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Butkovic A, Kraberger S, Smeele Z, Martin DP, Schmidlin K, Fontenele RS, Shero MR, Beltran RS, Kirkham AL, Aleamotu’a M, Burns JM, Koonin EV, Varsani A, Krupovic M. Evolution of anelloviruses from a circovirus-like ancestor through gradual augmentation of the jelly-roll capsid protein. Virus Evol 2023; 9:vead035. [PMID: 37325085 PMCID: PMC10266747 DOI: 10.1093/ve/vead035] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2023] [Revised: 05/15/2023] [Accepted: 05/22/2023] [Indexed: 06/17/2023] Open
Abstract
Anelloviruses are highly prevalent in diverse mammals, including humans, but so far have not been linked to any disease and are considered to be part of the 'healthy virome'. These viruses have small circular single-stranded DNA (ssDNA) genomes and encode several proteins with no detectable sequence similarity to proteins of other known viruses. Thus, anelloviruses are the only family of eukaryotic ssDNA viruses currently not included in the realm Monodnaviria. To gain insights into the provenance of these enigmatic viruses, we sequenced more than 250 complete genomes of anelloviruses from nasal and vaginal swab samples of Weddell seal (Leptonychotes weddellii) from Antarctica and a fecal sample of grizzly bear (Ursus arctos horribilis) from the USA and performed a comprehensive family-wide analysis of the signature anellovirus protein ORF1. Using state-of-the-art remote sequence similarity detection approaches and structural modeling with AlphaFold2, we show that ORF1 orthologs from all Anelloviridae genera adopt a jelly-roll fold typical of viral capsid proteins (CPs), establishing an evolutionary link to other eukaryotic ssDNA viruses, specifically, circoviruses. However, unlike CPs of other ssDNA viruses, ORF1 encoded by anelloviruses from different genera display remarkable variation in size, due to insertions into the jelly-roll domain. In particular, the insertion between β-strands H and I forms a projection domain predicted to face away from the capsid surface and function at the interface of virus-host interactions. Consistent with this prediction and supported by recent experimental evidence, the outermost region of the projection domain is a mutational hotspot, where rapid evolution was likely precipitated by the host immune system. Collectively, our findings further expand the known diversity of anelloviruses and explain how anellovirus ORF1 proteins likely diverged from canonical jelly-roll CPs through gradual augmentation of the projection domain. We suggest assigning Anelloviridae to a new phylum, 'Commensaviricota', and including it into the kingdom Shotokuvirae (realm Monodnaviria), alongside Cressdnaviricota and Cossaviricota.
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Affiliation(s)
- Anamarija Butkovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 25 rue du Dr Roux, Paris 75015, France
| | - Simona Kraberger
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Zoe Smeele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Darren P Martin
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Kara Schmidlin
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Rafaela S Fontenele
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
| | - Michelle R Shero
- Biology Department, Woods Hole Oceanographic Institution, 266 Woods Hole Rd, Woods Hole, MA 02543, USA
| | - Roxanne S Beltran
- Department of Ecology and Evolutionary Biology, University of California Santa Cruz, 130 McAllister Way, Santa Cruz, CA 95060, USA
| | - Amy L Kirkham
- U.S. Fish and Wildlife Service, Marine Mammals Management, 1011 E, Tudor Road, Anchorage, AK 99503, USA
| | - Maketalena Aleamotu’a
- School of Environmental and Life Sciences, The University of Newcastle, University Drive, Callaghan, NSW 2308, Australia
| | - Jennifer M Burns
- Department of Biological Sciences, Texas Tech University, 2500 Broadway, Lubbock, TX 79409, USA
| | - Eugene V Koonin
- National Center for Biotechnology Information, National Library of Medicine, 8600 Rockville Pike, Bethesda, MD 20894, USA
| | - Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, Center for Evolution and Medicine, School of Life Sciences, Arizona State University, 1001 S. McAllister Ave, Tempe, AZ 85287, USA
- Computational Biology Division, Department of Integrative Biomedical Sciences, Institute of Infectious Diseases and Molecular Medicine, University of Cape Town, Observatory, 1 Anzio Road, Cape Town 7925, South Africa
| | - Mart Krupovic
- Institut Pasteur, Université Paris Cité, CNRS UMR6047, Archaeal Virology Unit, 25 rue du Dr Roux, Paris 75015, France
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Kaczorowska J, Timmerman AL, Deijs M, Kinsella CM, Bakker M, van der Hoek L. Anellovirus evolution during long-term chronic infection. Virus Evol 2023; 9:vead001. [PMID: 36726484 PMCID: PMC9885978 DOI: 10.1093/ve/vead001] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 12/19/2022] [Accepted: 01/04/2023] [Indexed: 01/09/2023] Open
Abstract
Human anelloviruses (AVs) are extremely genetically diverse, are widespread in the human population, and cause chronic infections. However, the evolutionary dynamics of AVs within single hosts is currently unknown, and it is unclear whether these changes have an implication on the long-term persistence of AVs in the host. Here, we assessed the evolutionary dynamics of six AV lineages during 30 years of chronic infection at single host resolution. The total number of substitutions and the number of variable sites increased over time. However, not all substitutions reached population fixation, showing that AV lineages form heterogeneous swarms within the host. Most substitutions occurred within a hypervariable region (HVR) located between nucleotide positions 800 and 1,300 of ORF1, which is known to be located within the spike domain. Different regions of the ORF1 gene undergo either positive or negative selection pressure. Sites under strong diversifying selection pressure were detected in the HVR, while the majority of the sites under purifying selection were detected outside this region. The HVR may play the role of an immunological decoy that prevents antibodies from binding to more vulnerable parts of ORF1. Moreover, the frequent substitutions in this region may increase the chances of AV particles escaping immune recognition.
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Affiliation(s)
| | | | - Martin Deijs
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105 AZ, The Netherlands,Amsterdam Institute for Infection and Immunity, Postbus 22660, Amsterdam 1100 DD, The Netherlands
| | | | - Margreet Bakker
- Department of Medical Microbiology and Infection Prevention, Laboratory of Experimental Virology, Amsterdam UMC, University of Amsterdam, Meibergdreef 9, Amsterdam 1105 AZ, The Netherlands,Amsterdam Institute for Infection and Immunity, Postbus 22660, Amsterdam 1100 DD, The Netherlands
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3
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Virus Diversity, Abundance, and Evolution in Three Different Bat Colonies in Switzerland. Viruses 2022; 14:v14091911. [PMID: 36146717 PMCID: PMC9505930 DOI: 10.3390/v14091911] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/08/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Bats are increasingly recognized as reservoirs for many different viruses that threaten public health, such as Hendravirus, Ebolavirus, Nipahvirus, and SARS- and MERS-coronavirus. To assess spillover risk, viromes of bats from different parts of the world have been investigated in the past. As opposed to most of these prior studies, which determined the bat virome at a single time point, the current work was performed to monitor changes over time. Specifically, fecal samples of three endemic Swiss bat colonies consisting of three different bat species were collected over three years and analyzed using next-generation sequencing. Furthermore, single nucleotide variants of selected DNA and RNA viruses were analyzed to investigate virus genome evolution. In total, sequences of 22 different virus families were found, of which 13 are known to infect vertebrates. Most interestingly, in a Vespertilio murinus colony, sequences from a MERS-related beta-coronavirus were consistently detected over three consecutive years, which allowed us to investigate viral genome evolution in a natural reservoir host.
