scholarly journals An Analysis of SARS-CoV-2 Using ViReport

2020 ◽  
Author(s):  
Miranda Song ◽  
Niema Moshiri
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Phylogenetic Analyses ◽  
Full Genome ◽  
Genome Sequences ◽  
Link Type ◽  
Preventative Intervention ◽  
Viral Sequences

AbstractThe ongoing outbreak of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in millions of cases and hundreds of thousands of deaths. Given the current lack of treatments or vaccines available, it may be useful to trace the evolu-tion and spread of the virus to better develop methods of preventative intervention. In this study, we analyzed over 4,000 full genome sequences of human SARS-CoV-2 using novel tool ViReport [13], an automated workflow for performing phylogenetic analyses on viral sequences and generating comprehensive molecular epidemiologi-cal reports. The complete ViReport output can be found at https://github.com/mirandajsong/ViReport-SARS-CoV-2.

scholarly journals A snapshot of SARS-CoV-2 genome availability up to 30th March, 2020 and its implications

2020 ◽  
Author(s):  
Carla Mavian ◽  
Simone Marini ◽  
Mattia Prosperi ◽  
Marco Salemi
Keyword(s):  
Sufficient Information ◽  
Scientific Journals ◽  
Full Genome ◽  
Genome Sequences ◽  
Phylogenetic Information ◽  
Specific Data ◽  
Full Dataset ◽  
Viral Sequences ◽  
Country Specific

AbstractThe SARS-CoV-2 pandemic has been growing exponentially, affecting nearly 900 thousand people and causing enormous distress to economies and societies worldwide. A plethora of analyses based on viral sequences has already been published, in scientific journals as well as through non-peer reviewed channels, to investigate SARS-CoV-2 genetic heterogeneity and spatiotemporal dissemination. We examined full genome sequences currently available to assess the presence of sufficient information for reliable phylogenetic and phylogeographic studies in countries with the highest toll of confirmed cases. Although number of-available full-genomes is growing daily, and the full dataset contains sufficient phylogenetic information that would allow reliable inference of phylogenetic relationships, country-specific SARS-CoV-2 datasets still present severe limitations. Studies assessing within country spread or transmission clusters should be considered preliminary at best, or hypothesis generating. Hence the need for continuing concerted efforts to increase number and quality of the sequences required for robust tracing of the epidemic.Significance StatementAlthough genome sequences of SARS-CoV-2 are growing daily and contain sufficient phylogenetic information, country-specific data still present severe limitations and should be interpreted with caution.

scholarly journals Virus-derived sequences from the transcriptomes of two snail vectors of schistosomiasis, Biomphalaria pfeifferi and Bulinus globosus from Kenya

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12290
Author(s):  
Sijun Liu ◽  
Si-Ming Zhang ◽  
Sarah K. Buddenborg ◽  
Eric S. Loker ◽  
Bryony C. Bonning
Keyword(s):  
Phylogenetic Analyses ◽  
454 Sequencing ◽  
Genome Sequences ◽  
Bioinformatics Pipeline ◽  
Biomphalaria Pfeifferi ◽  
Rna Sequences ◽  
Positive Sense ◽  
Bulinus Globosus ◽  
Viral Sequences

Schistosomiasis, which infects more than 230 million people, is vectored by freshwater snails. We identified viral sequences in the transcriptomes of Biomphalaria pfeifferi (BP) and Bulinus globosus (BuG), two of the world’s most important schistosomiasis vectors in Africa. Sequences from 26 snails generated using Illumina Hi-Seq or 454 sequencing were assembled using Trinity and CAP3 and putative virus sequences were identified using a bioinformatics pipeline. Phylogenetic analyses were performed using viral RNA-dependent RNA polymerase and coat protein sequences to establish relatedness between virus sequences identified and those of known viruses. Viral sequences were identified from the entire snail holobiont, including symbionts, ingested material and organisms passively associated with the snails. Sequences derived from more than 17 different viruses were found including five near full-length genomes, most of which were small RNA viruses with positive sense RNA genomes (i.e., picorna-like viruses) and some of which are likely derived from adherent or ingested diatoms. Based on phylogenetic analysis, five of these viruses (including BPV2 and BuGV2) along with four Biomphalaria glabrata viruses reported previously, cluster with known invertebrate viruses and are putative viruses of snails. The presence of RNA sequences derived from four of these novel viruses in samples was confirmed. Identification of the genome sequences of candidate snail viruses provides a first step toward characterization of additional gastropod viruses, including from species of biomedical significance.

