Whole genome analysis of porcine astroviruses detected in Japanese pigs reveals genetic diversity and possible intra-genotypic recombination

2017 ◽  
Vol 50 ◽  
pp. 38-48 ◽  
Author(s):  
Mika Ito ◽  
Moegi Kuroda ◽  
Tsuneyuki Masuda ◽  
Masataka Akagami ◽  
Kei Haga ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genome Analysis ◽  
Whole Genome ◽  
Whole Genome Analysis

scholarly journals Whole-Genome Analysis of Porcine Circovirus Type 2 in Russia

Pathogens ◽  
2021 ◽  
Vol 10 (12) ◽  
pp. 1631
Author(s):  
Sergei Raev ◽  
Anton Yuzhakov ◽  
Taras Aliper
Keyword(s):  
Genetic Diversity ◽  
Genome Analysis ◽  
Porcine Circovirus Type ◽  
Porcine Circovirus Type 2 ◽  
Porcine Circovirus ◽  
Economic Losses ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Reading Frame

Porcine circovirus type 2 (PCV2) is the causative agent of porcine circovirus-associated diseases (PCVAD) that bring about significant economic losses in the pig industry all over the world. The aim of this study was to investigate the genetic diversity of PCV2 in Russia and characterize the available complete genome sequences. PCV2 DNA was detected at all investigated farms located in different regions of Russia. Whole-genome analysis demonstrated that the majority of PCV2 strains belonged to genotype PCV2d (12 out of 14), while PCV2a and PCV2b were only detected at 2 farms (one at each). Further analysis revealed that all antibody recognition sites in Russian PCV2 strains were different from the corresponding epitopes in a PCV2a vaccine strain, suggesting that PCV2a-based vaccines may only provide limited protection against these strains. PCV2d strains could be grouped into 3 distinct lines which shared 98.7–100% identity within open reading frame 2 (ORF2). It is the first study reporting the genetic diversity of PCV2 strains in Russia. Our data indicated that, similarly to China, Europe, and USA, PCV2a and PCV2b have largely been replaced by PCV2d.

Whole-genome analysis of vancomycin-resistant Enterococcus faecium causing nosocomial outbreaks suggests the occurrence of few endemic clonal lineages in Bavaria, Germany

2020 ◽  
Vol 75 (6) ◽  
pp. 1398-1404 ◽  
Author(s):  
David Eisenberger ◽  
Christian Tuschak ◽  
Markus Werner ◽  
Christian Bogdan ◽  
Thomas Bollinger ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genome Analysis ◽  
Enterococcus Faecium ◽  
Treatment Options ◽  
Health Concern ◽  
Snp Analysis ◽  
Whole Genome ◽  
Vancomycin Resistant Enterococcus ◽  
Whole Genome Analysis ◽  
Vancomycin Resistant

Abstract Objectives Infections caused by vancomycin-resistant Enterococcus faecium (VREfm) represent a major public health concern due to limited treatment options. Among invasive isolates of VREfm, ST117, ST80 and ST78 represent the most frequently detected STs by MLST in Germany. In this study, we investigated the genetic diversity of isolates of VREfm recovered from different nosocomial outbreaks in Bavaria, Germany, by WGS. Methods Between January 2018 and April 2019, 99 non-replicate isolates of VREfm originating from nosocomial outbreaks at eight different hospitals in Bavaria were investigated for genetic diversity by WGS. In detail, complex types (CTs) were identified by core-genome MLST. Furthermore, an SNP analysis was performed for all VREfm strains. Results Most of the isolates of this study (76%) belonged to three major clonal groups, which occurred in at least three hospitals: ST80/CT1065 vanB (n = 45; six hospitals), ST117/CT71 vanB (n = 11; four hospitals) and ST78/CT894like vanA (n = 19; three hospitals). Moreover, isolates of the predominant lineage ST80/CT1065 vanB showed a maximum difference of 36 SNPs as revealed by SNP analysis. Conclusions Whole-genome analysis of VREfm causing nosocomial outbreaks suggests the occurrence of few endemic clonal lineages in Bavarian hospital settings, namely ST80/CT1065 vanB, ST117/CT71 vanB and ST78/CT894like vanA. Further studies are needed for a better understanding of the factors affecting the successful spread of the above-mentioned lineages.

scholarly journals Whole-genome analysis uncovers loss of blaZ associated to carriage isolates belonging to MRSA clone ST5-VI in Cape Verde

2021 ◽  
Author(s):  
Magdalena Wysocka ◽  
Tamar Monteiro ◽  
Carine de Pina ◽  
Deisy Gonçalves ◽  
Sandrine de Pina ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Cape Verde ◽  
Whole Genome ◽  
Whole Genome Analysis

Next generation sequencing for whole genome analysis and surveillance of influenza A viruses

2016 ◽  
Vol 79 ◽  
pp. 44-50 ◽  
Author(s):  
Jana McGinnis ◽  
Jennifer Laplante ◽  
Matthew Shudt ◽  
Kirsten St. George
Keyword(s):  
Next Generation Sequencing ◽  
Genome Analysis ◽  
Influenza A ◽  
Whole Genome ◽  
Next Generation ◽  
Influenza A Viruses ◽  
Whole Genome Analysis ◽  
Generation Sequencing

Whole-genome analysis of the ammonia-oxidizing bacterium, Nitrosomonas eutropha C91: implications for niche adaptation

2007 ◽  
Vol 9 (12) ◽  
pp. 2993-3007 ◽  
Author(s):  
Lisa Y. Stein ◽  
Daniel J. Arp ◽  
Paul M. Berube ◽  
Patrick S. G. Chain ◽  
Loren Hauser ◽  
...  
Keyword(s):  
Genome Analysis ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Niche Adaptation ◽  
Ammonia Oxidizing Bacterium
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