scholarly journals Genomic surveillance of COVID-19 cases in Beijing

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Pengcheng Du ◽  
Nan Ding ◽  
Jiarui Li ◽  
Fujie Zhang ◽  
Qi Wang ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
High Frequency ◽  
Epidemiological Data ◽  
Genomic Diversity ◽  
Nucleotide Polymorphisms ◽  
Genomic Evolution ◽  
Single Nucleotide ◽  
Imported Cases ◽  
Single Nucleotide Variations ◽  
Local Transmission

Abstract The spread of SARS-CoV-2 in Beijing before May, 2020 resulted from transmission following both domestic and global importation of cases. Here we present genomic surveillance data on 102 imported cases, which account for 17.2% of the total cases in Beijing. Our data suggest that all of the cases in Beijing can be broadly classified into one of three groups: Wuhan exposure, local transmission and overseas imports. We classify all sequenced genomes into seven clusters based on representative high-frequency single nucleotide polymorphisms (SNPs). Genomic comparisons reveal higher genomic diversity in the imported group compared to both the Wuhan exposure and local transmission groups, indicating continuous genomic evolution during global transmission. The imported group show region-specific SNPs, while the intra-host single nucleotide variations present as random features, and show no significant differences among groups. Epidemiological data suggest that detection of cases at immigration with mandatory quarantine may be an effective way to prevent recurring outbreaks triggered by imported cases. Notably, we also identify a set of novel indels. Our data imply that SARS-CoV-2 genomes may have high mutational tolerance.

scholarly journals Complete Genome Sequence of Yersinia pestis Strains Antiqua and Nepal516: Evidence of Gene Reduction in an Emerging Pathogen

2006 ◽  
Vol 188 (12) ◽  
pp. 4453-4463 ◽  
Author(s):  
Patrick S. G. Chain ◽  
Ping Hu ◽  
Stephanie A. Malfatti ◽  
Lyndsay Radnedge ◽  
Frank Larimer ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Yersinia Pestis ◽  
Yersinia Pseudotuberculosis ◽  
Open Reading Frames ◽  
Genomic Diversity ◽  
Avirulent Strain ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Protein Coding ◽  
Definition Of

ABSTRACT Yersinia pestis, the causative agent of bubonic and pneumonic plagues, has undergone detailed study at the molecular level. To further investigate the genomic diversity among this group and to help characterize lineages of the plague organism that have no sequenced members, we present here the genomes of two isolates of the “classical” antiqua biovar, strains Antiqua and Nepal516. The genomes of Antiqua and Nepal516 are 4.7 Mb and 4.5 Mb and encode 4,138 and 3,956 open reading frames, respectively. Though both strains belong to one of the three classical biovars, they represent separate lineages defined by recent phylogenetic studies. We compare all five currently sequenced Y. pestis genomes and the corresponding features in Yersinia pseudotuberculosis. There are strain-specific rearrangements, insertions, deletions, single nucleotide polymorphisms, and a unique distribution of insertion sequences. We found 453 single nucleotide polymorphisms in protein-coding regions, which were used to assess the evolutionary relationships of these Y. pestis strains. Gene reduction analysis revealed that the gene deletion processes are under selective pressure, and many of the inactivations are probably related to the organism's interaction with its host environment. The results presented here clearly demonstrate the differences between the two biovar antiqua lineages and support the notion that grouping Y. pestis strains based strictly on the classical definition of biovars (predicated upon two biochemical assays) does not accurately reflect the phylogenetic relationships within this species. A comparison of four virulent Y. pestis strains with the human-avirulent strain 91001 provides further insight into the genetic basis of virulence to humans.

scholarly journals Transposable elements are important contributors to standing variation in gene expression in Capsella grandiflora

2018 ◽  
Author(s):  
Jasmina Uzunović ◽  
Emily B. Josephs ◽  
John R. Stinchcombe ◽  
Stephen I. Wright
Keyword(s):  
Gene Expression ◽  
Single Nucleotide Polymorphisms ◽  
Transposable Elements ◽  
Genomic Diversity ◽  
Nucleotide Polymorphisms ◽  
Mobile Dna ◽  
Gene Expression Variation ◽  
Single Nucleotide ◽  
Expression Variation ◽  
A Genome