scholarly journals Full Genome Evolutionary Studies of Wheat Streak Mosaic-Associated Viruses Using High-Throughput Sequencing

2021 ◽  
Vol 12 ◽  
Author(s):  
Carla Dizon Redila ◽  
Savannah Phipps ◽  
Shahideh Nouri
Keyword(s):  
Mosaic Virus ◽  
Rna Sequencing ◽  
Great Plains ◽  
High Throughput ◽  
Phylogenetic Analyses ◽  
Full Genome Sequence ◽  
Mixed Infections ◽  
Full Genome ◽  
Genome Sequences ◽  
Resistance Breaking

Wheat streak mosaic (WSM), a viral disease affecting cereals and grasses, causes substantial losses in crop yields. Wheat streak mosaic virus (WSMV) is the main causal agent of the complex, but mixed infections with Triticum mosaic virus (TriMV) and High plains wheat mosaic emaravirus (HPWMoV) were reported as well. Although resistant varieties are effective for the disease control, a WSMV resistance-breaking isolate and several potential resistance-breaking isolates have been reported, suggesting that viral populations are genetically diverse. Previous phylogenetic studies of WSMV were conducted by focusing only on the virus coat protein (CP) sequence, while there is no such study for either TriMV or HPWMoV. Here, we studied the genetic variation and evolutionary mechanisms of natural populations of WSM-associated viruses mainly in Kansas fields and fields in some other parts of the Great Plains using high-throughput RNA sequencing. In total, 28 historic and field samples were used for total RNA sequencing to obtain full genome sequences of WSM-associated viruses. Field survey results showed WSMV as the predominant virus followed by mixed infections of WSMV + TriMV. Phylogenetic analyses of the full genome sequences demonstrated that WSMV Kansas isolates are widely distributed in sub-clades. In contrast, phylogenetic analyses for TriMV isolates showed no significant diversity. Recombination was identified as the major evolutionary force of WSMV and TriMV variation in KS fields, and positive selection was detected in some encoding genomic regions in the genome of both viruses. Furthermore, the full genome sequence of a second Kansas HPWMoV isolate was reported. Here, we also identified previously unknown WSMV isolates in the Great Plains sharing clades and high nucleotide sequence similarities with Central Europe isolates. The findings of this study will provide more insights into the genetic structure of WSM-associated viruses and, in turn, help in improving strategies for disease management.

scholarly journals Improved molecular characterization of the Klebsiella oxytoca complex reveals the prevalence of the kleboxymycin biosynthetic gene cluster

2021 ◽  
Vol 7 (6) ◽  
Author(s):  
Preetha Shibu ◽  
Frazer McCuaig ◽  
Anne L. McCartney ◽  
Magdalena Kujawska ◽  
Lindsay J. Hall ◽  
...  
Keyword(s):  
Gene Cluster ◽  
Type Species ◽  
Phylogenetic Analyses ◽  
Klebsiella Oxytoca ◽  
Biosynthetic Gene Cluster ◽  
Biosynthetic Gene ◽  
Genome Sequences ◽  
Content Type ◽  
Link Type

