scholarly journals Possibility of Gene Rearrangement between Porcine Rotavirus H and Porcine Rotavirus C in Nonstructural Protein 3

2018 ◽  
Author(s):  
Tohru Suzuki ◽  
Daisuke Inoue
Keyword(s):  
Phylogenetic Analysis ◽  
Complete Genome ◽  
Gene Rearrangement ◽  
Nonstructural Protein ◽  
Genomic Sequences ◽  
Novel Gene ◽  
Nonstructural Protein 3 ◽  
Genome Information ◽  
Porcine Rotavirus ◽  
Nsp3 Gene

Rotavirus species H (RVH) has been detected in pigs, humans and bats. Moreover, porcine RVHs have been recently identified in several swine-producing countries. Despite their zoonotic impact, genome information of RVHs is still limited. This study aimed to establish a tentative complete genome-based genotyping system for RVHs, by appending genomic sequences from 12 porcine RVHs identified in Japan between 2013 and 2015 to those from human and other porcine RVHs reported in previous studies. Phylogenetic analysis of 11 RNA segments indicated that porcine RVHs could be classified into multiple genotypes. Consequently, the genotype classification for RVHs revealed the existence of genotypes 10G, 6P, 6I, 3R, 4C, 7M, 6A, 2N, 4T, 6E, 3H for the genes VP7, VP4, VP6, VP1, VP2, VP3, NSP1, NSP2, NSP3, NSP4 and NSP5, respectively. Surprisingly, two distinctive types in NSP1 and NSP3 genes were identified from among the twelve porcine RVHs. Our data suggest a potentially novel gene rearrangement event between porcine RVH and rotavirus species C in the NSP3 gene. These findings would provide a new insight in understanding for evolution of RV.

Phylogenetic analysis of nonstructural protein 5 (NSP5) gene sequences in porcine rotavirus B strains

2012 ◽  
Vol 12 (8) ◽  
pp. 1661-1668 ◽  
Author(s):  
Tohru Suzuki ◽  
Junichi Soma ◽  
Ayako Miyazaki ◽  
Hiroshi Tsunemitsu
Keyword(s):  
Phylogenetic Analysis ◽  
Nonstructural Protein ◽  
Gene Sequences ◽  
Nsp5 Gene ◽  
Porcine Rotavirus

scholarly journals Complete Genome Sequences of Six Human Bocavirus Strains from Patients with Acute Gastroenteritis in the North Region of Brazil

2018 ◽  
Vol 6 (17) ◽  
Author(s):  
Aripuanã Sakurada Aranha Watanabe ◽  
Adriana Luchs ◽  
Élcio Leal ◽  
Flavio Augusto de Pádua Milagres ◽  
Shirley Vasconcelos Komninakis ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Respiratory Tract ◽  
Acute Gastroenteritis ◽  
Complete Genome ◽  
Genomic Sequences ◽  
Human Bocavirus ◽  
Genome Sequences ◽  
The North ◽  
Respiratory Tract Illness ◽  
Complete Genomic

ABSTRACT Human bocavirus (HBoV) is commonly associated with acute respiratory tract illness and gastroenteritis. We report six complete genomic sequences of HBoV strains from patients with gastroenteritis in Belém do Pará and Tocantins in the North Region of Brazil. Phylogenetic analysis indicated that the six HBoV strains belong to genotypes 1, 2, and 3.

scholarly journals Mitochondrial Genomes from Two Specialized Subfamilies of Reduviidae (Insecta: Hemiptera) Reveal Novel Gene Rearrangements of True Bugs

Genes ◽  
2021 ◽  
Vol 12 (8) ◽  
pp. 1134
Author(s):  
Fei Ye ◽  
Hu Li ◽  
Qiang Xie
Keyword(s):  
Gene Rearrangement ◽  
Hot Spot ◽  
Phylogenetic Analyses ◽  
Mitochondrial Gene ◽  
Deep Understanding ◽  
Gene Arrangement ◽  
Mitochondrial Genomes ◽  
Current View ◽  
Novel Gene ◽  
Spot Group

