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De Maio FA, Winter M, Abate S, Birochio D, Iglesias NG, Barrio DA, Bellusci CP. Torque teno sus virus k2a (TTSuVk2a) in wild boars from northeastern Patagonia, Argentina. Braz J Microbiol 2024; 55:981-989. [PMID: 38286944 PMCID: PMC10920574 DOI: 10.1007/s42770-024-01261-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 01/14/2024] [Indexed: 01/31/2024] Open
Abstract
Torque teno sus virus k2a (TTSuVk2a) is a member of the family Anelloviridae that can establish persistent infections in both domestic pigs and wild boars. Its association with diseases has not been precisely elucidated, and it is often considered only as a commensal virus. This infectious agent has been reported in herds throughout the world. In this study, we investigated the detection rate and diversity of TTSuVk2a in free-living wild boars from northeastern Patagonia, Argentina. Total DNA was extracted from tonsil samples of 50 animals, nested PCR assays were carried out, and infection was verified in 60% of the cases. Sequence analysis of the viral non-coding region revealed distinct phylogenetic groups. These clusters showed contrasting patterns of spatial distribution, which presented statistically significant differences when evaluating spatial aggregation. In turn, the sequences were compared with those available in the database to find that the clusters were distinguished by having similarity with TTSuVk2a variants of different geographic origin. The results suggested that Patagonian wild boar populations are bearers of diverse viral strains of Asian, European, and South American provenance.
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Affiliation(s)
- Federico Andrés De Maio
- Universidad Nacional de Río Negro, Sede Atlántica, Centro de Investigaciones y Transferencia Río Negro (CONICET-UNRN), Ruta Provincial N°1 y Rotonda Cooperación, CP 8500, Viedma, Río Negro, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Marina Winter
- Universidad Nacional de Río Negro, Sede Atlántica, Centro de Investigaciones y Transferencia Río Negro (CONICET-UNRN), Ruta Provincial N°1 y Rotonda Cooperación, CP 8500, Viedma, Río Negro, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Sergio Abate
- Universidad Nacional de Río Negro, Sede Atlántica, Centro de Investigaciones y Transferencia Río Negro (CONICET-UNRN), Ruta Provincial N°1 y Rotonda Cooperación, CP 8500, Viedma, Río Negro, Argentina
| | - Diego Birochio
- Universidad Nacional de Río Negro, Sede Atlántica, Centro de Investigaciones y Transferencia Río Negro (CONICET-UNRN), Ruta Provincial N°1 y Rotonda Cooperación, CP 8500, Viedma, Río Negro, Argentina
| | - Néstor Gabriel Iglesias
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
- Laboratorio de Virología Molecular, Instituto de Biotecnología, Universidad Nacional de Hurlingham (UNAHUR), Buenos Aires, Argentina
| | - Daniel Alejandro Barrio
- Universidad Nacional de Río Negro, Sede Atlántica, Centro de Investigaciones y Transferencia Río Negro (CONICET-UNRN), Ruta Provincial N°1 y Rotonda Cooperación, CP 8500, Viedma, Río Negro, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Carolina Paula Bellusci
- Universidad Nacional de Río Negro, Sede Atlántica, Centro de Investigaciones y Transferencia Río Negro (CONICET-UNRN), Ruta Provincial N°1 y Rotonda Cooperación, CP 8500, Viedma, Río Negro, Argentina.
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Burrai GP, Hawko S, Dei Giudici S, Polinas M, Angioi PP, Mura L, Alberti A, Hosri C, Hassoun G, Oggiano A, Antuofermo E. The Synergic Role of Emerging and Endemic Swine Virus in the Porcine Respiratory Disease Complex: Pathological and Biomolecular Analysis. Vet Sci 2023; 10:595. [PMID: 37888547 PMCID: PMC10611356 DOI: 10.3390/vetsci10100595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Revised: 09/14/2023] [Accepted: 09/25/2023] [Indexed: 10/28/2023] Open
Abstract
Porcine respiratory disease complex (PRDC) represents a significant threat to the swine industry, causing economic losses in pigs worldwide. Recently, beyond the endemic viruses PRRSV and PCV2, emerging viruses such as TTSuV, PCV3, and PPV2, have been associated with PRDC, but their role remains unclear. This study investigates the presence of PCV2 and PRRSV and emerging viruses (PCV3, TTSuV, and PPV2) in the lungs of swine belonging to different age groups by histopathology and real-time PCR. The prevalent lung lesion was interstitial pneumonia with increased severity in post-weaning pigs. PRRSV was detected in 33% of piglets' lungs and in 20% of adults and post-weaning pigs with high Ct, while PCV2 was found in 100% of adult pigs, 33% of post-weaning pigs, and 22% of piglets, with low Ct in post-weaning pigs. PCV3 was present in all categories and coexisted with other viruses. TTSuV was detected in all swine in combination with other viruses, possibly influencing the disease dynamics, while PPV2 was detected in 100% of adults' and 90% of piglets' lungs. The detection of TTSuV, PCV3, and PPV2 in affected pigs prioritizes the need for comprehensive approaches in implementing appropriate control measures and minimizing economic losses associated with PRDC.
