scholarly journals Whole-Genome Sequence Analysis of Pseudorabies Virus Clinical Isolates from Pigs in China between 2012 and 2017 in China

Viruses ◽  
2021 ◽  
Vol 13 (7) ◽  
pp. 1322
Author(s):  
Ruiming Hu ◽  
Leyi Wang ◽  
Qingyun Liu ◽  
Lin Hua ◽  
Xi Huang ◽  
...  
Keyword(s):  
Selection Pressure ◽  
Pseudorabies Virus ◽  
Viral Evolution ◽  
Infectious Agent ◽  
Genomic Diversity ◽  
Whole Genome Sequence ◽  
Evolutionary Constraint ◽  
The Novel ◽  
Novel Variants ◽  
Pressure Analysis

Pseudorabies virus (PRV) is an economically significant swine infectious agent. A PRV outbreak took place in China in 2011 with novel virulent variants. Although the association of viral genomic variability with pathogenicity is not fully confirmed, the knowledge concerning PRV genomic diversity and evolution is still limited. Here, we sequenced 54 genomes of novel PRV variants isolated in China from 2012 to 2017. Phylogenetic analysis revealed that China strains and US/Europe strains were classified into two separate genotypes. PRV strains isolated from 2012 to 2017 in China are highly related to each other and genetically close to classic China strains such as Ea, Fa, and SC. RDP analysis revealed 23 recombination events within novel PRV variants, indicating that recombination contributes significantly to the viral evolution. The selection pressure analysis indicated that most ORFs were under evolutionary constraint, and 19 amino acid residue sites in 15 ORFs were identified under positive selection. Additionally, 37 unique mutations were identified in 19 ORFs, which distinguish the novel variants from classic strains. Overall, our study suggested that novel PRV variants might evolve from classical PRV strains through point mutation and recombination mechanisms.

scholarly journals Understanding genomic diversity, pan-genome, and evolution of SARS-CoV-2

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e9576
Author(s):  
Arohi Parlikar ◽  
Kishan Kalia ◽  
Shruti Sinha ◽  
Sucheta Patnaik ◽  
Neeraj Sharma ◽  
...  
Keyword(s):  
Genomic Diversity ◽  
Whole Genome Sequence ◽  
The Novel ◽  
Origin And Evolution ◽  
Pan Genome ◽  
Mutational Hotspots ◽  
Evolutionary Studies ◽  
Low Probability ◽  
Shed Light ◽  
Country Specific

Coronovirus disease 2019 (COVID-19) infection, which originated from Wuhan, China, has seized the whole world in its grasp and created a huge pandemic situation before humanity. Since December 2019, genomes of numerous isolates have been sequenced and analyzed for testing confirmation, epidemiology, and evolutionary studies. In the first half of this article, we provide a detailed review of the history and origin of COVID-19, followed by the taxonomy, nomenclature and genome organization of its causative agent Severe Acute Respiratory Syndrome-related Coronavirus-2 (SARS-CoV-2). In the latter half, we analyze subgenus Sarbecovirus (167 SARS-CoV-2, 312 SARS-CoV, and 5 Pangolin CoV) genomes to understand their diversity, origin, and evolution, along with pan-genome analysis of genus Betacoronavirus members. Whole-genome sequence-based phylogeny of subgenus Sarbecovirus genomes reasserted the fact that SARS-CoV-2 strains evolved from their common ancestors putatively residing in bat or pangolin hosts. We predicted a few country-specific patterns of relatedness and identified mutational hotspots with high, medium and low probability based on genome alignment of 167 SARS-CoV-2 strains. A total of 100-nucleotide segment-based homology studies revealed that the majority of the SARS-CoV-2 genome segments are close to Bat CoV, followed by some to Pangolin CoV, and some are unique ones. Open pan-genome of genus Betacoronavirus members indicates the diversity contributed by the novel viruses emerging in this group. Overall, the exploration of the diversity of these isolates, mutational hotspots and pan-genome will shed light on the evolution and pathogenicity of SARS-CoV-2 and help in developing putative methods of diagnosis and treatment.

Characterization of novel ybjG and dacC variants in Escherichia coli

2013 ◽  
Vol 62 (11) ◽  
pp. 1728-1734 ◽  
Author(s):  
Dongguo Wang ◽  
Enping Hu ◽  
Jiayu Chen ◽  
Xiulin Tao ◽  
Katelyn Gutierrez ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Multiple Drug Resistance ◽  
Multiple Drug ◽  
The Novel ◽  
Conventional Pcr ◽  
E Coli ◽  
Novel Variants ◽  
Restriction Sites ◽  
Genetic Structures

