Complete genome sequence of a rodent torque teno virus in Hainan Island, China
Objective: Torque teno virus(TTV), are reported in a wide range of mammals. In this study, we sequenced and analyzed the complete genome of a genetic variant of Rodent TTV, RoTTV3-HMU1 (Hainan Medical University). The virus was harbored by a Rattus norvegicus in the residential areas of Hainan Islan...
Published in: | Asian Pacific Journal of Tropical Medicine |
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Wolters Kluwer Medknow Publications
2018
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Online Access: | https://doi.org/10.4103/1995-7645.243096 https://doaj.org/article/2d1f221eb8184785a5869914edcce268 |
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ftdoajarticles:oai:doaj.org/article:2d1f221eb8184785a5869914edcce268 2023-05-15T15:15:34+02:00 Complete genome sequence of a rodent torque teno virus in Hainan Island, China Yue Wu Shan-shan Wang Yun-chun Chen Jasper Fuk-Woo Chan Li-hua Li Wen-qi Wang Huan-huan Zhou You Zhang Lei Zhang Xiu-ji Cui Gang Lu Kwok-Yung Yuen Fei-fei Yin 2018-01-01T00:00:00Z https://doi.org/10.4103/1995-7645.243096 https://doaj.org/article/2d1f221eb8184785a5869914edcce268 EN eng Wolters Kluwer Medknow Publications http://www.apjtm.org/article.asp?issn=1995-7645;year=2018;volume=11;issue=13;spage=29;epage=29;aulast=Wu https://doaj.org/toc/2352-4146 2352-4146 doi:10.4103/1995-7645.243096 https://doaj.org/article/2d1f221eb8184785a5869914edcce268 Asian Pacific Journal of Tropical Medicine, Vol 11, Iss 13, Pp 29-29 (2018) TTV Serotype Complete Genome Sequence Rattus norvegicus Arctic medicine. Tropical medicine RC955-962 article 2018 ftdoajarticles https://doi.org/10.4103/1995-7645.243096 2022-12-31T02:03:37Z Objective: Torque teno virus(TTV), are reported in a wide range of mammals. In this study, we sequenced and analyzed the complete genome of a genetic variant of Rodent TTV, RoTTV3-HMU1 (Hainan Medical University). The virus was harbored by a Rattus norvegicus in the residential areas of Hainan Island, China. Methods: Torque Teno virus (TTV) was found widely distributed throughout the world infecting an extensively wide range of mammals .We extracted the viral DNA from a Rattus norvegicus liver which was caught from the residential areas of Hainan Island. Purifying the amplicons in the range of 250-500 bp. Then Five hundred nanograms DNA was subjected to high-throughput sequencing. The contigs were compared with the NCBI nucleiotide database, designed the primers to cover the genome by PCR amplification and amplicons of each PCR which have been cloned and sequenced. Finally the genome was annotated by using NCBI ORF finder and FGENESV0. Phylogenetic analysis was implemented by the neighbor-joining method in the MEGA6 software package. Results: We sequenced the complete genome of a genetic variant of Rodent TTV, RoTTV3- HMU1. The genomic sequence of RoTTV3-HMU1 has been deposited in GenBank under accession number MF688246.1. The complete genome of RoTTV3-HMU1 is 2 570 nucleotides (nt) in length with a G+C content of 46.93%. RoTTV3-HMU1 encoded 3 unidirectional overlapping open reading frames (ORF). Sequence analysis indicated that the genome of RoTTV3-HMU1 virus was most closely related to RN_2_15 (GenBank accession no. KM668486.1). Phylogenetic analysis based on both ORF1 and the total genome sequence placed RoTTV3-HMU1 in to the clad RoTTV3 of the RoTTV. Conclusions: Hainan Island faces mainland across the sea, however, the same genotype of RoTTV was identified in both Hainan Island and the other part of China. The detection of RoTTV3-HMU1 contributed to a better understanding about the origin and evolution of RoTTV. Article in Journal/Newspaper Arctic Directory of Open Access Journals: DOAJ Articles Arctic Teno ENVELOPE(25.690,25.690,68.925,68.925) Asian Pacific Journal of Tropical Medicine 11 13 29 |
institution |
Open Polar |
collection |
Directory of Open Access Journals: DOAJ Articles |
op_collection_id |
ftdoajarticles |
language |
English |
topic |
TTV Serotype Complete Genome Sequence Rattus norvegicus Arctic medicine. Tropical medicine RC955-962 |
spellingShingle |
