scholarly journals Mutations in emerging variant of concern lineages disrupt genomic sequencing of SARS-CoV-2 clinical specimens

2021 ◽  
Author(s):  
Kevin S Kuchinski ◽  
Jason Nguyen ◽  
Tracy D Lee ◽  
Rebecca Hickman ◽  
Agatha N Jassem ◽  
...  
Keyword(s):  
British Columbia ◽  
Laboratory Data ◽  
Genomic Sequencing ◽  
Genome Sequences ◽  
High Quality ◽  
Laboratory Methods ◽  
Clinical Specimens ◽  
Recent Outbreak ◽  
High Quality Genome

Mutations in emerging SARS-CoV-2 lineages can interfere with the laboratory methods used to generate high-quality genome sequences for COVID-19 surveillance. Here, we identify 46 mutations in current variant of concern lineages affecting the widely used laboratory protocols for SARS-CoV-2 genomic sequencing by Freed et al. and the ARTIC network. We provide laboratory data showing how three of these mutations disrupted sequencing of P.1 lineage specimens during a recent outbreak in British Columbia, Canada, and we also demonstrate how we modified the Freed et al. protocol to restore performance.

scholarly journals High-Quality Complete Genome Sequences of Three Pseudomonas aeruginosa Isolates Retrieved from Patients Hospitalized in Intensive Care Units

2019 ◽  
Vol 8 (9) ◽  
Author(s):  
Bárbara Magalhães ◽  
Laurence Senn ◽  
Dominique S. Blanc
Keyword(s):  
Pseudomonas Aeruginosa ◽  
Intensive Care ◽  
Intensive Care Units ◽  
Genome Sequences ◽  
High Quality ◽  
Gram Negative ◽  
Content Type ◽  
Hospital Acquired Infections ◽  
Hospital Acquired ◽  
High Quality Genome

Pseudomonas aeruginosa is one of the major Gram-negative pathogens responsible for hospital-acquired infections. Here, we present high-quality genome sequences of isolates from three P. aeruginosa genotypes retrieved from patients hospitalized in intensive care units.

scholarly journals High-Quality Draft Genome Sequences of Three Cyanobacteria Isolated from the Limestone Walls of the Old Cathedral of Coimbra, Portugal

2020 ◽  
Vol 9 (26) ◽  
Author(s):  
Fabiana Soares ◽  
João Trovão ◽  
Catarina Coelho ◽  
Inês Costa ◽  
Nuno Mesquita ◽  
...  
Keyword(s):  
Draft Genome ◽  
World Heritage Site ◽  
The Novel ◽  
Genome Sequences ◽  
High Quality ◽  
Content Type ◽  
Heritage Site ◽  
Unesco World Heritage Site ◽  
Novel Taxa ◽  
High Quality Genome

ABSTRACT The recently described species Myxacorys almedinensis and two other cyanobacteria were isolated from the limestone walls of the Old Cathedral of Coimbra, Portugal (UNESCO World Heritage Site). The high-quality genome sequences presented here will be essential for characterization purposes and description of the novel taxa.

scholarly journals Evaluation and validation of de novo and hybrid assembly techniques to derive high-quality genome sequences

2014 ◽  
Vol 30 (19) ◽  
pp. 2709-2716 ◽  
Author(s):  
Sagar M. Utturkar ◽  
Dawn M. Klingeman ◽  
Miriam L. Land ◽  
Christopher W. Schadt ◽  
Mitchel J. Doktycz ◽  
...  
Keyword(s):  
De Novo ◽  
Hybrid Assembly ◽  
Genome Sequences ◽  
High Quality ◽  
High Quality Genome

scholarly journals High-quality genome sequences of uncultured microbes by assembly of read clouds

2018 ◽  
Vol 36 (11) ◽  
pp. 1067-1075 ◽  
Author(s):  
Alex Bishara ◽  
Eli L Moss ◽  
Mikhail Kolmogorov ◽  
Alma E Parada ◽  
Ziming Weng ◽  
...  
Keyword(s):  
Genome Sequences ◽  
High Quality ◽  
High Quality Genome

scholarly journals Characteristics and possible mechanisms of formation of microinversions distinguishing human and chimpanzee genomes

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Nadezhda A. Potapova ◽  
Alexey S. Kondrashov ◽  
Sergei M. Mirkin
Keyword(s):  
Dna Replication ◽  
Short Length ◽  
Inverted Repeats ◽  
Template Switching ◽  
Alternative Mechanism ◽  
Genome Sequences ◽  
High Quality ◽  
Mechanisms Of Formation ◽  
Break Induced Replication ◽  
High Quality Genome