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Affiliation(s)
- Giovanni Pietro Burrai
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy; (G.P.B.); (S.H.); (A.A.); (E.A.)
| | - Salwa Hawko
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy; (G.P.B.); (S.H.); (A.A.); (E.A.)
| | - Silvia Dei Giudici
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (S.D.G.); (P.P.A.); (L.M.); (A.O.)
| | - Marta Polinas
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy; (G.P.B.); (S.H.); (A.A.); (E.A.)
| | - Pier Paolo Angioi
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (S.D.G.); (P.P.A.); (L.M.); (A.O.)
| | - Lorena Mura
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (S.D.G.); (P.P.A.); (L.M.); (A.O.)
| | - Alberto Alberti
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy; (G.P.B.); (S.H.); (A.A.); (E.A.)
| | - Chadi Hosri
- Department of Veterinary Medicine, Faculty of Agricultural Sciences and Veterinary Medicine, Lebanese University, Beirut 1487, Lebanon; (C.H.); (G.H.)
| | - Georges Hassoun
- Department of Veterinary Medicine, Faculty of Agricultural Sciences and Veterinary Medicine, Lebanese University, Beirut 1487, Lebanon; (C.H.); (G.H.)
| | - Annalisa Oggiano
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy; (S.D.G.); (P.P.A.); (L.M.); (A.O.)
| | - Elisabetta Antuofermo
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy; (G.P.B.); (S.H.); (A.A.); (E.A.)
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Hawko S, Burrai GP, Polinas M, Angioi PP, Dei Giudici S, Oggiano A, Alberti A, Hosri C, Antuofermo E. A Review on Pathological and Diagnostic Aspects of Emerging Viruses—Senecavirus A, Torque teno sus virus and Linda Virus—In Swine. Vet Sci 2022; 9:vetsci9090495. [PMID: 36136710 PMCID: PMC9502770 DOI: 10.3390/vetsci9090495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 08/26/2022] [Accepted: 09/07/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Worldwide demand for food is expected to increase due to population growth and swine accounts for more than one-third of meat produced worldwide. Several factors affect the success of livestock production systems, including animal disease control. Despite the importance of infectious diseases to animal health and the productivity of the global swine industry, pathogens of swine, in particular emerging viruses, such as Senecavirus A, Torque teno sus virus, and Linda virus, have gained limited interest. We performed a systematic analysis of the literature, with a focus on the main macroscopical and histological findings related to those viruses to fill the gap and highpoint these potentially hazardous pathogens. Abstract Swine production represents a significant component in agricultural economies as it occupies over 30% of global meat demand. Infectious diseases could constrain the swine health and productivity of the global swine industry. In particular, emerging swine viral diseases are omnipresent in swine populations, but the limited knowledge of the pathogenesis and the scarce information related to associated lesions restrict the development of data-based control strategies aimed to reduce the potentially great impact on the swine industry. In this paper, we reviewed and summarized the main pathological findings related to emerging viruses, such as Senecavirus A, Torque teno sus virus, and Linda virus, suggesting a call for further multidisciplinary studies aimed to fill this lack of knowledge and better clarify the potential role of those viral diseases in swine pathology.
