scholarly journals Early Phylogenetic Diversification of SARS-CoV-2: Determination of Variants and the Effect on Epidemiology, Immunology, and Diagnostics

2020 ◽  
Vol 9 (6) ◽  
pp. 1615 ◽  
Author(s):  
Rene Kaden
Keyword(s):  
Sequence Data ◽  
Gene Prediction ◽  
Herd Immunity ◽  
Diagnostic Methods ◽  
Whole Genome Sequence ◽  
Primer Binding Site ◽  
Base Substitution ◽  
Phylogenetic Clustering ◽  
Source Tracing ◽  
Globally Distributed

The phylogenetic clustering of 95 SARS-CoV-2 sequences from the first 3 months of the pandemic reveals insights into the early evolution of the virus and gives first indications of how the variants are globally distributed. Variants might become a challenge in terms of diagnostics, immunology, and effectiveness of drugs. All available whole genome sequence data from the NCBI database (March 16, 2020) were phylogenetically analyzed, and gene prediction as well as analysis of selected variants were performed. Antigenic regions and the secondary protein structure were predicted for selected variants. While some clusters are presenting the same variant with 100% identical bases, other SARS-CoV-2 lineages show a beginning diversification and phylogenetic clustering due to base substitutions and deletions in the genomes. First molecular epidemiological investigations are possible with the results by adding metadata as travelling history to the presented data. The advantage of variants in source tracing can be a challenge in terms of virulence, immune response, and immunological memory. Variants of viruses often show differences in virulence or antigenicity. This must also be considered in decisions like herd immunity. Diagnostic methods might not work if the variations or deletions are in target regions for the detection of the pathogen. One base substitution was detected in a primer binding site.

scholarly journals Genome Sequence Data of the Soybean Pathogen Stagonosporopsis vannaccii: A Resource for Studies on Didymellaceae Evolution

2020 ◽  
Vol 33 (8) ◽  
pp. 1022-1024
Author(s):  
Giovanni Cafà ◽  
Thaís Regina Boufleur ◽  
Renata Rebellato Linhares de Castro ◽  
Nelson Sidnei Massola ◽  
Riccardo Baroncelli
Keyword(s):  
Comparative Genomics ◽  
Genome Sequence ◽  
Plant Pathogens ◽  
Sequence Data ◽  
Gene Prediction ◽  
Whole Genome Sequence ◽  
Future Research ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Associated Species

The genus Stagonosporopsis is classified within the Didymellaceae family and has around 40 associated species. Among them, several species are important plant pathogens responsible for significant losses in economically important crops worldwide. Stagonosporopsis vannaccii is a newly described species pathogenic to soybean. Here, we present the draft whole-genome sequence, gene prediction, and annotation of S. vannaccii isolate LFN0148 (also known as IMI 507030). To our knowledge, this is the first genome sequenced of this species and represents a new useful source for future research on fungal comparative genomics studies.

scholarly journals Whole genome sequence and gene annotation resource for Didymella bellidis, associated with tea leaf spot

Plant Disease ◽  
2020 ◽  
Author(s):  
Xue Wang ◽  
Xian Wu ◽  
Shilong Jiang ◽  
Qiaoxiu Yin ◽  
Dongxue Li ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Leaf Spot ◽  
Sequence Data ◽  
Gene Annotation ◽  
Gene Prediction ◽  
Guizhou Province ◽  
Whole Genome Sequence ◽  
Phytopathogenic Fungus ◽  
Future Research ◽  
Whole Genome

Didymella bellidis is a phytopathogenic fungus that causes leaf spot on tea plants (Camellia sinensis), which negatively affects the productivity and quality of tea leaves in Guizhou Province, China. D. bellidis isolate GZYQYQX2B was sequenced using Pacific Biosciences and Illumina technologies, and assembled into a whole genome of 35.5 Mbp. Transcripts of D. bellidis isolate GZYQYQX2B were predicted from the assembled genome and were further validated by RNA sequence data. In total, 10,731 genes were predicted by integrating three approaches, namely ab initio and homology-based gene prediction, as well as transcriptomics data. The whole-genome sequence of D. bellidis will provide a resource for future research on trait-specific genes of the pathogen and host-pathogen interactions.

