scholarly journals SARS-CoV-2 Entry Related Viral and Host Genetic Variations: Implications on COVID-19 Severity, Immune Escape, and Infectivity

2021 ◽  
Vol 22 (6) ◽  
pp. 3060
Author(s):  
Szu-Wei Huang ◽  
Sheng-Fan Wang
Keyword(s):  
Genetic Variation ◽  
Immune Escape ◽  
Driving Forces ◽  
Viral Evolution ◽  
Genetic Variations ◽  
Intercellular Adhesion Molecule ◽  
Human Populations ◽  
Host Proteins ◽  
Risk Variants ◽  
Geographical Regions

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has evolved to display particular patterns of genetic diversity in the genome across geographical regions. These variations in the virus and genetic variation in human populations can determine virus transmissibility and coronavirus disease 2019 (COVID-19) severity. Genetic variations and immune differences in human populations could be the driving forces in viral evolution. Recently emerged SARS-CoV-2 variants show several mutations at the receptor binding domain in the spike (S) glycoprotein and contribute to immune escape and enhanced binding with angiotensin 1-converting enzyme 2 (ACE2). Since ACE2 and transmembrane protease serine 2 (TMPRSS2) play important roles in SARS-CoV-2 entry into the cell, genetic variation in these host entry-related proteins may be a driving force for positive selection in the SARS-CoV-2 S glycoprotein. Dendritic or liver/lymph cell-specific intercellular adhesion molecule (ICAM)-3-grabbing non-integrin is also known to play vital roles in several pathogens. Genetic variations of these host proteins may affect the susceptibility to SARS-CoV-2. This review summarizes the latest research to describe the impacts of genetic variation in the viral S glycoprotein and critical host proteins and aims to provide better insights for understanding transmission and pathogenesis and more broadly for developing vaccine/antiviral drugs and precision medicine strategies, especially for high risk populations with genetic risk variants.

scholarly journals Insights into human genetic variation and population history from 929 diverse genomes

2019 ◽  
Author(s):  
Anders Bergström ◽  
Shane A. McCarthy ◽  
Ruoyun Hui ◽  
Mohamed A. Almarri ◽  
Qasim Ayub ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Central Africa ◽  
Population History ◽  
Human Populations ◽  
Genome Sequences ◽  
High Coverage ◽  
Geographical Regions ◽  
History Of ◽  
Different Populations ◽  
Source Populations

AbstractGenome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented private genetic variation in southern and central Africa and in Oceania and the Americas, but an absence of fixed, private variants between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the last 10,000 years, a potentially major population growth episode after the peopling of the Americas, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations. We also demonstrate benefits to the study of population relationships of genome sequences over ascertained array genotypes. These genome sequences are freely available as a resource with no access or analysis restrictions.

scholarly journals Insights into human genetic variation and population history from 929 diverse genomes

Science ◽  
2020 ◽  
Vol 367 (6484) ◽  
pp. eaay5012 ◽  
Author(s):  
Anders Bergström ◽  
Shane A. McCarthy ◽  
Ruoyun Hui ◽  
Mohamed A. Almarri ◽  
Qasim Ayub ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Central Africa ◽  
Population History ◽  
Human Populations ◽  
Genome Sequences ◽  
High Coverage ◽  
Geographical Regions ◽  
History Of ◽  
Different Populations ◽  
Source Populations

Genome sequences from diverse human groups are needed to understand the structure of genetic variation in our species and the history of, and relationships between, different populations. We present 929 high-coverage genome sequences from 54 diverse human populations, 26 of which are physically phased using linked-read sequencing. Analyses of these genomes reveal an excess of previously undocumented common genetic variation private to southern Africa, central Africa, Oceania, and the Americas, but an absence of such variants fixed between major geographical regions. We also find deep and gradual population separations within Africa, contrasting population size histories between hunter-gatherer and agriculturalist groups in the past 10,000 years, and a contrast between single Neanderthal but multiple Denisovan source populations contributing to present-day human populations.

