scholarly journals Genetic Diversity and Evolution of the Biological Features of the Pandemic SARS-CoV-2

Acta Naturae ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 77-89
Author(s):  
Aleksandra A. Nikonova ◽  
Eugene B. Faizuloev ◽  
Anastasia V. Gracheva ◽  
Igor Yu. Isakov ◽  
Vitaly V. Zverev
Keyword(s):  
Genetic Diversity ◽  
Genetic Variants ◽  
Large Scale ◽  
Biological Properties ◽  
Viral Genomes ◽  
Biological Features ◽  
Health Measures ◽  
Common Genetic Variants ◽  
Coronavirus Infection ◽  
The Relationship

The new coronavirus infection (COVID-19) represents a challenge for global health. Since the outbreak began, the number of confirmed cases has exceeded 117 million, with more than 2.6 million deaths worldwide. With public health measures aimed at containing the spread of the disease, several countries have faced a crisis in the availability of intensive care units. Currently, a large-scale effort is underway to identify the nucleotide sequences of the SARS-CoV-2 coronavirus that is an etiological agent of COVID-19. Global sequencing of thousands of viral genomes has revealed many common genetic variants, which enables the monitoring of the evolution of SARS-CoV-2 and the tracking of its spread over time. Understanding the current evolution of SARS-CoV-2 is necessary not only for a retrospective analysis of the new coronavirus infection spread, but also for the development of approaches to the therapy and prophylaxis of COVID-19. In this review, we have focused on the general characteristics of SARS-CoV-2 and COVID-19. Also, we have analyzed available publications on the genetic diversity of the virus and the relationship between the diversity and the biological properties of SARS-CoV-2, such as virulence and contagiousness.

scholarly journals Within-patient genetic diversity of SARS-CoV-2

2020 ◽  
Author(s):  
Jack Kuipers ◽  
Aashil A Batavia ◽  
Kim Philipp Jablonski ◽  
Fritz Bayer ◽  
Nico Borgsmüller ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Genetic Variants ◽  
Large Scale ◽  
Virus Genome ◽  
Spike Gene ◽  
Medical Interventions ◽  
Consensus Sequences ◽  
The Public ◽  
Number Of Patients ◽  
The Impact

AbstractSARS-CoV-2, the virus responsible for the current COVID-19 pandemic, is evolving into different genetic variants by accumulating mutations as it spreads globally. In addition to this diversity of consensus genomes across patients, RNA viruses can also display genetic diversity within individual hosts, and co-existing viral variants may affect disease progression and the success of medical interventions. To systematically examine the intra-patient genetic diversity of SARS-CoV-2, we processed a large cohort of 3939 publicly-available deeply sequenced genomes with specialised bioinformatics software, along with 749 recently sequenced samples from Switzerland. We found that the distribution of diversity across patients and across genomic loci is very unbalanced with a minority of hosts and positions accounting for much of the diversity. For example, the D614G variant in the Spike gene, which is present in the consensus sequences of 67.4% of patients, is also highly diverse within hosts, with 29.7% of the public cohort being affected by this coexistence and exhibiting different variants. We also investigated the impact of several technical and epidemiological parameters on genetic heterogeneity and found that age, which is known to be correlated with poor disease outcomes, is a significant predictor of viral genetic diversity.Author SummarySince it arose in late 2019, the new coronavirus (SARS-CoV-2) behind the COVID-19 pandemic has mutated and evolved during its global spread. Individual patients may host different versions, or variants, of the virus, hallmarked by different mutations. We examine the diversity of genetic variants coexisting within patients across a cohort of 3939 publicly accessible samples and 749 recently sequenced samples from Switzerland. We find that a small number of patients carry most of the diversity, and that patients with more diversity tend to be older. We also find that most of the diversity is concentrated in certain regions and positions of the virus genome. In particular, we find that a variant reported to increase infectivity is among the most diverse positions. Our study provides a large-scale survey of within-patient diversity of the SARS-CoV-2 genome.

