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Kumar A, Dutt M, Dehury B, Martinez GS, Singh KP, Kelvin DJ. Formulation of next-generation polyvalent vaccine candidates against three important poxviruses by targeting DNA-dependent RNA polymerase using an integrated immunoinformatics and molecular modeling approach. J Infect Public Health 2024; 17:102470. [PMID: 38865776 DOI: 10.1016/j.jiph.2024.102470] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Revised: 05/27/2024] [Accepted: 06/02/2024] [Indexed: 06/14/2024] Open
Abstract
BACKGROUND Poxviruses comprise a group of large double-stranded DNA viruses and are known to cause diseases in humans, livestock animals, and other animal species. The Mpox virus (MPXV; formerly Monkeypox), variola virus (VARV), and volepox virus (VPXV) are among the prevalent poxviruses of the Orthopoxviridae genera. The ongoing Mpox infectious disease pandemic caused by the Mpox virus has had a major impact on public health across the globe. To date, only limited repurposed antivirals and vaccines are available for the effective treatment of Mpox and other poxviruses that cause contagious diseases. METHODS The present study was conducted with the primary goal of formulating multi-epitope vaccines against three evolutionary closed poxviruses i.e., MPXV, VARV, and VPXV using an integrated immunoinformatics and molecular modeling approach. DNA-dependent RNA polymerase (DdRp), a potential vaccine target of poxviruses, has been used to determine immunodominant B and T-cell epitopes followed by interactions analysis with Toll-like receptor 2 at the atomic level. RESULTS Three multi-epitope vaccine constructs, namely DdRp_MPXV (V1), DdRp_VARV (V2), and DdRp_VPXV (V3) were designed. These vaccine constructs were found to be antigenic, non-allergenic, non-toxic, and soluble with desired physicochemical properties. Protein-protein docking and interaction profiling analysis depicts a strong binding pattern between the targeted immune receptor TLR2 and the structural models of the designed vaccine constructs, and manifested a number of biochemical bonds (hydrogen bonds, salt bridges, and non-bonded contacts). State-of-the-art all-atoms molecular dynamics simulations revealed highly stable interactions of vaccine constructs with TLR2 at the atomic level throughout the simulations on 300 nanoseconds. Additionally, the outcome of the immune simulation analysis suggested that designed vaccines have the potential to induce protective immunity against targeted poxviruses. CONCLUSIONS Taken together, formulated next-generation polyvalent vaccines were found to have good efficacy against closely related poxviruses (MPXV, VARV, and VPXV) as demonstrated by our extensive immunoinformatics and molecular modeling evaluations; however, further experimental investigations are still needed.
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Affiliation(s)
- Anuj Kumar
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Canada; Department of Pediatrics, IWK Health Center, Canadian Centre for Vaccinology CCfV, Halifax, Canada; Laboratory of Immunity, Shantou University Medical College, Shantou, China; BioForge Canada Limited, Halifax, Canada
| | - Mansi Dutt
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Canada; Department of Pediatrics, IWK Health Center, Canadian Centre for Vaccinology CCfV, Halifax, Canada; Laboratory of Immunity, Shantou University Medical College, Shantou, China; BioForge Canada Limited, Halifax, Canada
| | - Budheswar Dehury
- Department of Bioinformatics, Manipal School of Life Sciences, Manipal Academy of Higher Education, Manipal 576104, India
| | - Gustavo Sganzerla Martinez
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Canada; Department of Pediatrics, IWK Health Center, Canadian Centre for Vaccinology CCfV, Halifax, Canada; Laboratory of Immunity, Shantou University Medical College, Shantou, China; BioForge Canada Limited, Halifax, Canada
| | - Krishna Pal Singh
- Mahatma Jyotiba Phule Rohilkhand University, Bareilly, Uttar Pradesh, India
| | - David J Kelvin
- Department of Microbiology and Immunology, Faculty of Medicine, Dalhousie University, Halifax, Canada; Department of Pediatrics, IWK Health Center, Canadian Centre for Vaccinology CCfV, Halifax, Canada; Laboratory of Immunity, Shantou University Medical College, Shantou, China; BioForge Canada Limited, Halifax, Canada.
