|
1
|
Cosentino MAC, D’arc M, Moreira FRR, Cavalcante LTDF, Mouta R, Coimbra A, Schiffler FB, Miranda TDS, Medeiros G, Dias CA, Souza AR, Tavares MCH, Tanuri A, Soares MA, dos Santos AFA. Discovery of two novel Torque Teno viruses in Callithrix penicillata provides insights on Anelloviridae diversification dynamics. Front Microbiol 2022; 13:1002963. [PMID: 36160188 PMCID: PMC9493276 DOI: 10.3389/fmicb.2022.1002963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 08/18/2022] [Indexed: 11/13/2022] Open
Abstract
The development of high-throughput sequencing (HTS) technologies and metagenomics protocols deeply impacted the discovery of viral diversity. Moreover, the characterization of novel viruses in the Neotropical primates (NP) is central for the comprehension of viral evolution dynamics in those hosts, due to their evolutionary proximity to Old World primates, including humans. In the present work, novel anelloviruses were detected and characterized through HTS protocols in the NP Callithrix penicillata, the common black-tufted marmoset. De novo assembly of generated sequences was carried out, and a total of 15 contigs were identified with complete Anelloviridae ORF1 gene, two of them including a flanking GC-rich region, confirming the presence of two whole novel genomes of ~3 kb. The identified viruses were monophyletic within the Epsilontorquevirus genus, a lineage harboring previously reported anelloviruses infecting hosts from the Cebidae family. The genetic divergence found in the new viruses characterized two novel species, named Epsilontorquevirus callithrichensis I and II. The phylogenetic pattern inferred for the Epsilontorquevirus genus was consistent with the topology of their host species tree, echoing a virus-host diversification model observed in other viral groups. This study expands the host span of Anelloviridae and provides insights into their diversification dynamics, highlighting the importance of sampling animal viral genomes to obtain a clearer depiction of their long-term evolutionary processes.
Collapse
Affiliation(s)
- Matheus Augusto Calvano Cosentino
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Mirela D’arc
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Filipe Romero Rebello Moreira
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Department of Infectious Diseases Epidemiology, Imperial College London, London, United Kingdom
| | | | - Ricardo Mouta
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Amanda Coimbra
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Francine Bittencourt Schiffler
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Thamiris dos Santos Miranda
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Gabriel Medeiros
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Cecilia A. Dias
- Centro de Primatologia, Universidade de Brasília, Brasília, Brazil
| | | | | | - Amilcar Tanuri
- Laboratório de Virologia Molecular, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Marcelo Alves Soares
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- Programa de Oncovirologia, Instituto Nacional de Câncer, Rio de Janeiro, Brazil
| | - André Felipe Andrade dos Santos
- Laboratório de Diversidade e Doenças Virais, Departamento de Genética, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
- *Correspondence: André Felipe Andrade dos Santos,
| |
Collapse
|
|
2
|
Abstract
Anelloviruses are small negative-sense single-stranded DNA viruses with genomes ranging in size from 1.6 to 3.9 kb. The family Anelloviridae comprised 14 genera before the present changes. However, in the last five years, a large number of diverse anelloviruses have been identified in various organisms. Here, we undertake a global analysis of mammalian anelloviruses whose full genome sequences have been determined and have an intact open reading frame 1 (ORF1). We established new criteria for the classification of anelloviruses, and, based on our analyses, we establish new genera and species to accommodate the unclassified anelloviruses. We also note that based on the updated species demarcation criteria, some previously assigned species (n = 10) merge with other species. Given the rate at which virus sequence data are accumulating, and with the identification of diverse anelloviruses, we acknowledge that the taxonomy will have to be dynamic and continuously evolve to accommodate new members.
Collapse
|
|
3
|
Rogers AJ, Huang YW, Heffron CL, Opriessnig T, Patterson AR, Meng XJ. Prevalence of the NovelTorque Teno Sus VirusSpecies k2b from Pigs in the United States and Lack of Association with Post-Weaning Multisystemic Wasting Syndrome or Mulberry Heart Disease. Transbound Emerg Dis 2016; 64:1877-1883. [DOI: 10.1111/tbed.12586] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2016] [Indexed: 11/29/2022]
Affiliation(s)
- A. J. Rogers
- Department of Biomedical Sciences and Pathobiology; Virginia-Maryland College of Veterinary Medicine; Virginia Polytechnic Institute and State University; Blacksburg VA USA
| | - Y.-W. Huang
- College of Animal Sciences; Zhejiang University; Hangzhou China
| | - C. L. Heffron
- Department of Biomedical Sciences and Pathobiology; Virginia-Maryland College of Veterinary Medicine; Virginia Polytechnic Institute and State University; Blacksburg VA USA
| | - T. Opriessnig
- The Roslin Institute; University of Edinburgh; Midlothian Edinburgh UK
| | | | - X.-J. Meng
- Department of Biomedical Sciences and Pathobiology; Virginia-Maryland College of Veterinary Medicine; Virginia Polytechnic Institute and State University; Blacksburg VA USA
| |
Collapse
|
|
4
|
Hrazdilová K, Slaninková E, Brožová K, Modrý D, Vodička R, Celer V. New species of Torque Teno miniviruses infecting gorillas and chimpanzees. Virology 2015; 487:207-14. [PMID: 26547037 DOI: 10.1016/j.virol.2015.10.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2015] [Revised: 10/12/2015] [Accepted: 10/15/2015] [Indexed: 10/22/2022]
Abstract
Anelloviridae family is comprised of small, non-enveloped viruses of various genome lengths, high sequence diversity, sharing the same genome organization. Infections and co-infections by different genotypes in humans are ubiquitous. Related viruses were described in number of mammalian hosts, but very limited data are available from the closest human relatives - great apes and non-human primates. Here we report the 100% prevalence determined by semi-nested PCR from fecal samples of 16 captive primate species. Only the Mandrillus sphinx, showed the prevalence only 8%. We describe three new species of gorillas׳ and four new species of chimpanzees׳ Betatorqueviruses and their co-infections in one individual. This study is also first report and analysis of nearly full length TTMV genomes infecting gorillas. Our attempts to sequence the complete genomes of anelloviruses from host feces invariably failed. Broader usage of blood /tissue material is necessary to understand the diversity and interspecies transmission of anelloviruses.
