scholarly journals Complete Genome Sequences for Two Strains of a Novel Fastidious, Partially Acid-Fast, Gram-Positive Corynebacterineae Bacterium, Derived from Human Clinical Samples

2015 ◽  
Vol 3 (6) ◽  
Author(s):  
Ainsley C. Nicholson ◽  
Melissa Bell ◽  
Ben W. Humrighouse ◽  
John R. McQuiston
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Clinical Relevance ◽  
Complete Genome ◽  
Growth Characteristics ◽  
Clinical Samples ◽  
Whole Genome ◽  
The Novel ◽  
Genome Sequences ◽  
Gram Positive

Here we report the complete genome sequences of two strains of the novel fastidious, partially acid-fast, Gram-positive bacillus “ Lawsonella clevelandensis ” (proposed). Their clinical relevance and unusual growth characteristics make them intriguing candidates for whole-genome sequencing.

scholarly journals Assessment of Metagenomic MinION and Illumina sequencing as an approach for the recovery of whole genome sequences of chikungunya and dengue viruses directly from clinical samples

2018 ◽  
Author(s):  
Liana E. Kafetzopoulou ◽  
Kyriakos Efthymiadis ◽  
Kuiama Lewandowski ◽  
Ant Crook ◽  
Dan Carter ◽  
...  
Keyword(s):  
Dengue Virus ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Illumina Miseq ◽  
Clinical Samples ◽  
Whole Genome ◽  
Metagenomic Sequencing ◽  
Front Line ◽  
Genome Sequences ◽  
Oxford Nanopore

AbstractThe recent global emergence and re-emergence of arboviruses has caused significant human disease. Common vectors, symptoms and geographical distribution make differential diagnosis both important and challenging. We performed metagenomic sequencing using both the Illumina MiSeq and the portable Oxford Nanopore MinION to study the feasibility of whole genome sequencing from clinical samples containing chikungunya or dengue virus, two of the most important arboviruses. Direct metagenomic sequencing of nucleic acid extracts from serum and plasma without viral enrichment allowed for virus and coinfection identification, subtype determination and in the majority of cases elucidated complete or near-complete genomes adequate for phylogenetic analysis. This work demonstrates that metagenomic whole genome sequencing is feasible for over 90% and 80% of chikungunya and dengue virus PCR-positive patient samples respectively. It confirms the feasibility of field metagenomic sequencing for these and likely other RNA viruses, highlighting the applicability of this approach to front-line public health.

scholarly journals Relative Consolidation of the Kappa Variant Pre-Dates the Massive Second Wave of COVID-19 in India

Genes ◽  
2021 ◽  
Vol 12 (11) ◽  
pp. 1803
Author(s):  
Jitendra Singh ◽  
Anvita Gupta Malhotra ◽  
Debasis Biswas ◽  
Prem Shankar ◽  
Leena Lokhande ◽  
...  
Keyword(s):  
Phylogenetic Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Spike Protein ◽  
Whole Genome ◽  
The Novel ◽  
Genome Sequences ◽  
Second Wave ◽  
Insight Into

India experienced a tragic second wave after the end of March 2021, which was far more massive than the first wave and was driven by the emergence of the novel delta variant (B.1.617.2) of the SARS-CoV-2 virus. In this study, we explored the local and national landscape of the viral variants in the period immediately preceding the second wave to gain insight into the mechanism of emergence of the delta variant and thus improve our understanding of the causation of the second wave. We randomly selected 20 SARS-CoV-2 positive samples diagnosed in our lab between 3 February and 8 March 2021 and subjected them to whole genome sequencing. Nine of the 20 sequenced genomes were classified as kappa variant (B.1.617.1). The phylogenetic analysis of pan-India SARS-CoV-2 genome sequences also suggested the gradual replacement of the α variant with the kappa variant during this period. This relative consolidation of the kappa variant was significant, since it shared 3 of the 4 signature mutations (L452R, E484Q and P681R) observed in the spike protein of delta variant and thus was likely to be the precursor in its evolution. This study demonstrates the predominance of the kappa variant in the period immediately prior to the second wave and underscores its role as the “bridging variant” between the α and delta variants that drove the first and second waves of COVID-19 in India, respectively.

