scholarly journals Genome sequencing guide: An introductory toolbox to whole‐genome analysis methods

2021 ◽  
Author(s):  
Alexis N. Burian ◽  
Wufan Zhao ◽  
Te‐Wen Lo ◽  
Deborah M. Thurtle‐Schmidt
Keyword(s):  
Genome Sequencing ◽  
Genome Analysis ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Analysis Methods

scholarly journals Whole-Genome Sequencing Confirms that Burkholderia pseudomallei Multilocus Sequence Types Common to Both Cambodia and Australia Are Due to Homoplasy

2014 ◽  
Vol 53 (1) ◽  
pp. 323-326 ◽  
Author(s):  
Birgit De Smet ◽  
Derek S. Sarovich ◽  
Erin P. Price ◽  
Mark Mayo ◽  
Vanessa Theobald ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Analysis ◽  
Burkholderia Pseudomallei ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Content Type ◽  
Sequence Types

Burkholderia pseudomalleiisolates with shared multilocus sequence types (STs) have not been isolated from different continents. We identified two STs shared between Australia and Cambodia. Whole-genome analysis revealed substantial diversity within STs, correctly identified the Asian or Australian origin, and confirmed that these shared STs were due to homoplasy.

scholarly journals Detection of SARS-CoV-2 from Patient Fecal Samples by Whole Genome Sequencing

2020 ◽  
Author(s):  
Andreas Papoutsis ◽  
Thomas Borody ◽  
Siba Dolai ◽  
Jordan Daniels ◽  
Skylar Steinberg ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Analysis ◽  
Nasopharyngeal Swab ◽  
Whole Genome ◽  
Rt Pcr ◽  
Whole Genome Analysis ◽  
Fecal Samples ◽  
Oral Transmission ◽  
Study Participants

Abstract Background SARS-CoV-2 has been detected not only in respiratory secretions, but also in stool collections. Here were sought to identify SARS-CoV-2 by enrichment NGS from fecal samples, and to utilize whole genome analysis to characterize SARS-CoV-2 mutational variations in COVID-19 patients. Results Study participants underwent testing for SARS-CoV-2 from fecal samples by whole genome enrichment NGS (n = 14), and RT-PCR nasopharyngeal swab analysis (n = 12). The concordance of SARS-CoV-2 detection by enrichment NGS from stools with RT-PCR nasopharyngeal analysis was 100%. Unique variants were identified in four patients, with a total of 33 different mutations among those in which SARS-CoV-2 was detected by whole genome enrichment NGS. Conclusion These results highlight the potential viability of SARS-CoV-2 in feces, its ongoing mutational accumulation, and its possible role in fecal-oral transmission. This study also elucidates the advantages of SARS-CoV-2 enrichment NGS, which may be a key methodology to document complete viral eradication.

scholarly journals Surveillance of Influenza A resistance to polymerase complex inhibitors by whole genome analysis, 2016-17, 2017-18 and 2018-19 Seasons, Eastern Spain

2021 ◽  
Author(s):  
Beatriz Mengual-Chuliá ◽  
Andrés Alonso-Cordero ◽  
Laura Cano ◽  
M. del Mar Mosquera ◽  
Patricia de Molina ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Analysis ◽  
Influenza A ◽  
Natural Resistance ◽  
Whole Genome ◽  
Influenza A Viruses ◽  
Whole Genome Analysis ◽  
Molecular Surveillance ◽  
Polymerase Complex

Molecular surveillance by whole genome sequencing was used to monitor the susceptibility of circulating Influenza A viruses to three polymerase complex inhibitors. A total of 12 resistance substitutions were found among 285 genomes analysed, but none associated with high levels of resistance. Natural resistance to these influenza A antivirals is currently uncommon.

scholarly journals Co-circulation of multiple subtypes of enterovirus A71 (EV- A71) genotype C, including novel recombinants characterised by use of whole genome sequencing (WGS), Denmark 2016

2017 ◽  
Vol 22 (26) ◽  
Author(s):  
Sofie E Midgley ◽  
Astrid G Nielsen ◽  
Ramona Trebbien ◽  
Mille W. Poulsen ◽  
Peter H Andersen ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Genome Analysis ◽  
Neurological Disease ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Highly Pathogenic ◽  
Enterovirus A71 ◽  
Recent Emergence ◽  
Sporadic Cases ◽  
Genotype C

In Europe, enterovirus A71 (EV-A71) has primarily been associated with sporadic cases of neurological disease. The recent emergence of new genotypes and larger outbreaks with severely ill patients demonstrates a potential for the spread of new, highly pathogenic EV-A71 strains. Detection and characterisation of these new emerging EV variants is challenging as standard EV assays may not be adequate, necessitating the use of whole genome analysis.