Collapse
Affiliation(s)
- Kristýna Hrazdilová
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic; CEITEC - Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic.
| | - Eva Slaninková
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic; Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic
| | - Kristýna Brožová
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic; Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic
| | - David Modrý
- CEITEC - Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic; Department of Pathology and Parasitology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic; Biology Centre, Institute of Parasitology, Czech Academy of Sciences, Branišovská 31, 37005 České Budějovice, Czech Republic
| | - Roman Vodička
- The Prague Zoological Garden, Prague 171 00, Czech Republic
| | - Vladimír Celer
- Department of Infectious Diseases and Microbiology, Faculty of Veterinary Medicine, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic; CEITEC - Central European Institute of Technology, University of Veterinary and Pharmaceutical Sciences Brno,612 42 Brno, Czech Republic
| |
Collapse
|
|
5
|
Phylogeny, spatio-temporal phylodynamics and evolutionary scenario of Torque teno sus virus 1 (TTSuV1) and 2 (TTSuV2) in wild boars: Fast dispersal and high genetic diversity. Vet Microbiol 2013; 166:200-13. [DOI: 10.1016/j.vetmic.2013.06.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2013] [Revised: 05/29/2013] [Accepted: 06/10/2013] [Indexed: 01/09/2023]
|
|
6
|
Zhang Z, Dai W, Wang Y, Lu C, Fan H. Analysis of synonymous codon usage patterns in torque teno sus virus 1 (TTSuV1). Arch Virol 2012; 158:145-54. [PMID: 23011310 PMCID: PMC7086873 DOI: 10.1007/s00705-012-1480-y] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Accepted: 08/07/2012] [Indexed: 11/14/2022]
Abstract
Torque teno sus virus 1 (TTSuV1) is a novel virus that has been found widely distributed in the swine population in recent years. Analysis of codon usage can reveal much about the molecular evolution of TTSuV1. In this study, synonymous codon usage patterns and the key determinants in the coding region of 29 available complete TTSuV1 genome sequences were examined. By calculating the nucleotide content and relative synonymous codon usage (RSCU) of TTSuV1 coding sequences, we found that the preferentially used codons were mostly those ending with A or C nucleotides; less-used codons were mostly codons ending with U or G nucleotides, and these were mainly affected by composition constraints. Although there was a variation in codon usage bias among different TTSuV1 genomes, the codon usage bias and GC content in the TTSuV1 coding region was lower, which was mainly determined by the base composition in the third codon position and the effective number of codons (ENC) value. Moreover, the results of correspondence analysis (COA) indicated that the codon usage patterns of TTSuV1 isolated from different countries varied greatly and had significant differences. In addition, Spearman’s rank correlation analysis and an ENC plot revealed that apart from mutation pressure, which was critical in determining the codon usage pattern, other factors were involved in shaping the evolution of codon usage bias in TTSuV1, such as natural selection. Those results suggested that synonymous codon usage patterns of TTSuV1 genomes were the result of interaction between mutation pressure and natural selection. The information from this study not only provides important insights into the synonymous codon usage pattern of TTSuV1, but also helps to identify the main factors affecting codon usage by this virus.
Collapse
|
|
7
|
Xiao CT, Giménez-Lirola L, Huang YW, Meng XJ, Halbur PG, Opriessnig T. The prevalence of Torque teno sus virus (TTSuV) is common and increases with the age of growing pigs in the United States. J Virol Methods 2012; 183:40-4. [DOI: 10.1016/j.jviromet.2012.03.026] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2011] [Revised: 03/17/2012] [Accepted: 03/21/2012] [Indexed: 11/25/2022]
|
|
8
|
Zhu CX, Yuan CL, Cui L, Yu Y, Liu RA, Zhao W, Hua XG. Molecular detection of Torque teno sus virus from tissues samples of sick pigs in China. Virus Res 2012; 165:225-30. [PMID: 22361032 DOI: 10.1016/j.virusres.2012.02.007] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2011] [Revised: 02/06/2012] [Accepted: 02/07/2012] [Indexed: 10/28/2022]
Abstract
In the present study, Torque teno sus virus (TTSuV) was detected from different tissues, stool and serum samples of 25 sick pigs. The total prevalence of TTSuV1 and TTSuV2 were 64% (16/25) and 28% (7/25), 24% (6/25) were co-infected with both TTSuV1 and TTSuV2. The prevalence of TTSuV infection in spleen is a slightly higher, with positive rates of 52% (13/25) for TTSuV1 and 24% (6/25) for TTSuV2. Phylogenetic analysis of TTSuV1 showed that 21 isolates were distributed into two clusters (genotype TTSuV1a and TTSuV1b), with genotype TTSuV1b was the dominant genotype. Phylogenetic analysis of TTSuV2 showed that the nine isolates shared 80.9-99.2% nucleotide homology with each other, and were distributed in different genotypes (TTSuV2a-TTSuV2f). TTSuV2d was the most prevalent genotype in this study, which contained five Spanish strains and nine Chinese strains, and shared 94.2-96.8% homology.
Collapse
Affiliation(s)
- C X Zhu
- Shanghai Key Laboratory of Veterinary Biotechnology, School of Agriculture and Biology, Shanghai JiaoTong University, Shanghai 200240, China
| | | | | | | | | | | | | |
Collapse
|
|
9
|
Abstract
The newly established family Anelloviridae includes a number of viruses infecting humans (Torque teno viruses) and other animal species. The ones infecting domestic swine and wild boar are nowadays named Torque teno sus viruses (TTSuV), which are small circular single-stranded DNA viruses highly prevalent in the pig population. So far, two genetically distinct TTSuV species are infecting swine. Both TTSuVs appear to efficiently spread by vertical and horizontal transmission routes; in fact, foetuses may be infected and the prevalence and viral loads increase by age of the animals. Detailed immunological studies on TTSuVs are still lacking, but it seems that there are no efficient immunological responses limiting viraemia. These viruses are currently receiving more attention due to the latest results on disease association. Torque teno sus viruses have been circulating unnoticed in pigs for a long time, and even considered non-pathogenic by themselves; there is increasing evidence that points to influence the development of some diseases or even affect their outcome. Such link has been mainly established with porcine circovirus diseases.
