | - Paula Dieguez
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Winnie Eckardt
- Dian Fossey Gorilla Fund International, Atlanta, GA, USA.,Department of Environmental Sciences and Program in Population Biology, Ecology and Evolution, Emory University, Druid Hills, GA, USA
| | - Barbara Fruth
- School of Biological & Environmental Sciences, Liverpool John Moores University, Liverpool, United Kingdom.,Centre for Research and Conservation, Royal Zoological Society of Antwerp, Antwerp, Belgium
| | | | - Sorrel Jones
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Royal Society for the Protection of Birds, Centre for Conservation Science, Cambridge, United Kingdom
| | - Hjalmar Kuehl
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany
| | - Kevin E Langergraber
- School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Institute of Human Origins, Arizona State University, Tempe, AZ, USA
| | - Kevin Lee
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,School of Human Evolution and Social Change, Arizona State University, Tempe, AZ, USA.,Institute of Human Origins, Arizona State University, Tempe, AZ, USA
| | - Nadege F Madinda
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany.,Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Sonja Metzger
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany.,Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Lucy Jayne Ormsby
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Martha M Robbins
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Volker Sommer
- Department of Anthropology, University College London, London, United Kingdom.,Gashaka Primate Project, Serti/Taraba, Nigeria
| | - Tara Stoinski
- Dian Fossey Gorilla Fund International, Atlanta, GA, USA.,Department of Environmental Sciences and Program in Population Biology, Ecology and Evolution, Emory University, Druid Hills, GA, USA
| | - Erin G Wessling
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany.,Human Evolutionary Biology, Harvard University, Cambridge, MA, USA
| | - Roman M Wittig
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Yisa Ginath Yuh
- Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Fabian H Leendertz
- Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Sébastien Calvignac-Spencer
- Viral Evolution, Robert Koch Institute, Berlin, Germany.,Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
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9
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Casto AM, Roychoudhury P, Xie H, Selke S, Perchetti GA, Wofford H, Huang ML, Verjans GMGM, Gottlieb GS, Wald A, Jerome KR, Koelle DM, Johnston C, Greninger AL. Large, Stable, Contemporary Interspecies Recombination Events in Circulating Human Herpes Simplex Viruses. J Infect Dis 2021; 221:1271-1279. [PMID: 31016321 DOI: 10.1093/infdis/jiz199] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Accepted: 04/20/2019] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND The ubiquitous human pathogens, herpes simplex virus (HSV)-1 and HSV-2, are distinct viral species that diverged approximately 6 million years ago. At least 4 small, ancient HSV-1 × HSV-2 interspecies recombination events have affected the HSV-2 genome, with recombinants and nonrecombinants at each locus circulating today. However, it is unknown whether interspecies recombination can affect other loci and whether new recombinants continue to be generated. METHODS Using 255 newly sequenced and 230 existing HSV genome sequences, we comprehensively assessed interspecies recombination in HSV. RESULTS Our findings show that the sizes and locations of interspecies recombination events in HSV-2 are significantly more variable than previously appreciated and that they can impact species-specific T-cell recognition of HSV. CONCLUSIONS We describe 2 large (>5 kb) recombination events, one of which arose in its current host, demonstrating that interspecies recombination continues to occur today. These results raise concerns about the use of live-attenuated HSV-2 vaccines in high HSV-1 prevalence areas.
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Affiliation(s)
- Amanda M Casto
- Departments of Medicine, University of Washington, Seattle
| | | | - Hong Xie
- Laboratory Medicine, University of Washington, Seattle
| | - Stacy Selke
- Departments of Medicine, University of Washington, Seattle
| | | | - Haley Wofford
- Departments of Medicine, University of Washington, Seattle
| | - Meei-Li Huang
- Laboratory Medicine, University of Washington, Seattle
| | - Georges M G M Verjans
- Department of Viroscience, Erasmus MC, Rotterdam, The Netherlands.,Research Center for Emerging Infectious and Zoonoses, University of Veterinary Medicine Hannover, Germany
| | - Geoffrey S Gottlieb
- Departments of Medicine, University of Washington, Seattle.,Global Health, University of Washington, Seattle.,Center for Emerging and Re-Emerging Infectious Diseases, University of Washington, Seattle
| | - Anna Wald
- Departments of Medicine, University of Washington, Seattle
| | - Keith R Jerome
- Laboratory Medicine, University of Washington, Seattle.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
| | - David M Koelle
- Departments of Medicine, University of Washington, Seattle.,Laboratory Medicine, University of Washington, Seattle.,Global Health, University of Washington, Seattle.,Center for Emerging and Re-Emerging Infectious Diseases, University of Washington, Seattle.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington.,Benaroya Research Institute, Seattle, Washington
| | - Christine Johnston
- Departments of Medicine, University of Washington, Seattle.,Vaccine and Infectious Diseases Division, Fred Hutchinson Cancer Research Center, Seattle, Washington
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10
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[B virus]. Uirusu 2021; 71:125-136. [PMID: 37245975 DOI: 10.2222/jsv.71.125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
B virus is a herpes virus that natutaly infects macaque monkeys. It is extremely neuropathogenic when infection occurs in humans. B virus infection has been reported only in laboratory workers and breeders of macaque monkeys in North America and the United Kingdom, and it is therefore recognized as a rare infectious disease. The first cases of B virus disease were reported in Japan in 2019 and in China in 2021, although no cases had been reported since 1997. Although B virus disease has not been reported for more than 20 years, the potential threat has always existed. The viral factors responsible for the strong neuropathogenicity of B virus to humans has not been identified. There are no reports of infection by contact with wild macaque monkeys, but the possibility can not been ruled out. In this paper, we describe its virological properties, findings from B virus disease from patient-reported cases, and the genotype of B virus.