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Affiliation(s)
- Salwa Hawko
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Giovanni P. Burrai
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
- Correspondence: ; Tel.: +39-079-229440
| | - Marta Polinas
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Pier Paolo Angioi
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy
| | - Silvia Dei Giudici
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy
| | - Annalisa Oggiano
- Department of Animal Health, Istituto Zooprofilattico Sperimentale della Sardegna, 07100 Sassari, Italy
| | - Alberto Alberti
- Department of Veterinary Medicine, University of Sassari, 07100 Sassari, Italy
| | - Chadi Hosri
- Department of Veterinary Medicine, Faculty of Agronomy and Veterinary Sciences, Lebanese University, Beirut 14/6573, Lebanon
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da Silva Andrade J, Loiko MR, Schmidt C, Vidalett MR, Lopes BC, Cerva C, Varela APM, Tochetto C, Maciel ALG, Bertagnolli AC, Rodrigues RO, Roehe PM, Lunge VR, Mayer FQ. Molecular survey of Porcine Respiratory Disease Complex pathogens in Brazilian wild boars. Prev Vet Med 2022; 206:105698. [DOI: 10.1016/j.prevetmed.2022.105698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Revised: 03/16/2022] [Accepted: 06/17/2022] [Indexed: 11/30/2022]
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Righi F, Arnaboldi S, Filipello V, Ianiro G, Di Bartolo I, Calò S, Bellini S, Trogu T, Lelli D, Bianchi A, Bonardi S, Pavoni E, Bertasi B, Lavazza A. Torque Teno Sus Virus (TTSuV) Prevalence in Wild Fauna of Northern Italy. Microorganisms 2022; 10:microorganisms10020242. [PMID: 35208696 PMCID: PMC8875128 DOI: 10.3390/microorganisms10020242] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2021] [Revised: 01/20/2022] [Accepted: 01/20/2022] [Indexed: 11/24/2022] Open
Abstract
Torque teno sus virus (TTSuV) is a non-enveloped circular ssDNA virus which frequently infects swine and has been associated with hepatic, respiratory, and autoimmune disorders. TTSuV’s pathogenic role is still uncertain, and clear data in the literature on virus reservoirs are lacking. The aims of this study were to investigate the presence of potentially zoonotic TTSuV in wild animals in Northern Italy and to evaluate their role as reservoirs. Liver samples were collected between 2016 and 2020 during four hunting seasons from wild boars (Sus scrofa), red deer (Cervus elaphus), roe deer (Capreolus capreolus), and chamois (Rupicapra rupicapra). Samples originated from areas in Northern Italy characterized by different traits, i.e., mountains and flatland with, respectively low and high farm density and anthropization. Viral identification was carried out by end-point PCR with specific primers for TTSuV1a and TTSuVk2a species. TTSuV prevalence in wild boars was higher in the mountains than in the flatland (prevalence of 6.2% and 2.3%, respectively). In wild ruminants only TTSuVk2a was detected (with a prevalence of 9.4%). Our findings shed light on the occurrence and distribution of TTSuV in some wild animal species, investigating their possible role as reservoirs.
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Affiliation(s)
- Francesco Righi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy; (F.R.); (V.F.); (S.C.); (S.B.); (T.T.); (D.L.); (E.P.); (B.B.); (A.L.)
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 20133 Milan, Italy
| | - Sara Arnaboldi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy; (F.R.); (V.F.); (S.C.); (S.B.); (T.T.); (D.L.); (E.P.); (B.B.); (A.L.)
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 20133 Milan, Italy
- Correspondence: ; Tel.: +39-030-229-0781
| | - Virginia Filipello
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy; (F.R.); (V.F.); (S.C.); (S.B.); (T.T.); (D.L.); (E.P.); (B.B.); (A.L.)
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 20133 Milan, Italy
| | - Giovanni Ianiro
- Emerging Zoonoses Unit, Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (G.I.); (I.D.B.)
| | - Ilaria Di Bartolo
- Emerging Zoonoses Unit, Department of Food Safety, Nutrition and Veterinary Public Health, Istituto Superiore di Sanità, 00161 Rome, Italy; (G.I.); (I.D.B.)
| | - Stefania Calò
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy; (F.R.); (V.F.); (S.C.); (S.B.); (T.T.); (D.L.); (E.P.); (B.B.); (A.L.)
| | - Silvia Bellini
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy; (F.R.); (V.F.); (S.C.); (S.B.); (T.T.); (D.L.); (E.P.); (B.B.); (A.L.)
| | - Tiziana Trogu
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy; (F.R.); (V.F.); (S.C.); (S.B.); (T.T.); (D.L.); (E.P.); (B.B.); (A.L.)
| | - Davide Lelli
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy; (F.R.); (V.F.); (S.C.); (S.B.); (T.T.); (D.L.); (E.P.); (B.B.); (A.L.)
| | - Alessandro Bianchi
- Istituto Zooprofilattico della Lombardia e dell’Emilia Romagna (IZSLER), 23100 Sondrio, Italy;
| | - Silvia Bonardi
- Veterinary Science Department, Università degli Studi di Parma, 43100 Parma, Italy;
| | - Enrico Pavoni
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy; (F.R.); (V.F.); (S.C.); (S.B.); (T.T.); (D.L.); (E.P.); (B.B.); (A.L.)
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 20133 Milan, Italy
| | - Barbara Bertasi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy; (F.R.); (V.F.); (S.C.); (S.B.); (T.T.); (D.L.); (E.P.); (B.B.); (A.L.)
- National Reference Centre for Emerging Risks in Food Safety (CRESA), Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 20133 Milan, Italy
| | - Antonio Lavazza
- Istituto Zooprofilattico Sperimentale della Lombardia e dell’Emilia Romagna (IZSLER), 25124 Brescia, Italy; (F.R.); (V.F.); (S.C.); (S.B.); (T.T.); (D.L.); (E.P.); (B.B.); (A.L.)