A total of 69 strains of Escherichia coli from patients in the Taizhou Municipal Hospital, China, were isolated, and 11 strains were identified that were resistant to bacitracin, chloramphenicol, tetracycline and erythromycin. These strains were PCR positive for at least two out of three genes, ybjG, dacC and mdfA, by gene mapping with conventional PCR detection. Conjugation experiments demonstrated that these genes existed in plasmids that conferred resistance. Novel ybjG and dacC variants were isolated from E. coli strains EC2163 and EC2347, which were obtained from the sputum of intensive care unit patients. Genetic mapping showed that the genes were located on 8200 kb plasmid regions flanked by EcoRI restriction sites. Three distinct genetic structures were identified among the 11 PCR-positive strains of E. coli, and two contained the novel ybjG and dacC variants. The putative amino acid differences in the ybjG and dacC gene variants were characterized. These results provide evidence for novel variants of ybjG and dacC, and suggest that multiple drug resistance in hospital strains of E. coli depends on the synergistic function of ybjG, dacC and mdfA within three distinct genetic structures in conjugative plasmids.

scholarly journals The Whole-Genome Sequence of the Novel Yeast Species Metschnikowia persimmonesis Isolated from Medicinal Plant Diospyros kaki Thunb

2021 ◽  
Author(s):  
Endang Rahmat ◽  
Inkyu Park ◽  
Youngmin Kang
Keyword(s):  
Gc Content ◽  
Whole Genome Sequence ◽  
Diospyros Kaki ◽  
Whole Genome ◽  
The Novel ◽  
Data Set ◽  
Draft Assembly ◽  
Future Possibility ◽  
Complete Set ◽  
New Yeast

Abstract The new yeast Metschnikowia persimmonesis KCTC 12991BP (KIOM G15050 strain) exhibits strong antimicrobial activity against some pathogens. This activity may be related to the medicinal profile of secondary metabolites that could be found in the genome of this species. Therefore, to explore its future possibility of producing some beneficial activities, including medicinal ability, we report high quality whole-genome assembly of M. persimmonesis produced by PacBio RSII sequencer. The final draft assembly consisted of 16 scaffolds with GC content of 45.90% and comprised a fairly complete set (82.8%) of BUSCO result using Saccharomycetales lineage data set. The total length of the genome was 16.473 Mb, with a scaffold N50 of 1.982 Mb. Annotation of the M. persimmonesis genome revealed presence of 7,029 genes and 6,939 functionally annotated proteins. Based on the analysis of phylogenetic relationship and the average nucleotide identities (ANI), M. persimmonesis was proved to a novel species within the Metschnikowia genus. This finding is expected to significantly contribute to the discovery of high-value natural products from M. persimmonesis as well as for genome biology and evolution comparative analysis within Metschnikowia species.

scholarly journals Genomic Characteristics of Invasive Streptococcus pneumoniae Serotype 1 in New Caledonia Prior to the Introduction of PCV13

2020 ◽  
Vol 14 ◽  
pp. 117793222096210 ◽  
Author(s):  
Mariem Hanachi ◽  
Anmol Kiran ◽  
Jennifer Cornick ◽  
Emna Harigua-Souiai ◽  
Dean Everett ◽  
...  
Keyword(s):  
Population Structure ◽  
Streptococcus Pneumoniae ◽  
Virulence Genes ◽  
New Caledonia ◽  
Disease Outbreaks ◽  
Genomic Diversity ◽  
Whole Genome Sequence ◽  
Serotype 1 ◽  
The Impact ◽  
Sequence Types

Streptococcus pneumoniae serotype 1 is a common cause of global invasive pneumococcal disease. In New Caledonia, serotype 1 is the most prevalent serotype and led to two major outbreaks reported in the 2000s. The pneumococcal conjugate vaccine 13 (PCV13) was introduced into the vaccination routine, intending to prevent the expansion of serotype 1 in New Caledonia. Aiming to provide a baseline for monitoring the post-PCV13 changes, we performed a whole-genome sequence analysis on 67 serotype 1 isolates collected prior to the PCV13 introduction. To highlight the S. pneumoniae serotype 1 population structure, we performed a multilocus sequence typing (MLST) analysis revealing that NC serotype 1 consisted of 2 sequence types: ST3717 and the highly dominant ST306. Both sequence types harbored the same resistance genes to beta-lactams, macrolide, streptogramin B, fluoroquinolone, and lincosamide antibiotics. We have also identified 36 virulence genes that were ubiquitous to all the isolates. Among these virulence genes, the pneumolysin sequence presented an allelic profile associated with disease outbreaks and reduced hemolytic activity. Moreover, recombination hotspots were identified in 4 virulence genes and more notably in the cps locus ( cps2L), potentially leading to capsular switching, a major mechanism of the emergence of nonvaccine types. In summary, this study represents the first overview of the genomic characteristics of S. pneumoniae serotype 1 in New Caledonia prior to the introduction of PCV13. This preliminary description represents a baseline to assess the impact of PCV13 on serotype 1 population structure and genomic diversity.

scholarly journals Comparative Genomic and Morphological Analyses of Listeria Phages Isolated from Farm Environments

2014 ◽  
Vol 80 (15) ◽  
pp. 4616-4625 ◽  
Author(s):  
Thomas Denes ◽  
Kitiya Vongkamjan ◽  
Hans-Wolfgang Ackermann ◽  
Andrea I. Moreno Switt ◽  
Martin Wiedmann ◽  
...  
Keyword(s):  
New York ◽  
Dairy Farm ◽  
Morphological Diversity ◽  
Genomic Diversity ◽  
Comparative Genomic ◽  
The Novel ◽  
Important Food ◽  
Content Type ◽  
Small Genome ◽  
Food Borne