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11
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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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12
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Mody PH, Pathak S, Hanson LK, Spencer JV. Herpes Simplex Virus: A Versatile Tool for Insights Into Evolution, Gene Delivery, and Tumor Immunotherapy. Virology (Auckl) 2020; 11:1178122X20913274. [PMID: 34093008 PMCID: PMC8142529 DOI: 10.1177/1178122x20913274] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 02/19/2020] [Indexed: 12/20/2022] Open
Abstract
Herpesviruses are prevalent throughout the animal kingdom, and they have coexisted and coevolved along with their host species for millions of years. Herpesviruses carry a large (120-230 kb) double-stranded DNA genome surrounded by a protein capsid, a tegument layer consisting of viral and host proteins, and a lipid bilayer envelope with surface glycoproteins. A key characteristic of these viruses is their ability to enter a latent state following primary infection, allowing them to evade the host's immune system and persist permanently. Herpesviruses can reactivate from their dormant state, usually during times of stress or when the host's immune responses are impaired. While herpesviruses can cause complications with severe disease in immune-compromised people, most of the population experiences few ill effects from herpesvirus infections. Indeed, herpes simplex virus 1 (HSV-1) in particular has several features that make it an attractive tool for therapeutic gene delivery. Herpes simplex virus 1 targets and infects specific cell types, such as epithelial cells and neurons. The HSV-1 genome can also accommodate large insertions of up to 14 kb. The HSV-1-based vectors have already achieved success for the oncolytic treatment of melanoma. In addition to serving as a vehicle for therapeutic gene delivery and targeted cell lysis, comparative genomics of herpesviruses HSV-1 and 2 has revealed valuable information about the evolutionary history of both viruses and their hosts. This review focuses on the adaptability of HSV-1 as an instrument for gene delivery and an evolutionary marker. Overall, HSV-1 shows great promise as a tool for treating human disease and studying human migration patterns, disease outbreaks, and evolution.
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Affiliation(s)
- Prapti H Mody
- Department of Biology, Texas Woman’s University, Denton, TX, USA
| | - Sushila Pathak
- Department of Biology, Texas Woman’s University, Denton, TX, USA
| | - Laura K Hanson
- Department of Biology, Texas Woman’s University, Denton, TX, USA
| | - Juliet V Spencer
- Department of Biology, Texas Woman’s University, Denton, TX, USA
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13
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Mozzi A, Forni D, Cagliani R, Clerici M, Pozzoli U, Sironi M. Intrinsically disordered regions are abundant in simplexvirus proteomes and display signatures of positive selection. Virus Evol 2020; 6:veaa028. [PMID: 32411391 PMCID: PMC7211401 DOI: 10.1093/ve/veaa028] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Whereas the majority of herpesviruses co-speciated with their mammalian hosts, human herpes simplex virus 2 (HSV-2, genus Simplexvirus) most likely originated from the cross-species transmission of chimpanzee herpesvirus 1 to an ancestor of modern humans. We exploited the peculiar evolutionary history of HSV-2 to investigate the selective events that drove herpesvirus adaptation to a new host. We show that HSV-2 intrinsically disordered regions (IDRs)-that is, protein domains that do not adopt compact three-dimensional structures-are strongly enriched in positive selection signals. Analysis of viral proteomes indicated that a significantly higher portion of simplexvirus proteins is disordered compared with the proteins of other human herpesviruses. IDR abundance in simplexvirus proteomes was not a consequence of the base composition of their genomes (high G + C content). Conversely, protein function determines the IDR fraction, which is significantly higher in viral proteins that interact with human factors. We also found that the average extent of disorder in herpesvirus proteins tends to parallel that of their human interactors. These data suggest that viruses that interact with fast-evolving, disordered human proteins, in turn, evolve disordered viral interactors poised for innovation. We propose that the high IDR fraction present in simplexvirus proteomes contributes to their wider host range compared with other herpesviruses.