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Li Z, Sinha A, Zhang Y, Tanner N, Cheng HT, Premsrirut P, Carlow CKS. Extraction-free LAMP assays for generic detection of Old World Orthopoxviruses and specific detection of Mpox virus. Sci Rep 2023; 13:21093. [PMID: 38036581 PMCID: PMC10689478 DOI: 10.1038/s41598-023-48391-z] [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: 07/21/2023] [Accepted: 11/26/2023] [Indexed: 12/02/2023] Open
Abstract
Mpox is a neglected zoonotic disease endemic in West and Central Africa. The Mpox outbreak with more than 90,000 cases worldwide since 2022 generated great concern about future outbreaks and highlighted the need for a simple and rapid diagnostic test. The Mpox virus, MPV, is a member of the Orthopoxvirus (OPV) genus that also contains other pathogenic viruses including variola virus, vaccinia virus, camelpox virus, and cowpox virus. Phylogenomic analysis of 200 OPV genomes identified 10 distinct phylogroups with the New World OPVs placed on a very long branch distant from the Old World OPVs. Isolates derived from infected humans were found to be distributed across multiple phylogroups interspersed with isolates from animal sources, indicating the zoonotic potential of these viruses. In this study, we developed a simple and sensitive colorimetric LAMP assay for generic detection of Old World OPVs. We also developed an MPV-specific probe that differentiates MPV from other OPVs in the N1R LAMP assay. In addition, we described an extraction-free protocol for use directly with swab eluates in LAMP assays, thereby eliminating the time and resources needed to extract DNA from the sample. Our direct LAMP assays are well-suited for low-resource settings and provide a valuable tool for rapid and scalable diagnosis and surveillance of OPVs and MPV.
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Affiliation(s)
- Zhiru Li
- Molecular Genetics and Genomics Division, New England Biolabs, Ipswich, MA, 01938, USA.
| | - Amit Sinha
- Molecular Genetics and Genomics Division, New England Biolabs, Ipswich, MA, 01938, USA
| | - Yinhua Zhang
- Molecular Genetics and Genomics Division, New England Biolabs, Ipswich, MA, 01938, USA
| | - Nathan Tanner
- Molecular Genetics and Genomics Division, New England Biolabs, Ipswich, MA, 01938, USA
| | | | | | - Clotilde K S Carlow
- Molecular Genetics and Genomics Division, New England Biolabs, Ipswich, MA, 01938, USA
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3
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Genomic Sequencing and Phylogenomics of Cowpox Virus. Viruses 2022; 14:v14102134. [PMID: 36298689 PMCID: PMC9611595 DOI: 10.3390/v14102134] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2022] [Revised: 09/16/2022] [Accepted: 09/24/2022] [Indexed: 11/30/2022] Open
Abstract
Cowpox virus (CPXV; genus Orthopoxvirus; family Poxviridae) is the causative agent of cowpox, a self-limiting zoonotic infection. CPXV is endemic in Eurasia, and human CPXV infections are associated with exposure to infected animals. In the Fennoscandian region, five CPXVs isolated from cats and humans were collected and used in this study. We report the complete sequence of their genomes, which ranged in size from 220–222 kbp, containing between 215 and 219 open reading frames. The phylogenetic analysis of 87 orthopoxvirus strains, including the Fennoscandian CPXV isolates, confirmed the division of CPXV strains into at least five distinct major clusters (CPXV-like 1, CPXV-like 2, VACV-like, VARV-like and ECTV-Abatino-like) and can be further divided into eighteen sub-species based on the genetic and patristic distances. Bayesian time-scaled evolutionary history of CPXV was reconstructed employing concatenated 62 non-recombinant conserved genes of 55 CPXV. The CPXV evolution rate was calculated to be 1.65 × 10−5 substitution/site/year. Our findings confirmed that CPXV is not a single species but a polyphyletic assemblage of several species and thus, a reclassification is warranted.