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Glud HA, George S, Skovgaard K, Larsen LE. Zoonotic and reverse zoonotic transmission of viruses between humans and pigs. APMIS 2021; 129:675-693. [PMID: 34586648 PMCID: PMC9297979 DOI: 10.1111/apm.13178] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 08/28/2021] [Indexed: 12/30/2022]
Abstract
Humans and pigs share a close contact relationship, similar biological traits, and one of the highest estimated number of viruses compared to other mammalian species. The contribution and directionality of viral exchange between humans and pigs remain unclear for some of these viruses, but their transmission routes are important to characterize in order to prevent outbreaks of disease in both host species. This review collects and assesses the evidence to determine the likely transmission route of 27 viruses between humans and pigs.
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Affiliation(s)
- Helena Aagaard Glud
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Sophie George
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Kerstin Skovgaard
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lars Erik Larsen
- Department of Veterinary and Animal Sciences, University of Copenhagen, Copenhagen, Denmark
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Techera C, Marandino A, Tomás G, Grecco S, Hernández M, Hernández D, Panzera Y, Pérez R. Origin, spreading and genetic variability of chicken anaemia virus. Avian Pathol 2021; 50:311-320. [PMID: 33928817 DOI: 10.1080/03079457.2021.1919289] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Chicken anaemia virus (CAV) is a widespread pathogen that causes immunosuppression in chickens. The virus-induced immunosuppression often results in secondary infections and a sub-optimal response to vaccinations, leading to high mortality rates and significant economic losses in the poultry industry. The small circular ssDNA genome (2.3 kb) has three partially overlapping genes: vp1, vp2 and vp3. VP1 capsid protein is highly variable and contains the neutralizing epitopes. Here, we analysed CAV strains from Uruguay using the full-length vp1 gene and performed a global comparative analysis to provide new evidence about the origin, dispersion and genetic variability of the virus. The phylogenetic analysis classified CAV in three or four major clades. Two clades (II and III) grouped most of the strains circulating worldwide including the Uruguayan strains. The phylodynamic analyses indicated that CAV emerged in the early 1900s and diverged to originate clade II and III. This early period of viral emergence was characterised by local diversification promoted by the extremely high substitution rate inferred for the virus (3.8 × 10-4 substitutions/site/year). Later, the virus underwent a global spreading by intra- and inter-continental migrations that correlates with a significant rise in the effective population size. In South America, CAV was introduced in three different migratory events and spread across the continent. Our findings suggest that the current CAV distribution is the consequence of its continuous expansion capability that homogenizes the populations and prevents the detection of clear temporal and geographic patterns of evolution in most strains.RESEARCH HIGHLIGHTS Current strains of chicken anaemia virus emerged in Asia in the early 1900s.Chicken anaemia virus has a high substitution rate.The phylogenetic analysis classified chicken anaemia virus in four major clades.Evolution in South America was characterized by long migration and local spreading.
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Affiliation(s)
- Claudia Techera
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República Montevideo, Uruguay
| | - Ana Marandino
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República Montevideo, Uruguay
| | - Gonzalo Tomás
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República Montevideo, Uruguay
| | - Sofía Grecco
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República Montevideo, Uruguay
| | - Martín Hernández
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República Montevideo, Uruguay
| | - Diego Hernández
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República Montevideo, Uruguay
| | - Yanina Panzera
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República Montevideo, Uruguay
| | - Ruben Pérez
- Sección Genética Evolutiva, Departamento de Biología Animal, Instituto de Biología, Facultad de Ciencias, Universidad de la República Montevideo, Uruguay
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Leng C, Ma Y, Yuan Z, Zhai H, Ding Y, Bao Y, Li H, Ayra-Pardo C, Shi H, Qiu R, Zhang H, Chen K, Kan Y, Yao L, Tian Z. Characterization of two newly emerged torque teno sus virus isolates from a large-scale pig farm in China, in 2018. Res Vet Sci 2021; 136:18-24. [PMID: 33578290 DOI: 10.1016/j.rvsc.2021.01.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2020] [Revised: 12/30/2020] [Accepted: 01/07/2021] [Indexed: 11/19/2022]
Abstract
Torque teno sus virus (TTSuV) infection is common in China's pig herd. Although of uncertain pathogenicity, TTSuVs have been reported as a worsening factor of other porcine diseases, including porcine circovirus associated disease (PCVAD), porcine respiratory diseases complex (PRDC) or porcine dermatitis and nephropathy syndrome (PDNS). To better understand the genetic diversity in TTSuVs, the complete genomes of two newly emerged isolates, referred to as HeN1-A9 and HeN1-A11, collected from pig samples at a large-scale pig farm in China, were analyzed. Phylogenetic relationships of TTSuV sequences separated TTSuV1 and TTSuVk2a groups and divided TTSuV1 into two major subtypes, including TTSuV1a and TTSuV1b; HeN1-A9 and HeN1-A11 strains classified into the TTSuV1a subtype. Recombination analysis demonstrated HeN1-A9 and HeN1-A11 were generated via recombination in the overlapping ORF1/ORF3 region of TTSuV1a genome, which we report for the first time. Furthermore, we found that HeN1-A9 could be replicated in cultured MARC-145 cells for 18 passages. Our findings may be useful for elucidating the characteristics and epidemic status of TTSuVs in China.
