Characterization of a Novel Alphaherpesvirus Isolated from the Fruit Bat Pteropus lylei in Vietnam

ABSTRACT Herpesviruses exist in nature within each host animal. Ten herpesviruses have been isolated from bats and their biological properties reported. A novel bat alphaherpesvirus, which we propose to name “Pteropus lylei-associated alphaherpesvirus (PLAHV),” was isolated from urine of the fruit bat Pteropus lylei in Vietnam and characterized. The entire genome sequence was determined to be 144,008 bp in length and predicted to include 72 genes. PLAHV was assigned to genus Simplexvirus with other bat alphaherpesviruses isolated from pteropodid bats in Southeast Asia and Africa. The replication capacity of PLAHV in several cells was evaluated in comparison with that of herpes simplex virus 1 (HSV-1). PLAHV replicated better in the bat-originated cell line and less in human embryonic lung fibroblasts than HSV-1 did. PLAHV was serologically related to another bat alphaherpesvirus, Pteropodid alphaherpesvirus 1 (PtAHV1), isolated from a Pteropus hypomelanus-related bat captured in Indonesia, but not with HSV-1. PLAHV caused lethal infection in mice. PLAHV was as susceptible to acyclovir as HSV-1 was. Characterization of this new member of bat alphaherpesviruses, PLAHV, expands the knowledge on bat-associated alphaherpesvirology. IMPORTANCE A novel bat alphaherpesvirus, Pteropus lylei-associated alphaherpesvirus (PLAHV), was isolated from urine of the fruit bat Pteropus lylei in Vietnam. The whole-genome sequence was determined and was predicted to include 72 open reading frames in the 144,008-bp genome. PLAHV is circulating in a species of fruit bats, Pteropus lylei, in Asia. This study expands the knowledge on bat-associated alphaherpesvirology.

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Whole-Genome Sequence Characterization of Primary Auxin-Responsive Aux/IAA Gene Family in Sorghum (Sorghum bicolor L.)

ACTA AGRONOMICA SINICA ◽

10.3724/sp.j.1006.2010.00688 ◽

2010 ◽

Vol 36 (4) ◽

pp. 688-694

Author(s):

Yi-Jun WANG ◽

Yan-Ping LÜ ◽

Qin XIE ◽

De-Xiang DENG ◽

Yun-Long BIAN

Keyword(s):

Sorghum Bicolor ◽

Gene Family ◽

Genome Sequence ◽

Whole Genome Sequence ◽

Whole Genome ◽

Sequence Characterization ◽

I Gene

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Whole-Genome Sequence of Multidrug-ResistantPseudomonas aeruginosaStrain BAMCPA07-48, Isolated from a Combat Injury Wound

Genome Announcements ◽

10.1128/genomea.00547-16 ◽

2016 ◽

Vol 4 (4) ◽

Cited By ~ 2

Author(s):

Fatemeh Sanjar ◽

S. L. Rajasekhar Karna ◽

Tsute Chen ◽

Ping Chen ◽

Johnathan J. Abercrombie ◽

...

Keyword(s):

Pseudomonas Aeruginosa ◽

Genome Sequence ◽

Complete Genome Sequence ◽

Complete Genome ◽

Whole Genome Sequence ◽

Whole Genome ◽

Valuable Resource ◽

Combat Injury ◽

Pathogen Surveillance

We report here the complete genome sequence ofPseudomonas aeruginosastrain BAMCPA07-48, isolated from a combat injury wound. The closed genome sequence of this isolate is a valuable resource for pathogenome characterization ofP. aeruginosaassociated with wounds, which will aid in the development of a higher-resolution phylogenomic framework for molecular-guided pathogen-surveillance.

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Prevalence and Molecular Characterization of Novel Pathogenic Strains of Macrococcus Caseolyticus Isolated From External Wounds of Donkeys in Khartoum State –Sudan

10.21203/rs.3.rs-867901/v1 ◽

2021 ◽

Author(s):

Dania Ali ◽

Mushal Allam ◽

Hisham Altayb ◽

Dalia Mursi ◽

M. A Abdalla ◽

...

Keyword(s):

Sequence Analysis ◽

Molecular Characterization ◽

Genome Sequence ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequence Analysis ◽

Resistant Genes ◽

Different Seasons ◽

Novel Alleles

Abstract A pathogenic strains of Macrococcus caseolyticus was isolated from wounds infection during investigation on donkeys in Khartoum State. Samples were collected from external wounds (head, abdomin, back and leg), during different seasons of the year. One isolate (124B) was identified using whole-genome sequence analysis. RAST software identified thirty-one virulent genes of disease and defense including methicillin resistant genes, TatR family and ANT(4’)-Ib. Plasmid rep22 wasidentified by PlasmidFindet-2.0 Server and a CRISPR. MILST-2.0 predicted many novel alleles. NCBI notated the genome as a novel strain of M.caseolyticus strain (DaniaSudan). The MLST-tree-V1 revealed that DaniaSudan and KM0211a strains were interrelated. Strain Daniasudan was resistant to ciprofloxacin, ceftazidime, erythromycin, oxacillin, clindamycin and kanamycin. The prevalence of the strain was 4.73%, with significant differences between collection seasons and locations of wounds. Mice modling showen bacteremia and many clinical (swelling, allergy, wounds and loss of hair). Enlarged, hyperemia, adhesions and abscesses were observed in many organs. This represents the first report of pathogenic strains of M.caseolyticus worldwide.

