1
|
Diaz-Cánova D, Moens U, Brinkmann A, Nitsche A, Okeke MI. Whole genome sequencing of recombinant viruses obtained from co-infection and superinfection of Vero cells with modified vaccinia virus ankara vectored influenza vaccine and a naturally occurring cowpox virus. Front Immunol 2024; 15:1277447. [PMID: 38633245 PMCID: PMC11021749 DOI: 10.3389/fimmu.2024.1277447] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 03/19/2024] [Indexed: 04/19/2024] Open
Abstract
Modified vaccinia virus Ankara (MVA) has been widely tested in clinical trials as recombinant vector vaccine against infectious diseases and cancers in humans and animals. However, one biosafety concern about the use of MVA vectored vaccine is the potential for MVA to recombine with naturally occurring orthopoxviruses in cells and hosts in which it multiplies poorly and, therefore, producing viruses with mosaic genomes with altered genetic and phenotypic properties. We previously conducted co-infection and superinfection experiments with MVA vectored influenza vaccine (MVA-HANP) and a feline Cowpox virus (CPXV-No-F1) in Vero cells (that were semi-permissive to MVA infection) and showed that recombination occurred in both co-infected and superinfected cells. In this study, we selected the putative recombinant viruses and performed genomic characterization of these viruses. Some putative recombinant viruses displayed plaque morphology distinct of that of the parental viruses. Our analysis demonstrated that they had mosaic genomes of different lengths. The recombinant viruses, with a genome more similar to MVA-HANP (>50%), rescued deleted and/or fragmented genes in MVA and gained new host ranges genes. Our analysis also revealed that some MVA-HANP contained a partially deleted transgene expression cassette and one recombinant virus contained part of the transgene expression cassette similar to that incomplete MVA-HANP. The recombination in co-infected and superinfected Vero cells resulted in recombinant viruses with unpredictable biological and genetic properties as well as recovery of delete/fragmented genes in MVA and transfer of the transgene into replication competent CPXV. These results are relevant to hazard characterization and risk assessment of MVA vectored biologicals.
Collapse
Affiliation(s)
- Diana Diaz-Cánova
- Molecular Inflammation Research Group, Department of Medical Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Ugo Moens
- Molecular Inflammation Research Group, Department of Medical Biology, UiT - The Arctic University of Norway, Tromsø, Norway
| | - Annika Brinkmann
- WHO Reference Laboratory for SARS-CoV-2 and WHO Collaborating Centre for Emerging Infections and Biological Threats, Robert Koch Institute, Berlin, Germany
| | - Andreas Nitsche
- 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
| |
Collapse
|
2
|
Mazloum A, Van Schalkwyk A, Babiuk S, Venter E, Wallace DB, Sprygin A. Lumpy skin disease: history, current understanding and research gaps in the context of recent geographic expansion. Front Microbiol 2023; 14:1266759. [PMID: 38029115 PMCID: PMC10652407 DOI: 10.3389/fmicb.2023.1266759] [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: 07/25/2023] [Accepted: 09/28/2023] [Indexed: 12/01/2023] Open
Abstract
Lumpy skin disease is recognized as a transboundary and emerging disease of cattle, buffaloes and other wild ruminants. Being initially restricted to Africa, and since 1989 the Middle East, the unprecedented recent spread across Eurasia demonstrates how underestimated and neglected this disease is. The initial identification of the causative agent of LSD as a poxvirus called LSD virus, was well as findings on LSDV transmission and epidemiology were pioneered at Onderstepoort, South Africa, from as early as the 1940s by researchers such as Weiss, Haig and Alexander. As more data emerges from an ever-increasing number of epidemiological studies, previously emphasized research gaps are being revisited and discussed. The currently available knowledge is in agreement with the previously described South African research experience that LSDV transmission can occur by multiple routes, including indirect contact, shared water sources and arthropods. The virus population is prone to molecular evolution, generating novel phylogenetically distinct variants resulting from a diverse range of selective pressures, including recombination between field and homologous vaccine strains in cell culture that produce virulent recombinants which pose diagnostic challenges. Host restriction is not limited to livestock, with certain wild ruminants being susceptible, with unknown consequences for the epidemiology of the disease.