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Affiliation(s)
- Alessandra Mozzi
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, Bosisio Parini 23842, Italy
| | - Diego Forni
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, Bosisio Parini 23842, Italy
| | - Rachele Cagliani
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, Bosisio Parini 23842, Italy
| | - Mario Clerici
- Department of Physiopathology and Transplantation, University of Milan, Milan 20090, Italy.,Don C. Gnocchi Foundation ONLUS, IRCCS, Milan 20148, Italy
| | - Uberto Pozzoli
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, Bosisio Parini 23842, Italy
| | - Manuela Sironi
- Scientific Institute, IRCCS E. MEDEA, Bioinformatics, Bosisio Parini 23842, Italy
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14
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Rahman RU, Liebhoff AM, Bansal V, Fiosins M, Rajput A, Sattar A, Magruder DS, Madan S, Sun T, Gautam A, Heins S, Liwinski T, Bethune J, Trenkwalder C, Fluck J, Mollenhauer B, Bonn S. SEAweb: the small RNA Expression Atlas web application. Nucleic Acids Res 2020; 48:D204-D219. [PMID: 31598718 PMCID: PMC6943056 DOI: 10.1093/nar/gkz869] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2019] [Revised: 09/14/2019] [Accepted: 10/01/2019] [Indexed: 12/12/2022] Open
Abstract
We present the Small RNA Expression Atlas (SEAweb), a web application that allows for the interactive querying, visualization and analysis of known and novel small RNAs across 10 organisms. It contains sRNA and pathogen expression information for over 4200 published samples with standardized search terms and ontologies. In addition, SEAweb allows for the interactive visualization and re-analysis of 879 differential expression and 514 classification comparisons. SEAweb's user model enables sRNA researchers to compare and re-analyze user-specific and published datasets, highlighting common and distinct sRNA expression patterns. We provide evidence for SEAweb's fidelity by (i) generating a set of 591 tissue specific miRNAs across 29 tissues, (ii) finding known and novel bacterial and viral infections across diseases and (iii) determining a Parkinson's disease-specific blood biomarker signature using novel data. We believe that SEAweb's simple semantic search interface, the flexible interactive reports and the user model with rich analysis capabilities will enable researchers to better understand the potential function and diagnostic value of sRNAs or pathogens across tissues, diseases and organisms.
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Affiliation(s)
- Raza-Ur Rahman
- Institute of Medical Systems Biology, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Anna-Maria Liebhoff
- Institute of Medical Systems Biology, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Vikas Bansal
- Institute of Medical Systems Biology, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
- German Center for Neurodegenerative Diseases, 72076 Tübingen, Germany
| | - Maksims Fiosins
- Institute of Medical Systems Biology, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
- German Center for Neurodegenerative Diseases, 72076 Tübingen, Germany
- Genevention GmbH, 37079 Göttingen, Germany
| | - Ashish Rajput
- Institute of Medical Systems Biology, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Abdul Sattar
- Institute of Medical Systems Biology, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Daniel S Magruder
- Institute of Medical Systems Biology, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
- Genevention GmbH, 37079 Göttingen, Germany
| | - Sumit Madan
- Fraunhofer Institute for Algorithms and Scientific Computing, Schloss Birlinghoven, 53757 Sankt Augustin, Germany
- Rheinische Friedrich-Wilhelms-Universität Bonn, 53113 Bonn, Germany
| | - Ting Sun
- Institute of Medical Systems Biology, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
- Department of Neurogenetics, Max Planck Institute of Experimental Medicine, 37075 Göttingen, Germany
| | - Abhivyakti Gautam
- Institute of Medical Systems Biology, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Sven Heins
- Institute of Medical Systems Biology, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Timur Liwinski
- Department of Medicine, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Jörn Bethune
- Institute of Medical Systems Biology, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
| | - Claudia Trenkwalder