Collapse
Affiliation(s)
- T Kekarainen
- Centre de Recerca en Sanitat Animal (CReSA), UAB-IRTA, Campus de la Universitat Autònoma de Barcelona, Barcelona, Spain.
| | | |
Collapse
|
|
10
|
TSHERING C, TAKAGI M, DEGUCHI E. Seroprevalence of Torque Teno Sus Virus Types 1 and 2 in Postweaning Multisystemic Wasting Syndrome-Suspected Pigs and Porcine Circovirus Type 2-Vaccinated Normal Pigs in Southern Japan. J Vet Med Sci 2012; 74:107-10. [DOI: 10.1292/jvms.11-0233] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Chenga TSHERING
- United Graduate School of Veterinary Medicine, Yamaguchi University
- Laboratory of Farm Animal Production Medicine, Department of Veterinary Medicine, Faculty of Agriculture, Kagoshima University
| | - Mitsuhiro TAKAGI
- Laboratory of Farm Animal Production Medicine, Department of Veterinary Medicine, Faculty of Agriculture, Kagoshima University
| | - Eisaburo DEGUCHI
- Laboratory of Farm Animal Production Medicine, Department of Veterinary Medicine, Faculty of Agriculture, Kagoshima University
- Transboundary Animal Disease Research Center, Faculty of Agriculture, Kagoshima University
| |
Collapse
|
|
11
|
TSHERING C, TAKAGI M, DEGUCHI E. Detection of Torque Teno Sus Virus Types 1 and 2 by Nested Polymerase Chain Reaction in Sera of Sows at Parturition and of Their Newborn Piglets Immediately after Birth Without Suckling Colostrum and at 24 hr after Suckling Colostrum. J Vet Med Sci 2012; 74:315-9. [DOI: 10.1292/jvms.11-0155] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Chenga TSHERING
- United Graduate School of Veterinary Medicine, Yamaguchi University
- Laboratory of Farm Animal Production Medicine, Department of Veterinary Medicine, Faculty of Agriculture, Kagoshima University
| | - Mitsuhiro TAKAGI
- Laboratory of Farm Animal Production Medicine, Department of Veterinary Medicine, Faculty of Agriculture, Kagoshima University
| | - Eisaburo DEGUCHI
- Laboratory of Farm Animal Production Medicine, Department of Veterinary Medicine, Faculty of Agriculture, Kagoshima University
- Transboundary Animal Disease Control and Research Center, Faculty of Agriculture, Kagoshima University
| |
Collapse
|
|
12
|
TSHERING C, TAKAGI M, DEGUCHI E. Infection Dynamics of Torque Teno Sus Virus Types 1 and 2 in Serum and Peripheral Blood Mononuclear Cells. J Vet Med Sci 2012; 74:513-7. [DOI: 10.1292/jvms.11-0382] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Chenga TSHERING
- United Graduate School of Veterinary Medicine, Yamaguchi University, Yamaguchi 753-8515, Japan
- Laboratory of Farm Animal Production Medicine, Department of Veterinary Medicine, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
| | - Mitsuhiro TAKAGI
- Laboratory of Farm Animal Production Medicine, Department of Veterinary Medicine, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
| | - Eisaburo DEGUCHI
- Laboratory of Farm Animal Production Medicine, Department of Veterinary Medicine, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
- Transboundary Animal Disease Control and Research Center, Faculty of Agriculture, Kagoshima University, Kagoshima 890-0065, Japan
| |
Collapse
|
|
13
|
Zhu C, Shan T, Cui L, Luo X, Liu Z, Tang S, Liu Z, Yuan C, Lan D, Zhao W, Hua X. Molecular detection and sequence analysis of feline Torque teno virus (TTV) in China. Virus Res 2011; 156:13-6. [DOI: 10.1016/j.virusres.2010.12.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Revised: 12/05/2010] [Accepted: 12/10/2010] [Indexed: 11/29/2022]
|
|
14
|
Huang YW, Ni YY, Dryman BA, Meng XJ. Multiple infection of porcine Torque teno virus in a single pig and characterization of the full-length genomic sequences of four U.S. prototype PTTV strains: implication for genotyping of PTTV. Virology 2009; 396:289-97. [PMID: 19913866 DOI: 10.1016/j.virol.2009.10.031] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2009] [Revised: 09/23/2009] [Accepted: 10/19/2009] [Indexed: 11/17/2022]
Abstract
Porcine Torque teno virus (PTTV) was recently shown to partially contribute to the experimental induction of porcine dermatitis and nephropathy syndrome and postweaning multisystemic wasting syndrome in pigs in the United States. We report here the identification of four distinct full-length genomic sequences of PTTV strains from a single pig in Virginia. Detailed analyses of the genomic organization, the degree of variability and the characteristics of conserved nucleotide and amino acid motifs of PTTV were conducted. The results showed that these four prototype U.S. strains of PTTV identified from the same pig represent distinct genotypes or subtypes and a revised classification system for PPTV is subsequently proposed. This is the first study documenting multiple PTTV infections with distinct genotypes or subtypes in a single pig. The identification of novel PTTV strains from pigs in the United States also pave the way for future disease characterization and genotyping of PTTV.