Collapse
Affiliation(s)
- Ali Mazloum
- Federal Center for Animal Health, Vladimir, Russia
| | - Antoinette Van Schalkwyk
- Agricultural Research Council – Onderstepoort Veterinary Institute, Onderstepoort, South Africa
- Department of Biotechnology, University of the Western Cape, Bellville, South Africa
| | - Shawn Babiuk
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada
| | - Estelle Venter
- College of Public Health, Medical and Veterinary Sciences, Discipline Veterinary Science, James Cook University, Townsville, QLD, Australia
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | - David B. Wallace
- Agricultural Research Council – Onderstepoort Veterinary Institute, Onderstepoort, South Africa
- Department of Veterinary Tropical Diseases, Faculty of Veterinary Science, University of Pretoria, Onderstepoort, South Africa
| | | |
Collapse
|
3
|
Sprygin A, Mazloum A, van Schalkwyk A, Babiuk S. Capripoxviruses, leporipoxviruses, and orthopoxviruses: Occurrences of recombination. Front Microbiol 2022; 13:978829. [PMID: 36274700 PMCID: PMC9584655 DOI: 10.3389/fmicb.2022.978829] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2022] [Accepted: 09/12/2022] [Indexed: 11/13/2022] Open
Abstract
Poxviruses are double-stranded DNA viruses with several members displaying restricted host ranges. They are genetically stable with low nucleotide mutation rates compared to other viruses, due to the poxviral high-fidelity DNA polymerase. Despite the low accumulation of mutations per replication cycle, poxvirus genomes can recombine with each other to generate genetically rearranged viruses through recombination, a process directly associated with replication and the aforementioned DNA polymerase. Orthopoxvirus replication is intimately tethered to high frequencies of homologous recombination between co-infecting viruses, duplicated sequences of the same virus, and plasmid DNA transfected into poxvirus-infected cells. Unfortunately, the effect of these genomic alterations on the cellular context for all poxviruses across the family Poxviridae remains elusive. However, emerging sequence data on currently circulating and archived poxviruses, such as the genera orthopoxviruses and capripoxviruses, display a wide degree of divergence. This genetic variability cannot be explained by clonality or genetic drift alone, but are probably a result of significant genomic alterations, such as homologous recombination, gene loss and gain, or gene duplications as the major selection forces acting on viral progeny. The objective of this review is to cross-sectionally overview the currently available findings on natural and laboratory observations of recombination in orthopoxviruses, capripoxviruses, and leporipoxviruses, as well as the possible mechanisms involved. Overall, the reviewed available evidence allows us to conclude that the current state of knowledge is limited in terms of the relevance of genetic variations across even a genus of poxviruses as well as fundamental features governing and precipitating intrinsic gene flow and recombination events.
Collapse
Affiliation(s)
- Alexander Sprygin
- Federal Center for Animal Health, Vladimir, Russia
- *Correspondence: Alexander Sprygin,
| | - Ali Mazloum
- Federal Center for Animal Health, Vladimir, Russia
| | | | - Shawn Babiuk
- National Centre for Foreign Animal Disease, Canadian Food Inspection Agency, Winnipeg, MB, Canada
| |
Collapse
|
4
|
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.
Collapse
|
5
|
Sahu BP, Majee P, Singh RR, Sahoo N, Nayak D. Recombination drives the emergence of orf virus diversity: evidence from the first complete genome sequence of an Indian orf virus isolate and comparative genomic analysis. Arch Virol 2022; 167:1571-1576. [PMID: 35546377 PMCID: PMC9094603 DOI: 10.1007/s00705-022-05443-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2021] [Accepted: 03/07/2022] [Indexed: 11/02/2022]
Abstract
Contagious pustular dermatitis is a disease that primarily infects small ruminants and possesses zoonotic potential. It is caused by orf virus (ORFV), a member of the genus Parapoxvirus. In this study, we evaluated an ORFV outbreak in goats in Madhya Pradesh, a state in central India, during 2017. The transboundary potential of this virus was evaluated by constructing phylogenetic trees. The complete genome sequence of an ORFV isolate named Ind/MP/17 was found to be 139,807 bp in length with 63.7% GC content and 132 open reading frames (ORFs) flanked by 3,910-bp inverted terminal repeats (ITRs). An investigation into evolutionary parameters such as selection pressure (θ = dN/dS) and nucleotide diversity (π) demonstrated that ORFV has undergone purifying selection. A total of 40 recombination events were identified, 21 of which were evident in the Ind/MP/17 genome, indicating its ability to generate new variants.
Collapse
Affiliation(s)
- Basanta Pravas Sahu
- Department of Biological Sciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, MP, 453331, India
| | - Prativa Majee
- Department of Biological Sciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, MP, 453331, India
| | - Ravi Raj Singh
- Department of Biological Sciences and Biomedical Engineering, Indian Institute of Technology Indore, Indore, MP, 453331, India
| | - Niranjana Sahoo
- Centre for Wildlife Health, College of Veterinary Sciences and Animal Husbandry, Bhubaneswar, 751030, India
| | - Debasis Nayak
- Department of Biological Science, Indian Institute of Science Education and Research (IISER) Bhopal, Bhopal Bypass Road, Bhauri, Madhya Pradesh, 462066, India.
| |
Collapse
|
6
|
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.