Whole genome sequence-based haplotypes reveal a single origin of the 1393 bp HBB deletion

2020 ◽  
Vol 57 (8) ◽  
pp. 567-570 ◽  
Author(s):  
Xunde Wang ◽  
Julia Z Xu ◽  
Anna Conrey ◽  
Laurel Mendelsohn ◽  
Daniel Shriner ◽  
...  
Keyword(s):  
Genome Sequence ◽  
Sequence Data ◽  
Point Mutations ◽  
Pairwise Comparison ◽  
Large Deletion ◽  
Whole Genome Sequence ◽  
Base Substitution ◽  
Whole Genome ◽  
Single Origin ◽  
Haemoglobin Disorders

BackgroundMutations of HBB give rise to two prevalent haemoglobin disorders—sickle cell disease (SCD) and β-thalassaemia. While SCD is caused by a single base substitution, nearly 300 mutations that downregulate expression of HBB have been described. The vast majority of β-thalassaemia alleles are point mutations or small insertion/deletions within the HBB gene; deletions causing β-thalassaemia are very rare. We have identified three individuals with haemoglobin Sβ0-thalassaemia in which the β0-thalassaemia mutation is caused by a large deletion.ObjectiveTo use whole genome sequence data to determine whether these deletions arose from a single origin.MethodsWe used two approaches to confirm unrelatedness: pairwise comparison of SNPs and identity by descent analysis. Eagle, V.2.4, was used to generate phased haplotypes for the 683 individuals. The Neighbor-Net method implemented in SplitsTree V.4.13.1 was used to construct the network of haplotypes.ResultsAll three deletions involved 1393 bp, encompassing the β-promoter, exons 1 and 2, and part of intron 2, with identical breakpoints. The cases were confirmed to be unrelated. Haplotypes based on 29 SNPs in the HBB cluster showed that the three individuals harboured different βS haplotypes. In contrast, the haplotype harbouring the 1393 bp deletion was the same in all three individuals.ConclusionWe suggest that all the reported cases of the 1393 bp HBB deletion, including the three cases here, are likely to be of the same ancestral origin.

scholarly journals High and Highly Variable Spontaneous Mutation Rates in Daphnia

2020 ◽  
Vol 37 (11) ◽  
pp. 3258-3266 ◽  
Author(s):  
Eddie K H Ho ◽  
Fenner Macrae ◽  
Leigh C Latta ◽  
Peter McIlroy ◽  
Dieter Ebert ◽  
...  
Keyword(s):  
Intraspecific Variation ◽  
Sequence Data ◽  
Spontaneous Mutation ◽  
Nuclear Genome ◽  
Mutation Accumulation ◽  
Whole Genome Sequence ◽  
Critical Parameters ◽  
Mutation Rates ◽  
Base Substitution ◽  
Conversion Rates

Abstract The rate and spectrum of spontaneous mutations are critical parameters in basic and applied biology because they dictate the pace and character of genetic variation introduced into populations, which is a prerequisite for evolution. We use a mutation–accumulation approach to estimate mutation parameters from whole-genome sequence data from multiple genotypes from multiple populations of Daphnia magna, an ecological and evolutionary model system. We report extremely high base substitution mutation rates (µ-n,bs = 8.96 × 10−9/bp/generation [95% CI: 6.66–11.97 × 10−9/bp/generation] in the nuclear genome and µ-m,bs = 8.7 × 10−7/bp/generation [95% CI: 4.40–15.12 × 10−7/bp/generation] in the mtDNA), the highest of any eukaryote examined using this approach. Levels of intraspecific variation based on the range of estimates from the nine genotypes collected from three populations (Finland, Germany, and Israel) span 1 and 3 orders of magnitude, respectively, resulting in up to a ∼300-fold difference in rates among genomic partitions within the same lineage. In contrast, mutation spectra exhibit very consistent patterns across genotypes and populations, suggesting the mechanisms underlying the mutational process may be similar, even when the rates at which they occur differ. We discuss the implications of high levels of intraspecific variation in rates, the importance of estimating gene conversion rates using a mutation–accumulation approach, and the interacting factors influencing the evolution of mutation parameters. Our findings deepen our knowledge about mutation and provide both challenges to and support for current theories aimed at explaining the evolution of the mutation rate, as a trait, across taxa.