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Affiliation(s)
- Chaoliang Leng
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Key Laboratory of Insect Biology in Funiu Mountain, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang, PR China
| | - Yujing Ma
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Key Laboratory of Insect Biology in Funiu Mountain, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang, PR China
| | - Zhiqiao Yuan
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Key Laboratory of Insect Biology in Funiu Mountain, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang, PR China
| | - Hongyue Zhai
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Key Laboratory of Insect Biology in Funiu Mountain, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang, PR China
| | - Yushan Ding
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Key Laboratory of Insect Biology in Funiu Mountain, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang, PR China
| | - Yin Bao
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Key Laboratory of Insect Biology in Funiu Mountain, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang, PR China
| | - Huimin Li
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Key Laboratory of Insect Biology in Funiu Mountain, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang, PR China
| | - Camilo Ayra-Pardo
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Key Laboratory of Insect Biology in Funiu Mountain, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang, PR China
| | - Hongfei Shi
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Key Laboratory of Insect Biology in Funiu Mountain, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang, PR China
| | - Reng Qiu
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Key Laboratory of Insect Biology in Funiu Mountain, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang, PR China
| | - Hongliang Zhang
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, PR China
| | - Ke Chen
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Key Laboratory of Insect Biology in Funiu Mountain, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang, PR China
| | - Yunchao Kan
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Key Laboratory of Insect Biology in Funiu Mountain, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang, PR China
| | - Lunguang Yao
- Henan Provincial Engineering and Technology Center of Animal Disease Diagnosis and Integrated Control, Henan Provincial Engineering and Technology Center of Health Products for Livestock and Poultry, Henan Key Laboratory of Insect Biology in Funiu Mountain, China-UK-NYNU-RRes Joint Laboratory of Insect Biology, Nanyang Normal University, Nanyang, PR China
| | - Zhijun Tian
- State Key Laboratory of Veterinary Biotechnology, Harbin Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Harbin, PR China.
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9
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Deb B, Uddin A, Chakraborty S. Composition, codon usage pattern, protein properties, and influencing factors in the genomes of members of the family Anelloviridae. Arch Virol 2021; 166:461-474. [PMID: 33392821 PMCID: PMC7779081 DOI: 10.1007/s00705-020-04890-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 10/02/2020] [Indexed: 01/31/2023]
Abstract
The present study was carried out on 62 genome sequences of members of the family Anelloviridae, as there have been no reports of genome analysis of these DNA viruses using a bioinformatics approach. The genes were found to be rich in AC content with low codon usage bias (CUB). Relative synonymous codon usage (RSCU) values identified the preferred codons for each amino acid in the family. The codon AGA was overrepresented, while the codons TCG, TTG, CGG, CGT, ACG, GCG and GAT were underrepresented in all of the genomes. A significant correlation was found between the effective number of codons (ENC) and base constraints, indicating that compositional properties might have influenced the CUB. A highly significant correlation was observed between the overall base content and the base content at the third codon position, indicating that mutations might have affected the CUB. A highly significant positive correlation was observed between GC12 and GC3 (r = 0.904, p < 0.01), which indicated that directional mutation pressure influenced all three codon positions. A neutrality plot revealed that the contribution of mutation and natural selection in determining the CUB was 58.6% and 41.4%, respectively.
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Affiliation(s)
- Bornali Deb
- Department of Biotechnology, Assam University, Silchar, Assam 788150 India
| | - Arif Uddin
- Department of Zoology, Moinul Hoque Choudhury Memorial Science College, Algapur, Hailakandi, Assam 788150 India
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10
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Webb B, Rakibuzzaman A, Ramamoorthy S. Torque teno viruses in health and disease. Virus Res 2020; 285:198013. [PMID: 32404273 DOI: 10.1016/j.virusres.2020.198013] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 05/02/2020] [Accepted: 05/04/2020] [Indexed: 12/19/2022]
Abstract
Torque teno viruses (TTVs) are small, ubiquitous, viruses with a highly diverse, single-stranded, negative sense DNA genome and wide host range. They are detected at high rates in both healthy and diseased individuals and are considered a significant part of the mammalian virome. Similar to human TTVs, swine TTVs (TTSuVs) are epidemiologically linked to several coinfections including porcine circovirus types 2 and 3 and the porcine reproductive and respiratory disease syndrome virus. Experimental infection of gnotobiotic pigs with TTSuVs resulted in lesions in multiple organs and exacerbation of coinfections, making TTSuVs the only members of the Anelloviridae family with experimental evidence for pathogenicity. However, due to the lack of reliable cell culture and animal models, mechanistic studies on viral immunity and pathogenesis are limited. The objective of this review is to summarize the current status of knowledge regarding the biology, detection, pathogenesis and public health significance of TTSuVs, while identifying gaps in knowledge which limit the field.
