scholarly journals Estimated Spike Evolution and Impact of Emerging SARS-CoV-2 Variants

2021 ◽  
Author(s):  
Yong Lu ◽  
Kun Han ◽  
Gang Xue ◽  
Ningbo Zheng ◽  
Guangxu Jin
Keyword(s):  
Selection Pressure ◽  
Mutation Rates ◽  
Future Trends ◽  
New Wave ◽  
Virus Population ◽  
Supportive Evidence ◽  
Accelerated Evolution ◽  
Genomic Location ◽  
Rate Selection ◽  
Statistic Result

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the virus that causes COVID-19, has been mutating and thus variants emerged. This suggests that SARS-CoV-2 could mutate at an unsteady pace. Supportive evidence comes from the accelerated evolution which was revealed by tracking mutation rates of the genomic location of Spike protein. This process is sponsored by a small portion of the virus population but not the largest viral clades. Moreover, it generally took one to six months for current variants that caused peaks of COVID-19 cases and deaths to survive selection pressure. Based on this statistic result and the above speedy Spike evolution, another upcoming peak would come around July 2021 and disastrously attack Africa, Asia, Europe, and North America. This is the prediction generated by a mathematical model on evolutionary spread. The reliability of this model and future trends out of it comes from the comprehensive consideration of factors mainly including mutation rate, selection course, and spreading speed. Notably, if the prophecy is true, then the new wave will be the first determined by accelerated Spike evolution.

scholarly journals Metagenomic analyses and genetic diversity of Tomato leaf curl Arusha virus affecting tomato plants in Kenya

2021 ◽  
Vol 18 (1) ◽  
Author(s):  
Edith Khamonya Avedi ◽  
Adedapo Olutola Adediji ◽  
Dora Chao Kilalo ◽  
Florence Mmogi Olubayo ◽  
Isaac Macharia ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Selection Pressure ◽  
Management Strategies ◽  
Purifying Selection ◽  
Tomato Leaf ◽  
Amino Acid Sequences ◽  
Virus Population ◽  
Tomato Production ◽  
Tomato Leaf Curl ◽  
Leaf Curl

Abstract Background Tomato production is threatened worldwide by the occurrence of begomoviruses which are associated with tomato leaf curl diseases. There is little information on the molecular properties of tomato begomoviruses in Kenya, hence we investigated the population and genetic diversity of begomoviruses associated with tomato leaf curl in Kenya. Methods Tomato leaf samples with virus-like symptoms were obtained from farmers’ field across the country in 2018 and Illumina sequencing undertaken to determine the genetic diversity of associated begomoviruses. Additionally, the occurrence of selection pressure and recombinant isolates within the population were also evaluated. Results Twelve complete begomovirus genomes were obtained from our samples with an average coverage of 99.9%. The sequences showed 95.7–99.7% identity among each other and 95.9–98.9% similarities with a Tomato leaf curl virus Arusha virus (ToLCArV) isolate from Tanzania. Analysis of amino acid sequences showed the highest identities in the regions coding for the coat protein gene (98.5–100%) within the isolates, and 97.1–100% identity with the C4 gene of ToLCArV. Phylogenetic algorithms clustered all Kenyan isolates in the same clades with ToLCArV, thus confirming the isolates to be a variant of the virus. There was no evidence of recombination within our isolates. Estimation of selection pressure within the virus population revealed the occurrence of negative or purifying selection in five out of the six coding regions of the sequences. Conclusions The begomovirus associated with tomato leaf curl diseases of tomato in Kenya is a variant of ToLCArV, possibly originating from Tanzania. There is low genetic diversity within the virus population and this information is useful in the development of appropriate management strategies for the disease in the country.

Error Thresholds in Genetic Algorithms

2006 ◽  
Vol 14 (2) ◽  
pp. 157-182 ◽  
Author(s):  
Gabriela Ochoa
Keyword(s):  
Genetic Algorithms ◽  
Selection Pressure ◽  
Evolutionary Process ◽  
Critical Value ◽  
Mutation Rates ◽  
Genomic Information ◽  
Quasispecies Model ◽  
Error Catastrophe ◽  
Important Notion ◽  
Quasispecies Evolution

The error threshold of replication is an important notion in the quasispecies evolution model; it is a critical mutation rate (error rate) beyond which structures obtained by an evolutionary process are destroyed more frequently than selection can reproduce them. With mutation rates above this critical value, an error catastrophe occurs and the genomic information is irretrievably lost. Therefore, studying the factors that alter this magnitude has important implications in the study of evolution. Here we use a genetic algorithm, instead of the quasispecies model, as the underlying model of evolution, and explore whether the phenomenon of error thresholds is found on finite populations of bit strings evolving on complex landscapes. Our empirical results verify the occurrence of error thresholds in genetic algorithms. In this way, this notion is brought from molecular evolution to evolutionary computation. We also study the effect of modifying the most prominent evolutionary parameters on the magnitude of this critical value, and found that error thresholds depend mainly on the selection pressure and genotype length.