Collapse
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
| |
Collapse
|
7
|
Hutson CL, Kondas AV, Ritter JM, Reed Z, Ostergaard SD, Morgan CN, Gallardo-Romero N, Tansey C, Mauldin MR, Salzer JS, Hughes CM, Goldsmith CS, Carroll D, Olson VA. Teaching a new mouse old tricks: Humanized mice as an infection model for Variola virus. PLoS Pathog 2021; 17:e1009633. [PMID: 34547055 PMCID: PMC8454956 DOI: 10.1371/journal.ppat.1009633] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2020] [Accepted: 05/11/2021] [Indexed: 01/12/2023] Open
Abstract
Smallpox, caused by the solely human pathogen Variola virus (VARV), was declared eradicated in 1980. While known VARV stocks are secure, smallpox remains a bioterrorist threat agent. Recent U.S. Food and Drug Administration approval of the first smallpox anti-viral (tecovirimat) therapeutic was a successful step forward in smallpox preparedness; however, orthopoxviruses can become resistant to treatment, suggesting a multi-therapeutic approach is necessary. Animal models are required for testing medical countermeasures (MCMs) and ideally MCMs are tested directly against the pathogen of interest. Since VARV only infects humans, a representative animal model for testing therapeutics directly against VARV remains a challenge. Here we show that three different humanized mice strains are highly susceptible to VARV infection, establishing the first small animal model using VARV. In comparison, the non-humanized, immunosuppressed background mouse was not susceptible to systemic VARV infection. Following an intranasal VARV challenge that mimics the natural route for human smallpox transmission, the virus spread systemically within the humanized mouse before mortality (~ 13 days post infection), similar to the time from exposure to symptom onset for ordinary human smallpox. Our identification of a permissive/representative VARV animal model can facilitate testing of MCMs in a manner consistent with their intended use.
Collapse
Affiliation(s)
- Christina L. Hutson
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Ashley V. Kondas
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Jana M. Ritter
- Infectious Diseases Pathology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Zachary Reed
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Sharon Dietz Ostergaard
- Comparative Medicine Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Clint N. Morgan
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Nadia Gallardo-Romero
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Cassandra Tansey
- Comparative Medicine Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Matthew R. Mauldin
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Johanna S. Salzer
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Christine M. Hughes
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Cynthia S. Goldsmith
- Infectious Diseases Pathology Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Darin Carroll
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| | - Victoria A. Olson
- Poxvirus and Rabies Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, United States of America
| |
Collapse
|
8
|
Patrono LV, Pléh K, Samuni L, Ulrich M, Röthemeier C, Sachse A, Muschter S, Nitsche A, Couacy-Hymann E, Boesch C, Wittig RM, Calvignac-Spencer S, Leendertz FH. Monkeypox virus emergence in wild chimpanzees reveals distinct clinical outcomes and viral diversity. Nat Microbiol 2020; 5:955-965. [PMID: 32341480 DOI: 10.1038/s41564-020-0706-0] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Accepted: 03/09/2020] [Indexed: 12/17/2022]
Abstract
Monkeypox is a viral zoonotic disease on the rise across endemic habitats. Despite the growing importance of monkeypox virus, our knowledge on its host spectrum and sylvatic maintenance is limited. Here, we describe the recent repeated emergence of monkeypox virus in a wild, human-habituated western chimpanzee (Pan troglodytes verus, hereafter chimpanzee) population from Taï National Park, Ivory Coast. Through daily monitoring, we show that further to causing its typical exanthematous syndrome, monkeypox can present itself as a severe respiratory disease without a diffuse rash. By analysing 949 non-invasively collected samples, we identify the circulation of at least two distinct monkeypox virus lineages and document the shedding of infectious particles in faeces and flies, suggesting that they could mediate indirect transmission. We also show that the carnivorous component of the Taï chimpanzees' diet, mainly consisting of the sympatric monkeys they regularly hunt, did not change nor shift towards rodent consumption (the presumed reservoir) before the outbreaks, suggesting that the sudden emergence of monkeypox virus in this population is probably due to changes in the ecology of the virus itself. Using long-term mortality surveillance data from Taï National Park, we provide evidence of little to no prior viral activity over at least two decades. We conclude that great ape sentinel systems devoted to the longitudinal collection of behavioural and health data can help clarify the epidemiology and clinical presentation of zoonotic pathogens.