scholarly journals Different historical generation intervals in human populations inferred from Neanderthal fragment lengths and patterns of mutation accumulation

2021 ◽  
Author(s):  
Moisès Coll Macià ◽  
Laurits Skov ◽  
Benjamin Marco Peter ◽  
Mikkel Heide Schierup
Keyword(s):  
Fragment Length ◽  
Human Populations ◽  
Female Age ◽  
Generation Interval ◽  
The Past ◽  
Geographical Regions ◽  
Neanderthal Admixture ◽  
Rate Of Decay ◽  
Out Of Africa ◽  
Insight Into

AbstractAfter the main out-of-Africa event, humans interbred with Neanderthals leaving 1-2% of Neanderthal DNA scattered in small fragments in all non-African genomes today1,2. Here we investigate the size distribution of these fragments in non-African genomes3. We find consistent differences in fragment length distributions across Eurasia with 11% longer fragments in East Asians than in West Eurasians. By comparing extant populations and ancient samples, we show that these differences are due to a different rate of decay in length by recombination since the Neanderthal admixture. In line with this, we observe a strong correlation between the average fragment length and the accumulation of derived mutations, similar to what is expected by changing the ages at reproduction as estimated from trio studies4. Altogether, our results suggest consistent differences in the generation interval across Eurasia, by up to 20% (e.g. 25 versus 30 years), over the past 40,000 years. We use sex-specific accumulations of derived alleles to infer how these changes in generation intervals between geographical regions could have been mainly driven by shifts in either male or female age of reproduction, or both. We also find that previously reported variation in the mutational spectrum5 may be largely explained by changes to the generation interval and not by changes to the underlying mutational mechanism. We conclude that Neanderthal fragment lengths provide unique insight into differences of a key demographic parameter among human populations over the recent history.

scholarly journals RR:C19 Editorial: Immune Escape and Viral Evolution

2021 ◽  
Author(s):  
Gina Borgo ◽  
Yash S. Huilgol ◽  
Michael Cronce ◽  
Stefano M. Bertozzi
Keyword(s):  
Immune Escape ◽  
Viral Evolution

scholarly journals Genomic and demographic processes differentially influence genetic variation across the X chromosome

2021 ◽  
Author(s):  
Daniel J. Cotter ◽  
Timothy H. Webster ◽  
Melissa A. Wilson
Keyword(s):  
Genetic Diversity ◽  
Genetic Variation ◽  
Linkage Disequilibrium ◽  
X Chromosome ◽  
Global Scale ◽  
Careful Consideration ◽  
Human Populations ◽  
Evolutionary Forces ◽  
Ideal System ◽  
Demographic Patterns

AbstractMutation, recombination, selection, and demography affect genetic variation across the genome. Increased mutation and recombination both lead to increases in genetic diversity in a region-specific manner, while complex demographic patterns shape patterns of diversity on a more global scale. The X chromosome is particularly interesting because it contains several distinct regions that are subject to different combinations and strengths of these processes, notably the pseudoautosomal regions (PARs) and the X-transposed region (XTR). The X chromosome thus can serve as a unique model for studying how genetic and demographic forces act in different contexts to shape patterns of observed variation. Here we investigate diversity, divergence, and linkage disequilibrium in each region of the X chromosome using genomic data from 26 human populations. We find that both diversity and substitution rate are consistently elevated in PAR1 and the XTR compared to the rest of the X chromosome. In contrast, linkage disequilibrium is lowest in PAR1 and highest on the non-recombining X chromosome, with the XTR falling in between, suggesting that the XTR (usually included in the non-recombining X) may need to be considered separately in future studies. We also observed strong population-specific effects on genetic diversity; not only does genetic variation differ on the X and autosomes among populations, but the effects of linked selection on the X relative to autosomes have been shaped by population-specific history. The substantial variation in patterns of variation across these regions provides insight into the unique evolutionary history contained within the X chromosome.Significance StatementDemography and selection affect the X chromosome differently from non-sex chromosomes. However, the X chromosome can be subdivided into multiple distinct regions that facilitate even more fine-scaled assessment of these processes. Here we study regions of the human X chromosome in 26 populations to find evidence that recombination may be mutagenic in humans and that the X-transposed region may undergo recombination. Further we observe that the effects of selection and demography act differently on the X chromosome relative to the autosomes across human populations. Together, our results highlight profound regional differences across the X chromosome, simultaneously making it an ideal system for exploring the action of evolutionary forces as well as necessitating its careful consideration and treatment in genomic analyses.

