scholarly journals Emerging Novel GII.P16 Noroviruses Associated with Multiple Capsid Genotypes

Viruses ◽  
2019 ◽  
Vol 11 (6) ◽  
pp. 535 ◽  
Author(s):  
Leslie Barclay ◽  
Jennifer L. Cannon ◽  
Mary E. Wikswo ◽  
Annie R. Phillips ◽  
Hannah Browne ◽  
...  
Keyword(s):  
Amino Acid ◽  
Severe Case ◽  
Molecular Data ◽  
Antigenic Drift ◽  
The Novel ◽  
Structural Protein ◽  
Protein Coding ◽  
Recombinant Viruses ◽  
The Us ◽  
Genomic Regions

Noroviruses evolve by antigenic drift and recombination, which occurs most frequently at the junction between the non-structural and structural protein coding genomic regions. In 2015, a novel GII.P16-GII.4 Sydney recombinant strain emerged, replacing the predominance of GII.Pe-GII.4 Sydney among US outbreaks. Distinct from GII.P16 polymerases detected since 2010, this novel GII.P16 was subsequently detected among GII.1, GII.2, GII.3, GII.10 and GII.12 viruses, prompting an investigation on the unique characteristics of these viruses. Norovirus positive samples (n = 1807) were dual-typed, of which a subset (n = 124) was sequenced to yield near-complete genomes. CaliciNet and National Outbreak Reporting System (NORS) records were matched to link outbreak characteristics and case outcomes to molecular data and GenBank was mined for contextualization. Recombination with the novel GII.P16 polymerase extended GII.4 Sydney predominance and increased the number of GII.2 outbreaks in the US. Introduction of the novel GII.P16 noroviruses occurred without unique amino acid changes in VP1, more severe case outcomes, or differences in affected population. However, unique changes were found among NS1/2, NS4 and VP2 proteins, which have immune antagonistic functions, and the RdRp. Multiple polymerase-capsid combinations were detected among GII viruses including 11 involving GII.P16. Molecular surveillance of protein sequences from norovirus genomes can inform the functional importance of amino acid changes in emerging recombinant viruses and aid in vaccine and antiviral formulation.

scholarly journals Extensive Horizontal Gene Transfer in Cheese-Associated Bacteria

2016 ◽  
Author(s):  
Kevin S. Bonham ◽  
Benjamin E. Wolfe ◽  
Rachel J. Dutton
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Molecular Mechanisms ◽  
Protein Coding ◽  
Associated Bacteria ◽  
The Us ◽  
Selective Forces ◽  
Genomic Regions ◽  
Microbiome Assembly ◽  
Insight Into

AbstractAcquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly-sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4,733 protein coding genes. The largest of these regions are enriched for genes involved in siderophore acquisition, and are widely distributed in cheese rinds in both Europe and the US. These results suggest that horizontal gene transfer (HGT) is prevalent in cheese rind microbiomes, and the identification of genes that are frequently transferred in a particular environment may provide insight into the selective forces shaping microbial communities.

scholarly journals Mobuck virus genome sequence and phylogenetic analysis: identification of a novel Orbivirus isolated from a white-tailed deer in Missouri, USA

2014 ◽  
Vol 95 (1) ◽  
pp. 110-116 ◽  
Author(s):  
Elyse Cooper ◽  
Srivishnupriya Anbalagan ◽  
Patricia Klumper ◽  
Gail Scherba ◽  
Randy R. Simonson ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Clinical Signs ◽  
Amino Acid Identity ◽  
Virus Genome ◽  
The Novel ◽  
Structural Protein ◽  
Middle Point ◽  
Wide Range ◽  
Haemorrhagic Disease

The genus Orbivirus includes a diverse group of segmented dsRNA viruses that are transmitted via arthropods, have a global distribution and affect a wide range of hosts. A novel orbivirus was co-isolated with epizootic haemorrhagic disease virus (EHDV) from a white-tailed deer (Odocoileus virginianus) exhibiting clinical signs characteristic of EHDV. Using antiserum generated against EHDV, a pure isolate of the novel non-cytopathic orbivirus was obtained in Aedes albopictus cell culture. Genomic sequencing and phylogenetic analysis of predicted ORFs showed that eight of the ten ORFs were most homologous to Peruvian horse sickness virus (PHSV), with amino acid identities of 44.3–73.7 %. The remaining two ORFs, VP3 and VP5, were most similar to Middle Point orbivirus (35.9 %) and Yunnan orbivirus (59.8 %), respectively. Taxonomic classification of orbiviruses is largely based on homology of the major subcore structural protein VP2(T2), encoded by segment 2 for mobuck virus. With only 69.1 % amino acid identity to PHSV, we propose mobuck virus as the prototype of a new species of Orbivirus.

