Full‐length genome sequencing of RNA viruses—How the approach can enlighten us on hepatitis C and hepatitis E viruses

2020 ◽  
Author(s):  
Elodie Laugel ◽  
Cédric Hartard ◽  
Hélène Jeulin ◽  
Sibel Berger ◽  
Véronique Venard ◽  
...  
Keyword(s):  
Hepatitis C ◽  
Genome Sequencing ◽  
Rna Viruses ◽  
Hepatitis E ◽  
Full Length ◽  
Full Length Genome

Full-length genome of a novel genotype 3 hepatitis E virus strain obtained from domestic pigs in Japan

2017 ◽  
Vol 240 ◽  
pp. 147-153 ◽  
Author(s):  
Putu Prathiwi Primadharsini ◽  
Masao Miyake ◽  
Satoshi Kunita ◽  
Tsutomu Nishizawa ◽  
Masaharu Takahashi ◽  
...  
Keyword(s):  
Virus Strain ◽  
Hepatitis E Virus ◽  
Hepatitis E ◽  
Full Length ◽  
Genotype 3 ◽  
Domestic Pigs ◽  
Novel Genotype ◽  
Full Length Genome

Full-Length Genome Sequencing of HIV Type 1 Group O Viruses Isolated from a Heterosexual Transmission Cluster in Senegal

2001 ◽  
Vol 17 (12) ◽  
pp. 1211-1216 ◽  
Author(s):  
Coumba Toure Kane ◽  
Celine Montavon ◽  
Mama Awa Toure ◽  
Mame Awa Faye ◽  
Aissatou Gueye Ndiaye ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Full Length ◽  
Heterosexual Transmission ◽  
Hiv Type 1 ◽  
Full Length Genome

Analysis of the full-length genome of genotype 4 hepatitis E virus isolates from patients with fulminant or acute self-limited hepatitis E

2006 ◽  
Vol 78 (4) ◽  
pp. 476-484 ◽  
Author(s):  
Jun Inoue ◽  
Tsutomu Nishizawa ◽  
Masaharu Takahashi ◽  
Tatsuya Aikawa ◽  
Hitoshi Mizuo ◽  
...  
Keyword(s):  
Hepatitis E Virus ◽  
Hepatitis E ◽  
Full Length ◽  
Genotype 4 ◽  
Full Length Genome ◽  
Virus Isolates

scholarly journals HIV-1 Unique Recombinant Forms Identified in Slovenia and Their Characterization by Near Full-Length Genome Sequencing

Viruses ◽  
2020 ◽  
Vol 12 (1) ◽  
pp. 63
Author(s):  
Lunar ◽  
Mlakar ◽  
Zorec ◽  
Poljak
Keyword(s):  
Genome Sequencing ◽  
Recombination Event ◽  
Patient Management ◽  
Full Length ◽  
Base Pairs ◽  
Comprehensive Collection ◽  
Subtype B ◽  
Full Length Genome ◽  
Hiv 1 ◽  
Hiv Diversity

Surveillance of HIV circulating recombinant forms (CRFs) is important because HIV diversity can affect various aspects of HIV infection from prevention to diagnosis and patient management. A comprehensive collection of pol sequences obtained from individuals diagnosed with HIV-1 from 2000 to 2016 in Slovenia was subtyped to identify possible unique recombinant forms (URFs). Selected samples were subjected to near full-length genome (NFLG) sequencing and detailed recombination analyses. Discordant subtyping results were observed for 68/387 (17.6%) sequences and 20 sequences were identified as the most probable URFs and selected for NFLG characterization. Further, 11 NFLGs and two sequences of >7000 base pairs were obtained. Seven sequences were identified as “pure” subtypes or already characterized CRFs: subtype B (n = 5), sub-subtype A6 (n = 1), and CRF01_AE (n = 1). The remaining six sequences were determined to be URFs; four displayed a single recombination event and two exhibited a complex recombination pattern involving several subtypes or CRFs. Finally, three HIV strains were recognized as having epidemic potential and could be further characterized as new CRFs. Our study shows that the identification of new CRFs is possible, even in countries where HIV diversity is considered limited, emphasizing the importance of the surveillance of HIV recombinant forms.