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Kaczorowska J, van der Hoek L. Human anelloviruses: diverse, omnipresent and commensal members of the virome. FEMS Microbiol Rev 2021; 44:305-313. [PMID: 32188999 PMCID: PMC7326371 DOI: 10.1093/femsre/fuaa007] [Citation(s) in RCA: 87] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2019] [Accepted: 03/02/2020] [Indexed: 12/12/2022] Open
Abstract
Anelloviruses are small, single stranded circular DNA viruses. They are extremely diverse and have not been associated with any disease so far. Strikingly, these small entities infect most probably the complete human population, and there are no convincing examples demonstrating viral clearance from infected individuals. The main transmission could be via fecal-oral or airway route, as infections occur at an early age. However, due to the lack of an appropriate culture system, the virus–host interactions remain enigmatic. Anelloviruses are obviously mysterious viruses, and their impact on human life is not yet known, but, with no evidence of a disease association, a potential beneficial effect on human health should also be investigated.
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Affiliation(s)
- Joanna Kaczorowska
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Location AMC, University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands
| | - Lia van der Hoek
- Laboratory of Experimental Virology, Department of Medical Microbiology, Amsterdam UMC, Location AMC, University of Amsterdam, Meibergdreef 9, Amsterdam, the Netherlands
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Mrzljak A, Tabain I, Premac H, Bogdanic M, Barbic L, Savic V, Stevanovic V, Jelic A, Mikulic D, Vilibic-Cavlek T. The Role of Emerging and Neglected Viruses in the Etiology of Hepatitis. Curr Infect Dis Rep 2019; 21:51. [PMID: 31754812 DOI: 10.1007/s11908-019-0709-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
PURPOSE OF REVIEW In this review, we present the overview of emerging and neglected viruses associated with liver involvement. RECENT FINDINGS Hepatitis E virus (HEV) emerged in the last two decades, causing hepatitis in many parts of the world. Moreover, liver involvement was also described in some emerging arboviral infections. Many reports showed dengue-associated liver injury; however, chikungunya, West Nile, tick-borne encephalitis, and Zika virus are rarely associated with clinically manifest liver disease. In addition, some neglected highly prevalent viruses such as adenoviruses and parvovirus B19 are capable of causing hepatitis in specific population groups. Anelloviruses (torque teno virus/torque teno mini virus/torque teno midi virus, SEN virus), human bocavirus, pegiviruses, and lymphocytic choriomeningitis virus have shown a little potential for causing hepatitis, but their role in the etiology of liver disease remains to be determined. In addition to the well-known hepatotropic viruses, many emerging and neglected viruses have been associated with liver diseases. The number of emerging zoonotic viruses has been increasingly recognized. While zoonotic potential of HEV is well documented, the recent identification of new hepatitis-related animal viruses such as HEV strains from rabbits and camels, non-primate hepaciviruses in domestic dogs and horses, as well as equine and porcine pegivirus highlights the possible zoonotic transmission in the context of "One Health." However, zoonotic potential and hepatotropism of animal hepatitis viruses remain to be determined.
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Affiliation(s)
- Anna Mrzljak
- Department of Medicine, Merkur University Hospital, Salata 3b, 10000, Zagreb, Croatia.
- School of Medicine, University of Zagreb, Zagreb, Croatia.
| | - Irena Tabain
- Department of Virology, Croatian Institute of Public Health, Zagreb, Croatia
| | - Hrvoje Premac
- Department of Medicine, Varazdin General Hospital, Varazdin, Croatia
| | - Maja Bogdanic
- Department of Virology, Croatian Institute of Public Health, Zagreb, Croatia
| | - Ljubo Barbic
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Vladimir Savic
- Poultry Center, Laboratory for Virology and Serology, Croatian Veterinary Institute, Zagreb, Croatia
| | - Vladimir Stevanovic
- Department of Microbiology and Infectious Diseases with Clinic, Faculty of Veterinary Medicine, University of Zagreb, Zagreb, Croatia
| | - Ana Jelic
- Department of Medicine, Merkur University Hospital, Salata 3b, 10000, Zagreb, Croatia
| | - Danko Mikulic
- Department of Surgery, Merkur University Hospital, Zagreb, Croatia
| | - Tatjana Vilibic-Cavlek
- School of Medicine, University of Zagreb, Zagreb, Croatia
- Department of Virology, Croatian Institute of Public Health, Zagreb, Croatia
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Bédarida S, Dussol B, Signoli M, Biagini P. Analysis of Anelloviridae sequences characterized from serial human and animal biological samples. INFECTION GENETICS AND EVOLUTION 2017; 53:89-93. [PMID: 28536071 DOI: 10.1016/j.meegid.2017.05.017] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 04/28/2017] [Accepted: 05/19/2017] [Indexed: 11/19/2022]
Abstract
Rolling-circle amplification-sequence-independent single primer amplifications (RCA-SISPA) and/or RCA-PCR-based approaches were applied to serial human plasma and animal (domestic cat) saliva samples. Complete SENV-H-related and PRA4 Anelloviridae genomes were characterized and analysed over time (~16 and 6.5years for human and animal samples, respectively). Genomic sequences and deduced putative coding regions were compared. Comparable values, i.e. ~2×10-4subs/site/year, were obtained for estimated rates of non-synonymous substitutions. A "hot-spot" of mutations located on the SENV-H-related ORF1 was identified. These results are first data concerning Anelloviridae evolution in a human and an animal host based on the analysis of complete sequences.
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Affiliation(s)
- Sandra Bédarida
- EFS Alpes-Méditerranée, Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France
| | - Bertrand Dussol
- Nephrology and Renal Transplantation Centre, CHU Conception, Marseille, France
| | | | - Philippe Biagini
- EFS Alpes-Méditerranée, Aix Marseille Univ, CNRS, EFS, ADES, Marseille, France.
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Streck AF, Canal CW, Truyen U. Molecular epidemiology and evolution of porcine parvoviruses. INFECTION GENETICS AND EVOLUTION 2015; 36:300-306. [DOI: 10.1016/j.meegid.2015.10.007] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 10/03/2015] [Accepted: 10/06/2015] [Indexed: 11/16/2022]
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Sarker S, Ghorashi SA, Forwood JK, Bent SJ, Peters A, Raidal SR. Phylogeny of beak and feather disease virus in cockatoos demonstrates host generalism and multiple-variant infections within Psittaciformes. Virology 2014; 460-461:72-82. [PMID: 25010272 DOI: 10.1016/j.virol.2014.04.021] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Revised: 01/09/2014] [Accepted: 04/17/2014] [Indexed: 01/18/2023]
Abstract
Phylogenetic analyses of the highly genetically diverse but antigenically conserved, single-stranded circular, DNA genome of the avian circovirus, beak and feather disease virus (BFDV) from cockatoo species throughout Australia demonstrated a high mutation rate for BFDV (orders of magnitude fall in the range of 10(-4) substitutions/site/year) along with strong support for recombination indicating active cross-species transmission in various subpopulations. Multiple variants of BFDV were demonstrated with at least 30 genotypic variants identified within nine individual birds, with one containing up to 7 variants. Single genetic variants were detected in feathers from 2 birds but splenic tissue provided further variants. The rich BFDV genetic diversity points to Australasia as the most likely geographical origin of this virus and supports flexible host switching. We propose this as evidence of Order-wide host generalism in the Psittaciformes characterised by high mutability that is buffered by frequent recombination and slow replication strategy.