Reduviidae, a hyper-diverse family, comprise 25 subfamilies with nearly 7000 species and include many natural enemies of crop pests and vectors of human disease. To date, 75 mitochondrial genomes (mitogenomes) of assassin bugs from only 11 subfamilies have been reported. The limited sampling of mitogenome at higher categories hinders a deep understanding of mitogenome evolution and reduviid phylogeny. In this study, the first mitogenomes of Holoptilinae (Ptilocnemus lemur) and Emesinae (Ischnobaenella hainana) were sequenced. Two novel gene orders were detected in the newly sequenced mitogenomes. Combined 421 heteropteran mitogenomes, we identified 21 different gene orders and six gene rearrangement units located in three gene blocks. Comparative analyses of the diversity of gene order for each unit reveal that the tRNA gene cluster trnI-trnQ-trnM is the hotspot of heteropteran gene rearrangement. Furthermore, combined analyses of the gene rearrangement richness of each unit and the whole mitogenome among heteropteran lineages confirm Reduviidae as a ‘hot-spot group’ of gene rearrangement in Heteroptera. The phylogenetic analyses corroborate the current view of phylogenetic relationships between basal groups of Reduviidae with high support values. Our study provides deeper insights into the evolution of mitochondrial gene arrangement in Heteroptera and the early divergence of reduviids.

scholarly journals Metagenomic Analysis of Marigold: Mixed Infection Including Two New Viruses

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1254
Author(s):  
Hang Yin ◽  
Zheng Dong ◽  
Xulong Wang ◽  
Shuhao Lu ◽  
Fei Xia ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Mosaic Virus ◽  
Complete Genome ◽  
Plum Pox Virus ◽  
Cryptic Virus ◽  
Sequence Identity ◽  
Complete Genome Sequence Analysis ◽  
Wilt Virus ◽  
Broad Bean Wilt Virus

Marigold plants with symptoms of mosaic, crinkle, leaf curl and necrosis were observed and small RNA and ribo-depleted total RNA deep sequencing were conducted to identify the associated viruses. Broad bean wilt virus 2, cucumber mosaic virus, turnip mosaic virus, a new potyvirus tentatively named marigold mosaic virus (MMV) and a new partitivirus named as marigold cryptic virus (MCV) were finally identified. Complete genome sequence analysis showed MMV was 9811 nt in length, encoding a large polyprotein with highest aa sequence identity (57%) with the putative potyvirus polygonatumkingianum virus 1. Phylogenetic analysis with the definite potyviruses based on the polyprotein sequence showed MMV clustered closest to plum pox virus. The complete genome of MCV comprised of dsRNA1 (1583 bp) and dsRNA2 (1459 bp), encoding the RNA-dependent RNA polymerase (RdRp), and coat protein (CP), respectively. MCV RdRp shared the highest (75.7%) aa sequence identity with the unclassified partitivirus ambrosia cryptic virus 2, and 59.0%, 57.1%, 56.1%, 54.5% and 33.7% with the corresponding region of the definite delta-partitiviruses, pepper cryptic virus 2, beet cryptic virus 3, beet cryptic virus 2, pepper cryptic virus 1 and fig cryptic virus, respectively. Phylogenetic analysis based on the RdRp aa sequence showed MCV clustered into the delta-partitivirus group. These findings enriched our knowledge of viruses infecting marigold, but the association of the observed symptom and the identified viruses and the biological characterization of the new viruses should be further investigated.

scholarly journals p53 down-regulates SARS coronavirus replication and is targeted by the SARS-unique domain and PLprovia E3 ubiquitin ligase RCHY1

