scholarly journals Novel enteric viruses in fatal enteritis of grey squirrels

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.

scholarly journals Genomic Characterization of a New Enamovirus Infecting Common Bean

2021 ◽  
Author(s):  
Ruo-bin Lu ◽  
Ping-xiu Lan ◽  
Ru-jing Kang ◽  
Guan-lin Tan ◽  
Xiao-jiao Chen ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Novel Species ◽  
Open Reading Frames ◽  
Amino Acid Sequence Level ◽  
Disease Symptoms ◽  
Bean Plants ◽  
Genomic Characterization ◽  
Pea Enation Mosaic Virus ◽  
Reading Frames

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”.

scholarly journals Genomic Characterization and Phylogenetic Classification of Bovine Coronaviruses Through Whole Genome Sequence Analysis

Viruses ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 183 ◽  
Author(s):  
Tohru Suzuki ◽  
Yoshihiro Otake ◽  
Satoko Uchimoto ◽  
Ayako Hasebe ◽  
Yusuke Goto
Keyword(s):  
Phylogenetic Analysis ◽  
Sequence Analysis ◽  
Molecular Characterization ◽  
Genome Sequence ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Wild Ruminant ◽  
Genome Sequence Analysis ◽  
Genomic Characterization

Bovine coronavirus (BCoV) is zoonotically transmissible among species, since BCoV-like viruses have been detected in wild ruminants and humans. BCoV causing enteric and respiratory disease is widespread in cattle farms worldwide; however, limited information is available regarding the molecular characterization of BCoV because of its large genome size, despite its significant economic impact. This study aimed to better understand the genomic characterization and evolutionary dynamics of BCoV via comparative sequence and phylogenetic analyses through whole genome sequence analysis using 67 BCoV isolates collected throughout Japan from 2006 to 2017. On comparing the genomic sequences of the 67 BCoVs, genetic variations were detected in 5 of 10 open reading frames (ORFs) in the BCoV genome. Phylogenetic analysis using whole genomes from the 67 Japanese BCoV isolates in addition to those from 16 reference BCoV strains, revealed the existence of two major genotypes (classical and US wild ruminant genotypes). All Japanese BCoV isolates originated from the US wild ruminant genotype, and they tended to form the same clusters based on the year and farm of collection, not the disease type. Phylogenetic trees on hemagglutinin-esterase protein (HE), spike glycoprotein (S), nucleocapsid protein (N) genes and ORF1 revealed clusters similar to that on whole genome, suggesting that the evolution of BCoVs may be closely associated with variations in these genes. Furthermore, phylogenetic analysis of BCoV S genes including those of European and Asian BCoVs and human enteric coronavirus along with the Japanese BCoVs revealed that BCoVs differentiated into two major types (European and American types). Moreover, the European and American types were divided into eleven and three genotypes, respectively. Our analysis also demonstrated that BCoVs with different genotypes periodically emerged and predominantly circulated within the country. These findings provide useful information to elucidate the detailed molecular characterization of BCoVs, which have spread worldwide. Further genomic analyses of BCoV are essential to deepen the understanding of the evolution of this virus.

scholarly journals Genomic characterization of a turkey reovirus field strain by Next-Generation Sequencing

2015 ◽  
Vol 32 ◽  
pp. 313-321 ◽  
Author(s):  
Yi Tang ◽  
Huaguang Lu ◽  
Aswathy Sebastian ◽  
Yin-Ting Yeh ◽  
Craig A. Praul ◽  
...  
Keyword(s):  
Next Generation Sequencing ◽  
Field Strain ◽  
Next Generation ◽  
Genomic Characterization ◽  
Turkey Reovirus ◽  
Generation Sequencing

scholarly journals Genomic Characterization of VIM Metallo-β-Lactamase-Producing Alcaligenes faecalis from Gaza, Palestine

