Pre-vaccination genomic diversity of human papillomavirus genotype 6 (HPV 6): A comparative analysis of 21 full-length genome sequences

2011 ◽  
Vol 11 (7) ◽  
pp. 1805-1810 ◽  
Author(s):  
Boštjan J. Kocjan ◽  
Mateja M. Jelen ◽  
Polona J. Maver ◽  
Katja Seme ◽  
Mario Poljak
Keyword(s):  
Human Papillomavirus ◽  
Comparative Analysis ◽  
Full Length ◽  
Genomic Diversity ◽  
Genome Sequences ◽  
Full Length Genome

Prevaccination genomic diversity of human papillomavirus genotype 11: A study on 63 clinical isolates and 10 full-length genome sequences

2011 ◽  
Vol 83 (3) ◽  
pp. 461-470 ◽  
Author(s):  
Polona J. Maver ◽  
Boštjan J. Kocjan ◽  
Katja Seme ◽  
Marko Potočnik ◽  
Nina Gale ◽  
...  
Keyword(s):  
Human Papillomavirus ◽  
Full Length ◽  
Genomic Diversity ◽  
Clinical Isolates ◽  
Genome Sequences ◽  
Full Length Genome

scholarly journals Emergence of Salmonid Alphavirus Genotype 2 in Norway—Molecular Characterization of Viral Strains Circulating in Norway and Scotland

Viruses ◽  
2021 ◽  
Vol 13 (8) ◽  
pp. 1556
Author(s):  
Monika J. Hjortaas ◽  
Elena Fringuelli ◽  
Adérito L. Monjane ◽  
Aase B. Mikalsen ◽  
Christine M. Jonassen ◽  
...  
Keyword(s):  
Full Length ◽  
Genomic Diversity ◽  
Last Common Ancestor ◽  
Source Of Infection ◽  
New Variant ◽  
Genotype 2 ◽  
Boat Traffic ◽  
Horizontal Spread ◽  
Full Length Genome

Pancreas disease (PD) and sleeping disease (SD), caused by an alphavirus, are endemic in European salmonid aquaculture, causing significant mortality, reduced growth and poor flesh quality. In 2010, a new variant of salmonid alphavirus emerged in Norway, marine salmonid alphavirus genotype 2 (SAV2). As this genotype is highly prevalent in Scotland, transmission through well boat traffic was hypothesized as one possible source of infection. In this study, we performed full-length genome sequencing of SAV2 sampled between 2006 and 2012 in Norway and Scotland, and present the first comprehensive full-length characterization of Norwegian marine SAV2 strains. We analyze their relationship with selected Scottish SAV2 strains and explore the genetic diversity of SAV. Our results show that all Norwegian marine SAV2 share a recent last common ancestor with marine SAV2 circulating in Scotland and a higher level of genomic diversity among the Scottish marine SAV2 strains compared to strains from Norway. These findings support the hypothesis of a single introduction of SAV2 to Norway sometime from 2006–2010, followed by horizontal spread along the coast.

scholarly journals Full-Length Genome Sequences of Recombinant and Nonrecombinant Sympatric Strains of Rice yellow mottle virus from Western Kenya

2018 ◽  
Vol 6 (8) ◽  
Author(s):  
Antony Kigaru Adego ◽  
Nils Poulicard ◽  
Agnès Pinel-Galzi ◽  
Benard Mukoye ◽  
Denis Fargette ◽  
...  
Keyword(s):  
Full Length ◽  
Mottle Virus ◽  
Rice Yellow Mottle Virus ◽  
Genome Sequences ◽  
Western Kenya ◽  
Yellow Mottle ◽  
Full Length Genome

ABSTRACT Five isolates of Rice yellow mottle virus from western Kenya were fully sequenced. One isolate of strain S4lv had been collected in 1966. Two isolates belonged to the emerging strain S4ug recently described in Uganda. Two isolates collected in 2012 are putative recombinants between the S4lv and S4ug strains.

scholarly journals Natural infection of Atlantic salmon (Salmo salar L.) with salmonid alphavirus 3 generates numerous viral deletion mutants

2013 ◽  
Vol 94 (9) ◽  
pp. 1945-1954 ◽  
Author(s):  
Elin Petterson ◽  
Marit Stormoen ◽  
Øystein Evensen ◽  
Aase B. Mikalsen ◽  
Øyvind Haugland
Keyword(s):  
Atlantic Salmon ◽  
Salmo Salar ◽  
Natural Infection ◽  
Sequence Divergence ◽  
Heart Tissue ◽  
Full Length ◽  
Deletion Mutants ◽  
Genome Sequences ◽  
Pancreas Disease ◽  
Full Length Genome