scholarly journals Analyzing genetic mutations of porcine reproductive and respiratory syndrome virus strains by serial passages in cell line from field wild strain

2020 ◽  
Vol 4 (4) ◽  
pp. 857-867
Author(s):  
Bui Anh Thy ◽  
Lê Thanh Hòa ◽  
Trần Xuân Hạnh ◽  
Trần Linh Thước
Keyword(s):  
Amino Acid ◽  
Clinical Symptoms ◽  
Virulent Strain ◽  
Wild Strain ◽  
Variable Region ◽  
Molecular Data ◽  
Genetic Mutation ◽  
Respiratory Syndrome Virus ◽  
Structural Protein ◽  
Nucleotide Substitutions

In this study, we compared the genetic mutation and virulence of the attenuated PRRSV strains obtained by 95 serial passages in Marc-145 cells with the parental virulent strain (designated as BG81) isolated in Vietnam. Results showed that there were marked changes in virulence: pigs inoculated with BG81 exhibited high fever ( 41◦C), which lasted for 12 days, and presented typical clinical symptoms of PRRSV; otherwise, pigs inoculated with BG895 (from passage 95), maintained mean rectal temperature from 39,5oC to 39,9oC, did not develop any significant clinical symptoms. Whole genomes of the attenuated strains were significantly different, but their sequence lengths were conserved, i.e., 15,321 nucleotides. The attenuated strain from passage 95 (BG895) contained 38 nucleotide substitutions that resulted in 14 amino acid changes. Most of these changes (about 65%) occurred before passage 50. The 14 amino acid changes were distributed in Nsp1, Nsp4, Nsp9, Nsp10, GP2, E, GP3, GP4, GP5 and N. Specially, there were two single substitutes within a codon in ORF3, corresponding to parallel mutation at position F143L. However, structural protein (M) and eight non-structural proteins (Nsp2, Nsp3, Nsp5, Nsp6, Nsp7, Nsp8, Nsp11 and Nsp12) among the 19 PRRSV proteins, remained conserved, without any mutations and supposed for consideration as irrelative to the attenuation process. It is interesting that in the gene coding for the smallest structural protein (E protein), there was the highest mutation rate among all of the structural genes analyzed, and genetically, seemed to be a highly variable region. These changes may provide the molecular bases for the observation of the attenuated phenotype in pigs. Thus, our variation results obtained between the attenuated BG895 and the parental virulent BG81 strains provide appropriate molecular data for potential use to test and control the masterseed strain in production of a PRRSV vaccine in Vietnam.

scholarly journals Tissue tropism of recombinant coxsackieviruses in an adult mouse model

2005 ◽  
Vol 86 (7) ◽  
pp. 1897-1907 ◽  
Author(s):  
Heli Harvala ◽  
Hannu Kalimo ◽  
Jeffrey Bergelson ◽  
Glyn Stanway ◽  
Timo Hyypiä
Keyword(s):  
Neutralizing Antibodies ◽  
Plaque Assay ◽  
Tissue Tropism ◽  
Structural Protein ◽  
Coding Region ◽  
Protein Coding ◽  
Recombinant Viruses ◽  
Adult Mice ◽  
The Central Nervous System ◽  
Structural Region

Recombinant viruses, constructed by exchanging the 5′ non-coding region (5′NCR), structural and non-structural protein coding sequences were used to investigate determinants responsible for differences between coxsackievirus A9 (CAV9) and coxsackievirus B3 (CBV3) infections in adult mice and two cell lines. Plaque assay titration of recombinant and parental viruses from different tissues from adult BALB/c mice demonstrated that the structural region of CBV3 determined tropism to the liver tissue due to receptor recognition, and the 5′NCR of CBV3 enhanced viral multiplication in the mouse pancreas. Infection with a chimeric virus, containing the structural region from CBV3 and the rest of the genome from CAV9, and the parental CBV3 strain, caused high levels of viraemia in adult mice. The ability of these viruses to infect the central nervous system suggested that neurotropism is associated with high replication levels and the presence of the CBV3 capsid proteins, which also enhanced formation of neutralizing antibodies. Moreover, the appearance of neutralizing antibodies correlated directly with the clearance of the viruses from the tissues. These results demonstrate potential pathogenicity of intraspecies recombinant coxsackieviruses, and the complexity of the genetic determinants underlying tissue tropism.