AbstractGenomic inversions come in various sizes. While long inversions are relatively easy to identify by aligning high-quality genome sequences, unambiguous identification of microinversions is more problematic. Here, using a set of extra stringent criteria to distinguish microinversions from other mutational events, we describe microinversions that occurred after the divergence of humans and chimpanzees. In total, we found 59 definite microinversions that range from 17 to 33 nucleotides in length. In majority of them, human genome sequences matched exactly the reverse-complemented chimpanzee genome sequences, implying that the inverted DNA segment was copied precisely. All these microinversions were flanked by perfect or nearly perfect inverted repeats pointing to their key role in their formation. Template switching at inverted repeats during DNA replication was previously discussed as a possible mechanism for the microinversion formation. However, many of definite microinversions found by us cannot be easily explained via template switching owing to the combination of the short length and imperfect nature of their flanking inverted repeats. We propose a novel, alternative mechanism that involves repair of a double-stranded break within the inverting segment via microhomology-mediated break-induced replication, which can consistently explain all definite microinversion events.

scholarly journals Draft genome resources for Brassicaceae pathogens Fusarium oxysporum f. sp. raphani and Fusarium oxysporum f. sp. rapae

2021 ◽  
Author(s):  
Shuta Asai ◽  
Yu Ayukawa ◽  
Pamela Gan ◽  
Ken Shirasu
Keyword(s):  
Comparative Genomics ◽  
Fusarium Oxysporum ◽  
Brassica Rapa ◽  
Raphanus Sativus ◽  
Species Complex ◽  
Draft Genome ◽  
Genome Sequences ◽  
High Quality ◽  
Cultivated Plant ◽  
High Quality Genome

The soil-borne filamentous fungus Fusarium oxysporum causes devastating diseases of many cultivated plant species. F. oxysporum f. sp. raphani (Forpi) and f. sp. rapae (Forpe) are two of four formae speciales that are pathogenic to Brassicaceae plants. Here, we present high-quality genome sequences of Forpi strain Tf1262 and Forpe strain Tf1208 that were isolated from radish (Raphanus sativus) and turnip (Brassica rapa var. rapa), respectively. These genome resources should facilitate in-depth investigation of interactions between F. oxysporum and Brassicaceae plants, and enable comparative genomics of F. oxysporum species complex to uncover how pathogenicity evolved within F. oxysporum.

High-quality genome assembly of Huazhan and Tianfeng, the parents of an elite rice hybrid Tian-you-hua-zhan

2021 ◽  
Author(s):  
Hui Zhang ◽  
Yuexing Wang ◽  
Ce Deng ◽  
Sheng Zhao ◽  
Peng Zhang ◽  
...  
Keyword(s):  
Genome Assembly ◽  
High Quality ◽  
Rice Hybrid ◽  
High Quality Genome

scholarly journals Concurrent mutations in RNA-dependent RNA polymerase and spike protein emerged as the epidemiologically most successful SARS-CoV-2 variant

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Sten Ilmjärv ◽  
Fabien Abdul ◽  
Silvia Acosta-Gutiérrez ◽  
Carolina Estarellas ◽  
Ioannis Galdadas ◽  
...  
Keyword(s):  
Rna Polymerase ◽  
Molecular Modelling ◽  
Spike Protein ◽  
Genome Sequences ◽  
Viral Polymerase ◽  
Rna Dependent Rna Polymerase ◽  
High Quality

AbstractThe D614G mutation in the Spike protein of the SARS-CoV-2 has effectively replaced the early pandemic-causing variant. Using pseudotyped lentivectors, we confirmed that the aspartate replacement by glycine in position 614 is markedly more infectious. Molecular modelling suggests that the G614 mutation facilitates transition towards an open state of the Spike protein. To explain the epidemiological success of D614G, we analysed the evolution of 27,086 high-quality SARS-CoV-2 genome sequences from GISAID. We observed striking coevolution of D614G with the P323L mutation in the viral polymerase. Importantly, the exclusive presence of G614 or L323 did not become epidemiologically relevant. In contrast, the combination of the two mutations gave rise to a viral G/L variant that has all but replaced the initial D/P variant. Our results suggest that the P323L mutation, located in the interface domain of the RNA-dependent RNA polymerase, is a necessary alteration that led to the epidemiological success of the present variant of SARS-CoV-2. However, we did not observe a significant correlation between reported COVID-19 mortality in different countries and the prevalence of the Wuhan versus G/L variant. Nevertheless, when comparing the speed of emergence and the ultimate predominance in individual countries, it is clear that the G/L variant displays major epidemiological supremacy over the original variant.

Sign in / Sign up

Export Citation Format

Share Document