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Affiliation(s)
- Subir Sarker
- School of Animal and Veterinary Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia; Graham Centre for Agricultural Innovation, NSW Department of Primary Industries and Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia.
| | - Seyed A Ghorashi
- School of Animal and Veterinary Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia; Graham Centre for Agricultural Innovation, NSW Department of Primary Industries and Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia.
| | - Jade K Forwood
- School of Biomedical Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia; Graham Centre for Agricultural Innovation, NSW Department of Primary Industries and Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia.
| | - Stephen J Bent
- Molecular and Biomedical Science, Faculty of Sciences, The University of Adelaide, Australia.
| | - Andrew Peters
- School of Animal and Veterinary Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia; Graham Centre for Agricultural Innovation, NSW Department of Primary Industries and Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia.
| | - Shane R Raidal
- School of Animal and Veterinary Sciences, Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia; Graham Centre for Agricultural Innovation, NSW Department of Primary Industries and Charles Sturt University, Boorooma Street, Wagga Wagga, New South Wales 2678, Australia.
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Abstract
Studying phage codon adaptation is important not only for understanding the process of translation elongation, but also for reengineering phages for medical and industrial purposes. To evaluate the effect of mutation and selection on phage codon usage, we developed an index to measure selection imposed by host translation machinery, based on the difference in codon usage between all host genes and highly expressed host genes. We developed linear and nonlinear models to estimate the C→T mutation bias in different phage lineages and to evaluate the relative effect of mutation and host selection on phage codon usage. C→T-biased mutations occur more frequently in single-stranded DNA (ssDNA) phages than in double-stranded DNA (dsDNA) phages and affect not only synonymous codon usage, but also nonsynonymous substitutions at second codon positions, especially in ssDNA phages. The host translation machinery affects codon adaptation in both dsDNA and ssDNA phages, with a stronger effect on dsDNA phages than on ssDNA phages. Strand asymmetry with the associated local variation in mutation bias can significantly interfere with codon adaptation in both dsDNA and ssDNA phages.
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10
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Sarker S, Patterson EI, Peters A, Baker GB, Forwood JK, Ghorashi SA, Holdsworth M, Baker R, Murray N, Raidal SR. Mutability dynamics of an emergent single stranded DNA virus in a naïve host. PLoS One 2014; 9:e85370. [PMID: 24416396 PMCID: PMC3885698 DOI: 10.1371/journal.pone.0085370] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2013] [Accepted: 11/26/2013] [Indexed: 01/21/2023] Open
Abstract
Quasispecies variants and recombination were studied longitudinally in an emergent outbreak of beak and feather disease virus (BFDV) infection in the orange-bellied parrot (Neophema chrysogaster). Detailed health monitoring and the small population size (<300 individuals) of this critically endangered bird provided an opportunity to longitudinally track viral replication and mutation events occurring in a circular, single-stranded DNA virus over a period of four years within a novel bottleneck population. Optimized PCR was used with different combinations of primers, primer walking, direct amplicon sequencing and sequencing of cloned amplicons to analyze BFDV genome variants. Analysis of complete viral genomes (n = 16) and Rep gene sequences (n = 35) revealed that the outbreak was associated with mutations in functionally important regions of the normally conserved Rep gene and immunogenic capsid (Cap) gene with a high evolutionary rate (3.41×10−3 subs/site/year) approaching that for RNA viruses; simultaneously we observed significant evidence of recombination hotspots between two distinct progenitor genotypes within orange-bellied parrots indicating early cross-transmission of BFDV in the population. Multiple quasispecies variants were also demonstrated with at least 13 genotypic variants identified in four different individual birds, with one containing up to seven genetic variants. Preferential PCR amplification of variants was also detected. Our findings suggest that the high degree of genetic variation within the BFDV species as a whole is reflected in evolutionary dynamics within individually infected birds as quasispecies variation, particularly when BFDV jumps from one host species to another.
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Affiliation(s)
- Subir Sarker
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
- Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga, New South Wales, Australia
| | - Edward I. Patterson
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
- Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga, New South Wales, Australia
| | - Andrew Peters
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
- Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga, New South Wales, Australia
| | - G. Barry Baker
- Institute of Marine and Antarctic Studies, University of Tasmania, Hobart, Tasmania, Australia
| | - Jade K. Forwood
- School of Biomedical Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
- Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga, New South Wales, Australia
| | - Seyed A. Ghorashi
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
- Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga, New South Wales, Australia
| | - Mark Holdsworth
- Biodiversity Conservation Branch, Department of Primary Industries, Parks, Water and Environment, Hobart, Tasmania, Australia
| | - Rupert Baker
- Healesville Sanctuary, Zoos Victoria, Healesville, Victoria, Australia
| | - Neil Murray
- Department of Genetics, La Trobe University, Bundoora, Victoria, Australia
| | - Shane R. Raidal
- School of Animal and Veterinary Sciences, Charles Sturt University, Wagga Wagga, New South Wales, Australia
- Graham Centre for Agricultural Innovation (NSW Department of Primary Industries and Charles Sturt University), Wagga Wagga, New South Wales, Australia
- * E-mail:
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Kew MC. Hepatitis viruses (other than hepatitis B and C viruses) as causes of hepatocellular carcinoma: an update. J Viral Hepat 2013; 20:149-57. [PMID: 23383653 DOI: 10.1111/jvh.12043] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2012] [Accepted: 11/01/2012] [Indexed: 12/13/2022]
Abstract
Chronic hepatitis B and C virus infections are universally accepted as causes of hepatocellular carcinoma in humans. Hepatitis A and E viruses cause only acute self-limiting infections of the liver. Of the remaining hepatitis viruses - Delta hepatitis, hepatitis G (GB-C), TT and SEN - all have at some time been incriminated as causes of hepatocellular carcinoma. Delta hepatitis virus requires helper functions from hepatitis B virus to become invasive. Chronic Delta/hepatitis B viral co-infection runs a more severe course than that resulting from chronic hepatitis B virus infection alone, with progression to cirrhosis being more likely and more rapid. A substantial majority of the early studies did not find an increased incidence of hepatocellular carcinoma in co-infected individuals. But more recently, an increased incidence of the tumour has been recorded more often than no increase. Further studies are needed to draw a firm conclusion with regard to the hepatocarcinogenic effect of dual Delta/hepatitis B virus co-infection. With one exception, no published study (of 13) has incriminated chronic infection with hepatitis G virus as a cause of hepatocellular carcinoma. The dissenting study, published in 1999, was the only one performed in the United States. Fewer studies of the hepatocarcinogenic effect of TT virus have been performed. Apart from one study, published in 1999, no convincing evidence is available that supports a causal role for TT virus in hepatocarcinogenesis. The exception was in Japanese patients with high hepatitis C viral loads but independent of chronic hepatitis C virus infection. No evidence has been produced to indicate that SEN virus causes hepatocellular carcinoma.
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Affiliation(s)
- M C Kew
- Department of Medicine, Groote Schuur Hospital and University of Cape Town, Cape Town, South Africa.