Collapse
Affiliation(s)
- Livia V Patrono
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Kamilla Pléh
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Ivory Coast
| | - Liran Samuni
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Ivory Coast
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Markus Ulrich
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Caroline Röthemeier
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Andreas Sachse
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany
| | - Silvia Muschter
- Centre for Biological Threats and Special Pathogens and German Reference Laboratory for Poxviruses (ZBS1), Robert Koch Institute, Berlin, Germany
| | - Andreas Nitsche
- Centre for Biological Threats and Special Pathogens and German Reference Laboratory for Poxviruses (ZBS1), Robert Koch Institute, Berlin, Germany
| | - Emmanuel Couacy-Hymann
- Laboratoire National D'appui au Développement Agricole/Laboratoire Central de Pathologie Animale, Bingerville, Ivory Coast
| | - Christophe Boesch
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Ivory Coast
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | - Roman M Wittig
- Taï Chimpanzee Project, Centre Suisse de Recherches Scientifiques, Abidjan, Ivory Coast
- Department of Primatology, Max Planck Institute for Evolutionary Anthropology, Leipzig, Germany
| | | | - Fabian H Leendertz
- Project Group Epidemiology of Highly Pathogenic Microorganisms, Robert Koch Institute, Berlin, Germany.
| |
Collapse
|
9
|
Isolation and Characterization of Akhmeta Virus from Wild-Caught Rodents ( Apodemus spp.) in Georgia. J Virol 2019; 93:JVI.00966-19. [PMID: 31554682 PMCID: PMC6880181 DOI: 10.1128/jvi.00966-19] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 09/10/2019] [Indexed: 12/31/2022] Open
Abstract
Akhmeta virus is a unique Orthopoxvirus that was described in 2013 from the country of Georgia. This paper presents the first isolation of this virus from small mammal (Rodentia; Apodemus spp.) samples and the molecular characterization of those isolates. The identification of the virus in small mammals is an essential component to understanding the natural history of this virus and its transmission to human populations and could guide public health interventions in Georgia. Akhmeta virus genomes harbor evidence suggestive of recombination with a variety of other orthopoxviruses; this has implications for the evolution of orthopoxviruses, their ability to infect mammalian hosts, and their ability to adapt to novel host species. In 2013, a novel orthopoxvirus was detected in skin lesions of two cattle herders from the Kakheti region of Georgia (country); this virus was named Akhmeta virus. Subsequent investigation of these cases revealed that small mammals in the area had serological evidence of orthopoxvirus infections, suggesting their involvement in the maintenance of these viruses in nature. In October 2015, we began a longitudinal study assessing the natural history of orthopoxviruses in Georgia. As part of this effort, we trapped small mammals near Akhmeta (n = 176) and Gudauri (n = 110). Here, we describe the isolation and molecular characterization of Akhmeta virus from lesion material and pooled heart and lung samples collected from five wood mice (Apodemus uralensis and Apodemus flavicollis) in these two locations. The genomes of Akhmeta virus obtained from rodents group into 2 clades: one clade represented by viruses isolated from A. uralensis samples, and one clade represented by viruses isolated from A. flavicollis samples. These genomes also display several presumptive recombination events for which gene truncation and identity have been examined. IMPORTANCE Akhmeta virus is a unique Orthopoxvirus that was described in 2013 from the country of Georgia. This paper presents the first isolation of this virus from small mammal (Rodentia; Apodemus spp.) samples and the molecular characterization of those isolates. The identification of the virus in small mammals is an essential component to understanding the natural history of this virus and its transmission to human populations and could guide public health interventions in Georgia. Akhmeta virus genomes harbor evidence suggestive of recombination with a variety of other orthopoxviruses; this has implications for the evolution of orthopoxviruses, their ability to infect mammalian hosts, and their ability to adapt to novel host species.
Collapse
|
10
|
Abstract
In recent years, there have been numerous technological advances in the field of molecular biology; these include next- and third-generation sequencing of DNA genomes and mRNA transcripts and mass spectrometry of proteins. Perhaps, however, it is genome sequencing that impacts a virologist the most. In 2017, more than 480 complete genome sequences of poxviruses have been generated, and are constantly used in many different ways by almost all molecular virologists. Matching this growth in data acquisition is an explosion of the relatively new field of bioinformatics, providing databases to store and organize this valuable/expensive data and algorithms to analyze it. For the bench virologist, access to intuitive, easy-to-use, software is often critical for performing bioinformatics-based experiments. Three common hurdles for the researcher are (1) selection, retrieval, and reformatting genomics data from large databases; (2) use of tools to compare/analyze the genomics data; and (3) display and interpretation of complex sets of results. This chapter is directed at the bench virologist and describes the software that helps overcome these obstacles, with a focus on the comparison and analysis of poxvirus genomes. Although poxvirus genomes are stored in public databases such as GenBank, this resource can be cumbersome and tedious to use if large amounts of data must to be collected. Therefore, we also highlight our Viral Orthologous Clusters database system and integrated tools that we developed specifically for the management and analysis of complete viral genomes.