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Diaz-Cánova D, Moens UL, Brinkmann A, Nitsche A, Okeke MI. Genomic Sequencing and Analysis of a Novel Human Cowpox Virus With Mosaic Sequences From North America and Old World Orthopoxvirus. Front Microbiol 2022; 13:868887. [PMID: 35592007 PMCID: PMC9112427 DOI: 10.3389/fmicb.2022.868887] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Accepted: 02/24/2022] [Indexed: 11/13/2022] Open
Abstract
Orthopoxviruses (OPXVs) not only infect their natural hosts, but some OPXVs can also cause disease in humans. Previously, we partially characterized an OPXV isolated from an 18-year-old male living in Northern Norway. Restriction enzyme analysis and partial genome sequencing characterized this virus as an atypical cowpox virus (CPXV), which we named CPXV-No-H2. In this study, we determined the complete genome sequence of CPXV-No-H2 using Illumina and Nanopore sequencing. Our results showed that the whole CPXV-No-H2 genome is 220,276 base pairs (bp) in length, with inverted terminal repeat regions of approximately 7 kbp, containing 217 predicted genes. Seventeen predicted CPXV-No-H2 proteins were most similar to OPXV proteins from the Old World, including Ectromelia virus (ECTV) and Vaccinia virus, and North America, Alaskapox virus (AKPV). CPXV-No-H2 has a mosaic genome with genes most similar to other OPXV genes, and seven potential recombination events were identified. The phylogenetic analysis showed that CPXV-No-H2 formed a separate clade with the German CPXV isolates CPXV_GerMygEK938_17 and CPXV_Ger2010_MKY, sharing 96.4 and 96.3% nucleotide identity, respectively, and this clade clustered closely with the ECTV-OPXV Abatino clade. CPXV-No-H2 is a mosaic virus that may have arisen out of several recombination events between OPXVs, and its phylogenetic clustering suggests that ECTV-Abatino-like cowpox viruses form a distinct, new clade of cowpox viruses.
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Affiliation(s)
- Diana Diaz-Cánova
- Molecular Inflammation Research Group, Department of Medical Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Ugo L Moens
- Molecular Inflammation Research Group, Department of Medical Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Annika Brinkmann
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Andreas Nitsche
- Highly Pathogenic Viruses, Centre for Biological Threats and Special Pathogens, WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Malachy Ifeanyi Okeke
- Section of Biomedical Sciences, Department of Natural and Environmental Sciences, School of Arts and Sciences, American University of Nigeria, Yola, Nigeria
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5
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Ferrari G, Neukamm J, Baalsrud HT, Breidenstein AM, Ravinet M, Phillips C, Rühli F, Bouwman A, Schuenemann VJ. Variola virus genome sequenced from an eighteenth-century museum specimen supports the recent origin of smallpox. Philos Trans R Soc Lond B Biol Sci 2020; 375:20190572. [PMID: 33012235 PMCID: PMC7702794 DOI: 10.1098/rstb.2019.0572] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/10/2020] [Indexed: 12/15/2022] Open
Abstract
Smallpox, caused by the variola virus (VARV), was a highly virulent disease with high mortality rates causing a major threat for global human health until its successful eradication in 1980. Despite previously published historic and modern VARV genomes, its past dissemination and diversity remain debated. To understand the evolutionary history of VARV with respect to historic and modern VARV genetic variation in Europe, we sequenced a VARV genome from a well-described eighteenth-century case from England (specimen P328). In our phylogenetic analysis, the new genome falls between the modern strains and another historic strain from Lithuania, supporting previous claims of larger diversity in early modern Europe compared to the twentieth century. Our analyses also resolve a previous controversy regarding the common ancestor between modern and historic strains by confirming a later date around the seventeenth century. Overall, our results point to the benefit of historic genomes for better resolution of past VARV diversity and highlight the value of such historic genomes from around the world to further understand the evolutionary history of smallpox as well as related diseases. This article is part of the theme issue 'Insights into health and disease from ancient biomolecules'.