scholarly journals Evolution of ST-4821 clonal complex hyperinvasive and quinolone-resistant meningococci: the next meningococcal pandemic?

2020 ◽  
Author(s):  
Mingliang Chen ◽  
Odile B. Harrison ◽  
Holly B. Bratcher ◽  
Zhiyan Bo ◽  
Keith A. Jolley ◽  
...  
Keyword(s):  
Clonal Complex ◽  
Sequence Data ◽  
Indirect Evidence ◽  
Whole Genome Sequence ◽  
Resistant Clone ◽  
Penicillin Binding Protein ◽  
Global Pandemic ◽  
Typical Strain ◽  
The Relationship ◽  
Globally Distributed

AbstractThe expansion of quinolone-resistant Neisseria meningitidis clone ChinaCC4821-R1-C/B from ST-4821 clonal complex (cc4821) caused a serogroup shift from serogroup A to C in invasive meningococcal disease (IMD) in China. To establish the relationship among globally distributed cc4821 meningococci, we analysed whole genome sequence data from 173 cc4821 meningococci isolated in four continents from 1972-2019. These meningococci clustered into four sub-lineages (1-4), with sub-lineage 1 primarily comprising serogroup C IMD isolates (82%, 41/50). Most isolates from outside China formed a distinct sub-lineage (81.6%, 40/49, the Europe-USA cluster), with the typical strain designation B:P1.17-6,23:F3-36:ST-3200(cc4821) and harbouring mutations in penicillin-binding protein 2. These data show that the quinolone-resistant clone ChinaCC4821-R1-C/B has expanded to other countries. The increasing global distribution of B:cc4821 meningococci raises concern that cc4821 has the potential to cause a global pandemic and, this would be challenging to control though there is indirect evidence that Trumenba® vaccine might afford some protection.

scholarly journals Mutability of mononucleotide repeats, not oxidative stress, explains the discrepancy between laboratory-accumulated mutations and the natural allele-frequency spectrum in C. elegans

2021 ◽  
Author(s):  
Moein Rajaei ◽  
Ayush Shekhar Saxena ◽  
Lindsay M. Johnson ◽  
Michael C. Snyder ◽  
Timothy A. Crombie ◽  
...  
Keyword(s):  
Oxidative Stress ◽  
Sequence Data ◽  
Wild Strain ◽  
Whole Genome Sequence ◽  
Base Substitution ◽  
Wild Type ◽  
Deletion Mutations ◽  
C Elegans ◽  
Mutational Spectra ◽  
Mutational Process

AbstractImportant clues about natural selection can be gleaned from discrepancies between the properties of segregating genetic variants and of mutations accumulated experimentally under minimal selection, provided the mutational process is the same in the lab as in nature. The ratio of transitions to transversions (Ts/Tv) is consistently lower in C. elegans mutation accumulation (MA) experiments than in nature, which has been argued to be in part due to increased oxidative stress in the lab environment. Using whole-genome sequence data from a set of C. elegans MA lines carrying a mutation (mev-1) that increases the cellular titer of reactive oxygen species (ROS), leading to increased endogenous oxidative stress, we find that the base-substitution spectrum is similar between mev-1 lines, its wild-type progenitor (N2), and another set of MA lines derived from a different wild strain (PB306). By contrast, the rate of short insertions is greater in the mev-1 lines, consistent with studies in other organisms in which environmental stress led to an increase in the rate of insertion-deletion mutations. Further, the mutational properties of mononucleotide repeats in all strains are qualitatively different from those of non-mononucleotide sequence, both for indels and base-substitutions, and whereas the non-mononucleotide spectra are fairly similar between MA lines and wild isolates, the mononucleotide spectra are very different. The discrepancy in mutational spectra between lab MA experiments and natural variation is likely due to a consistent (but unknown) effect of the lab environment that manifests itself via different modes of mutability and/or repair at mononucleotide loci.