Collapse
Affiliation(s)
- Shin-Lin Tu
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Chris Upton
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada.
| |
Collapse
|
11
|
Adam DC, Scotch M, MacIntyre CR. Bayesian Phylogeography and Pathogenic Characterization of Smallpox Based on HA, ATI, and CrmB Genes. Mol Biol Evol 2018; 35:2607-2617. [PMID: 30099520 PMCID: PMC6231489 DOI: 10.1093/molbev/msy153] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Variola virus is at risk of re-emergence either through accidental release, bioterrorism, or synthetic biology. The use of phylogenetics and phylogeography to support epidemic field response is expected to grow as sequencing technology becomes miniaturized, cheap, and ubiquitous. In this study, we aimed to explore the use of common VARV diagnostic targets hemagglutinin (HA), cytokine response modifier B (CrmB), and A-type inclusion protein (ATI) for phylogenetic characterization as well as the representativeness of modelling strategies in phylogeography to support epidemic response should smallpox re-emerge. We used Bayesian discrete-trait phylogeography using the most complete data set currently available of whole genome (n = 51) and partially sequenced (n = 20) VARV isolates. We show that multilocus models combining HA, ATI, and CrmB genes may represent a useful heuristic to differentiate between VARV Major and subclades of VARV Minor which have been associated with variable case-fatality rates. Where whole genome sequencing is unavailable, phylogeography models of HA, ATI, and CrmB may provide preliminary but uncertain estimates of transmission, while supplementing whole genome models with additional isolates sequenced only for HA can improve sample representativeness, maintaining similar support for transmission relative to whole genome models. We have also provided empirical evidence delineating historic international VARV transmission using phylogeography. Due to the persistent threat of re-emergence, our results provide important research for smallpox epidemic preparedness in the posteradication era as recommended by the World Health Organisation.
Collapse
Affiliation(s)
- Dillon C Adam
- Biosecurity Program, Kirby Institute, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
| | - Matthew Scotch
- School of Public Health and Community Medicine, University of New South Wales, Sydney, NSW
- Biodesign Center for Environmental Health Engineering, Biodesign Institute, Arizona State University, Tempe, AZ
- Department of Biomedical Informatics, College of Health Solutions, Arizona State University, Tempe, AZ
| | - Chandini Raina MacIntyre
- Biosecurity Program, Kirby Institute, Faculty of Medicine, University of New South Wales, Sydney, NSW, Australia
- College of Public Service and Community Solutions and College of Health Solutions, Arizona State University, Tempe, AZ
| |
Collapse
|
12
|
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] [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.
Collapse
|
13
|
Smithson C, Imbery J, Upton C. Re-Assembly and Analysis of an Ancient Variola Virus Genome. Viruses 2017; 9:v9090253. [PMID: 28885569 PMCID: PMC5618019 DOI: 10.3390/v9090253] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2017] [Revised: 09/04/2017] [Accepted: 09/05/2017] [Indexed: 12/17/2022] Open
Abstract
We report a major improvement to the assembly of published short read sequencing data from an ancient variola virus (VARV) genome by the removal of contig-capping sequencing tags and manual searches for gap-spanning reads. The new assembly, together with camelpox and taterapox genomes, permitted new dates to be calculated for the last common ancestor of all VARV genomes. The analysis of recently sequenced VARV-like cowpox virus genomes showed that single nucleotide polymorphisms (SNPs) and amino acid changes in the vaccinia virus (VACV)-Cop-O1L ortholog, predicted to be associated with VARV host specificity and virulence, were introduced into the lineage before the divergence of these viruses. A comparison of the ancient and modern VARV genome sequences also revealed a measurable drift towards adenine + thymine (A + T) richness.
Collapse
Affiliation(s)
- Chad Smithson
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada.
| | - Jacob Imbery
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada.
| | - Chris Upton
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC V8W 3P6, Canada.
| |
Collapse
|
14
|
Smithson C, Meyer H, Gigante CM, Gao J, Zhao H, Batra D, Damon I, Upton C, Li Y. Two novel poxviruses with unusual genome rearrangements: NY_014 and Murmansk. Virus Genes 2017; 53:883-897. [PMID: 28762208 DOI: 10.1007/s11262-017-1501-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 07/27/2017] [Indexed: 10/19/2022]
Abstract
The genome sequence and annotation of two novel poxviruses, NY_014 and Murmansk, are presented. Despite being isolated on different continents and from different hosts, the viruses are relatively similar, albeit distinct species. The closest known relative of the novel viruses is Yoka poxvirus. Five novel genes were found in these genomes, two of which were MHC class I homologs. Although the core of these genomes was well conserved, the terminal regions showed significant variability with large deletions and surprising evidence of recombination with orthopoxviruses.
