scholarly journals Genomic Analyses of Human Sapoviruses Detected over a 40-Year Period Reveal Disparate Patterns of Evolution among Genotypes and Genome Regions

Viruses ◽  
2020 ◽  
Vol 12 (5) ◽  
pp. 516 ◽  
Author(s):  
Kentaro Tohma ◽  
Michael Kulka ◽  
Suzie Coughlan ◽  
Kim Y. Green ◽  
Gabriel I. Parra
Keyword(s):  
Evolutionary Dynamics ◽  
Age Groups ◽  
Similar Rate ◽  
Full Length ◽  
Phylogenetic Clustering ◽  
Sequencing Platform ◽  
Viral Genomes ◽  
Amino Acid Mutations ◽  
Genomic Regions ◽  
Full Length Genome

Human sapovirus is a causative agent of acute gastroenteritis in all age groups. The use of full-length viral genomes has proven beneficial to investigate evolutionary dynamics and transmission chains. In this study, we developed a full-length genome sequencing platform for human sapovirus and sequenced the oldest available strains (collected in the 1970s) to analyse diversification of sapoviruses. Sequence analyses from five major genotypes (GI.1, GI.2, GII.1, GII.3, and GIV.1) showed limited intra-genotypic diversification for over 20–40 years. The accumulation of amino acid mutations in VP1 was detected for GI.2 and GIV.1 viruses, while having a similar rate of nucleotide evolution to the other genotypes. Differences in the phylogenetic clustering were detected between RdRp and VP1 sequences of our archival strains as well as other reported putative recombinants. However, the lack of the parental strains and differences in diversification among genomic regions suggest that discrepancies in the phylogenetic clustering of sapoviruses could be explained, not only by recombination, but also by disparate nucleotide substitution patterns between RdRp and VP1 sequences. Together, this study shows that, contrary to noroviruses, sapoviruses present limited diversification by means of intra-genotype variation and recombination.

scholarly journals Recombination Located over 2A-2B Junction Ribosome Frameshifting Region of Saffold Cardiovirus

Viruses ◽  
2018 ◽  
Vol 10 (10) ◽  
pp. 520 ◽  
Author(s):  
Antônio da Costa ◽  
Adriana Luchs ◽  
Flávio Milagres ◽  
Shirley Komninakis ◽  
Danielle Gill ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Acute Gastroenteritis ◽  
Empirical Studies ◽  
Full Length ◽  
Evolutionary Analysis ◽  
Ribosomal Frameshift ◽  
Rna Dependent Rna Polymerase ◽  
Recombination Hotspot ◽  
Viral Genomes ◽  
Full Length Genome

Here we report the nearly full-length genome of a recombinant Saffold virus strain (SAFV-BR-193) isolated from a child with acute gastroenteritis. Evolutionary analysis performed using all available near-full length Saffold picornavirus genomes showed that the breakpoint found in the Brazilian strain (SAFV-BR-193) is indeed a recombination hotspot. Notably, this hotspot is located just one nucleotide after the ribosomal frameshift GGUUUUU motif in the SAFV genome. Empirical studies will be necessary to determine if this motif also affects the binding affinity of RNA-dependent RNA-polymerase (RdRp) and therefore increases the changes of RdRp swap between molecules during the synthesis of viral genomes.

scholarly journals Defective Interfering Genomes and the Full-Length Viral Genome Trigger RIG-I After Infection With Vesicular Stomatitis Virus in a Replication Dependent Manner

2021 ◽  
Vol 12 ◽  
Author(s):  
Andreas Linder ◽  
Viktoria Bothe ◽  
Nicolas Linder ◽  
Paul Schwarzlmueller ◽  
Frank Dahlström ◽  
...  
Keyword(s):  
Vesicular Stomatitis Virus ◽  
Full Length ◽  
Oncolytic Viruses ◽  
Interferon Response ◽  
Response Analysis ◽  
Interferon Α ◽  
Dependent Manner ◽  
Viral Genomes ◽  
Vesicular Stomatitis ◽  
Full Length Genome

Replication competent vesicular stomatitis virus (VSV) is the basis of a vaccine against Ebola and VSV strains are developed as oncolytic viruses. Both functions depend on the ability of VSV to induce adequate amounts of interferon-α/β. It is therefore important to understand how VSV triggers interferon responses. VSV activates innate immunity via retinoic acid-inducible gene I (RIG-I), a sensor for viral RNA. Our results show that VSV needs to replicate for a robust interferon response. Analysis of RIG-I-associated RNA identified a copy-back defective-interfering (DI) genome and full-length viral genomes as main trigger of RIG-I. VSV stocks depleted of DI genomes lost most of their interferon-stimulating activity. The remaining full-length genome and leader-N-read-through sequences, however, still triggered RIG-I. Awareness for DI genomes as trigger of innate immune responses will help to standardize DI genome content and to purposefully deplete or use DI genomes as natural adjuvants in VSV-based therapeutics.

scholarly journals Characterization of HIV-1 recombinant and subtype B near full-length genome among men who have sex with men in South Korea

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sangmi Ryou ◽  
Myeongsu Yoo ◽  
Kisoon Kim ◽  
Sangsoo Kim ◽  
Sang Il Kim ◽  
...  
Keyword(s):  
Full Length ◽  
The Novel ◽  
Full Genome Sequencing ◽  
Viral Genomes ◽  
Subtype B ◽  
Predominant Variant ◽  
Sex With Men ◽  
Next Generation Sequencing Ngs ◽  
Full Length Genome ◽  
Hiv 1

AbstractIn Korea, subtype B is the predominant variant of HIV-1, but full genome sequencing and analysis of its viral variants are lacking. We performed near full-length genome (NFLG) sequencing and phylogenetic and recombination analyses of fifty plasma samples from HIV-positive men who have sex with men (MSM) from a Korea HIV/AIDS cohort study. Viral genomes were amplified and the near-full-length sequences were determined using next-generation sequencing (NGS) and Sanger sequencing. We focused on the HIV-1 subtype classification and identification of HIV recombinants. Twelve HIV-1 NFLGs were determined: ten were subtyped as pure HIV-1 subtype B and two recombinant strains as a common subtype CRF07_BC, and a novel subtype CRF43_02G recombined with CRF02_AG again, or a new CRF02_AG and subtype G recombinant. For the ten NFLGs determined by NGS, “the novel recombinant emerged at approximately 2003 and the other nine subtype B about 2004 or 2005”. This is the first report analyzing HIV-1 NFLG, including recombinants and clinical characteristics, by subtype among MSM in Korea. Our results provide novel insights for understanding the recombinants in the HIV-1 epidemic in Korea.

A Score Method for Comparison of Partial Genomic Regions in Their Representatives of Full-Length Genome of Hepatitis E Virus for Genotyping

Intervirology ◽  
2007 ◽  
Vol 50 (5) ◽  
pp. 328-335 ◽  
Author(s):  
Pengcheng Xun ◽  
Feng Chen ◽  
Chen Dong ◽  
Guohua Qian ◽  
Dejian Lai ◽  
...  
Keyword(s):  
Hepatitis E Virus ◽  
Hepatitis E ◽  
Full Length ◽  
Score Method ◽  
Genomic Regions ◽  
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.

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