- Paracelsus-Elena-Klinik, 34128 Kassel, Germany
- Department of Neurosurgery, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Juliane Fluck
- Fraunhofer Institute for Algorithms and Scientific Computing, Schloss Birlinghoven, 53757 Sankt Augustin, Germany
- Institute of Geodesy and Geoinformation, University of Bonn, 53115 Bonn, Germany
- German National Library of Medicine (ZB MED) - Information Centre for Life Sciences, 53115 Bonn, Germany
| | - Brit Mollenhauer
- Paracelsus-Elena-Klinik, 34128 Kassel, Germany
- Institute of Neurology, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Stefan Bonn
- Institute of Medical Systems Biology, Center for Molecular Neurobiology, University Medical Center Hamburg-Eppendorf, 20251 Hamburg, Germany
- German Center for Neurodegenerative Diseases, 72076 Tübingen, Germany
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15
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Zmasek CM, Knipe DM, Pellett PE, Scheuermann RH. Classification of human Herpesviridae proteins using Domain-architecture Aware Inference of Orthologs (DAIO). Virology 2019; 529:29-42. [PMID: 30660046 PMCID: PMC6502252 DOI: 10.1016/j.virol.2019.01.005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2018] [Revised: 01/04/2019] [Accepted: 01/04/2019] [Indexed: 12/13/2022]
Abstract
We developed a computational approach called Domain-architecture Aware Inference of Orthologs (DAIO) for the analysis of protein orthology by combining phylogenetic and protein domain-architecture information. Using DAIO, we performed a systematic study of the proteomes of all human Herpesviridae species to define Strict Ortholog Groups (SOGs). In addition to assessing the taxonomic distribution for each protein based on sequence similarity, we performed a protein domain-architecture analysis for every protein family and computationally inferred gene duplication events. While many herpesvirus proteins have evolved without any detectable gene duplications or domain rearrangements, numerous herpesvirus protein families do exhibit complex evolutionary histories. Some proteins acquired additional domains (e.g., DNA polymerase), whereas others show a combination of domain acquisition and gene duplication (e.g., betaherpesvirus US22 family), with possible functional implications. This novel classification system of SOGs for human Herpesviridae proteins is available through the Virus Pathogen Resource (ViPR, www.viprbrc.org).
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Affiliation(s)
| | - David M Knipe
- Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA
| | - Philip E Pellett
- Department of Biochemistry, Microbiology & Immunology, Wayne State University School of Medicine, Detroit, MI 48201, USA
| | - Richard H Scheuermann
- J. Craig Venter Institute, La Jolla, CA 92037, USA; Department of Pathology, University of California, San Diego, CA 92093, USA; Division of Vaccine Discovery, La Jolla Institute for Allergy and Immunology, La Jolla, CA 92037, USA.
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16
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Azab W, Dayaram A, Greenwood AD, Osterrieder N. How Host Specific Are Herpesviruses? Lessons from Herpesviruses Infecting Wild and Endangered Mammals. Annu Rev Virol 2018; 5:53-68. [PMID: 30052491 DOI: 10.1146/annurev-virology-092917-043227] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Herpesviruses are ubiquitous and can cause disease in all classes of vertebrates but also in animals of lower taxa, including molluscs. It is generally accepted that herpesviruses are primarily species specific, although a species can be infected by different herpesviruses. Species specificity is thought to result from host-virus coevolutionary processes over the long term. Even with this general concept in mind, investigators have recognized interspecies transmission of several members of the Herpesviridae family, often with fatal outcomes in non-definitive hosts-that is, animals that have no or only a limited role in virus transmission. We here summarize herpesvirus infections in wild mammals that in many cases are endangered, in both natural and captive settings. Some infections result from herpesviruses that are endemic in the species that is primarily affected, and some result from herpesviruses that cause fatal disease after infection of non-definitive hosts. We discuss the challenges of such infections in several endangered species in the absence of efficient immunization or therapeutic options.