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12
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Monjane AL, Pande D, Lakay F, Shepherd DN, van der Walt E, Lefeuvre P, Lett JM, Varsani A, Rybicki EP, Martin DP. Adaptive evolution by recombination is not associated with increased mutation rates in Maize streak virus. BMC Evol Biol 2012; 12:252. [PMID: 23268599 PMCID: PMC3556111 DOI: 10.1186/1471-2148-12-252] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2012] [Accepted: 12/12/2012] [Indexed: 12/29/2022] Open
Abstract
BACKGROUND Single-stranded (ss) DNA viruses in the family Geminiviridae are proving to be very useful in real-time evolution studies. The high mutation rate of geminiviruses and other ssDNA viruses is somewhat mysterious in that their DNA genomes are replicated in host nuclei by high fidelity host polymerases. Although strand specific mutation biases observed in virus species from the geminivirus genus Mastrevirus indicate that the high mutation rates in viruses in this genus may be due to mutational processes that operate specifically on ssDNA, it is currently unknown whether viruses from other genera display similar strand specific mutation biases. Also, geminivirus genomes frequently recombine with one another and an alternative cause of their high mutation rates could be that the recombination process is either directly mutagenic or produces a selective environment in which the survival of mutants is favoured. To investigate whether there is an association between recombination and increased basal mutation rates or increased degrees of selection favoring the survival of mutations, we compared the mutation dynamics of the MSV-MatA and MSV-VW field isolates of Maize streak virus (MSV; Mastrevirus), with both a laboratory constructed MSV recombinant, and MSV recombinants closely resembling MSV-MatA. To determine whether strand specific mutation biases are a general characteristic of geminivirus evolution we compared mutation spectra arising during these MSV experiments with those arising during similar experiments involving the geminivirus Tomato yellow leaf curl virus (Begomovirus genus). RESULTS Although both the genomic distribution of mutations and the occurrence of various convergent mutations at specific genomic sites indicated that either mutation hotspots or selection for adaptive mutations might elevate observed mutation rates in MSV, we found no association between recombination and mutation rates. Importantly, when comparing the mutation spectra of MSV and TYLCV we observed similar strand specific mutation biases arising predominantly from imbalances in the complementary mutations G → T: C → A. CONCLUSIONS While our results suggest that recombination does not strongly influence mutation rates in MSV, they indicate that high geminivirus mutation rates are at least partially attributable to increased susceptibility of all geminivirus genomes to oxidative damage while in a single stranded state.
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Affiliation(s)
- Adérito L Monjane
- Department of Molecular and Cell Biology, University of Cape Town, Rondebosch, Cape Town 7701, South Africa
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Phylogenetic networks to study the origin and evolution of porcine circovirus type 2 (PCV2) in Cuba. Vet Microbiol 2011; 151:245-54. [DOI: 10.1016/j.vetmic.2011.03.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2010] [Revised: 03/16/2011] [Accepted: 03/18/2011] [Indexed: 12/11/2022]
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Abstract
Based on their extremely high mutation rates, RNA viruses have been traditionally considered as the fastest evolving entities in nature. However, recent work has revealed that, despite their greater replication fidelity, single-stranded (ss) DNA viruses can evolve fast in a similar way. To further investigate this issue, we have compared the rates of adaptation and molecular evolution of ssRNA and ssDNA viruses under highly controlled laboratory conditions using the bacteriophages ΦX174, G4, f1, Qβ, SP, and MS2 as model systems. Our results indicate that ssRNA phages evolve faster than ssDNA phages under strong selective pressure, and that their extremely high mutation rates appear to be optimal for this kind of scenario. However, their performance becomes similar to that of ssDNA phages over the longer term or when the population is moderately well-adapted. Interestingly, the roughly 100-fold difference between the mutation rates of ssRNA and ssDNA phages yields less than a fivefold difference in adaptation and nucleotide substitution rates. The results are therefore consistent with the observation that, despite their lower mutation rates, ssDNA viruses can sometimes match the evolvability of RNA viruses.
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Affiliation(s)
- Pilar Domingo-Calap
- Institut Cavanilles de Biodiversitat i Biologia Evolutiva, Universitat de València, Spain Departament de Genètica, Universitat de València, Spain Unidad Mixta de Investigación en Genómica y Salud, Centro Superior de Investigación en Salud Pública (CSISP), Valencia, Spain E-mail:
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Karimi-Rastehkenari A, Bouzari M. High frequency of SEN virus infection in thalassemic patients and healthy blood donors in Iran. Virol J 2010; 7:1. [PMID: 20044930 PMCID: PMC2819036 DOI: 10.1186/1743-422x-7-1] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2009] [Accepted: 01/02/2010] [Indexed: 01/22/2023] Open
Abstract
Background SEN virus is a blood-borne, circular ssDNA virus and possessing nine genotypes (A to I). Among nine genotypes, SENV-D and SENV-H genotypes have the strong link with patients with unknown (none-A to E) hepatitis infections. Infection with blood-borne viruses is the second important cause of death in thalassemic patients. The aim of this study was to determine the frequency of SENV-D and SENV-H genotypes viremia by performing nested-PCR in 120 and 100 sera from healthy blood donors and thalassemic patients in Guilan Province, North of Iran respectively. Also, to explicate a possible role of SEN virus in liver disease and established changes in blood factors, the serum aminotransferases (ALT and AST) and some of the blood factors were measured. Results Frequency of SENV-D, SENV (SENV-H or SENV-D) and co-infection (both SENV-D and SENV-H) viremia was significantly higher among thalassemic patients than healthy individuals. Frequency of SENV-H viremia was significantly higher than SENV-D among healthy individuals. In comparison to SENV-D negative patients, the mean of mean corpuscular hemoglobin was significantly higher in SENV-D positive and co-infection cases (P < 0.05). The means of AST and ALT were significantly higher in thalassemic patients than healthy blood donors, but there were not any significant differences in the means of the liver levels between SENV-positive and -negative individuals in healthy blood donors and thalassemic patients. High nucleotide homology observed among PCR amplicon's sequences in healthy blood donors and thalassemic patients. Conclusions The high rate of co-infection shows that different genotypes of SENV have no negative effects on each other. The high frequency of SENV infection among thalassemic patients suggests blood transfusion as main route of transmission. High frequency of SENV infection in healthy individuals indicates that other routes rather than blood transfusion also are important. Frequency of 90.8% of SENV infection among healthy blood donors as well as high nucleotide homology of sequenced amplicons between two groups can probably suggest that healthy blood donors infected by SENV act partly as a source of SENV transmission to the thalassemic patients. In conclusion, SENV-D isolate in Guilan Province may be having a pathogenic agent for thalassemic patients.
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Domingo-Calap P, Cuevas JM, Sanjuán R. The fitness effects of random mutations in single-stranded DNA and RNA bacteriophages. PLoS Genet 2009; 5:e1000742. [PMID: 19956760 PMCID: PMC2776273 DOI: 10.1371/journal.pgen.1000742] [Citation(s) in RCA: 87] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2009] [Accepted: 10/26/2009] [Indexed: 11/18/2022] Open
Abstract
Mutational fitness effects can be measured with relatively high accuracy in viruses due to their small genome size, which facilitates full-length sequencing and genetic manipulation. Previous work has shown that animal and plant RNA viruses are very sensitive to mutation. Here, we characterize mutational fitness effects in single-stranded (ss) DNA and ssRNA bacterial viruses. First, we performed a mutation-accumulation experiment in which we subjected three ssDNA (ΦX174, G4, F1) and three ssRNA phages (Qβ, MS2, and SP) to plaque-to-plaque transfers and chemical mutagenesis. Genome sequencing and growth assays indicated that the average fitness effect of the accumulated mutations was similar in the two groups. Second, we used site-directed mutagenesis to obtain 45 clones of ΦX174 and 42 clones of Qβ carrying random single-nucleotide substitutions and assayed them for fitness. In ΦX174, 20% of such mutations were lethal, whereas viable ones reduced fitness by 13% on average. In Qβ, these figures were 29% and 10%, respectively. It seems therefore that high mutational sensitivity is a general property of viruses with small genomes, including those infecting animals, plants, and bacteria. Mutational fitness effects are important for understanding processes of fitness decline, but also of neutral evolution and adaptation. As such, these findings can contribute to explain the evolution of ssDNA and ssRNA viruses. The fitness effects of mutations are the raw material for natural selection. It has been shown that point mutations typically have strongly deleterious effects in plant and animal RNA viruses, whereas cellular organisms are comparatively more robust. Here, we characterize the fitness effects of random mutations in DNA viruses and compare them with those found in RNA viruses, using six phage species of similar genome sizes. To achieve this goal, we introduced mutations by chemical and site-directed mutagenesis, identified the genetic changes by sequencing, and quantified their fitness effects using growth-rate assays. In all cases, mutations had a strong average impact on fitness. We conclude that mutational sensitivity is a general property of viruses with small genomes and discuss the evolutionary implications of these findings.