Collapse
Affiliation(s)
- Chad Smithson
- Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada
| | - Hermann Meyer
- Bundeswehr Institute of Microbiology, Munich, Germany
| | - Crystal M Gigante
- The National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Jinxin Gao
- The National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Hui Zhao
- The National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Dhwani Batra
- The National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Inger Damon
- The National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA
| | - Chris Upton
- Biochemistry and Microbiology, University of Victoria, Victoria, BC, V8W 3P6, Canada.
| | - Yu Li
- The National Center for Emerging and Zoonotic Infectious Diseases, Centers for Disease Control and Prevention, Atlanta, GA, USA.
| |
Collapse
|
15
|
Pajer P, Dresler J, Kabíckova H, Písa L, Aganov P, Fucik K, Elleder D, Hron T, Kuzelka V, Velemínsky P, Klimentova J, Fucikova A, Pejchal J, Hrabakova R, Benes V, Rausch T, Dundr P, Pilin A, Cabala R, Hubalek M, Stríbrny J, Antwerpen MH, Meyer H. Characterization of Two Historic Smallpox Specimens from a Czech Museum. Viruses 2017; 9:E200. [PMID: 28749451 PMCID: PMC5580457 DOI: 10.3390/v9080200] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Revised: 07/22/2017] [Accepted: 07/25/2017] [Indexed: 11/25/2022] Open
Abstract
Although smallpox has been known for centuries, the oldest available variola virus strains were isolated in the early 1940s. At that time, large regions of the world were already smallpox-free. Therefore, genetic information of these strains can represent only the very last fraction of a long evolutionary process. Based on the genomes of 48 strains, two clades are differentiated: Clade 1 includes variants of variola major, and clade 2 includes West African and variola minor (Alastrim) strains. Recently, the genome of an almost 400-year-old Lithuanian mummy was determined, which fell basal to all currently sequenced strains of variola virus on phylogenetic trees. Here, we determined two complete variola virus genomes from human tissues kept in a museum in Prague dating back 60 and 160 years, respectively. Moreover, mass spectrometry-based proteomic, chemical, and microscopic examinations were performed. The 60-year-old specimen was most likely an importation from India, a country with endemic smallpox at that time. The genome of the 160-year-old specimen is related to clade 2 West African and variola minor strains. This sequence likely represents a new endemic European variant of variola virus circulating in the midst of the 19th century in Europe.
Collapse
Affiliation(s)
- Petr Pajer
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01 Prague 6, Czech Republic.
| | - Jiri Dresler
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01 Prague 6, Czech Republic.
| | - Hana Kabíckova
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01 Prague 6, Czech Republic.
| | - Libor Písa
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01 Prague 6, Czech Republic.
| | - Pavel Aganov
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01 Prague 6, Czech Republic.
| | - Karel Fucik
- Military Health Institute, Military Medical Agency, Tychonova 1, 160 01 Prague 6, Czech Republic.
| | - Daniel Elleder
- Institute of Molecular Genetics of the ASCR, v. v. i., Vídeňská 1083, 142 20 Prague 4, Czech Republic.
| | - Tomas Hron
- Institute of Molecular Genetics of the ASCR, v. v. i., Vídeňská 1083, 142 20 Prague 4, Czech Republic.
| | - Vitezslav Kuzelka
- National Museum, Department of Anthropology, Václavské náměstí 68, 115 79 Praha 1, Czech Republic.
| | - Petr Velemínsky
- National Museum, Department of Anthropology, Václavské náměstí 68, 115 79 Praha 1, Czech Republic.
| | - Jana Klimentova
- Faculty of Military Health Sciences, University of Defence, Třebešská 1575, 500 01 Hradec Králové, Czech Republic.
| | - Alena Fucikova
- Faculty of Military Health Sciences, University of Defence, Třebešská 1575, 500 01 Hradec Králové, Czech Republic.
| | - Jaroslav Pejchal
- Faculty of Military Health Sciences, University of Defence, Třebešská 1575, 500 01 Hradec Králové, Czech Republic.
| | - Rita Hrabakova
- Laboratory of Applied Proteome Analyses, Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, Rumburská 89, 277 21 Liběchov, Czech Republic.
| | - Vladimir Benes
- Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.
| | - Tobias Rausch
- Genomics Core Facility, EMBL Heidelberg, Meyerhofstraße 1, 69117 Heidelberg, Germany.
| | - Pavel Dundr
- Institute of Pathology of the First Faculty of Medicine and General Teaching Hospital, Studničkova 2, 128 00 Prague, Czech Republic.
| | - Alexander Pilin
- Institute of Forensic Medicine and Toxicology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 4, 128 21, Praha 2, Czech Republic.
| | - Radomir Cabala
- Institute of Forensic Medicine and Toxicology, First Faculty of Medicine, Charles University and General University Hospital in Prague, Studničkova 4, 128 21, Praha 2, Czech Republic.
| | - Martin Hubalek
- Institute of Organic Chemistry and Biochemistry of the CAS, Flemingovo náměstí 542/2, 166 10 Praha 6, Czech Republic.
