scholarly journals Genomic Investigation of the Coronavirus Disease-2019 Outbreak in the Republic of Korea

2020 ◽  
Author(s):  
Jeong-Min Kim ◽  
Sung Yong Park ◽  
Daesang Lee ◽  
Jun-Sub Kim ◽  
Youngjoon Park ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Close Contact ◽  
Contact Tracing ◽  
Whole Genome ◽  
Genome Sequences ◽  
South Korean Government ◽  
South Korean ◽  
Nucleotide Base ◽  
The Republic

Abstract The South Korean government effectively contained the coronavirus disease-2019 (COVID-19) outbreak primarily associated with the Shincheonji religious group. We conducted SARS-CoV-2 whole genome sequencing of 66 cases to investigate connections among the initial South Korean cases and the Shincheonji outbreak. We assessed the accuracy of genomic investigation by comparing the whole genome sequences with comprehensive contact tracing records. Five transmission clusters were estimated among the 15 initial cases. The six close-contact cases and two potential exposure pairs identified by contact tracing showed two or fewer nucleotide base differences. Additionally, we identified two transmission clusters from the Shincheonji outbreak that were phylogenetically distinct from the initial clusters, sharing common G11083T, G26144T, and C14805T markers. The strain closest to the two Shincheonji clusters was identified from a pair of identical sequences isolated from a couple who traveled from Wuhan to Milano. Our findings provide insights into the origins of community spread of COVID-19.

scholarly journals Genomic investigation of the coronavirus disease-2019 outbreak in the Republic of Korea

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jeong-Min Kim ◽  
Sung Yong Park ◽  
Daesang Lee ◽  
Jun-Sub Kim ◽  
Youngjoon Park ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Close Contact ◽  
Religious Group ◽  
Contact Tracing ◽  
Whole Genome ◽  
Genome Sequences ◽  
South Korean Government ◽  
South Korean ◽  
The Republic

AbstractThe South Korean government effectively contained the coronavirus disease-2019 (COVID-19) outbreak primarily associated with a religious group. We conducted SARS-CoV-2 whole genome sequencing of 66 cases to investigate connections among the initial South Korean cases and the religious group outbreak. We assessed the accuracy of genomic investigation by comparing the whole genome sequences with comprehensive contact tracing records. Five transmission clusters were estimated among the 15 initial cases. The six close-contact cases and two potential exposure pairs identified by contact tracing showed two or fewer nucleotide base differences. Additionally, we identified two transmission clusters that were phylogenetically distinct from the initial clusters, sharing common G11083T, G26144T, and C14805T markers. The strain closest to the two additional clusters was identified from a pair of identical sequences isolated from individuals who traveled from Wuhan to Italy. Our findings provide insights into the origins of community spread of COVID-19.

scholarly journals Genomic Investigation of the Coronavirus Disease-2019 Outbreak in the Republic of Korea

2020 ◽  
Author(s):  
Jeong-Min Kim ◽  
Sung Yong Park ◽  
Daesang Lee ◽  
Jun-Sub Kim ◽  
Youngjoon Park ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Close Contact ◽  
Religious Group ◽  
Contact Tracing ◽  
Whole Genome ◽  
Genome Sequences ◽  
South Korean Government ◽  
South Korean ◽  
The Republic

Abstract The South Korean government effectively contained the coronavirus disease-2019 (COVID-19) outbreak primarily associated with a religious group. We conducted SARS-CoV-2 whole genome sequencing of 66 cases to investigate connections among the initial South Korean cases and the religious group outbreak. We assessed the accuracy of genomic investigation by comparing the whole genome sequences with comprehensive contact tracing records. Five transmission clusters were estimated among the 15 initial cases. The six close-contact cases and two potential exposure pairs identified by contact tracing showed two or fewer nucleotide base differences. Additionally, we identified two transmission clusters from the religious group outbreak that were phylogenetically distinct from the initial clusters, sharing common G11083T, G26144T, and C14805T markers. The strain closest to the two religious group clusters was identified from a pair of identical sequences isolated from individuals who traveled from Wuhan to Italy. Our findings provide insights into the origins of community spread of COVID-19.

