Mitogenome of Knodus borki (Cypriniformes: Characidae): genomic characterization and phylogenetic analysis

Author(s):  
Cheng-He Sun ◽  
Ya-Nan Zhang ◽  
Xiao-Shu Zeng ◽  
Da-Wei Liu ◽  
Qi Huang ◽  
...  
Viruses ◽  
2020 ◽  
Vol 12 (2) ◽  
pp. 183 ◽  
Author(s):  
Tohru Suzuki ◽  
Yoshihiro Otake ◽  
Satoko Uchimoto ◽  
Ayako Hasebe ◽  
Yusuke Goto

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.


2015 ◽  
Vol 33 ◽  
pp. 206-211 ◽  
Author(s):  
Rashi Gautam ◽  
Slavica Mijatovic-Rustempasic ◽  
Sunando Roy ◽  
Mathew D. Esona ◽  
Beatriz Lopez ◽  
...  

2017 ◽  
Vol 5 (6) ◽  
Author(s):  
Shanhui Ren ◽  
Chongyang Wang ◽  
Xiaolong Gao ◽  
Xue Zhang ◽  
Xiangwei Wang ◽  
...  

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.


2021 ◽  
Author(s):  
Ruo-bin Lu ◽  
Ping-xiu Lan ◽  
Ru-jing Kang ◽  
Guan-lin Tan ◽  
Xiao-jiao Chen ◽  
...  

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”.


2020 ◽  
Vol 101 (7) ◽  
pp. 746-750
Author(s):  
Akbar Dastjerdi ◽  
Camilla Benfield ◽  
David Everest ◽  
Mark F. Stidworthy ◽  
Roland Zell

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.


2020 ◽  
Vol 92 (9) ◽  
pp. 1637-1640 ◽  
Author(s):  
Gianguglielmo Zehender ◽  
Alessia Lai ◽  
Annalisa Bergna ◽  
Luca Meroni ◽  
Agostino Riva ◽  
...  

2016 ◽  
Vol 43 ◽  
pp. 43-49 ◽  
Author(s):  
Qing Ye ◽  
Zhong-Yu Liu ◽  
Jian-Feng Han ◽  
Tao Jiang ◽  
Xiao-Feng Li ◽  
...  

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