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Affiliation(s)
- Giada Ferrari
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316, Oslo, Norway
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Judith Neukamm
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
- Institute for Bioinformatics and Medical Informatics, University of Tübingen, Sand 14, 72076 Tübingen, Germany
| | - Helle T. Baalsrud
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316, Oslo, Norway
| | - Abagail M. Breidenstein
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Mark Ravinet
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biosciences, University of Oslo, PO Box 1066 Blindern, 0316, Oslo, Norway
- School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
| | - Carina Phillips
- The Royal College of Surgeons of England, 35-43 Lincoln's Inn Fields, London WC2A 3PE, UK
| | - Frank Rühli
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Abigail Bouwman
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
| | - Verena J. Schuenemann
- Institute of Evolutionary Medicine, University of Zurich, Winterthurerstrasse 190, 8057 Zurich, Switzerland
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Gigante CM, Gao J, Tang S, McCollum AM, Wilkins K, Reynolds MG, Davidson W, McLaughlin J, Olson VA, Li Y. Genome of Alaskapox Virus, A Novel Orthopoxvirus Isolated from Alaska. Viruses 2019; 11:E708. [PMID: 31375015 PMCID: PMC6723315 DOI: 10.3390/v11080708] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Revised: 07/19/2019] [Accepted: 07/21/2019] [Indexed: 01/10/2023] Open
Abstract
Since the eradication of smallpox, there have been increases in poxvirus infections and the emergence of several novel poxviruses that can infect humans and domestic animals. In 2015, a novel poxvirus was isolated from a resident of Alaska. Diagnostic testing and limited sequence analysis suggested this isolate was a member of the Orthopoxvirus (OPXV) genus but was highly diverged from currently known species, including Akhmeta virus. Here, we present the complete 210,797 bp genome sequence of the Alaska poxvirus isolate, containing 206 predicted open reading frames. Phylogenetic analysis of the conserved central region of the genome suggested the Alaska isolate shares a common ancestor with Old World OPXVs and is diverged from New World OPXVs. We propose this isolate as a member of a new OPXV species, Alaskapox virus (AKPV). The AKPV genome contained host range and virulence genes typical of OPXVs but lacked homologs of C4L and B7R, and the hemagglutinin gene contained a unique 120 amino acid insertion. Seven predicted AKPV proteins were most similar to proteins in non-OPXV Murmansk or NY_014 poxviruses. Genomic analysis revealed evidence suggestive of recombination with Ectromelia virus in two putative regions that contain seven predicted coding sequences, including the A-type inclusion protein.
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Affiliation(s)
- Crystal M Gigante
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Jinxin Gao
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Shiyuyun Tang
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Andrea M McCollum
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Kimberly Wilkins
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Mary G Reynolds
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Whitni Davidson
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Joseph McLaughlin
- Alaska Division of Public Health, Section of Epidemiology, Anchorage, AK 99503, USA
| | - Victoria A Olson
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA
| | - Yu Li
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA 30329, USA.