scholarly journals Whole-Genome Sequencing of Nontyphoidal Salmonella enterica Isolates Obtained from Various Meat Types in Ghana

2019 ◽  
Vol 8 (15) ◽  
Author(s):  
Moon Y. F. Tay ◽  
Frederick Adzitey ◽  
Stella Amelia Sultan ◽  
Joseph Makija Tati ◽  
Kelyn L. G. Seow ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Draft Genome ◽  
Protein Source ◽  
Whole Genome ◽  
Genome Sequences ◽  
Content Type ◽  
Important Protein ◽  
Retail Meats

Here, we report the draft genome sequences of 16 nontyphoidal Salmonella enterica isolates obtained from locally produced meats in Tamale, Ghana, which are commonly consumed by most natives as an important protein source. The draft genomes will help provide a molecular snapshot of Salmonella enterica isolates found in these retail meats in Tamale.

scholarly journals Draft Genome Sequences of Six Strains Isolated from the InSight Spacecraft and Associated Surfaces Using Oxford Nanopore- and Illumina-Based Sequencing

2020 ◽  
Vol 9 (21) ◽  
Author(s):  
Daniel L. Vera ◽  
Arman Seuylemezian ◽  
Kyle S. Landry ◽  
Ryan Hendrickson
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Draft Genome ◽  
Whole Genome ◽  
Genome Sequences ◽  
Planetary Protection ◽  
Functional Capabilities ◽  
Oxford Nanopore ◽  
Associated Surfaces ◽  
Insight Mission

ABSTRACT Whole-genome sequencing and annotation have allowed planetary protection engineers to assess the functional capabilities of microorganisms isolated from spacecraft hardware and associated surfaces. Here, we report draft genomes of six strains isolated from the InSight mission, determined using Oxford Nanopore- and Illumina-based sequencing.

scholarly journals Draft Genome Sequences of 64 Type Strains of 50 Species and 25 Subspecies of the Genus Staphylococcus Rosenbach 1884

2019 ◽  
Vol 8 (17) ◽  
Author(s):  
Kevin Cole ◽  
Dona Foster ◽  
Julie E. Russell ◽  
Tanya Golubchik ◽  
Martin Llewelyn ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Draft Genome ◽  
Whole Genome ◽  
Genome Sequences ◽  
Accurate Identification ◽  
Access To Data ◽  
Type Strains

Members of the genus Staphylococcus have been isolated from humans, animals, and the environment. Accurate identification with whole-genome sequencing requires access to data derived from type strains.

scholarly journals Comparison of routine field epidemiology and whole genome sequencing to identify tuberculosis transmission in a remote setting

2020 ◽  
Vol 148 ◽  
Author(s):  
J. L. Guthrie ◽  
L. Strudwick ◽  
B. Roberts ◽  
M. Allen ◽  
J. McFadzen ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Tandem Repeats ◽  
Variable Number ◽  
Yukon Territory ◽  
Contact Tracing ◽  
Whole Genome ◽  
Attitudes And Practices ◽  
Genomic Epidemiology ◽  
Recent Transmission

Abstract Yukon Territory (YT) is a remote region in northern Canada with ongoing spread of tuberculosis (TB). To explore the utility of whole genome sequencing (WGS) for TB surveillance and monitoring in a setting with detailed contact tracing and interview data, we used a mixed-methods approach. Our analysis included all culture-confirmed cases in YT (2005–2014) and incorporated data from 24-locus Mycobacterial Interspersed Repetitive Units-Variable Number of Tandem Repeats (MIRU-VNTR) genotyping, WGS and contact tracing. We compared field-based (contact investigation (CI) data + MIRU-VNTR) and genomic-based (WGS + MIRU-VNTR + basic case data) investigations to identify the most likely source of each person's TB and assessed the knowledge, attitudes and practices of programme personnel around genotyping and genomics using online, multiple-choice surveys (n = 4) and an in-person group interview (n = 5). Field- and genomics-based approaches agreed for 26 of 32 (81%) cases on likely location of TB acquisition. There was less agreement in the identification of specific source cases (13/22 or 59% of cases). Single-locus MIRU-VNTR variants and limited genetic diversity complicated the analysis. Qualitative data indicated that participants viewed genomic epidemiology as a useful tool to streamline investigations, particularly in differentiating latent TB reactivation from the recent transmission. Based on this, genomic data could be used to enhance CIs, focus resources, target interventions and aid in TB programme evaluation.