| | - Jan Stríbrny
- Military Institute of Forensic Medicine, Military University Hospital Prague, U Vojenské nemocnice 1200, 169 02 Praha 6.
| | - Markus H Antwerpen
- Bundeswehr Institute of Microbiology, Neuherbergstr. 11, 80937 Munich, Germany.
| | - Hermann Meyer
- Bundeswehr Institute of Microbiology, Neuherbergstr. 11, 80937 Munich, Germany.
| |
Collapse
|
16
|
Characterization of Eptesipoxvirus, a novel poxvirus from a microchiropteran bat. Virus Genes 2017; 53:856-867. [PMID: 28685222 PMCID: PMC6504846 DOI: 10.1007/s11262-017-1485-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 06/30/2017] [Indexed: 01/14/2023]
Abstract
The genome of Eptesipoxvirus (EPTV) is the first poxvirus genome isolated from a microbat. The 176,688 nt sequence, which is believed to encompass the complete coding region of the virus, is 67% A+T and is predicted to encode 191 genes. 11 of these genes have no counterpart in GenBank and are therefore unique to EPTV. The presence of a distantly related ortholog of Vaccinia virus F5L in EPTV uncovered a link with fragmented F5L orthologs in Molluscum contagiosum virus/squirrelpox and clade II viruses. Consistent with the unique position of EPTV approximately mid-point between the orthopoxviruses and the clade II viruses, EPTV has 11 genes that are specific to the orthopoxviruses and 13 genes that are typical, if not exclusive, to the clade II poxviruses. This mosaic nature of EPTV blurs the distinction between the old description of the orthopoxvirus and clade II groups. Genome annotation and characterization failed to find any common virulence genes shared with the other poxvirus isolated from bat (pteropoxvirus); however, EPTV encodes 3 genes that may have been transferred to or from deerpox and squirrelpox viruses; 2 of these, a putative endothelin-like protein and a MHC class I-like protein are likely to have immunomodulatory roles.
Collapse
|
17
|
Sarker S, Das S, Lavers JL, Hutton I, Helbig K, Imbery J, Upton C, Raidal SR. Genomic characterization of two novel pathogenic avipoxviruses isolated from pacific shearwaters (Ardenna spp.). BMC Genomics 2017; 18:298. [PMID: 28407753 PMCID: PMC5390406 DOI: 10.1186/s12864-017-3680-z] [Citation(s) in RCA: 45] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2016] [Accepted: 04/05/2017] [Indexed: 01/18/2023] Open
Abstract
Background Over the past 20 years, many marine seabird populations have been gradually declining and the factors driving this ongoing deterioration are not always well understood. Avipoxvirus infections have been found in a wide range of bird species worldwide, however, very little is known about the disease ecology of avian poxviruses in seabirds. Here we present two novel avipoxviruses from pacific shearwaters (Ardenna spp), one from a Flesh-footed Shearwater (A. carneipes) (SWPV-1) and the other from a Wedge-tailed Shearwater (A. pacificus) (SWPV-2). Results Epidermal pox lesions, liver, and blood samples were examined from A. carneipes and A. pacificus of breeding colonies in eastern Australia. After histopathological confirmation of the disease, PCR screening was conducted for avipoxvirus, circovirus, reticuloendotheliosis virus, and fungal agents. Two samples that were PCR positive for poxvirus were further assessed by next generation sequencing, which yielded complete Shearwaterpox virus (SWPV) genomes from A. pacificus and A. carneipes, both showing the highest degree of similarity with Canarypox virus (98% and 67%, respectively). The novel SWPV-1 complete genome from A. carneipes is missing 43 genes compared to CNPV and contains 4 predicted genes which are not found in any other poxvirus, whilst, SWPV-2 complete genome was deemed to be missing 18 genes compared to CNPV and a further 15 genes significantly fragmented as to probably cause them to be non-functional. Conclusion These are the first avipoxvirus complete genome sequences that infect marine seabirds. In the comparison of SWPV-1 and −2 to existing avipoxvirus sequences, our results indicate that the SWPV complete genome from A. carneipes (SWPV-1) described here is not closely related to any other avipoxvirus genome isolated from avian or other natural host species, and that it likely should be considered a separate species. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3680-z) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Subir Sarker
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia.