scholarly journals Trends of Mutation Accumulation across Global SARS-CoV-2 Genomes: Implications for the Ecology and Evolution of the Novel Coronavirus

2020 ◽  
Author(s):  
Chayan Roy ◽  
Santi M Mandal ◽  
Suresh K Mondol ◽  
Shriparna Mukherjee ◽  
Wriddhiman Ghosh ◽  
...  
Keyword(s):  
Point Mutations ◽  
Phylogenomic Analysis ◽  
Whole Genome ◽  
The Novel ◽  
Structural Protein ◽  
Genome Sequences ◽  
Protein Coding ◽  
Pan Genome ◽  
Genome Wide ◽  
Novel Coronavirus

The all-pervasiveness and dynamic nature of the COVID-19 pandemic warrants comprehensive and constant surveillance of the numerous mutations that are accumulating in global SARS-CoV-2 genomes and contributing to the microevoution of the various lineages of the novel coronavirus. This would help us gain insights into the evolving pathogenicity of the virus, and thereby improvise our control and therapeutic strategies. This study explores the genome-wide frequency, gene-wise distribution, and molecular nature, of the large repertoire of point mutations detected across the global dataset of 3,608 SARS-CoV-2 RNA-genomes short-listed from a total 5,485 whole genome sequences deposited in GenBank till 4 June 2020 using a download filter that eliminated all incomplete/gapped sequences. Phylogenomic analysis involving all existing SARS-CoV-2 lineages, represented by 3,740 whole genome sequences from human-source (out of a total of 63,894 sequences stored in the GISAID repository, as on 15 July, 2020), illustrated that the two major-lineages of the virus contributed almost equivalently to the pandemic. However, entities belonging to the early lineages are still mostly spread over Asian countries, whereas those affiliated to recently-derived lineages have a relatively more global distribution. Mutation frequency in the SARS-CoV-2 pan genome was found to be 2.27 × 10-5 nucleotide positions mutated per nucleotide analyzed. An overwhelming majority (count: 1797) of the total 2452 instances of single nucleotide substitution detected (in the SARS-CoV-2 pan genome) were found to be transition mutations with cytidine to uridine (CàU) as the most ubiquitous molecular-type (count: 987). Of the 655 instances of transversion detected, the guanosine to uridine (GàU) variant was most widespread (count: 367). All transcribed and untranscribed loci of the pan genome were found to contain mutation(s). nsp3, and S, N and orf3a, were the most point-mutation-ridden non-structural and structural protein-coding genes, respectively, with 435, 300, 171 and 128 total mutations; 349/86, 192/108, 107/64 and 76/52 transitions/transversions; and 189/48, 106/55, 59/42 and 43/31 CàU/GàU substitutions respectively. Potential mechanistic backgrounds were envisaged for the molecular bias of mutations observed in SARS-CoV-2.

Resolving the phylogenetic position of the Wallemiomycetes: an enigmatic major lineage of Basidiomycota

2006 ◽  
Vol 84 (12) ◽  
pp. 1794-1805 ◽  
Author(s):  
P. Brandon Matheny ◽  
Jasmin A. Gossmann ◽  
Polona Zalar ◽  
T.K. Arun Kumar ◽  
David S. Hibbett
Keyword(s):  
Amino Acid ◽  
Ribosomal Rna ◽  
Gene Tree ◽  
Sister Group ◽  
Molecular Data ◽  
Amino Acid Sequences ◽  
Phylogenetic Position ◽  
Protein Coding ◽  
Branch Support ◽  
Robust Measures