scholarly journals Countrywide implementation of whole genome sequencing: an opportunity to improve tuberculosis management, surveillance and contact tracing in low incidence countries

2018 ◽  
Vol 51 (6) ◽  
pp. 1800387 ◽  
Author(s):  
Andrea Maurizio Cabibbe ◽  
Alberto Trovato ◽  
Maria Rosaria De Filippo ◽  
Arash Ghodousi ◽  
Laura Rindi ◽  
...  
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Contact Tracing ◽  
Whole Genome ◽  
Low Incidence

scholarly journals Whole-Genome Characterization and Genotyping of Global WU Polyomavirus Strains

2010 ◽  
Vol 84 (12) ◽  
pp. 6229-6234 ◽  
Author(s):  
Seweryn Bialasiewicz ◽  
Rebecca Rockett ◽  
David W. Whiley ◽  
Yacine Abed ◽  
Tobias Allander ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Discriminatory Power ◽  
Whole Genome ◽  
Nucleotide Variation ◽  
Genome Sequences ◽  
Typing Method ◽  
Genome Characterization ◽  
Wu Polyomavirus

ABSTRACT Exploration of the genetic diversity of WU polyomavirus (WUV) has been limited in terms of the specimen numbers and particularly the sizes of the genomic fragments analyzed. Using whole-genome sequencing of 48 WUV strains collected in four continents over a 5-year period and 16 publicly available whole-genome sequences, we identified three main WUV clades and five subtypes, provisionally termed Ia, Ib, Ic, II, IIIa, and IIIb. Overall nucleotide variation was low (0 to 1.2%). The discriminatory power of the previous VP2 fragment typing method was found to be limited, and a new, larger genotyping region within the VP2/1 interface was proposed.

scholarly journals Whole-Genome Sequencing Applied to the Molecular Epidemiology of Shiga Toxin-Producing Escherichia coli O157:H7 in Argentina: TABLE 1 

2016 ◽  
Vol 4 (6) ◽  
Author(s):  
Claudia Carolina Carbonari ◽  
Nahuel Fittipaldi ◽  
Sarah Teatero ◽  
Taryn B. T. Athey ◽  
Luis Pianciola ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Molecular Epidemiology ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Shiga Toxin ◽  
Whole Genome ◽  
Escherichia Coli O157 ◽  
Genome Sequences ◽  
High Quality ◽  
Human Infections

Shiga toxin-producing Escherichia coli strains are worldwide associated with sporadic human infections and outbreaks. In this work, we report the availability of high-quality draft whole-genome sequences for 19 O157:H7 strains isolated in Argentina.

scholarly journals Whole-Genome Sequencing of Salmonella enterica Serovar Infantis and Kentucky Isolates Obtained from Layer Poultry Farms in Ecuador

2020 ◽  
Vol 9 (13) ◽  
Author(s):  
William Calero-Cáceres ◽  
Joyce Villacís ◽  
Maria Ishida ◽  
Elton Burnett ◽  
Christian Vinueza-Burgos
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Salmonella Enterica ◽  
Egg Production ◽  
Illumina Miseq ◽  
Whole Genome ◽  
Genome Sequences ◽  
Content Type ◽  
Poultry Farms

Five strains of Salmonella enterica subsp. enterica serovar Infantis and two strains of S. enterica subsp. enterica serovar Kentucky isolated in 2017 from Ecuadorian layer poultry farms were sequenced using Illumina MiSeq technology. These isolates were collected on layer farms in central Ecuador, one of the most important areas of egg production in the country. The genome sequences of these isolates show valuable information for surveillance purposes.

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