| | - Shubhagata Das
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| | - Jennifer L Lavers
- Institute for Marine and Antarctic Studies, University of Tasmania, Hobart, TAS, 7004, Australia
| | - Ian Hutton
- Lord Howe Island Museum, Lord Howe Island, NSW, 2898, Australia
| | - Karla Helbig
- Department of Physiology, Anatomy and Microbiology, School of Life Sciences, La Trobe University, Melbourne, VIC, 3086, Australia
| | - Jacob Imbery
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Chris Upton
- Department of Biochemistry and Microbiology, University of Victoria, Victoria, BC, Canada
| | - Shane R Raidal
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW, 2678, Australia
| |
Collapse
|
18
|
The genomes of three North American orthopoxviruses. Virus Genes 2016; 53:21-34. [PMID: 27613417 DOI: 10.1007/s11262-016-1388-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Accepted: 08/31/2016] [Indexed: 10/21/2022]
Abstract
The complete genomes of a skunkpox, volepox, and raccoonpox virus were sequenced and annotated. Phylogenetic analysis of these genomes indicates that although these viruses are all orthopoxviruses, they form a distinct clade to the other known species. This supports the ancient divergence of the North American orthopoxviruses from other members of the orthopoxviruses. Only two open reading frames appear to be unique to this group of viruses, but a relatively small number of insertions/deletions contribute to the varied gene content of this clade. The availability of these genomes will help determine whether skunkpox and volepox viruses share the characteristics that make raccoonpox a useful vaccine vector.
Collapse
|
19
|
Babkin IV, Babkina IN. The origin of the variola virus. Viruses 2015; 7:1100-12. [PMID: 25763864 PMCID: PMC4379562 DOI: 10.3390/v7031100] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2014] [Revised: 01/14/2015] [Accepted: 02/26/2015] [Indexed: 11/16/2022] Open
Abstract
The question of the origin of smallpox, one of the major menaces to humankind, is a constant concern for the scientific community. Smallpox is caused by the agent referred to as the variola virus (VARV), which belongs to the genus Orthopoxvirus. In the last century, smallpox was declared eradicated from the human community; however, the mechanisms responsible for the emergence of new dangerous pathogens have yet to be unraveled. Evolutionary analyses of the molecular biological genomic data of various orthopoxviruses, involving a wide range of epidemiological and historical information about smallpox, have made it possible to date the emergence of VARV. Comparisons of the VARV genome to the genomes of the most closely related orthopoxviruses and the examination of the distribution their natural hosts' ranges suggest that VARV emerged 3000 to 4000 years ago in the east of the African continent. The VARV evolution rate has been estimated to be approximately 2 × 10-6 substitutions/site/year for the central conserved genomic region and 4 × 10-6 substitutions/site/year for the synonymous substitutions in the genome. Presumably, the introduction of camels to Africa and the concurrent changes to the climate were the particular factors that triggered the divergent evolution of a cowpox-like ancestral virus and thereby led to the emergence of VARV.
Collapse
Affiliation(s)
- Igor V Babkin
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia.
| | - Irina N Babkina
- Laboratory of Molecular Microbiology, Institute of Chemical Biology and Fundamental Medicine, Novosibirsk 630090, Russia.
- JSC VECTOR-BEST, Novosibirsk 630559, Russia.
| |
Collapse
|
20
|
|
21
|
Identification of nucleotide-level changes impacting gene content and genome evolution in orthopoxviruses. J Virol 2014; 88:13651-68. [PMID: 25231308 DOI: 10.1128/jvi.02015-14] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
UNLABELLED Poxviruses are composed of large double-stranded DNA (dsDNA) genomes coding for several hundred genes whose variation has supported virus adaptation to a wide variety of hosts over their long evolutionary history. Comparative genomics has suggested that the Orthopoxvirus genus in particular has undergone reductive evolution, with the most recent common ancestor likely possessing a gene complement consisting of all genes present in any existing modern-day orthopoxvirus species, similar to the current Cowpox virus species. As orthopoxviruses adapt to new environments, the selection pressure on individual genes may be altered, driving sequence divergence and possible loss of function. This is evidenced by accumulation of mutations and loss of protein-coding open reading frames (ORFs) that progress from individual missense mutations to gene truncation through the introduction of early stop mutations (ESMs), gene fragmentation, and in some cases, a total loss of the ORF. In this study, we have constructed a whole-genome alignment for representative isolates from each Orthopoxvirus species and used it to identify the nucleotide-level changes that have led to gene content variation. By identifying the changes that have led to ESMs, we were able to determine that short indels were the major cause of gene truncations and that the genome length is inversely proportional to the number of ESMs present. We also identified the number and types of protein functional motifs still present in truncated genes to assess their functional significance. IMPORTANCE This work contributes to our understanding of reductive evolution in poxviruses by identifying genomic remnants such as single nucleotide polymorphisms (SNPs) and indels left behind by evolutionary processes. Our comprehensive analysis of the genomic changes leading to gene truncation and fragmentation was able to detect some of the remnants of these evolutionary processes still present in orthopoxvirus genomes and suggests that these viruses are under continual adaptation due to changes in their environment. These results further our understanding of the evolutionary mechanisms that drive virus variation, allowing orthopoxviruses to adapt to particular environmental niches. Understanding the evolutionary history of these virus pathogens may help predict their future evolutionary potential.
Collapse
|