Shared genetic etiology between anxiety disorders and psychiatric and related intermediate phenotypes

2019 ◽  
Vol 50 (4) ◽  
pp. 692-704 ◽  
Author(s):  
Kazutaka Ohi ◽  
Takeshi Otowa ◽  
Mihoko Shimada ◽  
Tsukasa Sasaki ◽  
Hisashi Tanii
Keyword(s):  
Anxiety Disorders ◽  
Psychiatric Disorders ◽  
Genetic Variants ◽  
Large Scale ◽  
Genetic Correlations ◽  
Well Being ◽  
Subjective Well Being ◽  
Intermediate Phenotypes ◽  
Genome Wide ◽  
Common Genetic Variants

AbstractBackgroundPsychiatric disorders and related intermediate phenotypes are highly heritable and have a complex, overlapping polygenic architecture. A large-scale genome-wide association study (GWAS) of anxiety disorders identified genetic variants that are significant on a genome-wide. The current study investigated the genetic etiological overlaps between anxiety disorders and frequently cooccurring psychiatric disorders and intermediate phenotypes.MethodsUsing case–control and factor score models, we investigated the genetic correlations of anxiety disorders with eight psychiatric disorders and intermediate phenotypes [the volumes of seven subcortical brain regions, childhood cognition, general cognitive ability and personality traits (subjective well-being, loneliness, neuroticism and extraversion)] from large-scale GWASs (n= 7556–298 420) by linkage disequilibrium score regression.ResultsAmong psychiatric disorders, the risk of anxiety disorders was positively genetically correlated with the risks of major depressive disorder (MDD) (rg± standard error = 0.83 ± 0.16,p= 1.97 × 10−7), schizophrenia (SCZ) (0.28 ± 0.09,p= 1.10 × 10−3) and attention-deficit/hyperactivity disorder (ADHD) (0.34 ± 0.13,p= 8.40 × 10−3). Among intermediate phenotypes, significant genetic correlations existed between the risk of anxiety disorders and neuroticism (0.81 ± 0.17,p= 1.30 × 10−6), subjective well-being (−0.73 ± 0.18,p= 4.89 × 10−5), general cognitive ability (−0.23 ± 0.08,p= 4.70 × 10−3) and putamen volume (−0.50 ± 0.18,p= 5.00 × 10−3). No other significant genetic correlations between anxiety disorders and psychiatric or intermediate phenotypes were observed (p> 0.05). The case–control model yielded stronger genetic effect sizes than the factor score model.ConclusionsOur findings suggest that common genetic variants underlying the risk of anxiety disorders contribute to elevated risks of MDD, SCZ, ADHD and neuroticism and reduced quality of life, putamen volume and cognitive performance. We suggest that the comorbidity of anxiety disorders is partly explained by common genetic variants.

scholarly journals A Whole-Genome Association Approach for Large-scaled Inter-species Trait

2018 ◽  
Author(s):  
Qi Wu ◽  
Huizhong Fan ◽  
Lei Chen ◽  
Yibo Hu ◽  
Fuwen Wei
Keyword(s):  
Chromosome Number ◽  
Genetic Variants ◽  
Complex Traits ◽  
Large Scale ◽  
Association Studies ◽  
Species Traits ◽  
Genome Wide Association Studies ◽  
Dna Double Strand Breaks ◽  
Common Genetic Variants ◽  
Genome Association

AbstractGenome wide association studies (GWAS) have provided an avenue for the association between common genetic variants and complex traits. However, using SNP as a genetic marker, GWAS has been confined to detect genetic basis traits only for within species but not for the large-scale inter-species traits. Here, we propose a practical statistical approach that is using kmer frequencies as the genetic markers to associate genetic variants with large scale inter-species traits. We applied this new approach to the trait of chromosome number in 96 mammalian proteomes, and we prioritized 130 genes including TP53 and BAD, of which 6 were candidate genes. These genes were proved to be associated with cellular reaction of DNA double-strand breaks caused by chromosome fission/fusion. Our study provides a new effective genomic strategy to perform association studies for large-scaled inter-species traits, using the chromosome number as a case. We hope this approach could provide exploration for broadly widely traits.

scholarly journals Heritability of Regional Brain Volumes in Large-Scale Neuroimaging and Genetic Studies

2018 ◽  
Vol 29 (7) ◽  
pp. 2904-2914 ◽  
Author(s):  
Bingxin Zhao ◽  
Joseph G Ibrahim ◽  
Yun Li ◽  
Tengfei Li ◽  
Yue Wang ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Large Scale ◽  
Research Area ◽  
Nucleotide Polymorphisms ◽  
Uk Biobank ◽  
Volume Data ◽  
Brain Volumes ◽  
Symmetric Pattern ◽  
Regional Brain ◽  
Common Genetic Variants