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Affiliation(s)
| | - José M. Cuevas
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, València, Spain
| | - Rafael Sanjuán
- Instituto Cavanilles de Biodiversidad y Biología Evolutiva, València, Spain
- Departamento de Genética, Universitat de València, València, Spain
- * E-mail:
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17
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Abstract
The point mutation rate of phage PhiX174 was determined using the fluctuation test. After identifying the genetic changes associated with the selected phenotype, we obtained an estimate of 1.0x10(-6) substitutions per base per round of copying, which is consistent with Drake's rule (0.003 mutations per genome per round of copying in DNA-based microorganisms).
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Harkins GW, Delport W, Duffy S, Wood N, Monjane AL, Owor BE, Donaldson L, Saumtally S, Triton G, Briddon RW, Shepherd DN, Rybicki EP, Martin DP, Varsani A. Experimental evidence indicating that mastreviruses probably did not co-diverge with their hosts. Virol J 2009; 6:104. [PMID: 19607673 PMCID: PMC2719613 DOI: 10.1186/1743-422x-6-104] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2009] [Accepted: 07/16/2009] [Indexed: 02/06/2023] Open
Abstract
Background Despite the demonstration that geminiviruses, like many other single stranded DNA viruses, are evolving at rates similar to those of RNA viruses, a recent study has suggested that grass-infecting species in the genus Mastrevirus may have co-diverged with their hosts over millions of years. This "co-divergence hypothesis" requires that long-term mastrevirus substitution rates be at least 100,000-fold lower than their basal mutation rates and 10,000-fold lower than their observable short-term substitution rates. The credibility of this hypothesis, therefore, hinges on the testable claim that negative selection during mastrevirus evolution is so potent that it effectively purges 99.999% of all mutations that occur. Results We have conducted long-term evolution experiments lasting between 6 and 32 years, where we have determined substitution rates of between 2 and 3 × 10-4 substitutions/site/year for the mastreviruses Maize streak virus (MSV) and Sugarcane streak Réunion virus (SSRV). We further show that mutation biases are similar for different geminivirus genera, suggesting that mutational processes that drive high basal mutation rates are conserved across the family. Rather than displaying signs of extremely severe negative selection as implied by the co-divergence hypothesis, our evolution experiments indicate that MSV and SSRV are predominantly evolving under neutral genetic drift. Conclusion The absence of strong negative selection signals within our evolution experiments and the uniformly high geminivirus substitution rates that we and others have reported suggest that mastreviruses cannot have co-diverged with their hosts.
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Affiliation(s)
- Gordon W Harkins
- South African National Bioinformatics Institute, University of the Western Cape, Cape Town, South Africa.
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Duffy S, Holmes EC. Validation of high rates of nucleotide substitution in geminiviruses: phylogenetic evidence from East African cassava mosaic viruses. J Gen Virol 2009; 90:1539-1547. [PMID: 19264617 PMCID: PMC4091138 DOI: 10.1099/vir.0.009266-0] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2008] [Accepted: 02/17/2009] [Indexed: 12/16/2022] Open
Abstract
Whitefly-transmitted geminiviruses are major pathogens of the important crop cassava in Africa. The intensive sampling and sequencing of cassava mosaic disease-causing viruses that occurred in the wake of a severe outbreak in Central Africa (1997-2002) allowed us to estimate the rate of evolution of this virus. East African cassava mosaic virus and related species are obligately bipartite (DNA-A and DNA-B segments), and these two genome segments have different evolutionary histories. Despite these phylogenetic differences, we inferred high rates of nucleotide substitution in both segments: mean rates of 1.60x10(-3) and 1.33x10(-4) substitutions site(-1) year(-1) for DNA-A and DNA-B, respectively. While similarly high substitution rates were found in datasets free of detectable recombination, only that estimated for the coat protein gene (AV1), for which an additional DNA-A sequence isolated in 1995 was available, was statistically robust. These high substitution rates also confirm that those previously estimated for the monopartite tomato yellow leaf curl virus (TYLCV) are representative of multiple begomoviruses. We also validated our rate estimates by comparing them with those depicting the emergence of TYLCV in North America. These results further support the notion that geminiviruses evolve as rapidly as many RNA viruses.
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Affiliation(s)
- Siobain Duffy
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Department of Ecology, Evolution and Natural Resources, School of Environmental and Biological Sciences, Rutgers University, New Brunswick, NJ 08901, USA
| | - Edward C. Holmes
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA
- Fogarty International Center, National Institutes of Health, Bethesda, MD 20892, USA
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Discovery of a novel single-stranded DNA virus from a sea turtle fibropapilloma by using viral metagenomics. J Virol 2008; 83:2500-9. [PMID: 19116258 DOI: 10.1128/jvi.01946-08] [Citation(s) in RCA: 93] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Viral metagenomics, consisting of viral particle purification and shotgun sequencing, is a powerful technique for discovering viruses associated with diseases with no definitive etiology, viruses that share limited homology with known viruses, or viruses that are not culturable. Here we used viral metagenomics to examine viruses associated with sea turtle fibropapillomatosis (FP), a debilitating neoplastic disease affecting sea turtles worldwide. By means of purifying and shotgun sequencing the viral community directly from the fibropapilloma of a Florida green sea turtle, a novel single-stranded DNA virus, sea turtle tornovirus 1 (STTV1), was discovered. The single-stranded, circular genome of STTV1 was approximately 1,800 nucleotides in length. STTV1 has only weak amino acid level identities (25%) to chicken anemia virus in short regions of its genome; hence, STTV1 may represent the first member of a novel virus family. A total of 35 healthy turtles and 27 turtles with FP were tested for STTV1 using PCR, and only 2 turtles severely afflicted with FP were positive. The affected turtles were systemically infected with STTV1, since STTV1 was found in blood and all major organs. STTV1 exists as a quasispecies, with several genome variants identified in the fibropapilloma of each positive turtle, suggesting rapid evolution of this virus. The STTV1 variants were identical over the majority of their genomes but contained a hypervariable region with extensive divergence. This study demonstrates the potential of viral metagenomics for discovering novel viruses directly from animal tissue, which can enhance our understanding of viral evolution and diversity.
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Kakkola L, Bondén H, Hedman L, Kivi N, Moisala S, Julin J, Ylä-Liedenpohja J, Miettinen S, Kantola K, Hedman K, Söderlund-Venermo M. Expression of all six human Torque teno virus (TTV) proteins in bacteria and in insect cells, and analysis of their IgG responses. Virology 2008; 382:182-9. [PMID: 18947848 DOI: 10.1016/j.virol.2008.09.012] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Revised: 07/21/2008] [Accepted: 09/08/2008] [Indexed: 01/03/2023]
Abstract
Torque teno virus (TTV) is a non-enveloped human virus with a circular ( approximately 3800 nt) ssDNA genome. TTV transcription results in three viral mRNAs and six proteins, the function or antigenicity of which are unknown. The six open reading frames of TTV genotype 6 were expressed in bacteria and insect cells. Expression of the ORF1/1-encoded protein was inefficient, while expression of the others was successful, with ORF1 and ORF1/2 as arginine-rich region depleted. All six recombinant TTV proteins were antigenic. Of healthy adults, 11/25 (44%) showed strong IgG reactivity with one or more proteins. Four subjects, two of whom were genotype-6-DNA positive, were followed. One of the latter showed concurrently a strong IgG response against the ORF1 protein. The other showed appearance of IgG against the ORF2 protein concomitantly with resolution of the genotype-6 viremia. The genotype-6 sequences remained unaltered for years, suggesting that some mechanisms other than amino acid substitutions play a role in TTV immune evasion.