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7
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Zhang F, Meng X, Townsend MB, Satheshkumar PS, Xiang Y. Identification of CP77 as the Third Orthopoxvirus SAMD9 and SAMD9L Inhibitor with Unique Specificity for a Rodent SAMD9L. J Virol 2019; 93:e00225-19. [PMID: 30918078 PMCID: PMC6613757 DOI: 10.1128/jvi.00225-19] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 03/20/2019] [Indexed: 11/20/2022] Open
Abstract
Orthopoxviruses (OPXVs) have a broad host range in mammalian cells, but Chinese hamster ovary (CHO) cells are nonpermissive for vaccinia virus (VACV). Here, we revealed a species-specific difference in host restriction factor SAMD9L as the cause for the restriction and identified orthopoxvirus CP77 as a unique inhibitor capable of antagonizing Chinese hamster SAMD9L (chSAMD9L). Two known VACV inhibitors of SAMD9 and SAMD9L (SAMD9&L), K1 and C7, can bind human and mouse SAMD9&L, but neither can bind chSAMD9L. Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 knockout of chSAMD9L from CHO cells removed the restriction for VACV, while ectopic expression of chSAMD9L imposed the restriction for VACV in a human cell line, demonstrating that chSAMD9L is a potent restriction factor for VACV. In contrast to K1 and C7, cowpox virus CP77 can bind chSAMD9L and rescue VACV replication in cells expressing chSAMD9L, indicating that CP77 is yet another SAMD9L inhibitor but has a unique specificity for chSAMD9L. Binding studies showed that the N-terminal 382 amino acids of CP77 were sufficient for binding chSAMD9L and that both K1 and CP77 target a common internal region of SAMD9L. Growth studies with nearly all OPXV species showed that the ability of OPXVs to antagonize chSAMD9L correlates with CP77 gene status and that a functional CP77 ortholog was maintained in many OPXVs, including monkeypox virus. Our data suggest that a species-specific difference in rodent SAMD9L poses a barrier for cross-species OPXV infection and that OPXVs have evolved three SAMD9&L inhibitors with different specificities to overcome this barrier.IMPORTANCE Several OPXV species, including monkeypox virus and cowpox virus, cause zoonotic infection in humans. They are believed to use wild rodents as the reservoir or intermediate hosts, but the host or viral factors that are important for OPXV host range in rodents are unknown. Here, we showed that the abortive replication of several OPXV species in a Chinese hamster cell line was caused by a species-specific difference in the host antiviral factor SAMD9L, suggesting that SAMD9L divergence in different rodent species poses a barrier for cross-species OPXV infection. While the Chinese hamster SAMD9L could not be inhibited by two previously identified OPXV inhibitors of human and mouse SAMD9&L, it can be inhibited by cowpox virus CP77, indicating that OPXVs encode three SAMD9&L inhibitors with different specificities. Our data suggest that OPXV host range in broad rodent species depends on three SAMD9&L inhibitors with different specificities.
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Affiliation(s)
- Fushun Zhang
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Xiangzhi Meng
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
| | - Michael B Townsend
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Panayampalli Subbian Satheshkumar
- Poxvirus and Rabies Branch, Division of High-Consequence Pathogens and Pathology, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yan Xiang
- Department of Microbiology, Immunology and Molecular Genetics, University of Texas Health Science Center at San Antonio, San Antonio, Texas, USA
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Gruber CEM, Giombini E, Selleri M, Tausch SH, Andrusch A, Tyshaieva A, Cardeti G, Lorenzetti R, De Marco L, Carletti F, Nitsche A, Capobianchi MR, Ippolito G, Autorino GL, Castilletti C. Whole Genome Characterization of Orthopoxvirus (OPV) Abatino, a Zoonotic Virus Representing a Putative Novel Clade of Old World Orthopoxviruses. Viruses 2018; 10:v10100546. [PMID: 30301229 PMCID: PMC6212904 DOI: 10.3390/v10100546] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 10/02/2018] [Accepted: 10/03/2018] [Indexed: 12/15/2022] Open
Abstract
Orthopoxviruses (OPVs) are diffused over the complete Eurasian continent, but previously described strains are mostly from northern Europe, and few infections have been reported from Italy. Here we present the extended genomic characterization of OPV Abatino, a novel OPV isolated in Italy from an infected Tonkean macaque, with zoonotic potential. Phylogenetic analysis based on 102 conserved OPV genes (core gene set) showed that OPV Abatino is most closely related to the Ectromelia virus species (ECTV), although placed on a separate branch of the phylogenetic tree, bringing substantial support to the hypothesis that this strain may be part of a novel OPV clade. Extending the analysis to the entire set of genes (coding sequences, CDS) further substantiated this hypothesis. In fact the genome of OPV Abatino included more CDS than ECTV; most of the extra genes (mainly located in the terminal genome regions), showed the highest similarity with cowpox virus (CPXV); however vaccinia virus (VACV) and monkeypox virus (MPXV) were the closest OPV for certain CDS. These findings suggest that OPV Abatino could be the result of complex evolutionary events, diverging from any other previously described OPV, and may indicate that previously reported cases in Italy could represent the tip of the iceberg yet to be explored.