Collapse
Affiliation(s)
- Y W Huang
- Center for Molecular Medicine and Infectious Diseases, Department of Biomedical Sciences and Pathobiology, College of Veterinary Medicine, Virginia Polytechnic Institute and State University, Blacksburg, 1981 Kraft Drive, Blacksburg, VA 24061-0913, USA
| | | | | | | |
Collapse
|
|
15
|
Blomström AL, Belák S, Fossum C, McKillen J, Allan G, Wallgren P, Berg M. Detection of a novel porcine boca-like virus in the background of porcine circovirus type 2 induced postweaning multisystemic wasting syndrome. Virus Res 2009; 146:125-9. [PMID: 19748534 DOI: 10.1016/j.virusres.2009.09.006] [Citation(s) in RCA: 114] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2009] [Revised: 09/01/2009] [Accepted: 09/03/2009] [Indexed: 11/26/2022]
Abstract
Porcine circovirus type 2 (PCV-2) has been found to be the causative agent of postweaning multisystemic wasting syndrome (PMWS). However, PCV-2 is a ubiquitous virus in the swine population and a majority of pigs infected with PCV-2 do not develop the disease. Different factors such as age, maintenance, the genetics of PCV-2, other pathogens, etc. have been suggested to contribute to the development of PMWS. However, so far no proven connection between any of these factors and the disease development has been found. In this study we explored the possible presence of other so far unknown DNA containing infectious agents in lymph nodes collected from Swedish pigs with confirmed PMWS through random amplification and high-throughput sequencing. Although the vast majority of the amplified genetic sequences belonged to PCV-2, we also found genome sequences of Torque Teno virus (TTV) and of a novel parvovirus. The detection of TTV was expected since like PCV-2, TTV has been found to have high prevalence in pigs around the world. We were able to amplify a longer region of the parvovirus genome, consisting of the entire NP1 and partial VP1/2. By comparative analysis of the nucleotide sequences and phylogenetic studies we propose that this is a novel porcine parvovirus, with genetic relationship to bocaviruses.
Collapse
Affiliation(s)
- Anne-Lie Blomström
- Department of Biomedical Sciences and Veterinary Public Health, Division of Microbiology and Food Safety, Swedish University of Agricultural Sciences, S-750 07 Uppsala, Sweden.
| | | | | | | | | | | | | |
Collapse
|
|
16
|
Ellis JA, Allan G, Krakowka S. Effect of coinfection with genogroup 1 porcine torque teno virus on porcine circovirus type 2-associated postweaning multisystemic wasting syndrome in gnotobiotic pigs. Am J Vet Res 2009; 69:1608-14. [PMID: 19046008 DOI: 10.2460/ajvr.69.12.1608] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
OBJECTIVE To determine whether genogroup 1 porcine torque teno virus (g1-TTV) can potentiate clinical disease associated with porcine circovirus type 2 (PCV2). SAMPLE POPULATION 33 gnotobiotic baby pigs. PROCEDURES Pigs were allocated into 7 groups: group A, 5 uninoculated control pigs from 3 litters; group B, 4 pigs oronasally inoculated with PCV2 alone; group C, 4 pigs inoculated IP with first-passage g1-TTV alone; group D, 4 pigs inoculated IP with fourth-passage g1-TTV alone; group E, 6 pigs inoculated IP with first-passage g1-TTV and then oronasally inoculated with PCV2 7 days later; group F, 6 pigs inoculated IP with fourth-passage g1-TTV and then inoculated oronasally with PCV2 7 days later; and group G, 4 pigs inoculated oro-nasally with PCV2 and then inoculated IP with fourth-passage g1-TTV 7 days later. RESULTS 6 of 12 pigs inoculated with g1-TTV prior to PCV2 developed acute onset of postweaning multisystemic wasting syndrome (PMWS). None of the pigs inoculated with g1-TTV alone or PCV2 alone or that were challenge exposed to g1-TTV after establishment of infection with PCV2 developed clinical illness. Uninoculated control pigs remained healthy. CONCLUSIONS AND CLINICAL RELEVANCE These data implicated g1-TTV as another viral infection that facilitates PCV2-induced PMWS. This raises the possibility that torque teno viruses in swine may contribute to disease expression currently associated with only a single infectious agent.
Collapse
Affiliation(s)
- John A Ellis
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, SK S7N 5B4, Canada
| | | | | |
Collapse
|
|
17
|
Kekarainen T, Segalés J. Torque teno virus infection in the pig and its potential role as a model of human infection. Vet J 2009; 180:163-8. [DOI: 10.1016/j.tvjl.2007.12.005] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Revised: 12/02/2007] [Accepted: 12/13/2007] [Indexed: 01/01/2023]
|
|
18
|
Ninomiya M, Takahashi M, Hoshino Y, Ichiyama K, Simmonds P, Okamoto H. Analysis of the entire genomes of torque teno midi virus variants in chimpanzees: infrequent cross-species infection between humans and chimpanzees. J Gen Virol 2009; 90:347-358. [PMID: 19141443 DOI: 10.1099/vir.0.007385-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Humans are frequently infected with three anelloviruses which have circular DNA genomes of 3.6-3.9 kb [Torque teno virus (TTV)], 2.8-2.9 kb [Torque teno mini virus (TTMV)] and 3.2 kb [a recently discovered anellovirus named Torque teno midi virus (TTMDV)]. Unexpectedly, human TTMDV DNA was not detectable in any of 74 chimpanzees tested, although all but one tested positive for both human TTV and TTMV DNA. Using universal primers for anelloviruses, novel variants of TTMDV that are phylogenetically clearly separate from human TTMDV were identified from chimpanzees, and over the entire genome, three chimpanzee TTMDV variants differed by 17.9-20.3 % from each other and by 40.4-43.6 % from all 18 reported human TTMDVs. A newly developed PCR assay that uses chimpanzee TTMDV-specific primers revealed the high prevalence of chimpanzee TTMDV in chimpanzees (63/74, 85 %) but low prevalence in humans (1/100). While variants of TTV and TTMV from chimpanzees and humans were phylogenetically interspersed, those of TTMDV were monophyletic for each species, with sequence diversity of <33 and <20 % within the 18 human and three chimpanzee TTMDV variants, respectively. Maximum within-group divergence values for TTV and TTMV were 51 and 57 %, respectively; both of these values were substantially greater than the maximum divergence among TTMDV variants (44 %), consistent with a later evolutionary emergence of TTMDV. However, substantiation of this hypothesis will require further analysis of genetic diversity using an expanded dataset of TTMDV variants in humans and chimpanzees. Similarly, the underlying mechanism of observed infrequent cross-species infection of TTMDV between humans and chimpanzees deserves further analysis.