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Affiliation(s)
- Walid Azab
- Institut für Virologie, Zentrum für Infektionsmedizin, Freie Universität Berlin, 14163 Berlin, Germany;
| | - Anisha Dayaram
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), 10315 Berlin, Germany;
| | - Alex D Greenwood
- Department of Wildlife Diseases, Leibniz Institute for Zoo and Wildlife Research (IZW), 10315 Berlin, Germany;
| | - Nikolaus Osterrieder
- Institut für Virologie, Zentrum für Infektionsmedizin, Freie Universität Berlin, 14163 Berlin, Germany;
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17
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Molecular evolution of fibropapilloma-associated herpesviruses infecting juvenile green and loggerhead sea turtles. Virology 2018; 521:190-197. [PMID: 29960922 DOI: 10.1016/j.virol.2018.06.012] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 06/21/2018] [Accepted: 06/22/2018] [Indexed: 11/23/2022]
Abstract
Chelonid Alphaherpesvirus 5 (ChHV5) has long been associated with fibropapillomatosis (FP) tumor disease in marine turtles. Presenting primarily in juvenile animals, FP results in fibromas of the skin, connective tissue, and internal organs, which may indirectly affect fitness by obstructing normal turtle processes. ChHV5 is near-universally present in tumorous tissues taken from affected animals, often at very high concentrations. However, there is also considerable asymptomatic carriage amongst healthy marine turtles, suggesting that asymptomatic hosts play an important role in disease ecology. Currently, there is a paucity of studies investigating variation in viral genetics between diseased and asymptomatic hosts, which could potentially explain why only some ChHV5 infections lead to tumor formation. Here, we generated a database containing DNA from over 400 tissue samples taken from green and loggerhead marine turtles, including multiple tissue types, a twenty year time span, and both diseased and asymptomatic animals. We used two molecular detection techniques, quantitative (q)PCR and nested PCR, to characterize the presence and genetic lineage of ChHV5 in each sample. We found that nested PCR across multiple loci out-performed qPCR and is a more powerful technique for determining infection status. Phylogenetic reconstruction of three viral loci from all ChHV5-positive samples indicated widespread panmixia of viral lineages, with samples taken across decades, species, disease states, and tissues all falling within the same evolutionary lineages. Haplotype networks produced similar results in that viral haplotypes were shared across species, tissue types and disease states with no evidence that viral lineages associated significantly with disease dynamics. Additionally, tests of selection on viral gene trees indicated signals of selection dividing major clades, though this selection did not divide sample categories. Based on these data, neither the presence of ChHV5 infection nor neutral genetic divergence between viral lineages infecting a juvenile marine turtle is sufficient to explain the development of FP within an individual.
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18
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Eberle R, Jones-Engel L. Questioning the Extreme Neurovirulence of Monkey B Virus (Macacine alphaherpesvirus 1). Adv Virol 2018; 2018:5248420. [PMID: 29666644 PMCID: PMC5831965 DOI: 10.1155/2018/5248420] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 01/10/2018] [Indexed: 01/20/2023] Open
Abstract
Monkey B virus (Macacine alphaherpesvirus 1; BV) occurs naturally in macaques of the genus Macaca, which includes rhesus and long-tailed (cynomolgus) monkeys that are widely used in biomedical research. BV is closely related to the human herpes simplex viruses (HSV), and BV infections in its natural macaque host are quite similar to HSV infections in humans. Zoonotic BV is extremely rare, having been diagnosed in only a handful of North American facilities with the last documented case occurring in 1998. However, BV is notorious for its neurovirulence since zoonotic infections are serious, usually involving the central nervous system, and are frequently fatal. Little is known about factors underlying the extreme neurovirulence of BV in humans. Here we review what is actually known about the molecular biology of BV and viral factors affecting its neurovirulence. Based on what is known about related herpesviruses, areas for future research that may elucidate mechanisms underlying the neurovirulence of this intriguing virus are also reviewed.
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Affiliation(s)
- R. Eberle
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK 74078, USA
| | - L. Jones-Engel
- Department of Anthropology and Center for Studies in Ecology and Demography, University of Washington, Seattle, WA 98195, USA
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19
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Burrel S, Boutolleau D, Ryu D, Agut H, Merkel K, Leendertz FH, Calvignac-Spencer S. Ancient Recombination Events between Human Herpes Simplex Viruses. Mol Biol Evol 2017; 34:1713-1721. [PMID: 28369565 PMCID: PMC5455963 DOI: 10.1093/molbev/msx113] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Herpes simplex viruses 1 and 2 (HSV-1 and HSV-2) are seen as close relatives but also unambiguously considered as evolutionary independent units. Here, we sequenced the genomes of 18 HSV-2 isolates characterized by divergent UL30 gene sequences to further elucidate the evolutionary history of this virus. Surprisingly, genome-wide recombination analyses showed that all HSV-2 genomes sequenced to date contain HSV-1 fragments. Using phylogenomic analyses, we could also show that two main HSV-2 lineages exist. One lineage is mostly restricted to subSaharan Africa whereas the other has reached a global distribution. Interestingly, only the worldwide lineage is characterized by ancient recombination events with HSV-1. Our findings highlight the complexity of HSV-2 evolution, a virus of putative zoonotic origin which later recombined with its human-adapted relative. They also suggest that coinfections with HSV-1 and 2 may have genomic and potentially functional consequences and should therefore be monitored more closely.
