Identification and genomic characterization of a novel species of feline anellovirus

Abstract A novel enamovirus was identified from bean plants with disease symptoms. Its genome of 5,781 nucleotides (nt) encodes five open reading frames. The virus and other species of the genus Enamovirus share identities of 50.4%-68.4% at the complete genome, and 19.9%-51.9% of P0, 24.9%-52.5% of P1, 33.4%-62.9% of P1-P2, 30.6%-81.1% of P3, 32.3%-74.2% of P3-P5 at amino acid sequence level, respectively. Phylogenetic analysis showed that the virus is most closely related to Alfalfa enamovirus 1 and Pea enation mosaic virus 1 in the genus Enamovirus within family Solemoviridae. These results suggest that the virus should be considered as a novel species in the genus Enamovirus and tentatively named as “bean enamovirus 1”.

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Novel enteric viruses in fatal enteritis of grey squirrels

Journal of General Virology ◽

10.1099/jgv.0.001431 ◽

2020 ◽

Vol 101 (7) ◽

pp. 746-750

Author(s):

Akbar Dastjerdi ◽

Camilla Benfield ◽

David Everest ◽

Mark F. Stidworthy ◽

Roland Zell

Keyword(s):

Phylogenetic Analysis ◽

Recombination Event ◽

Novel Species ◽

Structural Proteins ◽

Virus Particles ◽

Orf2 Sequence ◽

Genomic Characterization ◽

Generation Sequencing ◽

Grey Squirrels

Astro- and kobuviruses infect both humans and animals. Here, we report on the disease history, detection and genomic characterization of novel astro- and kobuviruses from fatal diarrhoea of two juvenile grey squirrels. The virus particles had enterovirus-like morphology and a diameter of 28–32 nm. Next-generation sequencing confirmed astro- and kobuviruses and sequence analysis revealed typical astrovirus and picornavirus genome organizations. The astrovirus ORF2 sequence clustered with a clade of unassigned astroviruses, with marmot and rodent mamastroviruses as closest relatives. For the kobuvirus, divergences greater than 49.4 % for P1 and 43.5 % in the non-structural proteins indicated a novel species. However, phylogenetic analysis of the 3D polymerase showed that it clustered with that of the newly classified ludopivirus A1, suggesting a previous recombination event in the evolution of the kobuvirus. Our data provide further insights into the diversity of astro- and kobuviruses and broaden the spectrum of viruses infecting grey squirrels.

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Genomic characterization of Sebokele virus 1 (SEBV1) reveals a new candidate species among the genus Parechovirus

Journal of General Virology ◽

10.1099/vir.0.053157-0 ◽

2013 ◽

Vol 94 (7) ◽

pp. 1547-1553 ◽

Cited By ~ 9

Author(s):

M. L. Joffret ◽

C. Bouchier ◽

M. Grandadam ◽

H. Zeller ◽

C. Maufrais ◽

...

Keyword(s):

Central African Republic ◽

Novel Species ◽

Genomic Features ◽

Protein Motifs ◽

Ljungan Virus ◽

Candidate Species ◽

Genomic Characterization ◽

Bioinformatics Workflows

We determined the genomic features and the taxonomic classification of Sebokele virus 1 (SEBV1), a previously unclassified arbovirus isolated in 1972 from rodents collected in Botambi, Central African Republic. The complete genome sequence was obtained using a deep sequencing approach (Illumina technology) and dedicated bioinformatics workflows for data analysis. Molecular analysis identified SEBV1 as a picornavirus, most closely related to Ljungan viruses of the genus Parechovirus. The genome has a typical Ljungan virus-like organization, including the presence of two unrelated 2A protein motifs. Phylogenetic analysis confirmed that SEBV1 belongs to the parechovirus phylogroup and was most closely related to the Ljungan virus species. However, it appeared clearly distinct from all members of this phylogroup, suggesting that it represents a novel species of the genus Parechovirus.

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Description and genomic characterization of Streptococcus symci sp. nov., isolated from a child’s oropharynx

Antonie van Leeuwenhoek ◽

10.1007/s10482-020-01505-3 ◽

2021 ◽

Author(s):

He Qi ◽

Defeng Liu ◽

Yang Zou ◽

Nan Wang ◽

Han Tian ◽

...