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Affiliation(s)
- Brett Webb
- Veterinary Diagnostic Laboratory, North Dakota State University, Fargo, ND, United States
| | - Agm Rakibuzzaman
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, United States
| | - Sheela Ramamoorthy
- Department of Microbiological Sciences, North Dakota State University, Fargo, ND, United States.
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11
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Epidemiology and evolutionary analysis of Torque teno sus virus. Vet Microbiol 2020; 244:108668. [PMID: 32402339 DOI: 10.1016/j.vetmic.2020.108668] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 01/14/2020] [Accepted: 01/15/2020] [Indexed: 11/20/2022]
Abstract
Single stranded (ss) DNA viruses are increasingly being discovered due to the ongoing development of modern technologies in exploring the virosphere. Characterized by high rates of recombination and nucleotide substitutions, it could be comparable to RNA virus ones. Torque teno sus virus (TTSuV) is a standard ssDNA virus with a high population diversity, whose evolution is still obscure, further, it is frequently found in co-infections with other viruses threatening the porcine industry and therefore share the same host and epidemiological context. Here, we implement and describe approach to integrate viral nucleotide sequence analysis, surveillance data, and a structural approach to examine the evolution of TTSuVs, we collected samples from pigs displaying respiratory signs in China and revealed a high prevalence of TTSuV1 and TTSuVk2, frequently as part of co-infections with porcine circoviruses (PCVs), especially in spleen and lung. In addition, thirty six strains sequenced were obtained to investigate their genetic diversity in China. The evolutionary history of TTSuVs were unveiled as following: At the nucleotide sequence level, TTSuVs ORF1 was confirmed to be a robust phylogenetic maker to study evolution comparably to full genomes. Additionally, extensive recombination discovered within TTSuVk2a (also 5 out of the 36 sequenced strains in this study revealed to be recombination). Then, pairwise distance, phylogenetic trees, and amino acid analysis confirmed TTSuVs species, and allowed to define circulating genotypes (TTSuV1a-1, 1a-2, 1b-1, 1b-2, 1b-3, and k2a-1, k2a-2, k2b). Selection analysis uncovered seven and six positive selected sites in TTSuV1 and TTSuVk2, respectively. At the protein structure level, mapping of sites onto the three-dimensional structure revealed that several positive selected sites locate into potential epitopes, which might related to the potential escaping from host immune response. Our result could assist future studies on swine ssDNA virus classification, surveillance and control.
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12
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Li G, Zhang W, Wang R, Xing G, Wang S, Ji X, Wang N, Su S, Zhou J. Genetic Analysis and Evolutionary Changes of the Torque teno sus Virus. Int J Mol Sci 2019; 20:ijms20122881. [PMID: 31200479 PMCID: PMC6628323 DOI: 10.3390/ijms20122881] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Revised: 06/05/2019] [Accepted: 06/10/2019] [Indexed: 01/03/2023] Open
Abstract
The torque teno sus virus (TTSuV) is an emerging virus threating the Suidae species of unclear pathogenicity, although it was previously reported as a worsening factor of other porcine diseases, in particular, porcine circovirus associated disease (PCVAD). Here, a comprehensive codon usage analysis of the open reading frame 1 (ORF1), which encodes the viral capsid protein, was undertaken for the first time to reveal its evolutionary history. We revealed independent phylogenetic processes for the two genera during TTSuV evolution, which was confirmed by principal component analysis (PCA). A low codon usage bias was observed in different genera and different species, with Kappatorquevirus a (TTSuVk2a) displaying the highest, which was mainly driven by mutation pressure and natural selection, especially natural selection. Overall, ATs were more abundant than GCs, along with more A-ended synonymous codons in relative synonymous codon usage (RSCU) analysis. To further confirm the role of natural selection and TTSuV adaptation to the Suidae species, codon adaptation index (CAI), relative codon deoptimization index (RCDI), and similarity index (SiD) analyses were performed, which showed different adaptations for different TTSuVs. Importantly, we identified a more dominant role of Sus scrofa in the evolution of Iotatorquevirus (TTSuV1), with the highest CAI values and lowest RCDI values compared to Sus scrofa domestica. However, in TTSuVk2, the roles of Sus scrofa and Sus scrofa domestica were the same, regarding codon usage, with similar CAI and RCDI values. Our study provides a new perspective of the evolution of TTSuV and valuable information to develop control measures against TTSuV.