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Affiliation(s)
- Sonia Burrel
- National Reference Centre for Herpesviruses, Paris, France
- AP-HP, University Hospital La Pitié-Salpêtrière – Charles Foix, Virology Department and Sorbonne Universités, UPMC Univ Paris 06, CR7, CIMI, INSERM U1135, Paris, France
| | - David Boutolleau
- National Reference Centre for Herpesviruses, Paris, France
- AP-HP, University Hospital La Pitié-Salpêtrière – Charles Foix, Virology Department and Sorbonne Universités, UPMC Univ Paris 06, CR7, CIMI, INSERM U1135, Paris, France
| | - Diane Ryu
- Robert Koch Institut, Berlin, Germany
| | - Henri Agut
- AP-HP, University Hospital La Pitié-Salpêtrière – Charles Foix, Virology Department and Sorbonne Universités, UPMC Univ Paris 06, CR7, CIMI, INSERM U1135, Paris, France
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20
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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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21
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Sequence of the ateline alphaherpesvirus 1 (HVA1) genome. Arch Virol 2017; 162:1423-1425. [PMID: 28160144 DOI: 10.1007/s00705-017-3249-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 01/10/2017] [Indexed: 10/20/2022]
Abstract
Here, we report the genome sequence of a spider monkey alphaherpesvirus (ateline alphaherpesvirus 1, HVA1) and compare it with that of other primate alphaherpesviruses. The HVA1 genome is 147,346 bp long and contains 67 predicted ORFs. The genetic layout of the HVA1 genome is similar to that of the squirrel monkey alphaherpesvirus (saimirine alphaherpesvirus 1, HVS1) in that it lacks inverted repeat regions flanking the unique long region and homologues of the UL43, UL49.5, US8.5 and US10-12 genes. Unlike HVS1, HVA1 also lacks a homologue of the RL1 (γ34.5) gene and a replication origin near the end of the genome. Consistent with previous phylogenetic analyses, all predicted proteins of HVA1 are most closely related to those of HVS1.
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22
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Abstract
Viruses related to the herpes simplex viruses of humans are present in all nonhuman primate (NHP) species tested and cross species transmission has been documented. The herpesvirus present in macaques, Herpes B virus (BV) rarely causes disease in its natural macaque host. However, when transmitted to a nonnative host, BV has occasionally caused severe and even fatal disease if not treated immediately. Here we present a comprehensive review of the taxonomy, molecular biology, physiology, epidemiology, diagnosis and treatment of BV. We also summarizes what is known about related herpesviruses of other NHP species and the zoonotic potential of these viruses.
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Affiliation(s)
- R Eberle
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Oklahoma, USA
| | - L Jones-Engel
- Department of Anthropology and Center for Studies in Demography and Ecology, University of Washington, Washington, USA
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23
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Houldcroft CJ, Underdown SJ. Neanderthal genomics suggests a pleistocene time frame for the first epidemiologic transition. AMERICAN JOURNAL OF PHYSICAL ANTHROPOLOGY 2016; 160:379-88. [PMID: 27063929 DOI: 10.1002/ajpa.22985] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/14/2015] [Revised: 02/10/2016] [Accepted: 03/03/2016] [Indexed: 12/13/2022]
Abstract
High quality Altai Neanderthal and Denisovan genomes are revealing which regions of archaic hominin DNA have persisted in the modern human genome. A number of these regions are associated with response to infection and immunity, with a suggestion that derived Neanderthal alleles found in modern Europeans and East Asians may be associated with autoimmunity. As such Neanderthal genomes are an independent line of evidence of which infectious diseases Neanderthals were genetically adapted to. Sympathetically, human genome adaptive introgression is an independent line of evidence of which infectious diseases were important for AMH coming in to Eurasia and interacting with Neanderthals. The Neanderthals and Denisovans present interesting cases of hominin hunter-gatherers adapted to a Eurasian rather than African infectious disease package. Independent sources of DNA-based evidence allow a re-evaluation of the first epidemiologic transition and how infectious disease affected Pleistocene hominins. By combining skeletal, archaeological and genetic evidence from modern humans and extinct Eurasian hominins, we question whether the first epidemiologic transition in Eurasia featured a new package of infectious diseases or a change in the impact of existing pathogens. Coupled with pathogen genomics, this approach supports the view that many infectious diseases are pre-Neolithic, and the list continues to expand. The transfer of pathogens between hominin populations, including the expansion of pathogens from Africa, may also have played a role in the extinction of the Neanderthals and offers an important mechanism to understand hominin-hominin interactions well back beyond the current limits for aDNA extraction from fossils alone. Am J Phys Anthropol 160:379-388, 2016. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Charlotte J Houldcroft