Keyword(s):

Ribosomal Rna ◽

Novel Species ◽

Optimal Growth ◽

Whole Genome Sequence ◽

High Susceptibility ◽

Base Pairs ◽

Streptococcus Species ◽

Main Fatty Acid ◽

Genomic Characterization

AbstractUsing the culturomics approach, we isolated a new Streptococcus species, strain C17T, from the oropharynx mucosa sample of a healthy 5-year-old child living in Shenyang, China. We studied the phenotypic, phylogenetic, and genomic characteristics of strain C17T, which was identified as a Gram-positive, coccus-shaped, non-motile, aerobic, catalase-negative bacteria. Its growth temperatures ranged from 20 to 42 °C, with optimal growth at 37 °C. Acid production could be inhibited by two sugars, trehalose and raffinose. In C17T, the reactions for enzyme lipase (C14) were confirmed to be negative, whereas those for alkaline phosphatase, α-glucosidase, and hippuric acid hydrolysis were positive. The C17T genome contained 2,189,419 base pairs (bp), with an average G+C content of 39.95%, encoding 2092 genes in total. The 16S ribosomal RNA sequence showed 99.8% similarity with the newly identified Streptococcus pseudopneumoniae ATCC BAA-960T. The main fatty acid components in C17T were C16:0, C18:1 w7c, C18:0, and C18:1 w9c, all of which can be found in other species of the Streptococcus genus. Strain C17T showed high susceptibility to clindamycin, linezolid, vancomycin, chloramphenicol, and cefepime, and moderate susceptibility to erythromycin. The obtained dDDH value between strain C17T and the closest species was 52.9%. In addition, the whole genome sequence of strain C17T had an 82.21–93.40% average nucleotide identity (ANI) with those strains of closely related Streptococcus species, indicating that the strain C17T was unique among all Streptococcus species. Based on these characteristics, we determine that C17T is a novel species, named Streptococcus symci sp. nov. (= GDMCC 1.1633 = JCM 33582).

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Genomic Characterization of an Emerging Enterobacteriaceae Species for the First Case of Human Infection in Cooperation with a Typical Pathogen

10.21203/rs.2.22057/v1 ◽

2020 ◽

Author(s):

Zhao Zhang ◽

Daixi Li ◽

xing shi ◽

Yao Zhai ◽

Yatao Guo ◽

...

Keyword(s):

Continuous Monitoring ◽

Novel Species ◽

Human Infection ◽

Klebsiella Pneumonia ◽

Opportunistic Pathogens ◽

Antibiotic Resistant ◽

First Case ◽

Infection Treatment ◽

Genomic Characterization

Abstract Opportunistic pathogens are important for clinical practice as they often cause antibiotic resistant infections. However, little is documented for many emerging opportunistic pathogens and their biological characteristics. Here, we isolated a novel species of extended-spectrum β-lactamase-producing Enterobacteriaceae from a patient of biliary tract infection. The isolate grows very slowly but confers strong protection for the co-infected cephalosporin-sensitive Klebsiella pneumonia. As the initial laboratory testing failed to identify the taxonomy of the strain, great perplexity was caused in the etiological diagnosis, and anti-infection treatment for the patient. Rigorous sequencing efforts achieved the complete genome sequence of the isolate which we designated as AF18. AF18 is phylogenetically close to a few strains respectively isolated from soil, clinical sewage, and patients, forming a novel species together, while the taxonomic nomenclature of which is still under discussion. And this is the first report of human infection of this novel species. As its relatives, AF18 harbors many genes related to cell mobility, various genes adaptive to both wild environment and animal host, tens of genetic mobile elements, and a plasmid bearing blaCTX-M-3 gene, indicating its ability to disseminate antimicrobial resistant genes from wild to patients. Transcriptome sequencing identified two sRNAs that critically regulate the growth rate of AF18 which could serve as targets for novel antimicrobial strategies. These findings imply that AF18 and its species are not only infection-relevant but also potential disseminators in transferring antibiotic determinants, which highlights the need for continuous monitoring for this novel species and efforts to develop controlling strategies.

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