ABSTRACTThe genusListeriais ubiquitous in the environment and includes the globally important food-borne pathogenListeria monocytogenes. While the genomic diversity ofListeriahas been well studied, considerably less is known about the genomic and morphological diversity ofListeriabacteriophages. In this study, we sequenced and analyzed the genomes of 14Listeriaphages isolated mostly from New York dairy farm environments as well as one relatedEnterococcus faecalisphage to obtain information on genome characteristics and diversity. We also examined 12 of the phages by electron microscopy to characterize their morphology. TheseListeriaphages, based on gene orthology and morphology, together with previously sequencedListeriaphages could be classified into five orthoclusters, including one novel orthocluster. One orthocluster (orthocluster I) consists of large-genome (∼135-kb) myoviruses belonging to the genus “Twort-like viruses,” three orthoclusters (orthoclusters II to IV) contain small-genome (36- to 43-kb) siphoviruses with icosahedral heads, and the novel orthocluster V contains medium-sized-genome (∼66-kb) siphoviruses with elongated heads. A novel orthocluster (orthocluster VI) ofE. faecalisphages, with medium-sized genomes (∼56 kb), was identified, which grouped together and shares morphological features with the novelListeriaphage orthocluster V. This new group of phages (i.e., orthoclusters V and VI) is composed of putative lytic phages that may prove to be useful in phage-based applications for biocontrol, detection, and therapeutic purposes.

The selection pressure analysis of chicken anemia virus structural protein gene VP1

Virus Genes ◽  
2009 ◽  
Vol 38 (2) ◽  
pp. 259-262 ◽  
Author(s):  
Dong Wang ◽  
Wei Fan ◽  
Guan-Zhu Han ◽  
Cheng-Qiang He
Keyword(s):  
Selection Pressure ◽  
Protein Gene ◽  
Chicken Anemia Virus ◽  
Structural Protein ◽  
Anemia Virus ◽  
Structural Protein Gene ◽  
Pressure Analysis

scholarly journals Proposal to rename Carnobacterium inhibens as Carnobacterium inhibens subsp. inhibens subsp. nov. and description of Carnobacterium inhibens subsp. gilichinskyi subsp. nov., a psychrotolerant bacterium isolated from Siberian permafrost

2015 ◽  
Vol 65 (Pt_2) ◽  
pp. 556-561 ◽  
Author(s):  
Wayne L. Nicholson ◽  
Kateryna Zhalnina ◽  
Rafael R. de Oliveira ◽  
Eric W. Triplett
Keyword(s):  
Sequence Analysis ◽  
Type Species ◽  
Fatty Acid Content ◽  
Optimal Growth ◽  
Whole Genome Sequence ◽  
Rrna Gene ◽  
Positive Staining ◽  
The Novel ◽  
Content Type ◽  
Link Type

A novel, psychrotolerant facultative anaerobe, strain WN1359T, was isolated from a permafrost borehole sample collected at the right bank of the Kolyma River in Siberia, Russia. Gram-positive-staining, non-motile, rod-shaped cells were observed with sizes of 1–2 µm long and 0.4–0.5 µm wide. Growth occurred in the range of pH 5.8–9.0 with optimal growth at pH 7.8–8.6 (pH optimum 8.2). The novel isolate grew at temperatures from 0–37 °C and optimal growth occurred at 25 °C. The novel isolate does not require NaCl; growth was observed between 0 and 8.8 % (1.5 M) NaCl with optimal growth at 0.5 % (w/v) NaCl. The isolate was a catalase-negative, facultatively anaerobic chemo-organoheterotroph that used sugars but not several single amino acids or dipeptides as substrates. The major metabolic end-product was lactic acid in the ratio of 86 % l-lactate : 14 % d-lactate. Strain WN1359T was sensitive to ampicillin, chloramphenicol, fusidic acid, lincomycin, monocycline, rifampicin, rifamycin SV, spectinomycin, streptomycin, troleandomycin and vancomycin, and resistant to nalidixic acid and aztreonam. The fatty acid content was predominantly unsaturated (70.2 %), branched-chain unsaturated (11.7 %) and saturated (12.5 %). The DNA G+C content was 35.3 mol% by whole genome sequence analysis. 16S rRNA gene sequence analysis showed 98.7 % sequence identity between strain WN1359T and Carnobacterium inhibens . Genome relatedness was computed using both Genome-to-Genome Distance Analysis (GGDA) and Average Nucleotide Identity (ANI), which both strongly supported strain WN1359T belonging to the species C. inhibens . On the basis of these results, the permafrost isolate WN1359T represents a novel subspecies of C. inhibens , for which the name Carnobacterium inhibens subsp. gilichinskyi subsp. nov. is proposed. The type strain is WN1359T ( = ATCC BAA-2557T = DSM 27470T). The subspecies Carnobacterium inhibens subsp. inhibens subsp. nov. is created automatically. An emended description of C. inhibens is also provided.

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