- Division of Biological Anthropology, Department of Archaeology & Anthropology, University of Cambridge, Cambridge, CB2 3QG, UK.,Infection, Inflammation and Rheumatology Section, UCL Institute of Child Health, London, WC1N 1EH, UK
| | - Simon J Underdown
- Human Origins and Palaeoenvironmental Research Group (HOPE), Department of Anthropology & Geography, Oxford Brookes University, Oxford, OX3 0BP, UK
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24
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Genome Sequencing and Analysis of Geographically Diverse Clinical Isolates of Herpes Simplex Virus 2. J Virol 2015; 89:8219-32. [PMID: 26018166 DOI: 10.1128/jvi.01303-15] [Citation(s) in RCA: 64] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2015] [Accepted: 05/19/2015] [Indexed: 01/12/2023] Open
Abstract
UNLABELLED Herpes simplex virus 2 (HSV-2), the principal causative agent of recurrent genital herpes, is a highly prevalent viral infection worldwide. Limited information is available on the amount of genomic DNA variation between HSV-2 strains because only two genomes have been determined, the HG52 laboratory strain and the newly sequenced SD90e low-passage-number clinical isolate strain, each from a different geographical area. In this study, we report the nearly complete genome sequences of 34 HSV-2 low-passage-number and laboratory strains, 14 of which were collected in Uganda, 1 in South Africa, 11 in the United States, and 8 in Japan. Our analyses of these genomes demonstrated remarkable sequence conservation, regardless of geographic origin, with the maximum nucleotide divergence between strains being 0.4% across the genome. In contrast, prior studies indicated that HSV-1 genomes exhibit more sequence diversity, as well as geographical clustering. Additionally, unlike HSV-1, little viral recombination between HSV-2 strains could be substantiated. These results are interpreted in light of HSV-2 evolution, epidemiology, and pathogenesis. Finally, the newly generated sequences more closely resemble the low-passage-number SD90e than HG52, supporting the use of the former as the new reference genome of HSV-2. IMPORTANCE Herpes simplex virus 2 (HSV-2) is a causative agent of genital and neonatal herpes. Therefore, knowledge of its DNA genome and genetic variability is central to preventing and treating genital herpes. However, only two full-length HSV-2 genomes have been reported. In this study, we sequenced 34 additional HSV-2 low-passage-number and laboratory viral genomes and initiated analysis of the genetic diversity of HSV-2 strains from around the world. The analysis of these genomes will facilitate research aimed at vaccine development, diagnosis, and the evaluation of clinical manifestations and transmission of HSV-2. This information will also contribute to our understanding of HSV evolution.
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Genomic, phylogenetic, and recombinational characterization of herpes simplex virus 2 strains. J Virol 2015; 89:6427-34. [PMID: 25855744 DOI: 10.1128/jvi.00416-15] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 04/02/2015] [Indexed: 11/20/2022] Open
Abstract
UNLABELLED Herpes simplex virus 2 (HSV-2) is a major global pathogen, infecting 16% of people 15 to 49 years old worldwide and causing recurrent genital ulcers. Little is known about viral factors contributing to virulence, and there are currently only two genomic sequences available. In this study, we determined nearly complete genomic sequences of six additional HSV-2 isolates, using Illumina MiSeq. We report that HSV-2 has a genomic overall mean distance of 0.2355%, which is less than that of HSV-1. There were approximately 100 amino-acid-encoding and indels per genome. Microsatellite mapping found a bias toward intergenic regions in the nonconserved microsatellites and a genic bias in all detected tandem repeats. Extensive recombination between the HSV-2 strains was also strongly implied. This was the first study to analyze multiple HSV-2 sequences, and the data will be valuable in future evolutionary, virulence, and structure-function studies. IMPORTANCE HSV-2 is a significant worldwide pathogen, causing recurrent genital ulcers. Here we present six nearly complete HSV-2 genomic sequences, and, with the addition of two previously sequenced strains, for the first time genomic, phylogenetic, and recombination analysis was performed on multiple HSV-2 genomes. Our results show that microsatellite mapping found a bias toward intergenic regions in the nonconserved microsatellites and a genic bias in all detected tandem repeats and confirm that chimpanzee herpesvirus 1 (ChHV-1) is a separate species and that each of the HSV-2 strains is a genomic mosaic.