2017 ◽  
Vol 61 (11) ◽  
Author(s):  
Nahed Al Laham ◽  
Kalyan D. Chavda ◽  
Astrid V. Cienfuegos-Gallet ◽  
Barry N. Kreiswirth ◽  
Liang Chen
Keyword(s):  
Bacterial Species ◽  
Alcaligenes Faecalis ◽  
Gram Negative Bacteria ◽  
Sequencing Analysis ◽  
Large Hospital ◽  
Content Type ◽  
Next Generation Sequencing Analysis ◽  
Genomic Characterization ◽  
Generation Sequencing

ABSTRACT Carbapenemase-producing Gram-negative bacteria (CP-GNB) have increasingly spread worldwide, and different families of carbapenemases have been identified in various bacterial species. Here, we report the identification of five VIM metallo-β-lactamase-producing Alcaligenes faecalis isolates associated with a small outbreak in a large hospital in Gaza, Palestine. Next-generation sequencing analysis showed bla VIM-2 is harbored by a chromosomal genomic island among three strains, while bla VIM-4 is carried by a novel plasmid in two strains.

scholarly journals Full Genomic Characterization of a Lentogenic Newcastle Disease Virus Isolated from Farm-Reared Ostriches (Struthio camelus) in Northwest China

2017 ◽  
Vol 5 (6) ◽  
Author(s):  
Shanhui Ren ◽  
Chongyang Wang ◽  
Xiaolong Gao ◽  
Xue Zhang ◽  
Xiangwei Wang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Newcastle Disease Virus ◽  
Disease Virus ◽  
Newcastle Disease ◽  
Northwest China ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Struthio Camelus ◽  
Genomic Characterization

ABSTRACT To our knowledge, our study is the first to report the whole-genome sequence of an ostrich-origin Newcastle disease virus (NDV) isolate, abbreviated as Ostrich/SX-01/06. Phylogenetic analysis revealed that this isolate belongs to the subgenotype c in class II. The identification of the complete genome will provide useful information regarding ostrich diseases, especially NDV.

scholarly journals Identification and genomic characterization of a novel species of feline anellovirus

2016 ◽  
Vol 13 (1) ◽  
Author(s):  
Wen Zhang ◽  
Hua Wang ◽  
Yan Wang ◽  
Zhijian Liu ◽  
Jingjiao Li ◽  
...  
Keyword(s):  
Novel Species ◽  
Genomic Characterization

scholarly journals Genomic characterization of Canine circovirus detected in a dog with intermittent hemorrhagic gastroenteritis in Brazil

2020 ◽  
Vol 50 (5) ◽  
Author(s):  
Taís Fukuta Cruz ◽  
Thiago Neves Batista ◽  
Ester Mariane Vieira ◽  
Luiz Marcos Frediani Portela ◽  
Amanda Mahnke Baccarin ◽  
...  
Keyword(s):  
Complete Genome ◽  
The United States ◽  
Diagnostic Tools ◽  
German Shepherd ◽  
German Shepherd Dog ◽  
History Of ◽  
Genomic Characterization ◽  
And Control ◽  
Generation Sequencing

ABSTRACT: Because Canine circovirus (CanineCV) is a new species of the genus Circovirus, several issues related to its epidemiology, pathogenesis and clinical disease remain unknown. Thus, this study aimed to perform the characterization of the first complete genome sequence of CanineCV detected in a dog with diarrhea in Brazil. A stool sample was collected of a ten-month-old female German Shepherd dog which had signs of intermittent hemorrhagic gastroenteritis, vomiting, and a history of eating raw pork. The complete CanineCV genome was sequenced by Next-Generation Sequencing. The sequence had 2,063 nucleotides, showed a typical genomic organization for circovirus, and was grouped with strain 214 described in the United States by phylogenetic analysis. One amino acid change was found in the replicase protein, and because of that it was considered unique to CanineCV. Therefore, the characterization of the complete genome of Brazilian CanineCV can be used in future studies of molecular epidemiology, pathogenesis and development of diagnostic tools for the prevention and control of this disease.

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