TTV Serotype Complete Genome Sequence Rattus norvegicus Arctic medicine. Tropical medicine RC955-962 Yue Wu Shan-shan Wang Yun-chun Chen Jasper Fuk-Woo Chan Li-hua Li Wen-qi Wang Huan-huan Zhou You Zhang Lei Zhang Xiu-ji Cui Gang Lu Kwok-Yung Yuen Fei-fei Yin Complete genome sequence of a rodent torque teno virus in Hainan Island, China |
topic_facet |
TTV Serotype Complete Genome Sequence Rattus norvegicus Arctic medicine. Tropical medicine RC955-962 |
description |
Objective: Torque teno virus(TTV), are reported in a wide range of mammals. In this study, we sequenced and analyzed the complete genome of a genetic variant of Rodent TTV, RoTTV3-HMU1 (Hainan Medical University). The virus was harbored by a Rattus norvegicus in the residential areas of Hainan Island, China. Methods: Torque Teno virus (TTV) was found widely distributed throughout the world infecting an extensively wide range of mammals .We extracted the viral DNA from a Rattus norvegicus liver which was caught from the residential areas of Hainan Island. Purifying the amplicons in the range of 250-500 bp. Then Five hundred nanograms DNA was subjected to high-throughput sequencing. The contigs were compared with the NCBI nucleiotide database, designed the primers to cover the genome by PCR amplification and amplicons of each PCR which have been cloned and sequenced. Finally the genome was annotated by using NCBI ORF finder and FGENESV0. Phylogenetic analysis was implemented by the neighbor-joining method in the MEGA6 software package. Results: We sequenced the complete genome of a genetic variant of Rodent TTV, RoTTV3- HMU1. The genomic sequence of RoTTV3-HMU1 has been deposited in GenBank under accession number MF688246.1. The complete genome of RoTTV3-HMU1 is 2 570 nucleotides (nt) in length with a G+C content of 46.93%. RoTTV3-HMU1 encoded 3 unidirectional overlapping open reading frames (ORF). Sequence analysis indicated that the genome of RoTTV3-HMU1 virus was most closely related to RN_2_15 (GenBank accession no. KM668486.1). Phylogenetic analysis based on both ORF1 and the total genome sequence placed RoTTV3-HMU1 in to the clad RoTTV3 of the RoTTV. Conclusions: Hainan Island faces mainland across the sea, however, the same genotype of RoTTV was identified in both Hainan Island and the other part of China. The detection of RoTTV3-HMU1 contributed to a better understanding about the origin and evolution of RoTTV. |
format |
Article in Journal/Newspaper |
author |
Yue Wu Shan-shan Wang Yun-chun Chen Jasper Fuk-Woo Chan Li-hua Li Wen-qi Wang Huan-huan Zhou You Zhang Lei Zhang Xiu-ji Cui Gang Lu Kwok-Yung Yuen Fei-fei Yin |
author_facet |
Yue Wu Shan-shan Wang Yun-chun Chen Jasper Fuk-Woo Chan Li-hua Li Wen-qi Wang Huan-huan Zhou You Zhang Lei Zhang Xiu-ji Cui Gang Lu Kwok-Yung Yuen Fei-fei Yin |
author_sort |
Yue Wu |
title |
Complete genome sequence of a rodent torque teno virus in Hainan Island, China |
title_short |
Complete genome sequence of a rodent torque teno virus in Hainan Island, China |
title_full |
Complete genome sequence of a rodent torque teno virus in Hainan Island, China |
title_fullStr |
Complete genome sequence of a rodent torque teno virus in Hainan Island, China |
title_full_unstemmed |
Complete genome sequence of a rodent torque teno virus in Hainan Island, China |
title_sort |
complete genome sequence of a rodent torque teno virus in hainan island, china |
publisher |
Wolters Kluwer Medknow Publications |
publishDate |
2018 |
url |
https://doi.org/10.4103/1995-7645.243096 https://doaj.org/article/2d1f221eb8184785a5869914edcce268 |
long_lat |
ENVELOPE(25.690,25.690,68.925,68.925) |
geographic |
Arctic Teno |
geographic_facet |
Arctic Teno |
genre |
Arctic |
genre_facet |
Arctic |
op_source |
Asian Pacific Journal of Tropical Medicine, Vol 11, Iss 13, Pp 29-29 (2018) |
op_relation |
http://www.apjtm.org/article.asp?issn=1995-7645;year=2018;volume=11;issue=13;spage=29;epage=29;aulast=Wu https://doaj.org/toc/2352-4146 2352-4146 doi:10.4103/1995-7645.243096 https://doaj.org/article/2d1f221eb8184785a5869914edcce268 |
op_doi |
https://doi.org/10.4103/1995-7645.243096 |
container_title |
Asian Pacific Journal of Tropical Medicine |
container_volume |
11 |
container_issue |
13 |
container_start_page |
29 |
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1766345937521737728 |