scholarly journals Resequencing of 1,143 indica rice accessions reveals important genetic variations and different heterosis patterns

2020 ◽  
Vol 11 (1) ◽  
Author(s):  
Qiming Lv ◽  
Weiguo Li ◽  
Zhizhong Sun ◽  
Ning Ouyang ◽  
Xin Jing ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Hybrid Rice ◽  
Indica Rice ◽  
Genetic Variations ◽  
Hybrid Breeding ◽  
Rice Grain ◽  
Kinship Analysis ◽  
Cadmium Absorption ◽  
Hybrid Lines ◽  
Rice Genetic

Abstract Obtaining genetic variation information from indica rice hybrid parents and identification of loci associated with heterosis are important for hybrid rice breeding. Here, we resequence 1,143 indica accessions mostly selected from the parents of superior hybrid rice cultivars of China, identify genetic variations, and perform kinship analysis. We find different hybrid rice crossing patterns between 3- and 2-line superior hybrid lines. By calculating frequencies of parental variation differences (FPVDs), a more direct approach for studying rice heterosis, we identify loci that are linked to heterosis, which include 98 in superior 3-line hybrids and 36 in superior 2-line hybrids. As a proof of concept, we find two accessions harboring a deletion in OsNramp5, a previously reported gene functioning in cadmium absorption, which can be used to mitigate rice grain cadmium levels through hybrid breeding. Resource of indica rice genetic variation reported in this study will be valuable to geneticists and breeders.

scholarly journals Predicting Adaptive Genetic Variation of Loblolly Pine (Pinus taeda L.) Populations Under Projected Future Climates Based on Multivariate Models

2019 ◽  
Vol 110 (7) ◽  
pp. 857-865 ◽  
Author(s):  
Mengmeng Lu ◽  
Konstantin V Krutovsky ◽  
Carol A Loopstra
Keyword(s):  
Climate Change ◽  
South Carolina ◽  
Genetic Variation ◽  
Loblolly Pine ◽  
Greenhouse Gas Emission ◽  
Isolation By Distance ◽  
Adaptive Genetic Variation ◽  
Climate Conditions ◽  
Geographical Regions ◽  
Bioclimatic Variables

Abstract Greenhouse gas emission and global warming are likely to cause rapid climate change within the natural range of loblolly pine over the next few decades, thus bringing uncertainty to their adaptation to the environment. Here, we studied adaptive genetic variation of loblolly pine and correlated genetic variation with bioclimatic variables using multivariate modeling methods—Redundancy Analysis, Generalized Dissimilarity Modeling, and Gradient Forests. Studied trees (N = 299) were originally sampled from their native range across eight states on the east side of the Mississippi River. Genetic variation was calculated using a total of 44,317 single-nucleotide polymorphisms acquired by exome target sequencing. The fitted models were used to predict the adaptive genetic variation on a large spatial and temporal scale. We observed east-to-west spatial genetic variation across the range, which presented evidence of isolation by distance. Different key factors drive adaptation of loblolly pine from different geographical regions. Trees residing near the northeastern edge of the range, spanning across Delaware and Maryland and mountainous areas of  Virginia, North Carolina, South Carolina, and northern Georgia, were identified to be most likely impacted by climate change based on the large difference in genetic composition under current and future climate conditions. This study provides new perspectives on adaptive genetic variation of loblolly pine in response to different climate scenarios, and the results can be used to target particular populations while developing adaptive forest management guidelines.

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