The Wallemiomycetes includes three species of molds from the genus Wallemia . These fungi are adapted to environments of high osmotic stress, contaminate various foods, cause respiratory disease, and have an unusual mode of asexual reproduction. Wallemia was recently proposed as a new class based on 18S ribosomal RNA gene sequences to accommodate the isolated position of the clade in the Basidiomycota. We analyzed the phylogenetic position of the Wallemiomycetes using 3451 nucleotide characters of the 18S, 25S, and 5.8S ribosomal RNA genes and 1282 amino acid positions of rpb1, rpb2, and tef1 nuclear protein-coding genes across 91 taxa. Different gene regions and methods of phylogenetic inference produce mildly conflicting placements of the Wallemiomycetes. Parsimony analyses of nrDNA data suggest that the Wallemiomycetes is an early diverging lineage of Basidiomycota, occupying a basal position near the Entorrhizomycetidae. Ultrastructural data, some Bayesian analyses, and amino acid sequences suggest the Wallemiomycetes may be the sister group of the Agaricomycotina or Ustilaginomycotina. The combined gene tree supports the Wallemiomycetes as a lineage basal to a core clade of Pucciniomycotina, Ustilaginomycotina, and Agaricomycotina with robust measures of branch support. This study reinforces the isolated position of Wallemia in the Basidiomycota using molecular data from six nuclear genes. In total, five major lineages of Basidiomycota are recognized: the Agaricomycotina, Ustilaginomycotina, Pucciniomycotina, Entorrhizomycetidae, and the Wallemiomycetes.

scholarly journals Extensive horizontal gene transfer in cheese-associated bacteria

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Kevin S Bonham ◽  
Benjamin E Wolfe ◽  
Rachel J Dutton
Keyword(s):  
Gene Transfer ◽  
Horizontal Gene Transfer ◽  
Molecular Mechanisms ◽  
Protein Coding ◽  
Associated Bacteria ◽  
The Us ◽  
Selective Forces ◽  
Genomic Regions ◽  
Microbiome Assembly ◽  
Insight Into

Acquisition of genes through horizontal gene transfer (HGT) allows microbes to rapidly gain new capabilities and adapt to new or changing environments. Identifying widespread HGT regions within multispecies microbiomes can pinpoint the molecular mechanisms that play key roles in microbiome assembly. We sought to identify horizontally transferred genes within a model microbiome, the cheese rind. Comparing 31 newly sequenced and 134 previously sequenced bacterial isolates from cheese rinds, we identified over 200 putative horizontally transferred genomic regions containing 4733 protein coding genes. The largest of these regions are enriched for genes involved in siderophore acquisition, and are widely distributed in cheese rinds in both Europe and the US. These results suggest that HGT is prevalent in cheese rind microbiomes, and that identification of genes that are frequently transferred in a particular environment may provide insight into the selective forces shaping microbial communities.

scholarly journals Cryptococcus rajasthanensis sp. nov., an anamorphic yeast species related to Cryptococcus laurentii, isolated from Rajasthan, India

2007 ◽  
Vol 57 (2) ◽  
pp. 414-418 ◽  
Author(s):  
Puja Saluja ◽  
G. S. Prasad
Keyword(s):  
Large Subunit ◽  
Its Region ◽  
Molecular Data ◽  
Lsu Rdna ◽  
Cryptococcus Laurentii ◽  
The Novel ◽  
D2 Domain ◽  
Its Regions ◽  
Anamorphic Yeast ◽  
Physiological Tests

Two novel anamorphic yeast strains (S-15LT and 3-C1) were isolated from the inflorescences of plants collected in two different towns in Rajasthan State, India. Sequencing of the D1/D2 domains of the large-subunit (LSU) rDNA and the internal transcribed spacer (ITS) regions suggested they are strains of the same species. Phenotypic characteristics such as the absence of fermentation, the absence of sexual structures and ballistoconidia, the assimilation of myo-inositol and d-glucuronate, and positive Diazonium blue B and urease reactions indicated that these strains belong to the genus Cryptococcus. The novel strains differed from Cryptococcus laurentii in six physiological tests and differed from other related species in more than six tests. A phylogenetic analysis of the sequences of the D1/D2 domains of the LSU rDNA and the ITS regions placed these strains in the Bulleromyces clade within the order Tremellales, with C. laurentii as their closest described relative. The novel strains showed 1.6 and 7.5 % divergence in the D1/D2 domain of the LSU rDNA and ITS regions, respectively, with respect to C. laurentii. The divergence from other species was more than 3 % for the D1/D2 domain and more than 9 % for the ITS region. On the basis of the phenotypic and molecular data, strains S-15LT and 3-C1 represent a novel species within the genus Cryptococcus, for which the name Cryptococcus rajasthanensis sp. nov. is proposed. The type strain is S-15LT (=MTCC 7075T=CBS 10406T).

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