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Affiliation(s)
- Laura Kakkola
- Department of Virology, Haartman Institute and Helsinki University Central Hospital Laboratory, Haartmaninkatu 3, P.O. Box 21, University of Helsinki, FIN-00014, Finland.
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van der Walt E, Martin DP, Varsani A, Polston JE, Rybicki EP. Experimental observations of rapid Maize streak virus evolution reveal a strand-specific nucleotide substitution bias. Virol J 2008; 5:104. [PMID: 18816368 PMCID: PMC2572610 DOI: 10.1186/1743-422x-5-104] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2008] [Accepted: 09/24/2008] [Indexed: 12/18/2022] Open
Abstract
Background Recent reports have indicated that single-stranded DNA (ssDNA) viruses in the taxonomic families Geminiviridae, Parvoviridae and Anellovirus may be evolving at rates of ~10-4 substitutions per site per year (subs/site/year). These evolution rates are similar to those of RNA viruses and are surprisingly high given that ssDNA virus replication involves host DNA polymerases with fidelities approximately 10 000 times greater than those of error-prone viral RNA polymerases. Although high ssDNA virus evolution rates were first suggested in evolution experiments involving the geminivirus maize streak virus (MSV), the evolution rate of this virus has never been accurately measured. Also, questions regarding both the mechanistic basis and adaptive value of high geminivirus mutation rates remain unanswered. Results We determined the short-term evolution rate of MSV using full genome analysis of virus populations initiated from cloned genomes. Three wild type viruses and three defective artificial chimaeric viruses were maintained in planta for up to five years and displayed evolution rates of between 7.4 × 10-4 and 7.9 × 10-4 subs/site/year. Conclusion These MSV evolution rates are within the ranges observed for other ssDNA viruses and RNA viruses. Although no obvious evidence of positive selection was detected, the uneven distribution of mutations within the defective virus genomes suggests that some of the changes may have been adaptive. We also observed inter-strand nucleotide substitution imbalances that are consistent with a recent proposal that high mutation rates in geminiviruses (and possibly ssDNA viruses in general) may be due to mutagenic processes acting specifically on ssDNA molecules.
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Affiliation(s)
- Eric van der Walt
- Department of Molecular and Cell Biology, University of Cape Town, Cape Town, South Africa.
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Duffy S, Shackelton LA, Holmes EC. Rates of evolutionary change in viruses: patterns and determinants. Nat Rev Genet 2008; 9:267-76. [PMID: 18319742 DOI: 10.1038/nrg2323] [Citation(s) in RCA: 1006] [Impact Index Per Article: 62.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Understanding the factors that determine the rate at which genomes generate and fix mutations provides important insights into key evolutionary mechanisms. We review our current knowledge of the rates of mutation and substitution, as well as their determinants, in RNA viruses, DNA viruses and retroviruses. We show that the high rate of nucleotide substitution in RNA viruses is matched by some DNA viruses, suggesting that evolutionary rates in viruses are explained by diverse aspects of viral biology, such as genomic architecture and replication speed, and not simply by polymerase fidelity.
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Affiliation(s)
- Siobain Duffy
- Center for Infectious Disease Dynamics, Department of Biology, Mueller Laboratory, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
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Duffy S, Holmes EC. Phylogenetic evidence for rapid rates of molecular evolution in the single-stranded DNA begomovirus tomato yellow leaf curl virus. J Virol 2008; 82:957-65. [PMID: 17977971 PMCID: PMC2224568 DOI: 10.1128/jvi.01929-07] [Citation(s) in RCA: 193] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2007] [Accepted: 10/22/2007] [Indexed: 01/04/2023] Open
Abstract
Geminiviruses are devastating viruses of plants that possess single-stranded DNA (ssDNA) DNA genomes. Despite the importance of this class of phytopathogen, there have been no estimates of the rate of nucleotide substitution in the geminiviruses. We report here the evolutionary rate of the tomato yellow leaf curl disease-causing viruses, an intensively studied group of monopartite begomoviruses. Sequences from GenBank, isolated from diseased plants between 1988 and 2006, were analyzed using Bayesian coalescent methods. The mean genomic substitution rate was estimated to be 2.88 x 10(-4) nucleotide substitutions per site per year (subs/site/year), although this rate could be confounded by frequent recombination within Tomato yellow leaf curl virus genomes. A recombinant-free data set comprising the coat protein (V1) gene in isolation yielded a similar mean rate (4.63 x 10(-4) subs/site/year), validating the order of magnitude of genomic substitution rate for protein-coding regions. The intergenic region, which is known to be more variable, was found to evolve even more rapidly, with a mean substitution rate of approximately 1.56 x 10(-3) subs/site/year. Notably, these substitution rates, the first reported for a plant DNA virus, are in line with those estimated previously for mammalian ssDNA viruses and RNA viruses. Our results therefore suggest that the high evolutionary rate of the geminiviruses is not primarily due to frequent recombination and may explain their ability to emerge in novel hosts.
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Affiliation(s)
- Siobain Duffy
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, Mueller Laboratory, University Park, PA 16802, USA.
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Spataro P, Di Pietro A, Scoglio ME, Visalli G, Chirico C, Picerno I, Ferlazzo N, Campo S, Bellinghieri G, Savica V, Santoro D, Buemi M, Costantino F. Prevalence of SENV-H and SENV-D virus: epidemiological study in blood donors and dialysis patients. Ren Fail 2006; 28:441-8. [PMID: 16825095 DOI: 10.1080/08860220600684225] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022] Open
Abstract
INTRODUCTION Recently, the identification of the SEN virus as a possible etiological agent of parental transmission hepatitis led to the study of the prevalence of such pathogen agents, particularly SENV-H, in our population. This paper compares the rate prevalence in high-risk subjects, such as dialysis patients, and low-risk subjects, such as blood donors. MATERIAL AND METHODS The study was carried out on SEN virus DNA extracted from serum of dialysis patients and blood donors, and the presence of viral genomes was performed by the nested PCR method. RESULTS The results showed a higher prevalence in male blood donors, supporting the hypothesis of an epidemiological role for sexual and also parental transmission, as is clearly demonstrated by the high prevalence in dialysis patients. The result reduced the importance of the possible etiological role of the SEN virus due to the high percentage of positivity in healthy population, and it induces one to consider poorly significant the pathogenicity of such viral agents. CONCLUSION For this instance, the authors, in agreement with the phylogenically related TT virus, described SEN viruses as absolutely not pathogens and considered them as "simple guests."