Abstract Brain genetics is an active research area. The degree to which genetic variants impact variations in brain structure and function remains largely unknown. We examined the heritability of regional brain volumes (P ~ 100) captured by single-nucleotide polymorphisms (SNPs) in UK Biobank (n ~ 9000). We found that regional brain volumes are highly heritable in this study population and common genetic variants can explain up to 80% of their variabilities (median heritability 34.8%). We observed omnigenic impact across the genome and examined the enrichment of SNPs in active chromatin regions. Principal components derived from regional volume data are also highly heritable, but the amount of variance in brain volume explained by the component did not seem to be related to its heritability. Heritability estimates vary substantially across large-scale functional networks, exhibit a symmetric pattern across left and right hemispheres, and are consistent in females and males (correlation = 0.638). We repeated the main analysis in Alzheimer’s Disease Neuroimaging Initiative (n ~ 1100), Philadelphia Neurodevelopmental Cohort (n ~ 600), and Pediatric Imaging, Neurocognition, and Genetics (n ~ 500) datasets, which demonstrated that more stable estimates can be obtained from the UK Biobank.

scholarly journals Genetic Overlap between General Cognitive Function and Schizophrenia: A Review of Cognitive GWASs

2018 ◽  
Vol 19 (12) ◽  
pp. 3822 ◽  
Author(s):  
Kazutaka Ohi ◽  
Chika Sumiyoshi ◽  
Haruo Fujino ◽  
Yuka Yasuda ◽  
Hidenaga Yamamori ◽  
...  
Keyword(s):  
Cognitive Function ◽  
Genetic Variants ◽  
Large Scale ◽  
Molecular Mechanisms ◽  
Association Studies ◽  
Cognitive Impairments ◽  
Treatment Strategies ◽  
Genome Wide Association Studies ◽  
Common Genetic Variants ◽  
Health Related

General cognitive (intelligence) function is substantially heritable, and is a major determinant of economic and health-related life outcomes. Cognitive impairments and intelligence decline are core features of schizophrenia which are evident before the onset of the illness. Genetic overlaps between cognitive impairments and the vulnerability for the illness have been suggested. Here, we review the literature on recent large-scale genome-wide association studies (GWASs) of general cognitive function and correlations between cognitive function and genetic susceptibility to schizophrenia. In the last decade, large-scale GWASs (n > 30,000) of general cognitive function and schizophrenia have demonstrated that substantial proportions of the heritability of the cognitive function and schizophrenia are explained by a polygenic component consisting of many common genetic variants with small effects. To date, GWASs have identified more than 100 loci linked to general cognitive function and 108 loci linked to schizophrenia. These genetic variants are mostly intronic or intergenic. Genes identified around these genetic variants are densely expressed in brain tissues. Schizophrenia-related genetic risks are consistently correlated with lower general cognitive function (rg = −0.20) and higher educational attainment (rg = 0.08). Cognitive functions are associated with many of the socioeconomic and health-related outcomes. Current treatment strategies largely fail to improve cognitive impairments of schizophrenia. Therefore, further study is needed to understand the molecular mechanisms underlying both cognition and schizophrenia.

scholarly journals Common genetic variation influencing human white matter microstructure

2020 ◽  
Author(s):  
Bingxin Zhao ◽  
Tengfei Li ◽  
Yue Yang ◽  
Xifeng Wang ◽  
Tianyou Luo ◽  
...  
Keyword(s):  
White Matter ◽  
Genetic Variants ◽  
Complex Traits ◽  
Large Scale ◽  
Genetic Correlations ◽  
Neuropsychiatric Disorders ◽  
Regulatory Elements ◽  
Functional Principal Component Analysis ◽  
White Matter Microstructure ◽  
Common Genetic Variants

AbstractBrain regions communicate with each other via tracts of myelinated axons, commonly referred to as white matter. White matter microstructure can be measured in the living human brain using diffusion based magnetic resonance imaging (dMRI), and has been found to be altered in patients with neuropsychiatric disorders. Although under strong genetic control, few genetic variants influencing white matter microstructure have ever been identified. Here we identified common genetic variants influencing white matter microstructure using dMRI in 42,919 individuals (35,741 in the UK Biobank). The dMRIs were summarized into 215 white matter microstructure traits, including 105 measures from tract-specific functional principal component analysis. Genome-wide association analysis identified many novel white matter microstructure associated loci (P < 2.3 × 10−10). We identified shared genetic influences through genetic correlations between white matter tracts and 62 other complex traits, including stroke, neuropsychiatric disorders (e.g., ADHD, bipolar disorder, major depressive disorder, schizophrenia), cognition, neuroticism, chronotype, as well as non-brain traits. Common variants associated with white matter microstructure alter the function of regulatory elements in glial cells, particularly oligodendrocytes. White matter associated genes were enriched in pathways involved in brain disease pathogenesis, neurodevelopment process, and repair of white matter damage (P < 1.5 × 10−8). In summary, this large-scale tract-specific study provides a big step forward in understanding the genetic architecture of white matter and its genetic links to a wide spectrum of clinical outcomes.