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Wertheim JO, Smith MD, Smith DM, Scheffler K, Kosakovsky Pond SL. Evolutionary origins of human herpes simplex viruses 1 and 2. Mol Biol Evol 2014; 31:2356-64. [PMID: 24916030 PMCID: PMC4137711 DOI: 10.1093/molbev/msu185] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Herpesviruses have been infecting and codiverging with their vertebrate hosts for hundreds of millions of years. The primate simplex viruses exemplify this pattern of virus-host codivergence, at a minimum, as far back as the most recent common ancestor of New World monkeys, Old World monkeys, and apes. Humans are the only primate species known to be infected with two distinct herpes simplex viruses: HSV-1 and HSV-2. Human herpes simplex viruses are ubiquitous, with over two-thirds of the human population infected by at least one virus. Here, we investigated whether the additional human simplex virus is the result of ancient viral lineage duplication or cross-species transmission. We found that standard phylogenetic models of nucleotide substitution are inadequate for distinguishing among these competing hypotheses; the extent of synonymous substitutions causes a substantial underestimation of the lengths of some of the branches in the phylogeny, consistent with observations in other viruses (e.g., avian influenza, Ebola, and coronaviruses). To more accurately estimate ancient viral divergence times, we applied a branch-site random effects likelihood model of molecular evolution that allows the strength of natural selection to vary across both the viral phylogeny and the gene alignment. This selection-informed model favored a scenario in which HSV-1 is the result of ancient codivergence and HSV-2 arose from a cross-species transmission event from the ancestor of modern chimpanzees to an extinct Homo precursor of modern humans, around 1.6 Ma. These results provide a new framework for understanding human herpes simplex virus evolution and demonstrate the importance of using selection-informed models of sequence evolution when investigating viral origin hypotheses.
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Affiliation(s)
| | - Martin D Smith
- Bioinformatics and Systems Biology Graduate Program, University of California, San Diego
| | - Davey M Smith
- Department of Medicine, University of California, San DiegoVeterans Affairs San Diego Healthcare System, San Diego, CA
| | - Konrad Scheffler
- Department of Medicine, University of California, San DiegoDepartment of Mathematical Sciences, Stellenbosch University, Stellenbosch, South Africa
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Ohsawa K, Black D, Ohsawa M, Eberle R. Genome sequence of a pathogenic isolate of monkey B virus (species Macacine herpesvirus 1). Arch Virol 2014; 159:2819-21. [PMID: 24903602 DOI: 10.1007/s00705-014-2130-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2014] [Accepted: 05/22/2014] [Indexed: 11/28/2022]
Abstract
The only genome sequence for monkey B virus (BV; species Macacine herpesvirus 1) is that of an attenuated vaccine strain originally isolated from a rhesus monkey (BVrh). Here we report the genome sequence of a virulent BV strain isolated from a cynomolgus macaque (BVcy). The overall genome organization is the same, although sequence differences exist. The greatest sequence divergence is located in non-coding areas of the long and short repeat regions. Like BVrh, BVcy has duplicated Ori elements and lacks an ORF corresponding to the γ34.5 gene of herpes simplex virus. Nine of ten miRNAs and the majority of ORFs are conserved between BVrh and BVcy. The most divergent genes are several membrane-associated proteins and those encoding immediate early proteins.
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Affiliation(s)
- Kazutaka Ohsawa
- Division of Comparative Medicine, Center for Frontier Life Sciences, Nagasaki University, Nagasaki, Japan
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Black D, Ohsawa K, Tyler S, Maxwell L, Eberle R. A single viral gene determines lethal cross-species neurovirulence of baboon herpesvirus HVP2. Virology 2014; 452-453:86-94. [PMID: 24606686 DOI: 10.1016/j.virol.2013.12.038] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 11/25/2013] [Accepted: 12/27/2013] [Indexed: 11/24/2022]
Abstract
Alpha-herpesviruses can produce more severe infections in non-natural host species than in their natural host. Isolates of the baboon alpha-herpesvirus Papiine herpesvirus 2 (HVP2) are either very neurovirulent in mice (subtype nv) or non-virulent (subtype ap), but no such difference is evident in the natural baboon host. Comparative genome sequencing was used to identify subtype-specific sequence differences (SSDs) between HVP2nv and HVP2ap isolates. Some genes were identified that despite exhibiting sequence variation among isolates did not have any SSDs, while other genes had comparatively high levels of SSDs. Construction of genomic recombinants between HVP2nv and HVP2ap isolates mapped the mouse neurovirulence determinant to within three genes. Construction of gene-specific recombinants demonstrated that the UL39 ORF is responsible for determining the lethal neurovirulence phenotype of HVP2 in mice. These results demonstrate that differences in a single viral gene can determine the severity of herpesvirus infection in a non-natural host species.
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Affiliation(s)
- Darla Black
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, United States
| | - Kazutaka Ohsawa
- Center for Frontier Life Sciences, Division of Comparative Medicine, Nagasaki University, Nagasaki, Japan
| | - Shaun Tyler
- National Microbiology Laboratory, Public Health Agency of Canada, Canadian Science Centre for Human and Animal Health, Winnipeg, Canada R3E 3P6
| | - Lara Maxwell
- Department of Physiological Sciences, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, United States
| | - R Eberle
- Department of Veterinary Pathobiology, Center for Veterinary Health Sciences, Oklahoma State University, Stillwater, OK, United States.
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