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Affiliation(s)
- Pasquale Spataro
- Department of Hygiene, Preventive Medicine, and Public Health, University of Messina, Italy
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Akiba J, Umemura T, Alter HJ, Kojiro M, Tabor E. SEN virus: epidemiology and characteristics of a transfusion-transmitted virus. Transfusion 2005; 45:1084-8. [PMID: 15987351 DOI: 10.1111/j.1537-2995.2004.00209.x] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
SEN virus (SEN-V) is a blood-borne, single-stranded, nonenveloped DNA virus. Although its prevalence varies by geographic region, it has been detected in as many as 30 percent of postoperative transfusion recipients, compared to 3 percent of postoperative patients who did not receive transfusions. A significant association has been observed between transfusion volume and the occurrence of SEN-V infection. Transmission by transfusion also has been confirmed by the detection of greater than 99 percent homology between SEN-V in donor and recipient sera. Concurrent infections with SEN-V and hepatitis B virus, hepatitis C virus, or human immunodeficiency virus type 1 have been documented, and these observations probably reflect the blood-borne transmission of these viruses as well as SEN-V. Although SEN-V was discovered as part of a search for causes of posttransfusion hepatitis, there is no firm evidence so far that SEN-V infection either causes hepatitis or worsens the course of coexistent liver disease. Nevertheless, SEN-V appears to be transmitted by transfusion, and further studies may reveal more about its role in the future.
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Affiliation(s)
- Jun Akiba
- Division of Emerging and Transfusion Transmitted Diseases, Center for Biologics Evaluation and Research, Food and Drug Administration, Bethesda, Maryland, USA
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Rajic ZA, Jankovic GM, Vidovic A, Milic NM, Skoric D, Pavlovic M, Lazarevic V. Size of the protein-coding genome and rate of molecular evolution. J Hum Genet 2005; 50:217-229. [PMID: 15883855 DOI: 10.1007/s10038-005-0242-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2004] [Accepted: 02/17/2005] [Indexed: 11/25/2022]
Abstract
In diploid populations of size N, there will be 2 Nmu mutations per nucleotide (nt) site (or per locus) per generation (mu stands for mutation rate). If either the population or the coding genome double in size, one expects 4 Nmu mutations. What is important is not the population size per se but the number of genes (coding sites), the two being often interconverted. Here we compared the total physical length of protein-coding genomes (n) with the corresponding absolute rates of synonymous substitution (K(S)), an empirical neutral reference. In the classical occupancy problem and in the coupons collector (CC) problem, n was expressed as the mean rate of change (K(CC)). Despite inherently very low power of the approaches involving averaging of rates, the mode of molecular evolution of the total size phenotype of the coding genome could be evidenced through differences between the genomic estimates of K(CC) [K(CC)=1/(ln n + 0.57721) n] and rate of molecular evolution, K(S). We found that (1) the estimates of n and K(S) are reciprocally correlated across taxa (r=0.812; p<< 0.001); (2) the gamete-cell division hypothesis (Chang et al. Proc Natl Acad Sci USA 91:827-831, 1994) can be confirmed independently in terms of K(CC)/K(S) ratios; (3) the time scale of molecular evolution changes with change in mutation rate, as previously shown by Takahata (Proc Natl Acad Sci USA 87:2419-2423, 1990), Takahata et al. (Genetics 130:925-938, 1992), and Vekemans and Slatkin (Genetics 137:1157-1165, 1994); (4) the generation time and population size (Lynch and Conery, Science 302:1401-1404, 2003) effects left their "signatures" at the level of the size phenotype of the protein-coding genome.
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Affiliation(s)
- Zoran A Rajic
- Institute of Hematology, University Clinical Center, University of Belgrade, ul. Dr. Koste Todorovica br. 2, 11000, Belgrade, Serbia
| | - Gradimir M Jankovic
- Institute of Hematology, University Clinical Center, University of Belgrade, ul. Dr. Koste Todorovica br. 2, 11000, Belgrade, Serbia.
| | - Ana Vidovic
- Institute of Hematology, University Clinical Center, University of Belgrade, ul. Dr. Koste Todorovica br. 2, 11000, Belgrade, Serbia
| | - Natasa M Milic
- Faculty of Medicine, Institute for Medical Statistics and Informatics, Belgrade, Serbia
| | - Dejan Skoric
- University Children's Hospital, University of Belgrade, Belgrade, Serbia
| | - Milorad Pavlovic
- Institute of Hematology, University Clinical Center, University of Belgrade, ul. Dr. Koste Todorovica br. 2, 11000, Belgrade, Serbia
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Abstract
AIM: To establish nested-PCR methods for the detection of SENV-D and SENV-H and to investigate the epidemiology of SEN virus in China.
METHODS: According to published gene sequences, primers from the conserved region were designed. Then, 135 samples from healthy voluntary blood donors and 242 samples from patients with various forms of liver disease were detected by nested-PCR of SENV-D/H. Some PCR products were cloned and sequenced.
RESULTS: By sequencing, the specificity of genotype-specific PCR was confirmed. SENV-D/H DNA was detected in 31% of the blood donors, which was higher than those in America and Italy (2%), and in Japan and Taiwan (15%-20%). The prevalence of SENV-D/H viremia was significantly higher in patients with hepatitis B and hepatitis C than in blood donors (59%-85% vs 31%, P < 0.05). The prevalence among patients with non-A-E hepatitis was significantly higher than among blood donors (68% vs 31%, P < 0.01), and equivalent to that among patients with hepatitis B and C.
CONCLUSION: Nested-PCR with genotype-specific primers could serve as a useful SENV screening assay. SENV has the same transmission modes as HBV and HCV. The high prevalence in patients with non-A-E hepatitis may attribute to the transmission modes, and SENV may not serve as the causative agents.
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Affiliation(s)
- Shi-Jie Mu
- School of Life Sciences and Technology, Xi'an Jiaotong University, Xi'an 710049, Shaanxi Province, China.
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Sagir A, Adams O, Kirschberg O, Erhardt A, Heintges T, Haussinger D. SEN virus does not affect treatment response in hepatitis C virus coinfected patients but SEN virus response depends on SEN virus DNA concentration. World J Gastroenterol 2004; 10:1893-7. [PMID: 15222031 PMCID: PMC4572225 DOI: 10.3748/wjg.v10.i13.1893] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
AIM: To clarify the effect of SEN virus (SENV) infection on a combination therapy including interferon alfa (IFN-α) or pegylated-IFN with ribavirin in patients with chronic hepatitis and the effect of a combination therapy on SENV.
METHODS: SENV DNA was determined by polymerase chain reaction in serum samples from 95 patients with chronic hepatitis C. Quantitative analysis was done for SENV H DNA.
RESULTS: Twenty-one (22%) of 95 patients were positive for SENV DNA. There was no difference in clinical and biochemical parameters between patients with HCV infection alone and coinfected patients. The sustained response rate for HCV clearance after combination therapy did not differ between patients with SENV (52%) and without SENV (50%, n.s.). SENV DNA was undetectable in 76% of the initially SENV positive patients at the end of follow-up. SENV H response to combination therapy was significantly correlated with SENV DNA level (P = 0.05).
CONCLUSION: SENV infection had no influence on the HCV sustained response rate to the combination therapy. Response rate of SENV to the combination therapy depends on SENV DNA level.
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Affiliation(s)
- Abdurrahman Sagir
- Klinik fur Gastroenterologie, Hepatologie und Infektiologie, Universitatsklinikum Dusseldorf, Moorenstrasse 5, 40225 Dusseldorf, Germany.
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Tang W, Peng XM, Yang SM, Wang ZQ, Wang H, Jiang XL, Zhou BP. Demonstration of gene heterogeneity and quasispecies of SEN virus. Shijie Huaren Xiaohua Zazhi 2004; 12:604-606. [DOI: 10.11569/wcjd.v12.i3.604] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM: To describe the gene heterogeneity and quasispecies of SEN virus.