Collapse
Affiliation(s)
- Masashi Ninomiya
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi-Ken 329-0498, Japan
| | - Masaharu Takahashi
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi-Ken 329-0498, Japan
| | - Yu Hoshino
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi-Ken 329-0498, Japan
| | - Koji Ichiyama
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi-Ken 329-0498, Japan
| | - Peter Simmonds
- Virus Evolution Group, Centre for Infectious Diseases, University of Edinburgh, Summerhall, Edinburgh EH9 1QH, UK
| | - Hiroaki Okamoto
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi-Ken 329-0498, Japan
| |
Collapse
|
|
19
|
Kekarainen T, Martínez-Guinó L, Segalés J. Swine torque teno virus detection in pig commercial vaccines, enzymes for laboratory use and human drugs containing components of porcine origin. J Gen Virol 2009; 90:648-653. [DOI: 10.1099/vir.0.006841-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Torque teno viruses (TTVs) are vertebrate infecting, single-stranded circular DNA viruses. Two genetically distinct TTV genogroups (TTV1 and TTV2) infect swine worldwide with high prevalence. Currently, swine TTVs are considered non-pathogenic, although TTV2 has been linked to post-weaning multisystemic wasting syndrome, a porcine circovirus disease. On the other hand, pig materials are an important source of components used in porcine vaccine manufacturing, human drugs and commercial enzyme products. However, there is little information about the possible existence of extraneous viruses in products containing porcine-derived components. In the present study, 26 commercial swine vaccines, seven human drugs and three enzyme products from porcine origin were tested for the presence of TTV1 and TTV2 genomes by PCR. Four vaccines against Mycoplasma hyopneumoniae were positive for TTV2 by PCR. Three M. hyopneumoniae, one porcine parvovirus and one porcine reproductive and respiratory syndrome virus vaccines were PCR positive for TTV1. One human drug contained TTV1 DNA as well as a trypsin enzyme; a porcine-derived elastase product was positive for both TTV genogroups. These results show that swine TTVs are contaminants not only of swine vaccines but also of human drugs containing porcine components and enzymes for laboratory use.
Collapse
Affiliation(s)
- Tuija Kekarainen
- Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Laura Martínez-Guinó
- Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Joaquim Segalés
- Departament de Sanitat i d'Anatomia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
- Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| |
Collapse
|
|
20
|
Abstract
Infection with TT virus (Torque teno virus, TTV), a small, nonenveloped virus with a circular, single-stranded DNA genome classified in the floating genus Anellovirus, is not restricted to humans. Using highly conserved primers derived from the untranslated region of the human TTV genome, a variety of TTV-like viruses have been found circulating in nonhuman primates such as chimpanzees, macaques, and tamarins. TTV variants in nonhuman primates are species-specific, although some genetic groups of human and chimpanzee TTVs cluster to make human/chimpanzee clades. TTVs from macaques and tamarins are increasingly divergent from TTV variants infecting humans and chimpanzees. TTV-like mini virus (TTMV) infections have also been detected in chimpanzees, with genotypes distinct but interspersed with human TTMV genotypes. Pets are also naturally infected with species-specific TTVs, and several isolates have been found in cats and dogs. In addition, other mammals such as tupaias and pigs have species-specific TTVs: swine TTVs are found among pigs worldwide. The genomic organization and proposed transcriptional profiles of TTVs infecting nonhuman primate and other mammalian species are similar to those of human TTVs, and co-evolution of TTVs with their hosts has been suggested. To date, TTVs infecting nonhuman primates and other mammalian species have been under-examined. It is likely that essentially all animals are naturally infected with species-specific TTVs.
Collapse
|
|
21
|
Abstract
Many features of the Torque teno virus and the other anelloviruses (AVs) that have been identified after this virus was discovered in 1997 remain elusive. The immunobiology of the AVs is no exception. However, evidence is progressively accumulating that at least some AVs have an interesting interplay with cells and soluble factors known to contribute to the homeostasis of innate and adaptive immunity. Evidence is also accumulating that this interplay can have a significant impact on how effectively an infected host can deal with superimposed infectious and non-infectious noxae. This review article discusses the scanty information available on these aspects and highlights the ones that would be more urgent to precisely understand in order to get an adequate assessment of how important for human health these extremely ubiquitous and pervasive viruses really are.
Collapse
|
|
22
|
Les anellovirus (TTV et variants) : données actuelles dix ans après leur découverte. Transfus Clin Biol 2008; 15:406-15. [DOI: 10.1016/j.tracli.2008.10.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2008] [Accepted: 10/10/2008] [Indexed: 11/21/2022]
|
|
23
|
Kekarainen T, López-Soria S, Segalés J. Detection of swine Torque teno virus genogroups 1 and 2 in boar sera and semen. Theriogenology 2007; 68:966-71. [PMID: 17767950 DOI: 10.1016/j.theriogenology.2007.07.010] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2007] [Revised: 07/18/2007] [Accepted: 07/21/2007] [Indexed: 10/22/2022]
Abstract
Torque teno virus (TTV) is a non-enveloped, circular, single-stranded DNA virus infecting swine and several other species. TTV is nowadays considered a non-pathogenic virus in all species where it has been found. In the present study, the prevalence of two distinct swine TTV genogroups in boar semen and sera was determined by a nested PCR method. Furthermore, association between TTV infection and semen qualitative and quantitative parameters was analyzed. TTV was detected in 74% of boar sera and 72% in semen. The prevalence of genogroup 1 in sera and semen were 64% and 55%, respectively, while lower prevalence of genogroup 2 was observed in both sera (38%) and semen (32%). Some significant associations of TTV infection on semen characteristics in boar genetic lines were observed, but qualitative and quantitative semen parameters obtained in studied boars fall into normal expected ranges. Therefore, TTV semen infection was not evidenced to be harmful for the studied qualitative and quantitative parameters of semen. The high rate of TTV in semen suggests that sexual route might contribute to the transmission of the virus. It is presently unknown if this potential vertical transmission of swine TTV implies any effect on female reproductive tract. This study also represents the first description of swine TTV presence in semen.