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Affiliation(s)
- Gairu Li
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210000, China.
| | - Wenyan Zhang
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210000, China.
| | - Ruyi Wang
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210000, China.
| | - Gang Xing
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou 310027, China.
| | - Shilei Wang
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210000, China.
| | - Xiang Ji
- Department of Biomathematics, University of California, Los Angeles, CA 90095, USA.
| | - Ningning Wang
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210000, China.
| | - Shuo Su
- MOE International Joint Collaborative Research Laboratory for Animal Health & Food Safety, Jiangsu Engineering Laboratory of Animal Immunology, Institute of Immunology, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing 210000, China.
| | - Jiyong Zhou
- Key Laboratory of Animal Virology of Ministry of Agriculture, Zhejiang University, Hangzhou 310027, China.
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13
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Ramos N, Mirazo S, Botto G, Teixeira TF, Cibulski SP, Castro G, Cabrera K, Roehe PM, Arbiza J. High frequency and extensive genetic heterogeneity of TTSuV1 and TTSuVk2a in PCV2- infected and non-infected domestic pigs and wild boars from Uruguay. Vet Microbiol 2018; 224:78-87. [DOI: 10.1016/j.vetmic.2018.08.029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 08/28/2018] [Accepted: 08/29/2018] [Indexed: 01/16/2023]
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14
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Vargas-Ruiz A, García-Camacho LA, Ramírez-Alvarez H, Rangel-Rodriguez IC, Alonso-Morales RA, Sánchez-Betancourt JI. Molecular characterization of the ORF2 of Torque teno sus virus 1a and Torque teno sus virus 1b detected in cases of postweaning multisystemic wasting syndrome in Mexico. Transbound Emerg Dis 2018; 65:1806-1815. [PMID: 30035377 DOI: 10.1111/tbed.12956] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2017] [Revised: 05/28/2018] [Accepted: 06/18/2018] [Indexed: 02/05/2023]
Abstract
Worldwide Torque teno sus virus (TTSuV, genus Iotatorquevirus) species have been regarded as possible agents associated with porcine circovirus-associated disease. Iotatorquevirus species possess high genomic variability, suggesting that diverse genotypes are widely geographically distributed. In this study, we validated the genomic variability of Iotaroquevirus species in pigs with postweaned multisystemic wasting syndrome. Genomic DNA from nine TTSuV1a-positive tissues and 15 TTSuV1b-positive tissues was used to amplify the complete ORF2 of each species by nested PCR to perform a molecular characterization. It was found that Mexican TTSuV1a sequences belong to genotype B, sharing phylogenetic origin, high nucleic acid and amino acid sequence similarity and dominant epitope conformation with commercially linked countries, such as the United States, Canada and China, whereas the Mexican TTSuV1b sequences belong to genotype A, being more divergent among each other and displaying low nucleotide identity with worldwide genotype A sequences. In both Iotatorquevirus species, a PTPase-like signature motif was identified in the predicted amino acid sequence, being more conserved for Mexican TTSuV1b sequences than for Mexican TTSuV1a sequences, in which several substitutions were observed. These changes may influence the conformation of dominant epitopes as different arrays were determined among TTSuV1a genotypes. ORF2 variability may account for pathogenic differences by modifying viral replication and immune response, as depicted for human TTV.
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Affiliation(s)
- Alejandro Vargas-Ruiz
- College of Superior Studies (FESC), National University of Mexico (UNAM), Estado de México, México
| | | | - Hugo Ramírez-Alvarez
- College of Superior Studies (FESC), National University of Mexico (UNAM), Estado de México, México
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15
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Retrospective study of the relationship of Torque teno sus virus 1a and Torque teno sus virus 1b with porcine circovirus associated disease. CANADIAN JOURNAL OF VETERINARY RESEARCH = REVUE CANADIENNE DE RECHERCHE VETERINAIRE 2017; 81:178-185. [PMID: 28725107 DOI: pmid/28725107] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 09/22/2016] [Accepted: 01/20/2017] [Indexed: 02/08/2023]
Abstract
Genus Iotatorquevirus consists of 2 species, Torque teno sus virus 1a and Torque teno sus virus 1b, which are ubiquitous in swine populations, and are widely reported in association with porcine circovirus associated disease (PCVAD). To evaluate the relationship with PCVAD, 100 formalin-fixed paraffin-embedded tissue samples were used to detect both Iotatorquevirus species by nested PCR and sequencing. Sixty-eight PCVAD cases were selected as well as 32 porcine circovirus type 2 (PCV2) non-affected cases. Overall, 33 of the 100 cases were positive for Torque teno sus virus 1a and 8 of 100 were positive for Torque teno sus virus 1b. Only 24 of 68 (35%) PCVAD cases were positive for Torque teno sus virus 1a; 39% (9/23) of post-weaning multisystemic wasting syndrome, and 33% (15/45) of PCV2-associated reproductive failure cases. Among PCV2 non-affected cases, 28% were positive for Torque teno sus virus 1a and 6% were positive for Torque teno sus virus 1b. Torque teno sus virus 1b was not detected in PCV2-associated reproductive failure cases. Regardless of the PCV2-status, a lower frequency of both Iotatorquevirus species was found than depicted in other reports and there was no statistical relationship with PCVAD (χ 2 < 0.01). Given the worldwide genomic variability of Iotatorquevirus species, it is feasible that species prevalent in Mexico share a lower nucleotide sequence identity, leading to different pathogenic potential.