As part of the ongoing studies with clinically relevant Klebsiella spp., we characterized the genomes of three clinical GES-5-positive ST138 strains originally identified as Klebsiella oxytoca. bla OXY gene, average nucleotide identity and phylogenetic analyses showed the strains to be Klebsiella michiganensis . Affiliation of the strains to ST138 led us to demonstrate that the current multi-locus sequence typing scheme for K. oxytoca can be used to distinguish members of this genetically diverse complex of bacteria. The strains encoded the kleboxymycin biosynthetic gene cluster (BGC), previously only found in K. oxytoca strains and one strain of Klebsiella grimontii . The finding of this BGC, associated with antibiotic-associated haemorrhagic colitis, in K. michiganensis led us to carry out a wide-ranging study to determine the prevalence of this BGC in Klebsiella spp. Of 7170 publicly available Klebsiella genome sequences screened, 88 encoded the kleboxymycin BGC. All BGC-positive strains belonged to the K. oxytoca complex, with strains of four ( K. oxytoca , K. pasteurii , K. grimontii , K. michiganensis ) of the six species of complex found to encode the complete BGC. In addition to being found in K. grimontii strains isolated from preterm infants, the BGC was found in K. oxytoca and K. michiganensis metagenome-assembled genomes recovered from neonates. Detection of the kleboxymycin BGC across the K. oxytoca complex may be of clinical relevance and this cluster should be included in databases characterizing virulence factors, in addition to those characterizing BGCs.

scholarly journals Regaining perspective on SARS-CoV-2 molecular tracing and its implications

2020 ◽  
Author(s):  
Carla Mavian ◽  
Simone Marini ◽  
Costanza Manes ◽  
Ilaria Capua ◽  
Mattia Prosperi ◽  
...  
Keyword(s):  
Genetic Heterogeneity ◽  
Partial Information ◽  
Sufficient Information ◽  
Scientific Journals ◽  
Full Genome ◽  
Genome Sequences ◽  
The Past ◽  
Viral Sequences

AbstractDuring the past three months, a new coronavirus (SARS-CoV-2) epidemic has been growing exponentially, affecting over 100 thousand people worldwide, and causing enormous distress to economies and societies of affected countries. A plethora of analyses based on viral sequences has already been published, in scientific journals as well as through non-peer reviewed channels, to investigate SARS-CoV-2 genetic heterogeneity and spatiotemporal dissemination. We examined all full genome sequences currently available to assess the presence of sufficient information for reliable phylogenetic and phylogeographic studies. Our analysis clearly shows severe limitations in the present data, in light of which any finding should be considered, at the very best, preliminary and hypothesis-generating. Hence the need for avoiding stigmatization based on partial information, and for continuing concerted efforts to increase number and quality of the sequences required for robust tracing of the epidemic.

scholarly journals GET_PHYLOMARKERS, a software package to select optimal orthologous clusters for phylogenomics and inferring pan-genome phylogenies, used for a critical geno-taxonomic revision of the genusStenotrophomonas

2018 ◽  
Author(s):  
Pablo Vinuesa ◽  
Luz Edith Ochoa-Sánchez ◽  
Bruno Contreras-Moreira
Keyword(s):  
Core Genome ◽  
Phylogenetic Analyses ◽  
Superior Performance ◽  
Biological Research ◽  
Species Trees ◽  
Genome Sequences ◽  
Sequence Alignments ◽  
Multiple Sequence ◽  
Pan Genome ◽  
Link Type

AbstractThe massive accumulation of genome-sequences in public databases promoted the proliferation of genome-level phylogenetic analyses in many areas of biological research. However, due to diverse evolutionary and genetic processes, many loci have undesirable properties for phylogenetic reconstruction. These, if undetected, can result in erroneous or biased estimates, particularly when estimating species trees from concatenated datasets. To deal with these problems, we developed GET_PHYLOMARKERS, a pipeline designed to identify high-quality markers to estimate robust genome phylogenies from the orthologous clusters, or the pan-genome matrix (PGM), computed by GET_HOMOLOGUES. In the first context, a set of sequential filters are applied to exclude recombinant alignments and those producing anomalous or poorly resolved trees. Multiple sequence alignments and maximum likelihood (ML) phylogenies are computed in parallel on multi-core computers. A ML species tree is estimated from the concatenated set of top-ranking alignments at the DNA or protein levels, using either FastTree or IQ-TREE (IQT). The latter is used by default due to its superior performance revealed in an extensive benchmark analysis. In addition, parsimony and ML phylogenies can be estimated from the PGM.We demonstrate the practical utility of the software by analyzing 170Stenotrophomonasgenome sequences available in RefSeq and 10 new complete genomes of environmentalS. maltophiliacomplex (Smc) isolates reported herein. A combination of core-genome and PGM analyses was used to revise the molecular systematics of the genus. An unsupervised learning approach that uses a goodness of clustering statistic identified 20 groups within the Smc at a core-genome average nucleotide identity of 95.9% that are perfectly consistent with strongly supported clades on the core- and pan-genome trees. In addition, we identified 14 misclassified RefSeq genome sequences, 12 of them labeled asS. maltophilia, demonstrating the broad utility of the software for phylogenomics and geno-taxonomic studies. The code, a detailed manual and tutorials are freely available for Linux/UNIX servers under the GNU GPLv3 license athttps://github.com/vinuesa/get_phylomarkers. A docker image bundling GET_PHYLOMARKERS with GET_HOMOLOGUES is available athttps://hub.docker.com/r/csicunam/get_homologues/, which can be easily run on any platform.