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Affiliation(s)
- Cesare E M Gruber
- National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, via Portuense 292, 00149 Rome, Italy.
| | - Emanuela Giombini
- National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, via Portuense 292, 00149 Rome, Italy.
| | - Marina Selleri
- National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, via Portuense 292, 00149 Rome, Italy.
| | - Simon H Tausch
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Seestraße 10, 13353 Berlin, Germany.
| | - Andreas Andrusch
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Seestraße 10, 13353 Berlin, Germany.
| | - Alona Tyshaieva
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Seestraße 10, 13353 Berlin, Germany.
| | - Giusy Cardeti
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana M. Aleandri, via Appia Nuova 1411, 00178 Rome, Italy.
| | - Raniero Lorenzetti
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana M. Aleandri, via Appia Nuova 1411, 00178 Rome, Italy.
| | - Lorenzo De Marco
- Parco Faunistico Piano dell'Abatino, via Capo Farfa 50, 02030 Poggio San Lorenzo, Italy.
| | - Fabrizio Carletti
- National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, via Portuense 292, 00149 Rome, Italy.
| | - Andreas Nitsche
- Robert Koch Institute, Centre for Biological Threats and Special Pathogens 1, Seestraße 10, 13353 Berlin, Germany.
| | - Maria R Capobianchi
- National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, via Portuense 292, 00149 Rome, Italy.
| | - Giuseppe Ippolito
- National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, via Portuense 292, 00149 Rome, Italy.
| | - Gian Luca Autorino
- Istituto Zooprofilattico Sperimentale del Lazio e della Toscana M. Aleandri, via Appia Nuova 1411, 00178 Rome, Italy.
| | - Concetta Castilletti
- National Institute for Infectious Diseases Lazzaro Spallanzani IRCCS, via Portuense 292, 00149 Rome, Italy.
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Cardeti G, Gruber CEM, Eleni C, Carletti F, Castilletti C, Manna G, Rosone F, Giombini E, Selleri M, Lapa D, Puro V, Di Caro A, Lorenzetti R, Scicluna MT, Grifoni G, Rizzoli A, Tagliapietra V, De Marco L, Capobianchi MR, Autorino GL. Fatal Outbreak in Tonkean Macaques Caused by Possibly Novel Orthopoxvirus, Italy, January 2015 1. Emerg Infect Dis 2017; 23:1941-1949. [PMID: 28975882 PMCID: PMC5708245 DOI: 10.3201/eid2312.162098] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
In January 2015, during a 3-week period, 12 captive Tonkean macacques at a sanctuary in Italy died. An orthopoxvirus infection was suspected because of negative-staining electron microscopy results. The diagnosis was confirmed by histology, virus isolation, and molecular analysis performed on different organs from all animals. An epidemiologic investigation was unable to define the infection source in the surrounding area. Trapped rodents were negative by virologic testing, but specific IgG was detected in 27.27% of small rodents and 14.28% of rats. An attenuated live vaccine was administered to the susceptible monkey population, and no adverse reactions were observed; a detectable humoral immune response was induced in most of the vaccinated animals. We performed molecular characterization of the orthopoxvirus isolate by next-generation sequencing. According to the phylogenetic analysis of the 9 conserved genes, the virus could be part of a novel clade, lying between cowpox and ectromelia viruses.