AbstractTransposable elements (TEs) make up a significant portion of eukaryotic genomes, and thus are important drivers of genome evolution. However, the evolutionary forces controlling TE copy number and the extent to which TEs affect phenotypic variation on a genome-wide scale are still unclear. We characterised TE insertion polymorphism and its effects on gene expression in 124 whole genome sequences from a single population of Capsella grandiflora. The frequency of insertions was negatively correlated with distance to genes, as well as density of conserved non-coding elements, suggesting that the negative effects of TEs on gene regulation are important in limiting their abundance. Rare TE variants strongly influence gene expression variation, predominantly through downregulation. In contrast, rare single nucleotide polymorphisms (SNPs) contribute equally to up- and down-regulation, but have a weaker effect. Taken together, these results imply that TEs are a significant contributor to gene expression variation and can be more likely than rare SNPs to cause extreme changes in gene expression.Author SummaryTransposable elements (TEs), mobile DNA elements with the ability to excise from the genome and reinsert in new locations, are important components of genomic diversity. Due to their abundance and mobility, TEs play an influential role in genomic evolution, often deleterious. Here we show that TEs in a population of the plant Capsella grandiflora are most deleterious when they insert in genic and regulatory regions. We find that TEs indeed are associated with unusual levels of gene expression, predominantly decreased expression.Furthermore, this effect is stronger than the association of single nucleotide polymorphisms with gene expression variation, highlighting the importance of TE contribution to the maintenance of expression variation.

scholarly journals Specific detection ofCampylobacter jejunifrom faeces using single nucleotide polymorphisms

2006 ◽  
Vol 135 (5) ◽  
pp. 839-846 ◽  
Author(s):  
E. L. Best ◽  
A. J. Fox ◽  
R. J. Owen ◽  
J. Cheesbrough ◽  
F. J. Bolton
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Real Time ◽  
Real Time Pcr ◽  
Clonal Complex ◽  
Direct Detection ◽  
Epidemiological Data ◽  
Human Infection ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Human Faeces

SUMMARYSpecimens of human faeces were tested by a rapid strategy for detection ofCampylobacter jejunilineages by the presence of specific single nucleotide polymorphisms (SNPs) based on theC. jejunimulti locus sequence typing (MLST) scheme. This strategy was derived from analysis of the MLST databases to identify clonal complex specific SNPs followed by the design of real-time PCR assays to enable identification of six majorC. jejuniclonal complexes associated with cases of human infection. The objective was to use the MLST SNP-based assays for the direct detection ofC. jejuniby clonal complex from specimens of human faeces, and then confirm the accuracy of the clonal complex designation from the SNP-based assays by performing MLST on the cultured faecal material, this targeted at determining the validity of direct molecular specimen identification. Results showed it was possible to identify 38% of the isolates to one of the six major MLST clonal complexes using a rapid DNA extraction method directly from faeces in under 3 h. This method provides a novel strategy for the use of real-time PCR for detection and characterization beyond species level, supplying real-time epidemiological data, which is comparable with MLST results.

scholarly journals Genomic epidemiology of SARS-CoV-2 reveals multiple lineages and early spread of SARS-CoV-2 infections in Lombardy, Italy

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Claudia Alteri ◽  
Valeria Cento ◽  
Antonio Piralla ◽  
Valentino Costabile ◽  
Monica Tallarita ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genomic Epidemiology ◽  
Glycosylation Sites ◽  
Community Transmission ◽  
Local Transmission

AbstractFrom February to April 2020, Lombardy (Italy) reported the highest numbers of SARS-CoV-2 cases worldwide. By analyzing 346 whole SARS-CoV-2 genomes, we demonstrate the presence of seven viral lineages in Lombardy, frequently sustained by local transmission chains and at least two likely to have originated in Italy. Six single nucleotide polymorphisms (five of them non-synonymous) characterized the SARS-CoV-2 sequences, none of them affecting N-glycosylation sites. The seven lineages, and the presence of local transmission clusters within three of them, revealed that sustained community transmission was underway before the first COVID-19 case had been detected in Lombardy.

scholarly journals Single-Nucleotide Polymorphism-Based Genetic Diversity Analysis of Clinical Pseudomonas aeruginosa Isolates

2020 ◽  
Vol 12 (4) ◽  
pp. 396-406 ◽  
Author(s):  
Uthayakumar Muthukumarasamy ◽  
Matthias Preusse ◽  
Adrian Kordes ◽  
Michal Koska ◽  
Monika Schniederjans ◽  
...  
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Single Nucleotide Polymorphisms ◽  
Core Genome ◽  
Phenotypic Diversity ◽  
Bacterial Species ◽  
Genomic Variation ◽  
Genomic Diversity ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Genetic Changes

Abstract Extensive use of next-generation sequencing has the potential to transform our knowledge on how genomic variation within bacterial species impacts phenotypic versatility. Because different environments have unique selection pressures, they drive divergent evolution. However, there is also parallel or convergent evolution of traits in independent bacterial isolates inhabiting similar environments. The application of tools to describe population-wide genomic diversity provides an opportunity to measure the predictability of genetic changes underlying adaptation. Here, we describe patterns of sequence variations in the core genome among 99 individual Pseudomonas aeruginosa clinical isolates and identified single-nucleotide polymorphisms that are the basis for branching of the phylogenetic tree. We also identified single-nucleotide polymorphisms that were acquired independently, in separate lineages, and not through inheritance from a common ancestor. Although our results demonstrate that the Pseudomonas aeruginosa core genome is highly conserved and in general, not subject to adaptive evolution, instances of parallel evolution will provide an opportunity to uncover genetic changes that underlie phenotypic diversity.

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