Collapse
Affiliation(s)
- T Kekarainen
- Centre de Recerca en Sanitat Animal (CReSA), Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain.
| | | | | |
Collapse
|
|
24
|
Ninomiya M, Takahashi M, Shimosegawa T, Okamoto H. Analysis of the entire genomes of fifteen torque teno midi virus variants classifiable into a third group of genus Anellovirus. Arch Virol 2007; 152:1961-75. [PMID: 17712598 DOI: 10.1007/s00705-007-1046-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2007] [Accepted: 07/16/2007] [Indexed: 11/27/2022]
Abstract
Recently, we identified a novel human virus with a circular DNA genome of 3.2 kb, tentatively designated as torque teno midi virus (TTMDV), with a genomic organization resembling those of torque teno virus (TTV) of 3.8-3.9 kb and torque teno mini virus (TTMV) of 2.8-2.9 kb. To investigate the extent of genomic variability of TTMDV genomes, the full-length sequence was determined for 15 TTMDV isolates obtained from viremic individuals in Japan. The 15 TTMDV isolates comprised 3175-3230 bases and shared 67.0-90.3% identities with each other, and were only 68.4-73.0% identical to the 3 reported TTMDV isolates over the entire genome. TTMDV possessed a genomic organization with four open reading frames (ORF1-ORF4) with characteristic sequence motifs and stem and loop structures with high GC content, similar to TTV and TTMV. The total of 18 TTMDV genomes differed by up to 60.7% from each other in the amino acid sequence of ORF1 (658-677 amino acids), but segregated phylogenetically into the same cluster, which was distantly related to the TTVs and TTMVs. These results indicate that TTMDV with a circular DNA genome of 3.2 kb, has an extremely high degree of genomic variability, and is classifiable into a third group in the genus Anellovirus.
Collapse
Affiliation(s)
- M Ninomiya
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi, Japan
| | | | | | | |
Collapse
|
|
25
|
Ninomiya M, Nishizawa T, Takahashi M, Lorenzo FR, Shimosegawa T, Okamoto H. Identification and genomic characterization of a novel human torque teno virus of 3.2 kb. J Gen Virol 2007; 88:1939-1944. [PMID: 17554026 DOI: 10.1099/vir.0.82895-0] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In the process of searching for the recently described small anelloviruses 1 and 2 (SAVs) with the genomic DNA length of 2.2 or 2.6 kb in human sera, we isolated a novel virus with its genomic organization resembling those of torque teno virus (TTV) of 3.8-3.9 kb and torque teno mini virus (TTMV) of 2.8-2.9 kb. The entire genomic sequence of three isolates (MD1-032, MD1-073 and MD2-013), which comprised 3242-3253 bases and exhibited 76-99 % identities with the SAVs within the overlapping sequence, was determined. Although the MD1-032, MD1-073 and MD2-013 isolates differed by 10-28 % from each other over the entire genome, they segregated into the same cluster and were phylogenetically distinguishable from all reported TTVs and TTMVs. These results suggest that SAVs are deletion mutants of the novel virus with intermediate genomic length between those of TTV and TTMV and that the novel virus can be classified into a third group of the genus Anellovirus.
Collapse
Affiliation(s)
- Masashi Ninomiya
- Department of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi-Ken 329-0498, Japan
| | - Tsutomu Nishizawa
- International Research and Educational Institute for Integrated Medical Sciences, Tokyo Women's Medical University, Tokyo 162-8666, Japan
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi-Ken 329-0498, Japan
| | - Masaharu Takahashi
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi-Ken 329-0498, Japan
| | - Felipe R Lorenzo
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi-Ken 329-0498, Japan
| | - Tooru Shimosegawa
- Department of Gastroenterology, Tohoku University Graduate School of Medicine, Sendai 980-8574, Japan
| | - Hiroaki Okamoto
- Division of Virology, Department of Infection and Immunity, Jichi Medical University School of Medicine, Tochigi-Ken 329-0498, Japan
| |
Collapse
|
|
26
|
Al-Moslih MI, Perkins H, Hu YW. Genetic relationship of Torque Teno virus (TTV) between humans and camels in United Arab Emirates (UAE). J Med Virol 2007; 79:188-91. [PMID: 17177296 DOI: 10.1002/jmv.20776] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Torque Teno Virus (TTV) species-cross infection has been documented. However, the genetic relationship between human and animal TTV remains uncertain. In this study, genotypic characterization of TTV in different Camel specimens from the United Arab Emirates (UAE) was undertaken for comparison with human UAE TTV. A total of 56 specimens: 34 sera, 14 raw, and 8 pasteurized milk samples were tested for TTV. The results showed that the rate of infection was, 38.2% (13/34), 35.7% (5/14), and 100% (8/8), for the samples of sera, raw, and pasteurized milk respectively. The 5'untranslated region (5'UTR) of 23 clones that were generated from PCR products amplified from Camel samples (three sera, three raw, and two pasteurized milk samples) were subjected to sequence analysis. The camel TTV clones were classified as genotype 11 (47.8%), group 5 (43.5%), and SENV-H or genotype 16 (8.7%) which are among the predominant genotypes found in humans in the UAE. Phylogenetic analysis of representative sequences revealed that the similarity between isolates from camels and humans is 92%-97% for the same genotypes. The data lead to the conclusion that camels and humans share a common source of TTV infection in the UAE.
Collapse
Affiliation(s)
- Moslih I Al-Moslih
- College of Health Sciences, University of Sharjah, Sharjah, United Arab Emirates.