scholarly journals Enterovirus D68: molecular biological characteristics, features of infection

MediAl ◽  
2019 ◽  
pp. 40-54
Author(s):  
V. V. Zverev ◽  
N. A. Novikova
Keyword(s):  
Genetic Diversity ◽  
Respiratory Tract ◽  
Large Scale ◽  
Clinical Manifestations ◽  
The United States ◽  
Biological Properties ◽  
Steady Increase ◽  
Acid Sensitivity ◽  
Human Pathology ◽  
Wide Range

Human enteroviruses (genus Enterovirus, family Picornaviridae) are infectious agents characterized by a wide range of clinical manifestations. EV-D68, associated with respiratory and neurological diseases, plays a significant role in human pathology. The virus was discovered in 1962 and has long been detected only sporadically, but since the late 2000s there has been a steady increase in cases of detection of the virus in different countries of the world. A large-scale outbreak of EV-D68 infection occurred in the United States in 2014. The virus is characterized by unique biological properties, combining the characteristics of enteroviruses and rhinoviruses, has a significant genetic diversity and is currently represented by strains of four main phylogenetic lines. Due to the acid sensitivity, the main place of virus replication are epithelial cells of the respiratory tract. EV-D68 causes mainly pathology of the upper and lower respiratory tract of varying severity, but there are numerous data on the connection of the virus with the occurrence of acute flaccid paralysis and exacerbations of asthma. The risk groups for the disease EV-D68 infection are different age groups of the population, mainly young children. The analytical review provides information on the taxonomic position and classification history, the structural structure of the virion and genome, and the genetic diversity of the virus. Much of the material is devoted to clinical and epidemiological aspects of infection. The issues of the current state of specific prevention and therapy of EV-D68 infection are highlighted. Information on approaches and methods of virus identification is given.

scholarly journals Common genetic variants and health outcomes appear geographically structured in the UK Biobank sample: Old concerns returning and their implications

2018 ◽  
Author(s):  
Simon Haworth ◽  
Ruth Mitchell ◽  
Laura Corbin ◽  
Kaitlin H Wade ◽  
Tom Dudding ◽  
...  
Keyword(s):  
Genetic Variants ◽  
Complex Traits ◽  
Large Scale ◽  
Genetic Data ◽  
Population Based ◽  
Risk Scores ◽  
Phenotypic Variance ◽  
Uk Biobank ◽  
Common Genetic Variants ◽  
The Uk

Introductory paragraphThe inclusion of genetic data in large studies has enabled the discovery of genetic contributions to complex traits and their application in applied analyses including those using genetic risk scores (GRS) for the prediction of phenotypic variance. If genotypes show structure by location and coincident structure exists for the trait of interest, analyses can be biased. Having illustrated structure in an apparently homogeneous collection, we aimed to a) test for geographical stratification of genotypes in UK Biobank and b) assess whether stratification might induce bias in genetic association analysis.We found that single genetic variants are associated with birth location within UK Biobank and that geographic structure in genetic data could not be accounted for using routine adjustment for study centre and principal components (PCs) derived from genotype data. We found that GRS for complex traits do appear geographically structured and analysis using GRS can yield biased associations. We discuss the likely origins of these observations and potential implications for analysis within large-scale population based genetic studies.

Genetic Variation: Impact on Folate (and Choline) Bioefficacy

2010 ◽  
Vol 80 (45) ◽  
pp. 319-329 ◽  
Author(s):  
Allyson A. West ◽  
Marie A. Caudill
Keyword(s):  
Carbon Metabolism ◽  
Genetic Variants ◽  
Plasma Homocysteine ◽  
Water Soluble ◽  
Gene Interactions ◽  
Dietary Folate ◽  
Methyl Donors ◽  
Common Genetic Variants ◽  
One Carbon Metabolism ◽  
The Impact

Folate and choline are water-soluble micronutrients that serve as methyl donors in the conversion of homocysteine to methionine. Inadequacy of these nutrients can disturb one-carbon metabolism as evidenced by alterations in circulating folate and/or plasma homocysteine. Among common genetic variants that reside in genes regulating folate absorptive and metabolic processes, homozygosity for the MTHFR 677C > T variant has consistently been shown to have robust effects on status markers. This paper will review the impact of genetic variants in folate-metabolizing genes on folate and choline bioefficacy. Nutrient-gene and gene-gene interactions will be considered along with the need to account for these genetic variants when updating dietary folate and choline recommendations.

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