Salmon pancreas disease virus (SPDV) also referred to as salmonid alphavirus (SAV) is a virus causing pancreas disease in Atlantic salmon (Salmo salar L.) and rainbow trout (Oncorhynchus mykiss). Although the virus causes an economically important disease, relatively few full-length genome sequences of SAV strains are currently available. Here, we report full-length genome sequences of nine SAV3 strains from sites farming Atlantic salmon geographically spread along the Norwegian coastline. The virus genomes were sequenced directly from infected heart tissue, to avoid culture selection bias. Sequence analysis confirmed a high level of sequence identity within SAV3 strains, with a mean nucleotide diversity of 0.11 %. Sequence divergence was highest in 6K and E2, while lowest in the capsid protein and the non-structural proteins (nsP4 and nsP2). This study reports for the first time that numerous defective viruses containing genome deletions are generated during natural infection with SAV. Deletions occurred in all virus strains and were not distributed randomly throughout the genome but instead tended to aggregate in certain areas. We suggest imprecise homologous recombination as an explanation for generation of defective viruses with genome deletions. The presence of such viruses, provides a possible explanation for the difficulties in isolating SAV in cell culture. Primary virus isolation was successfully achieved for only two of eight strains, despite extensive attempts using three different cell lines. Both SAV isolates were easily propagated further and concomitant viral deletion mutants present in clinically infected heart tissue were maintained following serial passage in CHH-1 cells.

scholarly journals The full-length genome sequences of nine HCV genotype 4 variants representing a new subtype 4s and eight unclassified lineages

Virology ◽  
2015 ◽  
Vol 482 ◽  
pp. 111-116 ◽  
Author(s):  
Ling Lu ◽  
Yan Xu ◽  
Jie Yuan ◽  
Chunhua Li ◽  
Donald G. Murphy
Keyword(s):  
Full Length ◽  
Genome Sequences ◽  
Genotype 4 ◽  
Hcv Genotype ◽  
Full Length Genome

scholarly journals The Analysis of Near Full-Length Genome Sequences of HIV Type 1 Subtype A Viruses from Russia Supports the Monophyly of Major Intrasubtype Clusters

2012 ◽  
Vol 28 (10) ◽  
pp. 1340-1343 ◽  
Author(s):  
Aurora Fernández-García ◽  
Ana Revilla ◽  
Elena Vázquez-de Parga ◽  
Anna Vinogradova ◽  
Aza Rakhmanova ◽  
...  
Keyword(s):  
Full Length ◽  
Genome Sequences ◽  
Hiv Type 1 ◽  
Subtype A ◽  
Full Length Genome

scholarly journals Molecular Characterization of Novel Cucurbit Aphid Borne Yellows Virus Strains Infecting Squash and Watermelon in India

2022 ◽  
Author(s):  
Nagendran Krishnan ◽  
Shweta Kumari ◽  
Koshlendra Kumar Pandey ◽  
Sudhakar Pandey ◽  
Tusar Kanti Behera ◽  
...  
Keyword(s):  
Asian American ◽  
Recombinant Strain ◽  
Sequence Similarity ◽  
Uttar Pradesh ◽  
Amino Acid Sequences ◽  
Full Length ◽  
Rt Pcr ◽  
Genome Sequences ◽  
Species Demarcation Threshold ◽  
Full Length Genome

Abstract The pathogen responsible for yellowing and downward rolling of leaves of squash and watermelon plants from Uttar Pradesh state, India, was identified as probably strains of Cucurbit aphid-borne yellows virus (CABYV) through RT-PCR using universal Polerovirus primers followed by sequencing. The full-length genome sequences of an isolate from squash (POL-SQ - 5650 nt) and one from watermelon (POL-WM - 5647nt) were determined by sequencing the products from RT-PCR with six sets of primers with overlapping products. Sequence comparison and phylogenetic analysis showed that these isolates had closest identity with a recombinant strain obtained between CABYV and Melon aphid-borne yellows virus (MABYV) reported from Taiwan infecting Luffa aegyptiaca (CABYV-R-TW82) rather than other Asian, American, or European isolates. The deduced amino acid sequences of the P0, P1 and P1-P2 proteins showed >10% variation, whereas the P3, P4 and P3-P5 proteins showed <10% variation when compared to the corresponding proteins of other strains of CABYV worldwide. Thus, according to the Polerovirus species demarcation threshold, these new sequences should be regarded as representing strains of a novel previously undescribed Polerovirus species. However, based on their sequence similarity and phylogenetic grouping with the recombinant strain from Taiwan we suggest these sequences represent recombinant strains of CABYV. These are the first full-length genome sequences for CABYV strains from India and this study adds watermelon as host for CABYV in India.

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