| | | | | |
Collapse
|
|
27
|
Irshad M, Joshi YK, Sharma Y, Dhar I. Transfusion transmitted virus: A review on its molecular characteristics and role in medicine. World J Gastroenterol 2006; 12:5122-5134. [PMID: 16937521 PMCID: PMC4088008 DOI: 10.3748/wjg.v12.i32.5122] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/03/2006] [Revised: 05/15/2006] [Accepted: 05/22/2006] [Indexed: 02/06/2023] Open
Abstract
The present review gives an updated overview of transfusion transmitted virus (TTV), a novel agent, in relation to its molecular characteristics, epidemiological features, modes of transmission, tissue tropism, pathogenesis, role in various diseases and its eradication from the body. TTV, a DNA virus, is a single stranded, non-enveloped, 3.8 kb long DNA virus with a small and covalently closed circular genome comprising 3852 bases. It was tentatively designated Circinoviridae virus. TTV genome sequence is heterogeneous and reveals the existence of six different genotypes and several subtypes. TTV has been reported to transmit not only via parenteral routes, but also via alternate routes. This virus has been detected in different non-human primates as well. At present, TTV is detected by polymerase chain reaction (PCR) with no other available diagnostic assays. It shows its presence globally and was detected in high percent populations of healthy persons as well as in various disease groups. Initially it was supposed to have strong association with liver disease; however, there is little evidence to show its liver tropism and contribution in causing liver diseases. It shows high prevalence in hemodialysis patients, pointing towards its significance in renal diseases. In addition, TTV is associated with several infectious and non-infectious diseases. Though, its exact pathogenesis is not yet clear, TTV virus possibly resides and multiplies in bone marrow cells and peripheral blood mononuclear cells (PBMCs). Recently, attempts have been made to eradicate this virus with interferon treatment. More information is still needed to extricate various mysteries related to TTV.
Collapse
Affiliation(s)
- M Irshad
- Clinical Biochemistry Division, Department of Laboratory Medicine, PO Box -4938, A I I M S, New Delhi-110029, India.
| | | | | | | |
Collapse
|
|
28
|
Kekarainen T, Sibila M, Segalés J. Prevalence of swine Torque teno virus in post-weaning multisystemic wasting syndrome (PMWS)-affected and non-PMWS-affected pigs in Spain. J Gen Virol 2006; 87:833-837. [PMID: 16528032 DOI: 10.1099/vir.0.81586-0] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The present study was designed to investigate the prevalence of swine Torque teno virus (TTV) in post-weaning multisystemic wasting syndrome (PMWS)-affected and non-affected Spanish swine. Nested PCR (nPCR) assays to detect two distinct TTV genogroups were applied. A significantly higher prevalence of TTV infection was found in sera from PMWS-affected animals (97 %) than in sera from non-PMWS-affected animals (78 %). Whilst PMWS-affected pigs (91 %) were more likely to be infected with TTV from genogroup 2 than non-PMWS-affected swine (72 %), no such difference was observed with genogroup 1. Nucleotide sequences of nPCR products were 91-99 % identical between strains within a genogroup. In contrast, inter-genogroup sequence identities were 49-58 %. Phylogenetic analyses demonstrated that genogroups form different clusters without association with PMWS or porcine circovirus type 2 infection status of the animals. These results indicate a high prevalence of both swine TTV genogroups in Spain, being present more frequently in PMWS-affected animals than in non-PMWS-affected animals.
Collapse
Affiliation(s)
- Tuija Kekarainen
- Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Marina Sibila
- Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| | - Joaquim Segalés
- Departament de Sanitat i d'Anatomia Animals, Facultat de Veterinària, Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
- Centre de Recerca en Sanitat Animal (CReSA), Universitat Autònoma de Barcelona, 08193 Bellaterra, Barcelona, Spain
| |
Collapse
|
|
29
|
Jones MS, Kapoor A, Lukashov VV, Simmonds P, Hecht F, Delwart E. New DNA viruses identified in patients with acute viral infection syndrome. J Virol 2005; 79:8230-6. [PMID: 15956568 PMCID: PMC1143717 DOI: 10.1128/jvi.79.13.8230-8236.2005] [Citation(s) in RCA: 286] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
A sequence-independent PCR amplification method was used to identify viral nucleic acids in the plasma samples of 25 individuals presenting with symptoms of acute viral infection following high-risk behavior for human immunodeficiency virus type 1 transmission. GB virus C/hepatitis G virus was identified in three individuals and hepatitis B virus in one individual. Three previously undescribed DNA viruses were also detected, a parvovirus and two viruses related to TT virus (TTV). Nucleic acids in human plasma that were distantly related to bacterial sequences or with no detectable similarities to known sequences were also found. Nearly complete viral genome sequencing and phylogenetic analysis confirmed the presence of a new parvovirus distinct from known human and animal parvoviruses and of two related TTV-like viruses highly divergent from both the TTV and TTV-like minivirus groups. The detection of two previously undescribed viral species in a small group of individuals presenting acute viral syndrome with unknown etiology indicates that a rich yield of new human viruses may be readily identifiable using simple methods of sequence-independent nucleic acid amplification and limited sequencing.
Collapse
Affiliation(s)
- Morris S Jones
- Blood Systems Research Institute, 270 Masonic Ave., San Francisco, California 94118, USA
| | | | | | | | | | | |
Collapse
|
|
30
|
Thom K, Morrison C, Lewis JCM, Simmonds P. Distribution of TT virus (TTV), TTV-like minivirus, and related viruses in humans and nonhuman primates. Virology 2003; 306:324-33. [PMID: 12642105 DOI: 10.1016/s0042-6822(02)00049-1] [Citation(s) in RCA: 37] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
TT virus (TTV) and TTV-like minivirus (TLMV) are small DNA viruses with single-stranded, closed circular, antisense genomes infecting man. Despite their extreme sequence heterogeneity (>50%), a highly conserved region in the untranslated region (UTR) allows both viruses to be amplified by polymerase chain reaction (PCR). TTV/TLMV infection was detected in 88 of 100 human plasma samples; amplified sequences were differentiated into TTV and TLMV by analysis of melting profiles, showing that both viruses were similarly prevalent. PCR with UTR primers also detected frequent infection with TTV/TLMV-related viruses in a wide range of apes (chimpanzees, gorillas, orangutans, gibbons) and African monkey species (mangabeys, drills, mandrills). These findings support the hypothesis for the co-evolution of TTV-like viruses with their hosts over the period of primate speciation, potentially analogous to the evolution of primate herpesviruses.