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16
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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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17
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Varsani A, Krupovic M. Sequence-based taxonomic framework for the classification of uncultured single-stranded DNA viruses of the family Genomoviridae. Virus Evol 2017; 3:vew037. [PMID: 28458911 PMCID: PMC5399927 DOI: 10.1093/ve/vew037] [Citation(s) in RCA: 85] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Abstract
With the advent of metagenomics approaches, a large diversity of known and unknown viruses has been identified in various types of environmental, plant, and animal samples. One such widespread virus group is the recently established family Genomoviridae which includes viruses with small (∼2-2.4 kb), circular ssDNA genomes encoding rolling-circle replication initiation proteins (Rep) and unique capsid proteins. Here, we propose a sequence-based taxonomic framework for classification of 121 new virus genomes within this family. Genomoviruses display ∼47% sequence diversity, which is very similar to that within the well-established and extensively studied family Geminiviridae (46% diversity). Based on our analysis, we establish a 78% genome-wide pairwise identity as a species demarcation threshold. Furthermore, using a Rep sequence phylogeny-based analysis coupled with the current knowledge on the classification of geminiviruses, we establish nine genera within the Genomoviridae family. These are Gemycircularvirus (n = 73), Gemyduguivirus (n = 1), Gemygorvirus (n = 9), Gemykibivirus (n = 29), Gemykolovirus (n = 3), Gemykrogvirus (n = 3), Gemykroznavirus (n = 1), Gemytondvirus (n = 1), Gemyvongvirus (n = 1). The presented taxonomic framework offers rational classification of genomoviruses based on the sequence information alone and sets an example for future classification of other groups of uncultured viruses discovered using metagenomics approaches.
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Affiliation(s)
- Arvind Varsani
- The Biodesign Center for Fundamental and Applied Microbiomics, School of Life sciences, Center for Evolution and Medicine, Arizona State University, Tempe, AZ 85287, USA.,Structural Biology Research Unit, Department of Clinical Laboratory Sciences, University of Cape Town, Observatory 7700, South Africa
| | - Mart Krupovic
- Unité Biologie moléculaire du Gène chez les Extrêmophiles, Department of Microbiology, Institut Pasteur, 25 rue du Docteur Roux, Paris 75015, France
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18
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Shi C, Liu Y, Hu X, Xiong J, Zhang B, Yuan Z. A metagenomic survey of viral abundance and diversity in mosquitoes from Hubei province. PLoS One 2015; 10:e0129845. [PMID: 26030271 PMCID: PMC4452694 DOI: 10.1371/journal.pone.0129845] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 05/13/2015] [Indexed: 01/27/2023] Open
Abstract
Mosquitoes as one of the most common but important vectors have the potential to transmit or acquire a lot of viruses through biting, however viral flora in mosquitoes and its impact on mosquito-borne disease transmission has not been well investigated and evaluated. In this study, the metagenomic techniquehas been successfully employed in analyzing the abundance and diversity of viral community in three mosquito samples from Hubei, China. Among 92,304 reads produced through a run with 454 GS FLX system, 39% have high similarities with viral sequences belonging to identified bacterial, fungal, animal, plant and insect viruses, and 0.02% were classed into unidentified viral sequences, demonstrating high abundance and diversity of viruses in mosquitoes. Furthermore, two novel viruses in subfamily Densovirinae and family Dicistroviridae were identified, and six torque tenosus virus1 in family Anelloviridae, three porcine parvoviruses in subfamily Parvovirinae and a Culex tritaeniorhynchus rhabdovirus in Family Rhabdoviridae were preliminarily characterized. The viral metagenomic analysis offered us a deep insight into the viral population of mosquito which played an important role in viral initiative or passive transmission and evolution during the process.
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Affiliation(s)
- Chenyan Shi
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- University of Chinese Academy of Sciences, Beijing, China
| | - Yi Liu
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Xiaomin Hu
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Jinfeng Xiong
- Hubei Disease Control and Prevention Center, Wuhan, China
| | - Bo Zhang
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
| | - Zhiming Yuan
- Key Laboratory of Agricultural and Environmental Microbiology, Wuhan Institute of Virology, Chinese Academy of Sciences, Wuhan, China
- * E-mail:
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