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Sarker S, Roberts HK, Tidd N, Ault S, Ladmore G, Peters A, Forwood JK, Helbig K, Raidal SR. Molecular and microscopic characterization of a novel Eastern grey kangaroopox virus genome directly from a clinical sample. Sci Rep 2017; 7:16472. [PMID: 29184134 PMCID: PMC5705601 DOI: 10.1038/s41598-017-16775-7] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2017] [Accepted: 11/17/2017] [Indexed: 11/22/2022] Open
Abstract
Poxviruses are large DNA viruses with varying zoonotic potential, and are recognised in a broad range of wildlife. Although poxviruses have been detected in kangaroos, their genetic relationships to poxviruses in other animals and humans is not well understood. Here, we present a novel genome sequence of a marsupial poxvirus, the Eastern grey kangaroopox virus (EKPV-NSW), isolated from a wild eastern grey kangaroo. In the present study, histopathologically confirmed epidermal pox lesions were used to recover the full-length viral genome and perform electron microscopic analysis, with both immature virions and intracellular mature virions detected. Subsequent analysis of the EKPV-NSW genome demonstrated the highest degree of sequence similarity with EKPV-SC strain (91.51%), followed by WKPV-WA (87.93%), and MOCV1 (44.05%). The novel EKPV-NSW complete genome encompasses most of the chordopoxviruses protein coding genes (138) that are required for genome replication and expression, with only three essential protein coding genes being absent. The novel EKPV-NSW is missing 28 predicted genes compared to the recently isolated EKPV-SC, and carries 21 additional unique genes, encoding unknown proteins. Phylogenetic and recombination analyses showed EKPV-NSW to be the distinct available candidate genome of chordopoxviruses.
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Affiliation(s)
- Subir Sarker
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, VIC 3086, Australia.
| | - Hayley K Roberts
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, VIC 3086, Australia
| | - Naomie Tidd
- Veterinary Diagnostic Laboratory, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Shayne Ault
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
- Lake Road Veterinary Clinic, 327 Lake Albert Road, Kooringal, NSW 2650, Australia
| | - Georgia Ladmore
- Lake Road Veterinary Clinic, 327 Lake Albert Road, Kooringal, NSW 2650, Australia
| | - Andrew Peters
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
| | - Karla Helbig
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, VIC 3086, Australia
| | - Shane R Raidal
- Veterinary Diagnostic Laboratory, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
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11
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Okeke MI, Okoli AS, Diaz D, Offor C, Oludotun TG, Tryland M, Bøhn T, Moens U. Hazard Characterization of Modified Vaccinia Virus Ankara Vector: What Are the Knowledge Gaps? Viruses 2017; 9:v9110318. [PMID: 29109380 PMCID: PMC5707525 DOI: 10.3390/v9110318] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2017] [Revised: 10/21/2017] [Accepted: 10/26/2017] [Indexed: 12/17/2022] Open
Abstract
Modified vaccinia virus Ankara (MVA) is the vector of choice for human and veterinary applications due to its strong safety profile and immunogenicity in vivo. The use of MVA and MVA-vectored vaccines against human and animal diseases must comply with regulatory requirements as they pertain to environmental risk assessment, particularly the characterization of potential adverse effects to humans, animals and the environment. MVA and recombinant MVA are widely believed to pose low or negligible risk to ecosystem health. However, key aspects of MVA biology require further research in order to provide data needed to evaluate the potential risks that may occur due to the use of MVA and MVA-vectored vaccines. The purpose of this paper is to identify knowledge gaps in the biology of MVA and recombinant MVA that are of relevance to its hazard characterization and discuss ongoing and future experiments aimed at providing data necessary to fill in the knowledge gaps. In addition, we presented arguments for the inclusion of uncertainty analysis and experimental investigation of verifiable worst-case scenarios in the environmental risk assessment of MVA and recombinant MVA. These will contribute to improved risk assessment of MVA and recombinant MVA vaccines.