scholarly journals Estimation and Partition of Heritability in Human Populations Using Whole-Genome Analysis Methods

2013 ◽  
Vol 47 (1) ◽  
pp. 75-95 ◽  
Author(s):  
Anna A.E. Vinkhuyzen ◽  
Naomi R. Wray ◽  
Jian Yang ◽  
Michael E. Goddard ◽  
Peter M. Visscher
Keyword(s):  
Genome Analysis ◽  
Human Populations ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Analysis Methods

scholarly journals Application of Whole-Genome Sequencing to an Unusual Outbreak of Invasive Group A Streptococcal Disease

2016 ◽  
Vol 3 (1) ◽  
Author(s):  
Jessica Galloway-Peña ◽  
Meredith E. Clement ◽  
Batu K. Sharma Kuinkel ◽  
Felicia Ruffin ◽  
Anthony R. Flores ◽  
...  
Keyword(s):  
Point Source ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Analysis ◽  
Whole Genome ◽  
Whole Genome Analysis ◽  
Invasive Group ◽  
Streptococcal Disease ◽  
Group A ◽  
Genome Analyses

Abstract Whole-genome analysis was applied to investigate atypical point-source transmission of 2 invasive group A streptococcal (GAS) infections. Isolates were serotype M4, ST39, and genetically indistinguishable. Comparison with MGAS10750 revealed nonsynonymous polymorphisms in ropB and increased speB transcription. This study demonstrates the usefulness of whole-genome analyses for GAS outbreaks.

scholarly journals Detection of SARS-CoV-2 from Patient Fecal Samples by Whole Genome Sequencing

2020 ◽  
Author(s):  
Andreas Papoutsis ◽  
Thomas Borody ◽  
Siba Dolai ◽  
Jordan Daniels ◽  
Skylar Steinberg ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Analysis ◽  
Nasopharyngeal Swab ◽  
Whole Genome ◽  
Rt Pcr ◽  
Whole Genome Analysis ◽  
Fecal Samples ◽  
Oral Transmission ◽  
Study Participants

Abstract Background SARS-CoV-2 has been detected not only in respiratory secretions, but also in stool collections. Here were sought to identify SARS-CoV-2 by enrichment NGS from fecal samples, and to utilize whole genome analysis to characterize SARS-CoV-2 mutational variations in COVID-19 patients. Results Study participants underwent testing for SARS-CoV-2 from fecal samples by whole genome enrichment NGS (n = 14), and RT-PCR nasopharyngeal swab analysis (n = 12). The concordance of SARS-CoV-2 detection by enrichment NGS from stools with RT-PCR nasopharyngeal analysis was 100%. Unique variants were identified in four patients, with a total of 33 different mutations among those in which SARS-CoV-2 was detected by whole genome enrichment NGS. Conclusion These results highlight the potential viability of SARS-CoV-2 in feces, its ongoing mutational accumulation, and its possible role in fecal-oral transmission. This study also elucidates the advantages of SARS-CoV-2 enrichment NGS, which may be a key methodology to document complete viral eradication.

scholarly journals Detection of SARS-CoV-2 from Patient Fecal Samples by Whole Genome Sequencing

2021 ◽  
Author(s):  
Andreas Papoutsis ◽  
Thomas Borody ◽  
Siba Dolai ◽  
Jordan Daniels ◽  
Skylar Steinberg ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Analysis ◽  
Nasopharyngeal Swab ◽  
Whole Genome ◽  
Rt Pcr ◽  
Whole Genome Analysis ◽  
Fecal Samples ◽  
Oral Transmission ◽  
Study Participants

Abstract Background SARS-CoV-2 has been detected not only in respiratory secretions, but also in stool collections. Here were sought to identify SARS-CoV-2 by enrichment NGS from fecal samples, and to utilize whole genome analysis to characterize SARS-CoV-2 mutational variations in COVID-19 patients. Results Study participants underwent testing for SARS-CoV-2 from fecal samples by whole genome enrichment NGS (n = 14), and RT-PCR nasopharyngeal swab analysis (n = 12). The concordance of SARS-CoV-2 detection by enrichment NGS from stools with RT-PCR nasopharyngeal analysis was 100%. Unique variants were identified in four patients, with a total of 33 different mutations among those in which SARS-CoV-2 was detected by whole genome enrichment NGS. Conclusion These results highlight the potential viability of SARS-CoV-2 in feces, its ongoing mutational accumulation, and its possible role in fecal-oral transmission. This study also elucidates the advantages of SARS-CoV-2 enrichment NGS, which may be a key methodology to document complete viral eradication.

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