2016 ◽  
Vol 113 (35) ◽  
pp. E5192-E5201 ◽  
Author(s):  
Yue Ma-Lauer ◽  
Javier Carbajo-Lozoya ◽  
Marco Y. Hein ◽  
Marcel A. Müller ◽  
Wen Deng ◽  
...  
Keyword(s):  
Ubiquitin Ligase ◽  
Nonstructural Protein ◽  
E3 Ubiquitin Ligase ◽  
Ring Finger ◽  
Immune Recognition ◽  
Major Player ◽  
Nonstructural Protein 3 ◽  
Human Coronaviruses ◽  
Unique Domain

Highly pathogenic severe acute respiratory syndrome coronavirus (SARS-CoV) has developed strategies to inhibit host immune recognition. We identify cellular E3 ubiquitin ligase ring-finger and CHY zinc-finger domain-containing 1 (RCHY1) as an interacting partner of the viral SARS-unique domain (SUD) and papain-like protease (PLpro), and, as a consequence, the involvement of cellular p53 as antagonist of coronaviral replication. Residues 95–144 of RCHY1 and 389–652 of SUD (SUD-NM) subdomains are crucial for interaction. Association with SUD increases the stability of RCHY1 and augments RCHY1-mediated ubiquitination as well as degradation of p53. The calcium/calmodulin-dependent protein kinase II delta (CAMK2D), which normally influences RCHY1 stability by phosphorylation, also binds to SUD. In vivo phosphorylation shows that SUD does not regulate phosphorylation of RCHY1 via CAMK2D. Similarly to SUD, the PLpros from SARS-CoV, MERS-CoV, and HCoV-NL63 physically interact with and stabilize RCHY1, and thus trigger degradation of endogenous p53. The SARS-CoV papain-like protease is encoded next to SUD within nonstructural protein 3. A SUD–PLprofusion interacts with RCHY1 more intensively and causes stronger p53 degradation than SARS-CoV PLproalone. We show that p53 inhibits replication of infectious SARS-CoV as well as of replicons and human coronavirus NL63. Hence, human coronaviruses antagonize the viral inhibitor p53 via stabilizing RCHY1 and promoting RCHY1-mediated p53 degradation. SUD functions as an enhancer to strengthen interaction between RCHY1 and nonstructural protein 3, leading to a further increase in in p53 degradation. The significance of these findings is that down-regulation of p53 as a major player in antiviral innate immunity provides a long-sought explanation for delayed activities of respective genes.

scholarly journals Complete Genome Sequence of Porcine Deltacoronavirus Strain CH/JXJGS01/2016, Isolated in Jiangxi Province, China, 2016

2017 ◽  
Vol 5 (34) ◽  
Author(s):  
Min Zhang ◽  
Yu Ye ◽  
Wang Gong ◽  
Nannan Guo ◽  
Fanfan Zhang ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Amino Acid ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Jiangxi Province ◽  
Accession Number ◽  
Chinese Strain

ABSTRACT The complete genome sequence of a variant of porcine deltacoronavirus, isolated from a diarrheal piglet and designated CH/JXJGS01/2016, was sequenced and analyzed. Phylogenetic analysis demonstrated that CH/JXJGS01/2016 shares the highest nucleotide and amino acid identities with the Chinese strain NH (GenBank accession number KU981059).

scholarly journals Complete Genome Sequences of Two Subgenotype 1b Newcastle Disease Viruses Isolated from Sansui Sheldrake Ducks in Guizhou, China

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Yan Hu ◽  
Zhiqiang Duan ◽  
Xinqin Ji ◽  
Jiafu Zhao ◽  
Houqiang Xu ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Newcastle Disease ◽  
Complete Genome ◽  
Class I ◽  
Guizhou Province ◽  
Genome Sequences

Here, we report the complete genome sequences of two Newcastle disease viruses, Sheldrake duck/China/Guizhou/01/2016 and Sheldrake duck/China/Guizhou/02/2016, isolated from Sansui Sheldrake ducks in Guizhou Province, China. The genome of the isolates is 15,198 nucleotides in length. Phylogenetic analysis revealed that the isolates are clustered into subgenotype 1b in class I.

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