Following the very initial growth of biological RNA viral clones

2005 ◽  
Vol 86 (2) ◽  
pp. 435-443 ◽  
Author(s):  
José M. Cuevas ◽  
Andrés Moya ◽  
Rafael Sanjuán
Keyword(s):  
Environmental Changes ◽  
Rna Virus ◽  
Growth Dynamics ◽  
Direct Consequence ◽  
Mutation Rates ◽  
Initial Growth ◽  
Virus Population ◽  
High Genetic Diversity ◽  
Viral Yield ◽  
Fitness Parameters

Due to their extremely high genetic diversity, which is a direct consequence of high mutation rates, RNA viruses are often described as molecular quasispecies. According to this theory, RNA virus populations cannot be understood in terms of individual viral clones, as they are clouds of interconnected mutants, but this prediction has not yet been demonstrated experimentally. The goal of this study was to determine the fitness of individual clones sampled from a given RNA virus population, a necessary previous step to test the above prediction. To do so, limiting dilutions of a vesicular stomatitis virus population were employed to isolate single viral clones and their initial growth dynamics were followed, corresponding to the release of the first few hundred viral particles. This technique is useful for estimating basic fitness parameters, such as intracellular growth rate, viral yield per cell, rate at which cells are infected and time spent in cell-to-cell transmission. A combination of these parameters allows estimation of the fitness of individual clones, which seems to be determined mainly by their ability to complete infection cycles more quickly. Interestingly, fitness was systematically higher for initial clones than for their derived populations. In addition to environmental changes, such as cellular defence mechanisms, these differences are attributable to high RNA virus mutation rates.

THE EVOLUTIONARY ADVANTAGE OF BREEDING FOR TOLERANCE OVER RESISTANCE AGAINST VIRAL PLANT DISEASE

1999 ◽  
Vol 47 (3) ◽  
pp. 135-139 ◽  
Author(s):  
Raffi Salomon
Keyword(s):  
Virus Infection ◽  
Selection Pressure ◽  
Virus Population ◽  
Long Run ◽  
Virulent Type ◽  
Evolutionary Advantage ◽  
Virulent Virus ◽  
Large Virus ◽  
Minimal Damage ◽  
Virus Mutant

A tolerant strain of a crop permits the propagation of an entire virus population, thus exerting a much lower selection pressure in favor of a virus mutant overcoming resistance. One may suppose that a tolerant crop may build up a large virus reservoir and therefore increase the chance of emergence of a more virulent type. However, the tolerant crop exerts a much lower selective pressure for a given virus line, and therefore the new virulent type remains a very low proportion of the total virus population. Susceptible crops, into which resistance to a given virus was bred, may be immune to this virus infection, thus preventing the buildup of a large virus reservoir. However, other host crops around it, or wild weeds facilitate propagation of this virus. This peripheral buildup of virus reservoir in the vicinity of the resistant crop creates a strong selection pressure for the propagation of the mutants overcoming resistance. Therefore, the planting of monoculture of a resistant crop accelerates the emergence of virulent virus lines that overcome this resistance. There is no reason to assume that resistance introduced into transgenic plants will be different. In the long run, tolerant crops may have the advantage over resistant crops, preserving for a longer time conditions in which virus infection causes only minimal damage. The production of tolerance to virus infection is an approach not yet favored by breeders and seed producers. However, it may be regarded as a less expensive, additional route to reduce the damage to crops inflicted by viral diseases.

scholarly journals Metagenomic analyses and genetic diversity of Tomato leaf curl  Arusha virus affecting tomato plants in Kenya

2020 ◽  
Author(s):  
Edith Khamonya Avedi ◽  
Adedapo Olutola Adediji ◽  
Dora Chao Kilalo ◽  
Florence Mmogi Olubayo ◽  
Isaac Macharia ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Selection Pressure ◽  
Management Strategies ◽  
Purifying Selection ◽  
Tomato Leaf ◽  
Amino Acid Sequences ◽  
Virus Population ◽  
Tomato Production ◽  
Tomato Leaf Curl ◽  
Leaf Curl