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Affiliation(s)
- Malachy I Okeke
- Genome Editing Research Group, GenØk-Center for Biosafety, Siva Innovation Center, N-9294 Tromso, Norway.
| | - Arinze S Okoli
- Genome Editing Research Group, GenØk-Center for Biosafety, Siva Innovation Center, N-9294 Tromso, Norway.
| | - Diana Diaz
- Molecular Inflammation Research Group, Institute of Medical Biology, University i Tromsø (UiT)-The Arctic University of Norway, N-9037 Tromso, Norway.
| | - Collins Offor
- Department of Medical and Pharmaceutical Biotechnology, IMC University of Applied Sciences Piaristengasse 1, A-3500 Krems, Austria.
| | - Taiwo G Oludotun
- Department of Medical and Pharmaceutical Biotechnology, IMC University of Applied Sciences Piaristengasse 1, A-3500 Krems, Austria.
| | - Morten Tryland
- Genome Editing Research Group, GenØk-Center for Biosafety, Siva Innovation Center, N-9294 Tromso, Norway.
- Artic Infection Biology, Department of Artic and Marine Biology, UIT-The Artic University of Norway, N-9037 Tromso, Norway.
| | - Thomas Bøhn
- Genome Editing Research Group, GenØk-Center for Biosafety, Siva Innovation Center, N-9294 Tromso, Norway.
| | - Ugo Moens
- Molecular Inflammation Research Group, Institute of Medical Biology, University i Tromsø (UiT)-The Arctic University of Norway, N-9037 Tromso, Norway.
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12
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Farré D, Martínez-Vicente P, Engel P, Angulo A. Immunoglobulin superfamily members encoded by viruses and their multiple roles in immune evasion. Eur J Immunol 2017; 47:780-796. [PMID: 28383780 DOI: 10.1002/eji.201746984] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2017] [Revised: 03/11/2017] [Accepted: 03/29/2017] [Indexed: 12/31/2022]
Abstract
Pathogens have developed a plethora of strategies to undermine host immune defenses in order to guarantee their survival. For large DNA viruses, these immune evasion mechanisms frequently rely on the expression of genes acquired from host genomes. Horizontally transferred genes include members of the immunoglobulin superfamily, whose products constitute the most diverse group of proteins of vertebrate genomes. Their promiscuous immunoglobulin domains, which comprise the building blocks of these molecules, are involved in a large variety of functions mediated by ligand-binding interactions. The flexible structural nature of the immunoglobulin domains makes them appealing targets for viral capture due to their capacity to generate high functional diversity. Here, we present an up-to-date review of immunoglobulin superfamily gene homologs encoded by herpesviruses, poxviruses, and adenoviruses, that include CD200, CD47, Fc receptors, interleukin-1 receptor 2, interleukin-18 binding protein, CD80, carcinoembryonic antigen-related cell adhesion molecules, and signaling lymphocyte activation molecules. We discuss their distinct structural attributes, binding properties, and functions, shaped by evolutionary pressures to disarm specific immune pathways. We include several novel genes identified from extensive genome database surveys. An understanding of the properties and modes of action of these viral proteins may guide the development of novel immune-modulatory therapeutic tools.
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Affiliation(s)
- Domènec Farré
- Immunology Unit, Department of Biomedical Sciences, Medical School, University of Barcelona, Barcelona, Spain
| | - Pablo Martínez-Vicente
- Immunology Unit, Department of Biomedical Sciences, Medical School, University of Barcelona, Barcelona, Spain
| | - Pablo Engel
- Immunology Unit, Department of Biomedical Sciences, Medical School, University of Barcelona, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
| | - Ana Angulo
- Immunology Unit, Department of Biomedical Sciences, Medical School, University of Barcelona, Barcelona, Spain.,Institut d'Investigacions Biomèdiques August Pi i Sunyer, Barcelona, Spain
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