Collapse
Affiliation(s)
- K Thom
- TTI Theme Group, Scottish National Blood Transfusion Service, University of Edinburgh, Teviot Place, EH8 9AG Scotland, Edinburgh, UK
| | | | | | | |
Collapse
|
|
31
|
Okamoto H, Takahashi M, Nishizawa T, Tawara A, Fukai K, Muramatsu U, Naito Y, Yoshikawa A. Genomic characterization of TT viruses (TTVs) in pigs, cats and dogs and their relatedness with species-specific TTVs in primates and tupaias. J Gen Virol 2002; 83:1291-1297. [PMID: 12029143 DOI: 10.1099/0022-1317-83-6-1291] [Citation(s) in RCA: 162] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Using PCR with primers derived from a non-coding region of the human TT virus (TTV) genome, the TTV sequence in serum samples obtained from pigs (Sus domesticus), dogs (Canis familiaris) and cats (Felis catus) was identified and the entire genomic sequence was determined for each representative isolate. Three TTV isolates (Sd-TTV31 from a pig, Cf-TTV10 from a dog and Fc-TTV4 from a cat) comprising 2878, 2797 and 2064 nucleotides, respectively, each had three open reading frames (ORFs) encoding 436-635 (ORF1), 73-105 (ORF2) and 224-243 (ORF3) aa but lacked ORF4, similar to tupaia TTV. ORF3 was presumed to arise from a splicing of TTV mRNA, similar to human prototype TTV. Although the nucleotide sequence of Sd-TTV31, Cf-TTV10 and Fc-TTV4 differed by more than 50% from each other and from previously reported TTVs of 3.4-3.9 kb and TTV-like mini viruses (TLMVs) of 2.8-3.0 kb isolated from humans and non-human primates as well as tupaia TTVs of 2.2 kb, they resembled known TTVs and TLMVs with regard to genomic organization and presumed transcriptional profile rather than animal circoviruses of 1.7-2.3 kb. Phylogenetic analysis revealed that Sd-TTV31, Cf-TTV10 and Fc-TTV4 were closer to TTVs from lower-order primates and tupaias than to TTVs from higher-order primates and TLMVs. These results indicate that domestic pigs, cats and dogs are naturally infected with species-specific TTVs with small genomic size and suggest a wide distribution of TTVs with extremely divergent genomic sequence and length in animals.
Collapse
Affiliation(s)
- Hiroaki Okamoto
- Immunology Division and Division of Molecular Virology, Jichi Medical School, Tochigi-Ken 329-0498, Japan1
| | - Masaharu Takahashi
- Immunology Division and Division of Molecular Virology, Jichi Medical School, Tochigi-Ken 329-0498, Japan1
| | - Tsutomu Nishizawa
- Immunology Division and Division of Molecular Virology, Jichi Medical School, Tochigi-Ken 329-0498, Japan1
| | - Akio Tawara
- First Department of Internal Medicine, Yamanashi Medical University, Yamanashi-Ken 409-3898, Japan2
| | - Katsuhiko Fukai
- Central Animal Hygiene Service Center of Tochigi Prefecture, Tochigi-Ken 321-0905, Japan3
| | - Umetaro Muramatsu
- Central Animal Hygiene Service Center of Tochigi Prefecture, Tochigi-Ken 321-0905, Japan3
| | - Yoshihisa Naito
- Department of Clinical Veterinary Medicine, Faculty of Agriculture, Iwate University, Iwate-Ken 020-8550, Japan4
| | - Akira Yoshikawa
- Japanese Red Cross Saitama Blood Center, Saitama-Ken 338-0001, Japan5
| |
Collapse
|
|
32
|
Okamoto H, Nishizawa T, Takahashi M, Tawara A, Peng Y, Kishimoto J, Wang Y. Genomic and evolutionary characterization of TT virus (TTV) in tupaias and comparison with species-specific TTVs in humans and non-human primates. J Gen Virol 2001; 82:2041-2050. [PMID: 11514713 DOI: 10.1099/0022-1317-82-9-2041] [Citation(s) in RCA: 76] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
TT virus (TTV) was recovered from the sera of tupaias (Tupaia belangeri chinensis) by PCR using primers derived from the noncoding region of the human TTV genome, and its entire genomic sequence was determined. One tupaia TTV isolate (Tbc-TTV14) consisted of only 2199 nucleotides (nt) and had three open reading frames (ORFs), spanning 1506 nt (ORF1), 177 nt (ORF2) and 642 nt (ORF3), which were in the same orientation as the ORFs of the human prototype TTV (TA278). ORF3 was presumed to arise from a splicing of TTV mRNA, similar to reported human TTVs whose spliced mRNAs have been identified, and encoded a joint protein of 214 amino acids with a Ser-, Lys- and Arg-rich sequence at the C terminus. Tbc-TTV14 was less than 50% similar to previously reported TTVs of 3.4-3.9 kb and TTV-like mini viruses (TLMVs) of 2.8-3.0 kb isolated from humans and non-human primates, and known animal circoviruses. Although Tbc-TTV14 has a genomic length similar to animal circoviruses (1.8-2.3 kb), Tbc-TTV14 resembled TTVs and TLMVs with regard to putative genomic organization and transcription profile. Conserved motifs were commonly observed in the coding and noncoding regions of the Tbc-TTV14 genome and in all TTV and TLMV genomes. Phylogenetic analysis revealed that Tbc-TTV14 is the closest to TLMVs, and is closer to TTVs isolated from tamarin and douroucouli than to TTVs isolated from humans and chimpanzees. These results indicate that tupaias are naturally infected with a new TTV species that has not been identified among primates.
Collapse
Affiliation(s)
- Hiroaki Okamoto
- Immunology Division and Division of Molecular Virology, Jichi Medical School, Tochigi-Ken 329-0498, Japan1
| | - Tsutomu Nishizawa
- Immunology Division and Division of Molecular Virology, Jichi Medical School, Tochigi-Ken 329-0498, Japan1
| | - Masaharu Takahashi
- Immunology Division and Division of Molecular Virology, Jichi Medical School, Tochigi-Ken 329-0498, Japan1
| | - Akio Tawara
- First Department of Internal Medicine, Yamanashi Medical University, Yamanashi-Ken 409-3898, Japan2
| | - Yihong Peng
- Immunology Division and Division of Molecular Virology, Jichi Medical School, Tochigi-Ken 329-0498, Japan1
| | | | - Yu Wang
- Hepatology Institute, People's Hospital, Peking University, Beijing 100044, People's Republic of China4
| |
Collapse
|