Full-Length Genome Sequencing of the Polish HPAI H5N1 Viruses Suggests Separate Introductions in 2006 and 2007

2010 ◽  
Vol 5 (s1) ◽  
pp. e54-e54
Author(s):  
Krzysztof Smietanka ◽  
Alice Fusaro ◽  
Katarzyna Domanska-Blicharz ◽  
Annalisa Salviato ◽  
Isabella Monne ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Full Length ◽  
Hpai H5n1 ◽  
Full Length Genome

scholarly journals Analysis of the full-length genome of hepatitis E virus isolates obtained from wild boars in Japan

2005 ◽  
Vol 86 (12) ◽  
pp. 3321-3326 ◽  
Author(s):  
Tsutomu Nishizawa ◽  
Masaharu Takahashi ◽  
Kazunori Endo ◽  
Shinji Fujiwara ◽  
Nobuo Sakuma ◽  
...  
Keyword(s):  
Hepatitis E Virus ◽  
Hepatitis E ◽  
Full Length ◽  
Partial Sequence ◽  
Genotype 3 ◽  
Entire Genome ◽  
Wild Boars ◽  
Full Length Sequence ◽  
Full Length Genome ◽  
Virus Isolates

Two (2·3 %) of 87 wild-caught boars in Japan had detectable hepatitis E virus (HEV) RNA. The two boar HEV isolates (wbJTS1 and wbJYG1) obtained in the present study and a previously reported isolate (wbJSG1) whose partial sequence had been determined were sequenced over the entire genome. The wbJSG1, wbJTS1 and wbJYG1 isolates comprised 7225 or 7226 nt, excluding the poly(A) tail, and segregated into genotype 3. They differed by 8·5–11·2 % from each other and by 8·6–18·4 % from 17 reported genotype 3 HEV isolates, including one boar isolate, in the full-length sequence. When compared with 191 reported genotype 3 HEV isolates whose partial sequences were known, these three boar isolates were closer to Japanese isolates than to isolates of non-Japanese origin (89·2±2·6 vs 85·9±2·2 %; P<0·0001). A proportion of wild boars in Japan are infected with markedly heterogeneous HEV strains that are indigenous to Japan and may serve as reservoirs of HEV.

Near-Full-Length Genome Sequencing of Divergent African HIV Type 1 Subtype F Viruses Leads to the Identification of a New HIV Type 1 Subtype Designated K

2000 ◽  
Vol 16 (2) ◽  
pp. 139-151 ◽  
Author(s):  
Karine Triques ◽  
Anke Bourgeois ◽  
Nicole Vidal ◽  
Eitel Mpoudi-Ngole ◽  
Claire Mulanga-Kabeya ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Full Length ◽  
Hiv Type 1 ◽  
Full Length Genome

scholarly journals Full-length genome sequence of segmented RNA virus from ticks was obtained using small RNA sequencing data

BMC Genomics ◽  
2020 ◽  
Vol 21 (1) ◽  
Author(s):  
Xiaofeng Xu ◽  
Jinlong Bei ◽  
Yibo Xuan ◽  
Jiayuan Chen ◽  
Defu Chen ◽  
...  
Keyword(s):  
Rna Sequencing ◽  
Genome Sequence ◽  
Small Rna ◽  
Rna Viruses ◽  
Rna Virus ◽  
Full Length ◽  
Small Rna Sequencing ◽  
Sequencing Data ◽  
Geographical Regions ◽  
Full Length Genome

Abstract Background In 2014, a novel tick-borne virus of the Flaviviridae family was first reported in the Mogiana region of Brazil and named the Mogiana tick virus (MGTV). Thereafter, the Jingmen tick virus (JMTV), Kindia tick virus (KITV), and Guangxi tick virus (GXTV)—evolutionarily related to MGTV—were reported. Results In the present study, we used small RNA sequencing (sRNA-seq) to detect viruses in ticks and discovered a new MGTV strain in Amblyomma testudinarium ticks collected in China’s Yunnan Province in 2016. We obtained the full-length genome sequence of this MGTV strain Yunnan2016 (GenBank: MT080097, MT080098, MT080099 and MT080100) and recommended it for its inclusion in the NCBI RefSeq database for future studies on MGTV, JMTV, KITV and GXTV. Phylogenetic analysis showed that MGTV, JMTV, KITV and GXTV are monophyletic and belong to a MGTV group. Furthermore, this MGTV group of viruses may be phylogenetically related to geographical regions that were formerly part of the supercontinents Gondwana and Laurasia. Conclusions To the best of our knowledge, this is the first study in which 5′ and 3′ sRNAs were used to generate full-length genome sequences of, but not limited to, RNA viruses. We also demonstrated the feasibility of using the sRNA-seq based method for the detection of viruses in pooled two and even possible one small ticks. MGTV may preserve the characteristic of ancient RNA viruses, which can be used to study the origin and evolution of RNA viruses. In addition, MGTV can be used as novel species for studies in phylogeography.

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