TIGER: inferring DNA replication timing from whole-genome sequence data

2021 ◽  
Author(s):  
Amnon Koren ◽  
Dashiell J Massey ◽  
Alexa N Bracci
Keyword(s):  
Dna Replication ◽  
Genome Sequence ◽  
Genomic Dna ◽  
Sequence Data ◽  
Replication Timing ◽  
Whole Genome Sequence ◽  
Supplementary Information ◽  
Whole Genome ◽  
Genome Sequence Data ◽  
Dna Replication Timing

Abstract Motivation Genomic DNA replicates according to a reproducible spatiotemporal program, with some loci replicating early in S phase while others replicate late. Despite being a central cellular process, DNA replication timing studies have been limited in scale due to technical challenges. Results We present TIGER (Timing Inferred from Genome Replication), a computational approach for extracting DNA replication timing information from whole genome sequence data obtained from proliferating cell samples. The presence of replicating cells in a biological specimen leads to non-uniform representation of genomic DNA that depends on the timing of replication of different genomic loci. Replication dynamics can hence be observed in genome sequence data by analyzing DNA copy number along chromosomes while accounting for other sources of sequence coverage variation. TIGER is applicable to any species with a contiguous genome assembly and rivals the quality of experimental measurements of DNA replication timing. It provides a straightforward approach for measuring replication timing and can readily be applied at scale. Availability and Implementation TIGER is available at https://github.com/TheKorenLab/TIGER. Supplementary information Supplementary data are available at Bioinformatics online

scholarly journals SARS-CoV-2 IgG Antibodies Seroprevalence and Sera Neutralizing Activity in MEXICO: A National Cross-Sectional Study during 2020

2021 ◽  
Vol 9 (4) ◽  
pp. 850
Author(s):  
José Esteban Muñoz-Medina ◽  
Concepción Grajales-Muñiz ◽  
Angel Gustavo Salas-Lais ◽  
Larissa Fernandes-Matano ◽  
Constantino López-Macías ◽  
...  
Keyword(s):  
Immunosorbent Assay ◽  
Neutralizing Antibodies ◽  
Herd Immunity ◽  
Cross Sectional Study ◽  
Molecular Techniques ◽  
Diagnostic Methods ◽  
Molecular Diagnostic ◽  
Enzyme Linked Immunosorbent Assay ◽  
Cross Sectional ◽  
Neutralizing Activity

Until recently, the incidence of COVID-19 was primarily estimated using molecular diagnostic methods. However, the number of cases is vastly underreported using these methods. Seroprevalence studies estimate cumulative infection incidences and allow monitoring of transmission dynamics, and the presence of neutralizing antibodies in the population. In February 2020, the Mexican Social Security Institute began conducting anonymous unrelated sampling of residual sera from specimens across the country, excluding patients with fever within the previous two weeks and/or patients with an acute respiratory infection. Sampling was carried out weekly and began 17 days before Mexico’s first officially confirmed case. The 24,273 sera obtained were analyzed by chemiluminescent-linked immunosorbent assay (CLIA) IgG S1/S2 and, later, positive cases using this technique were also analyzed to determine the rate of neutralization using the enzyme-linked immunosorbent assay (ELISA). We identified 40 CLIA IgG positive cases before the first official report of SARS-CoV-2 infection in Mexico. The national seroprevalence was 3.5% in February and 33.5% in December. Neutralizing activity among IgG positives patients during overall study period was 86.1%. The extent of the SARS-CoV-2 infection in Mexico is 21 times higher than that reported by molecular techniques. Although the general population is still far from achieving herd immunity, epidemiological indicators should be re-estimated based on serological studies of this type.

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