METHODS: Three SEN virus subtype D or H positive sera from a SEN virus prevalence investigation in Shenzhen District were randomly selected and a nested-PCR were performed. 3 positive PCR products of each subtype were ligated into pMD18 T-vectors. 1-11 clones from every PCR product were randomly selected to be sequenced and aligned with SENV sequences retrieved from GeneBank representing strains from 4 different countries and district. Homology of nucleotide sequences were analysed and a phylogenic tree was conducted.
RESULTS: 13 clones of SENV D and 3 of SENV H were sequenced and demonstrated to belong to SENV. 81.8% (9/11) clones from a single host SZ-54 were quasispecies. The nucleotide sequence homology of 15 SENV D clones (11 of Shenzhen and 4 retrieved from GeneBank representing 4 other countries and district) were 77.7%-99.5%. The amount of mutated bases between each two of 9 clones from same host were 8.5±5.2, which was significantly different from that between each two of 11 clones from 3 hosts within Shenzhen district (28.9±3.2) and that between each two of 15 clones from different hosts and districts (29.6±7.8) (P < 0.001). The nucleotide sequence homology of 7 SENV H clones (3 of Shenzhen and 4 retrieved from GeneBank as described above) were 74.6%-95.0%. The phylogenic tree showed that clones from same patient were more related to each other than those from other patients and much closer than strains representing other countries and district.
CONCLUSION: There exist SENV quasispecies in SENV carriers. The heterogeneity of nucleic acid of SENV may be influnced by differences between hosts and regions. This unique characteristic should be taken in consideration when detecting the virus, determining sequence mutation and even discussing its clinical implication.
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Tang W, Peng XM, Zhang Y, Wang H, Jiang XL, Zhou BP. Establishment and application of polymerase chain reaction for detecting D and H subtypes of SEN virus. Shijie Huaren Xiaohua Zazhi 2003; 11:1540-1543. [DOI: 10.11569/wcjd.v11.i10.1540] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
AIM To establish a polymerase chain reaction (PCR) method to detect 2 SENV subtypes (SENV-D and SENV-H) in sera from patients with hepatitis and healthy adults.
METHODS The outer primers were designed based on the data of SENV D and H subtypes from geneBank, while sequences of the inner pair of primers were obtained from newly published medical literature, both of which were used to establish a nested-PCR. SENV-D and H in sera from 192 healthy adults and 48 patients with acute hepatitis A, 176 with chronic hepatitis B, 98 with chronic hepatitis C, and 38 with non A-E hepatitis were detected by this method.
RESULTS The specificity and sensitivity of the nested-PCR test were perfect. The prevalence of SENV-D and/or SENV-H (SENV-D/H) infections in healthy adults and patients with acute hepatitis A, chronic hepatitis B, chronic hepatitis C and non A-E hepatitis were 30.7%, 37.5%, 64.8%, 57.1% and 44.7%, respectively. SENV D/H infection were more frequent in patients with chronic hepatitis B and chronic hepatitis C than in healthy adults (P<0.001), but showed no significant difference between patients with non A-E and healthy adults (P>0.05).
CONCLUSION This nested PCR can be used to detect SEN virus. SENV infections do occur in Shenzhen. SENV may share similar modes of transmission to that of HBV and HCV, but whether it plays a causal role in non A-E hepatitis remains to be elucidated.
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Affiliation(s)
- Wei Tang
- Shenzhen Research Institute of Liver Disease, Shenzhen East Lake Hospital, Shenzhen 518020, Guangdong Province, China
| | - Xiao-Mou Peng
- Department of Infectious Disease, The Third Affiliated Hospital of Zhongshan University, Guangzhou 510630, Guangdong Province, China
| | - Ying Zhang
- Shenzhen Research Institute of Liver Disease, Shenzhen East Lake Hospital, Shenzhen 518020, Guangdong Province, China
| | - Hui Wang
- Shenzhen Research Institute of Liver Disease, Shenzhen East Lake Hospital, Shenzhen 518020, Guangdong Province, China
| | - Xiao-Ling Jiang
- Shenzhen Research Institute of Liver Disease, Shenzhen East Lake Hospital, Shenzhen 518020, Guangdong Province, China
| | - Bo-Ping Zhou
- Shenzhen Research Institute of Liver Disease, Shenzhen East Lake Hospital, Shenzhen 518020, Guangdong Province, China
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Abstract
The development of new technologies leads to the discovery of new viruses. For each of these new infectious agents, relevance to transfusion, including transmissibility by transfusion, pathogenicity, prevalence in blood donors, persistence and the availability of screening assays needs to be assessed. Since 1995, one virus and a new family of viruses have been identified. GB virus-C/hepatitis G virus (GBV-C/HGV), a flavi virus with some homology with and epidemiological features of HCV, is not related to post-transfusion hepatitis but seems to positively interfere with human immunodeficiency virus replication. Human circoviruses include TT virus (TTV) and SEN-V. Both are highly variable, constituting a large family of distantly related viruses. They appear ubiquitous, infecting humans very early in life and are largely persistent. No clinical symptoms or pathogenicity is associated with TTV, but SEN-V might be associated with some non-A-E post-transfusion hepatitis. Parvovirus B19 has been known for many years, but its transmission to recipients of plasma derivatives despite viral inactivation raised the issue of screening plasma pools by nucleic acid testing. Most fractionators quantify B19 DNA in plasma pools to ensure a viral load of <10(4) IU mL-1.
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Affiliation(s)
- J-P Allain
- Division of Transfusion Medicine, Department of Haematology, East Anglia Blood Centre, Cambridge, UK.
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Umemura T, Alter HJ, Tanaka E, Orii K, Yeo AET, Shih JWK, Matsumoto A, Yoshizawa K, Kiyosawa K. SEN virus: response to interferon alfa and influence on the severity and treatment response of coexistent hepatitis C. Hepatology 2002; 35:953-9. [PMID: 11915044 DOI: 10.1053/jhep.2002.32536] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The SEN virus (SENV) is a recently identified single-stranded, circular DNA virus. A strong association between 2 SENV variants (SENV-D and SENV-H) and transfusion-associated non-A-to-E hepatitis has been reported. To clarify the effect of SENV infection on coexisting chronic hepatitis C and the effect of interferon alfa (IFN-alpha) therapy on SENV replication, SENV DNA was quantitated by polymerase chain reaction in serum samples from 186 patients with chronic hepatitis C. Thirty-nine of 186 (21%) patients with chronic hepatitis C were positive for SENV DNA. There were no differences in the clinical, virologic and histologic features between patients with and without SENV infection. Eighteen of 102 patients with chronic hepatitis C who received IFN-alpha were positive for SENV DNA. The sustained response rate for hepatitis C virus (HCV) clearance after IFN-alpha treatment did not differ significantly between patients with SENV (28%) and without SENV infection (39%). SENV DNA levels decreased during therapy in 15 of 16 patients, and 11 of the 16 patients (69%) had a sustained loss of SENV DNA in response to IFN-alpha. In coinfected patients, SENV responses to IFN-alpha were significantly better in those who failed to clear HCV RNA than in those who lost HCV RNA (P =.013). In conclusion, SENV infection was frequently found in patients with chronic hepatitis C. SENV infection had no apparent influence on the severity of HCV-related liver disease or the HCV response to IFN-alpha. SENV was sensitive to IFN-alpha therapy and the majority of patients had a sustained virologic response.
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Affiliation(s)
- Takeji Umemura
- Second Department of Internal Medicine, Shinshu University School of Medicine, Matsumoto, Japan.
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