Prevotella illustrans sp. nov., derived from human oropharyngeal abscess puncture fluid

2021 ◽  
Vol 71 (12) ◽  
Author(s):  
Michael E. J. Buhl ◽  
Jan P. Meier-Kolthoff ◽  
Matthias Marschal
Keyword(s):  
Dna Hybridization ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Routine Care ◽  
Oral Microbiome ◽  
Rrna Gene ◽  
Long Chain Fatty Acids ◽  
Genome Sequences ◽  
Content Type ◽  
Link Type

An obligately anaerobic strain, designated as A2931T, was isolated from oropharyngeal abscess puncture fluid of a patient sampled during routine care at a hospital and further characterized both phenotypically, biochemically and genotypically. This Gram-negative rod-shaped bacterium was moderately saccharolytic and proteolytic. Phylogenetic analyses of full-length 16S rRNA gene and whole-genome sequences revealed it to be best placed in the genus Prevotella , but to be only comparatively distantly related to recognized species, with the closest relationship to Prevotella baroniae (average nucleotide identity and digital DNA–DNA hybridization values both well below the generally accepted thresholds). Strain A2931T had a genomic DNA G+C content of 47.7 mol%. Its most abundant cellular long-chain fatty acids were anteiso-C15 : 0, iso-C15 : 0 and C16 : 0. Taken together, this polyphasic data suggests strain A2931T to represent a novel species within the genus Prevotella , for which the name Prevotella illustrans sp. nov. is proposed. The type strain is A2931T (=DSM 108028T=CCOS 1232T=CCUG 72806T). Interestingly, we found strain A2931T to correspond to the oral taxon Prevotella HMT-820 in the Human Oral Microbiome Database, as supported by overall genome relatedness index analyses >99 %. Thus, our work not only closes one of the gaps of knowledge about hitherto unnamed species isolated from humans, but also will facilitate identification of this taxon both in the clinical microbiology context and in research alike.

scholarly journals Thermococcus paralvinellae sp. nov. and Thermococcus cleftensis sp. nov. of hyperthermophilic heterotrophs from deep-sea hydrothermal vents

2014 ◽  
Vol 64 (Pt_11) ◽  
pp. 3655-3659 ◽  
Author(s):  
Sarah A. Hensley ◽  
Jong-Hyun Jung ◽  
Cheon-Seok Park ◽  
James F. Holden
Keyword(s):  
Type Species ◽  
Hydrothermal Vents ◽  
Novel Species ◽  
Phylogenetic Analyses ◽  
Rrna Gene ◽  
Genome Sequences ◽  
Content Type ◽  
Link Type ◽  
The North ◽  
North Eastern

Two heterotrophic hyperthermophilic strains, ES1T and CL1T, were isolated from Paralvinella sp. polychaete worms collected from active hydrothermal vent chimneys in the north-eastern Pacific Ocean. Both were obligately anaerobic and produced H2S in the presence of elemental sulfur and H2. Complete genome sequences are available for both strains. Phylogenetic analyses based on 16S rRNA gene sequences showed that the strains are more than 97 % similar to most other species of the genus Thermococcus . Therefore, overall genome relatedness index analyses were performed to establish that these strains are novel species. For each analysis, strain ES1T was determined to be most similar to Thermococcus barophilus MPT, while strain CL1T was determined to be most similar to Thermococcus sp. 4557. The average nucleotide identity scores for these strains were 84 % for strain ES1T and 81 % for strain CL1T, genome-to-genome direct comparison scores were 23 % for strain ES1T and 47 % for strain CL1T, and the species identification scores were 89 % for strain ES1T and 88 % for strain CL1T. For each analysis, strains ES1T and CL1T were below the species delineation cut-off. Therefore, based on their whole genome sequences, strains ES1T and CL1T are suggested to represent novel species of the genus Thermococcus for which the names Thermococcus paralvinellae sp. nov. and Thermococcus cleftensis sp. nov. are proposed, respectively. The type strains are ES1T ( = DSM 27261T = KACC 17923T) and CL1T ( = DSM 27260T = KACC 17922T).