scholarly journals Complete Genome Sequences of 12 Species of Stable Defined Moderately Diverse Mouse Microbiota 2: TABLE 1 

2016 ◽  
Vol 4 (5) ◽  
Author(s):  
Yasuhiro Uchimura ◽  
Madeleine Wyss ◽  
Sandrine Brugiroux ◽  
Julien P. Limenitakis ◽  
Bärbel Stecher ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Complete Genome ◽  
Bacterial Species ◽  
Whole Genome ◽  
Genome Sequences ◽  
Pacbio Sequencing ◽  
Sequencing Platform ◽  
Germ Free

We report here the complete genome sequences of 12 bacterial species of stable defined moderately diverse mouse microbiota 2 (sDMDMm2) used to colonize germ-free mice with defined microbes. Whole-genome sequencing of these species was performed using the PacBio sequencing platform yielding circularized genome sequences of all 12 species.

scholarly journals Complete Genome Sequences of 10 Yersinia pseudotuberculosis Isolates Recovered from Wild Boars in Germany

2018 ◽  
Vol 6 (19) ◽  
Author(s):  
Marie Reinhardt ◽  
Jens A. Hammerl ◽  
Stefan Hertwig
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Complete Genome ◽  
Yersinia Pseudotuberculosis ◽  
Draft Genome ◽  
Whole Genome ◽  
Genome Sequences ◽  
Content Type ◽  
Wild Boars ◽  
Human Infections

ABSTRACT We report here the draft genome sequences of 10 Yersinia pseudotuberculosis isolates recovered from tonsils of wild boars hunted between 2015 and 2016 in Germany. Whole-genome sequencing and bioinformatic analyses were performed to assess the diversity of Y. pseudotuberculosis , which may result in human infections caused by the consumption of game meat.

scholarly journals Complete Genome Sequence of the Temperate Klebsiella pneumoniae Phage KPP5665-2

2017 ◽  
Vol 5 (43) ◽  
Author(s):  
Gaby Carl ◽  
Claudia Jäckel ◽  
Josephine Grützke ◽  
Stefan Hertwig ◽  
Mirjam Grobbel ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genome Sequence ◽  
Complete Genome Sequence ◽  
Complete Genome ◽  
Whole Genome ◽  
The Novel ◽  
Content Type ◽  
Narrow Host Range

ABSTRACT We describe here the genome sequence of the novel temperate Klebsiella pneumoniae phage KPP5665-2 isolated from a Klebsiella pneumoniae strain recovered from milk in Germany in 2016. The phage exhibited a narrow host range and a siphoviridal morphology. KPP5665-2-related prophage sequences were detected in whole-genome sequencing (WGS) data of various Klebsiella species isolates.

scholarly journals Complete Genome Sequences of Thermus thermophilus Strains HB5002 and HB5008, Isolated from Mine Hot Spring in Japan

2021 ◽  
Vol 10 (16) ◽  
Author(s):  
Kentaro Miyazaki ◽  
Toshiyuki Moriya ◽  
Natsuko Tokito ◽  
Tairo Oshima ◽  
Kei Yura ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Complete Genome ◽  
Hot Spring ◽  
Thermus Thermophilus ◽  
Nucleotide Identity ◽  
Whole Genome ◽  
Average Nucleotide Identity ◽  
Genome Sequences ◽  
Content Type

ABSTRACT We isolated Thermus thermophilus strains HB5002 and HB5008 from Mine Hot Spring in Japan. Whole-genome sequencing revealed that they showed ∼100% average nucleotide identity to each other, ≥98.53% to the T. thermophilus strains originating from the same spot but ≤97.64% to the T. thermophilus strains from geographically different places in Japan.

scholarly journals Cattle connection: molecular epidemiology of BVDV outbreaks via rapid nanopore whole-genome sequencing of clinical samples