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Genome Sequence of Venturia oleaginea, the Causal Agent of Olive Leaf Scab

Molecular Plant-Microbe Interactions ◽

10.1094/mpmi-03-20-0070-a ◽

2020 ◽

Vol 33 (9) ◽

pp. 1095-1097

Author(s):

Mohammed Y. Jaber ◽

Jiandong Bao ◽

Xiuqin Gao ◽

Limei Zhang ◽

Dou He ◽

...

Keyword(s):

Genetic Diversity ◽

Genome Sequence ◽

Population Genetic ◽

Whole Genome Sequence ◽

Whole Genome ◽

Olive Leaf ◽

Spot Disease ◽

Host Interaction ◽

Fungal Biology

Olive leaf scab, also known as peacock spot disease, caused by Venturia oleaginea (syn. Spilocaea oleaginea and Fusicladium oleagineum) is the most widespread and economically important fungal disease attacking olive in production countries. Here, we report the first highly contiguous whole-genome sequence (46.08 Mb) of one isolate, YUN35, of V. oleaginea. The described genome sequence and annotation resource will be useful to study the fungal biology, pathogen-host interaction, characterization of genes of interest, and population genetic diversity.

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

Viruses ◽

10.3390/v12020183 ◽

2020 ◽

Vol 12 (2) ◽

pp. 183 ◽

Cited By ~ 11

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.

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Whole genome sequence and phenotypic characterization of a Cbm+serotypeestrain ofStreptococcus mutans

Molecular Oral Microbiology ◽

10.1111/omi.12222 ◽

2018 ◽

Vol 33 (3) ◽

pp. 257-269 ◽

Cited By ~ 2

Author(s):

A. Avilés-Reyes ◽

I. A. Freires ◽

J.K. Kajfasz ◽

D. Barbieri ◽

J.H. Miller ◽

...

Keyword(s):

Genome Sequence ◽

Whole Genome Sequence ◽

Phenotypic Characterization ◽

Whole Genome

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Whole‐genome sequence data of Hypericum perforatum and functional characterization of melatonin biosynthesis by N‐acetylserotonin O‐methyltransferase

Journal of Pineal Research ◽

10.1111/jpi.12709 ◽

2020 ◽

Author(s):

Wen Zhou ◽

Ying Wang ◽

Bin Li ◽

Linda Petijová ◽

Suying Hu ◽

...

Keyword(s):

Genome Sequence ◽

Hypericum Perforatum ◽

Sequence Data ◽

Functional Characterization ◽

Whole Genome Sequence ◽

Whole Genome ◽

Genome Sequence Data

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Population-Sequencing as a Biomarker ofBurkholderia malleiandBurkholderia pseudomalleiEvolution through Microbial Forensic Analysis

Journal of Nucleic Acids ◽

10.1155/2013/801505 ◽

2013 ◽

Vol 2013 ◽

pp. 1-13

Author(s):

John P. Jakupciak ◽

Jeffrey M. Wells ◽

Richard J. Karalus ◽

David R. Pawlowski ◽

Jeffrey S. Lin ◽

...

Keyword(s):

Homeland Security ◽

Large Scale ◽

Direct Sequencing ◽

Forensic Analysis ◽

Population Diversity ◽

Whole Genome Sequence ◽

Whole Genome ◽

Department Of Homeland Security ◽

Entire Genome

Large-scale genomics projects are identifying biomarkers to detect human disease.B. pseudomalleiandB. malleiare two closely related select agents that cause melioidosis and glanders. Accurate characterization of metagenomic samples is dependent on accurate measurements of genetic variation between isolates with resolution down to strain level. Often single biomarker sensitivity is augmented by use of multiple or panels of biomarkers. In parallel with single biomarker validation, advances in DNA sequencing enable analysis of entire genomes in a single run: population-sequencing. Potentially, direct sequencing could be used to analyze an entire genome to serve as the biomarker for genome identification. However, genome variation and population diversity complicate use of direct sequencing, as well as differences caused by sample preparation protocols including sequencing artifacts and mistakes. As part of a Department of Homeland Security program in bacterial forensics, we examined how to implement whole genome sequencing (WGS) analysis as a judicially defensible forensic method for attributing microbial sample relatedness; and also to determine the strengths and limitations of whole genome sequence analysis in a forensics context. Herein, we demonstrate use of sequencing to provide genetic characterization of populations: direct sequencing of populations.

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