scholarly journals Full-Genome Sequences and Phylogenetic Analysis of Archived Danish European Bat Lyssavirus 1 (EBLV-1) Emphasize a Higher Genetic Resolution and Spatial Segregation for Sublineage 1a

Viruses ◽  
2021 ◽  
Vol 13 (4) ◽  
pp. 634
Author(s):  
Sten Calvelage ◽  
Conrad M. Freuling ◽  
Anthony R. Fooks ◽  
Dirk Höper ◽  
Denise A. Marston ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
High Throughput Sequencing ◽  
Phylogenetic Analyses ◽  
Spatial Segregation ◽  
Full Genome ◽  
Genome Sequences ◽  
Genetic Characteristics ◽  
Close Phylogenetic Relationship ◽  
Almost All ◽  
Relationship Of

European bat lyssavirus type 1 (EBLV-1) is the causative agent for almost all reported rabies cases found in European bats. In recent years, increasing numbers of available EBLV-1 full genomes and their phylogenetic analyses helped to further elucidate the distribution and genetic characteristics of EBLV-1 and its two subtypes, namely EBLV-1a and EBLV-1b. Nonetheless, the absence of full-genome sequences from regions with known detections of EBLV-1 still limit the understanding of the phylogeographic relations between viruses from different European regions. In this study, a set of 21 archived Danish EBLV-1 samples from the years 1985 to 2009 was processed for the acquisition of full-genome sequences using a high-throughput sequencing approach. Subsequent phylogenetic analysis encompassing all available EBLV-1 full genomes from databases revealed the Danish sequences belong to the EBLV-1a subtype and further highlighted the distinct, close phylogenetic relationship of Danish, Dutch and German isolates in this region. In addition, the formation of five putative groups nearly exclusively formed by Danish isolates and the overall increased resolution of the EBLV-1a branch indicate a higher genetic diversity and spatial segregation for this sublineage than was previously known. These results emphasize the importance of phylogenetic analyses of full-genome sequences of lyssaviruses for genetic geography.

scholarly journals Molecular Epidemiology and Whole-Genome Analysis of Bovine Foamy Virus in Japan

Viruses ◽  
2021 ◽  
Vol 13 (6) ◽  
pp. 1017
Author(s):  
Hirohisa Mekata ◽  
Tomohiro Okagawa ◽  
Satoru Konnai ◽  
Takayuki Miyazawa
Keyword(s):  
Phylogenetic Analyses ◽  
Foamy Virus ◽  
Pcr Analysis ◽  
Whole Genome ◽  
Genome Sequences ◽  
Whole Genome Analysis ◽  
Virus Family ◽  
Bovine Foamy Virus ◽  
Novel Genotype

Bovine foamy virus (BFV) is a member of the foamy virus family in cattle. Information on the epidemiology, transmission routes, and whole-genome sequences of BFV is still limited. To understand the characteristics of BFV, this study included a molecular survey in Japan and the determination of the whole-genome sequences of 30 BFV isolates. A total of 30 (3.4%, 30/884) cattle were infected with BFV according to PCR analysis. Cattle less than 48 months old were scarcely infected with this virus, and older animals had a significantly higher rate of infection. To reveal the possibility of vertical transmission, we additionally surveyed 77 pairs of dams and 3-month-old calves in a farm already confirmed to have BFV. We confirmed that one of the calves born from a dam with BFV was infected. Phylogenetic analyses revealed that a novel genotype was spread in Japan. In conclusion, the prevalence of BFV in Japan is relatively low and three genotypes, including a novel genotype, are spread in Japan.

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