2021 ◽  
Vol 17 (1) ◽  
Author(s):  
Jacqueline King ◽  
Anne Pohlmann ◽  
Kamila Dziadek ◽  
Martin Beer ◽  
Kerstin Wernike
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Economic Losses ◽  
Clinical Samples ◽  
Bovine Viral Diarrhea ◽  
Sequence Information ◽  
Whole Genome ◽  
Diarrhea Virus ◽  
Viral Diarrhea ◽  
Viral Loads

Abstract Background As a global ruminant pathogen, bovine viral diarrhea virus (BVDV) is responsible for the disease Bovine Viral Diarrhea with a variety of clinical presentations and severe economic losses worldwide. Classified within the Pestivirus genus, the species Pestivirus A and B (syn. BVDV-1, BVDV-2) are genetically differentiated into 21 BVDV-1 and four BVDV-2 subtypes. Commonly, the 5’ untranslated region and the Npro protein are utilized for subtyping. However, the genetic variability of BVDV leads to limitations in former studies analyzing genome fragments in comparison to a full-genome evaluation. Results To enable rapid and accessible whole-genome sequencing of both BVDV-1 and BVDV-2 strains, nanopore sequencing of twelve representative BVDV samples was performed on amplicons derived through a tiling PCR procedure. Covering a multitude of subtypes (1b, 1d, 1f, 2a, 2c), sample matrices (plasma, EDTA blood and ear notch), viral loads (Cq-values 19–32) and species (cattle and sheep), ten of the twelve samples produced whole genomes, with two low titre samples presenting 96 % genome coverage. Conclusions Further phylogenetic analysis of the novel sequences emphasizes the necessity of whole-genome sequencing to identify novel strains and supplement lacking sequence information in public repositories. The proposed amplicon-based sequencing protocol allows rapid, inexpensive and accessible obtainment of complete BVDV genomes.

scholarly journals A Half-Day Genome Sequencing Protocol for Middle East Respiratory Syndrome Coronavirus

2021 ◽  
Vol 12 ◽  
Author(s):  
Kwan Woo Kim ◽  
Sungmi Choi ◽  
Su-Kyoung Shin ◽  
Imchang Lee ◽  
Keun Bon Ku ◽  
...  
Keyword(s):  
Public Health ◽  
Middle East ◽  
Genome Sequencing ◽  
Complete Genome ◽  
Middle East Respiratory Syndrome ◽  
Universal Primers ◽  
Clinical Samples ◽  
Primary Concern ◽  
Whole Genome ◽  
Serum Samples

Recent coronavirus (CoV) outbreaks, including that of Middle East respiratory syndrome (MERS), have presented a threat to public health worldwide. A primary concern in these outbreaks is the extent of mutations in the CoV, and the content of viral variation that can be determined only by whole genome sequencing (WGS). We aimed to develop a time efficient WGS protocol, using universal primers spanning the entire MERS-CoV genome. MERS and synthetic Neoromicia capensis bat CoV genomes were successfully amplified using our developed PCR primer set and sequenced with MinION. All experimental and analytical processes took 6 h to complete and were also applied to synthetic animal serum samples, wherein the MERS-CoV genome sequence was completely recovered. Results showed that the complete genome of MERS-CoV and related variants could be directly obtained from clinical samples within half a day. Consequently, this method will contribute to rapid MERS diagnosis, particularly in future CoV epidemics.

scholarly journals Complete Genome Sequences of Three African Foot-and-Mouth Disease Viruses from Clinical Samples Isolated in 2009 and 2010

2016 ◽  
Vol 4 (3) ◽  
Author(s):  
Steven Van Borm ◽  
Toon Rosseel ◽  
Andy Haegeman ◽  
Mpolokang Elliot Fana ◽  
Latoa Seoke ◽  
...  
Keyword(s):  
Genome Sequencing ◽  
Complete Genome ◽  
Foot And Mouth Disease ◽  
Mouth Disease ◽  
Clinical Samples ◽  
Full Genome ◽  
Full Genome Sequencing ◽  
Genome Sequences ◽  
Foot And Mouth

The complete genome sequences of three foot-and-mouth disease viruses (one virus of each serotype SAT1, SAT2 and O) were directly sequenced from RNA extracted from clinical bovine samples, demonstrating the feasibility of full-genome sequencing from strong positive samples taken from symptomatic animals.

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