Abstract Background: Tomato production is threatened worldwide by the occurrence of begomoviruses which are associated with tomato leaf curl diseases. There is little information on the molecular properties of tomato begomoviruses in Kenya, hence we investigated the population and genetic diversity of begomoviruses associated with tomato leaf curl in Kenya.Methods: Tomato leaf samples with virus-like symptoms were obtained from farmers’ field across the country in 2018 and Illumina sequencing undertaken to determine the genetic diversity of associated begomoviruses. Additionally, the occurrence of selection pressure and recombinant isolates within the population were also evaluated.Results: Twelve complete begomovirus genomes were obtained from our samples with an average coverage of 99.9%. The sequences showed 95.7-99.7% identity among each other and 95.9-98.9% similarities with a Tomato leaf curl virus Arusha virus (ToLCArV) isolate from Tanzania. Analysis of amino acid sequences showed the highest identities in the regions coding for the coat protein gene (98.5-100%) within the isolates, and 97.1-100% identity with the C4 gene of ToLCArV. Phylogenetic algorithms clustered all Kenyan isolates in the same clades with ToLCArV, thus confirming the isolates to be a variant of the virus. There was no evidence of recombination within our isolates. Estimation of selection pressure within the virus population revealed the occurrence of negative or purifying selection in 5 out of the 6 coding regions of the sequences.Conclusions: The begomovirus associated with tomato leaf curl diseases of tomato in Kenya is a variant of ToLCArV, possibly originating from Tanzania. There is low genetic diversity within the virus population and this information is useful in the development of appropriate management strategies for the disease in the country.

scholarly journals An underlying mechanism for the increased mutagenesis of lagging-strand genes inBacillus subtilis

2015 ◽  
Vol 112 (10) ◽  
pp. E1096-E1105 ◽  
Author(s):  
Samuel Million-Weaver ◽  
Ariana N. Samadpour ◽  
Daniela A. Moreno-Habel ◽  
Patrick Nugent ◽  
Mitchell J. Brittnacher ◽  
...  
Keyword(s):  
Excision Repair ◽  
Underlying Mechanism ◽  
Mutation Rates ◽  
Dependent Manner ◽  
Lesion Bypass ◽  
Dna Lesion ◽  
Accelerated Evolution ◽  
Recombination Protein ◽  
Y Family ◽  
Lagging Strand

We previously reported that lagging-strand genes accumulate mutations faster than those encoded on the leading strand inBacillus subtilis. Although we proposed that orientation-specific encounters between replication and transcription underlie this phenomenon, the mechanism leading to the increased mutagenesis of lagging-strand genes remained unknown. Here, we report that the transcription-dependent and orientation-specific differences in mutation rates of genes require theB. subtilisY-family polymerase, PolY1 (yqjH). We find that without PolY1, association of the replicative helicase, DnaC, and the recombination protein, RecA, with lagging-strand genes increases in a transcription-dependent manner. These data suggest that PolY1 promotes efficient replisome progression through lagging-strand genes, thereby reducing potentially detrimental breaks and single-stranded DNA at these loci. Y-family polymerases can alleviate potential obstacles to replisome progression by facilitating DNA lesion bypass, extension of D-loops, or excision repair. We find that the nucleotide excision repair (NER) proteins UvrA, UvrB, and UvrC, but not RecA, are required for transcription-dependent asymmetry in mutation rates of genes in the two orientations. Furthermore, we find that the transcription-coupling repair factor Mfd functions in the same pathway as PolY1 and is also required for increased mutagenesis of lagging-strand genes. Experimental and SNP analyses ofB. subtilisgenomes show mutational footprints consistent with these findings. We propose that the interplay between replication and transcription increases lesion susceptibility of, specifically, lagging-strand genes, activating an Mfd-dependent error-prone NER mechanism. We propose that this process, at least partially, underlies the accelerated evolution of lagging-strand genes.

scholarly journals Spontaneous Mutations in HIV-1 Gag, Protease, RT p66 in the First Replication Cycle and How They Appear: Insights from an In Vitro Assay on Mutation Rates and Types

2020 ◽  
Vol 22 (1) ◽  
pp. 370
Author(s):  
Joshua Yi Yeo ◽  
Darius Wen-Shuo Koh ◽  
Ping Yap ◽  
Ghin-Ray Goh ◽  
Samuel Ken-En Gan
Keyword(s):  
Codon Usage ◽  
Selection Pressure ◽  
In Vitro Selection ◽  
Mutation Rates ◽  
Free Energies ◽  
Vitro Assay ◽  
Free System ◽  
Functional Sites ◽  
Hiv 1

While drug resistant mutations in HIV-1 are largely credited to its error prone HIV-1 RT, the time point in the infection cycle that these mutations can arise and if they appear spontaneously without selection pressures both remained enigmatic. Many HIV-1 RT mutational in vitro studies utilized reporter genes (LacZ) as a template to investigate these questions, thereby not accounting for the possible contribution of viral codon usage. To address this gap, we investigated HIV-1 RT mutation rates and biases on its own Gag, protease, and RT p66 genes in an in vitro selection pressure free system. We found rare clinical mutations with a general avoidance of crucial functional sites in the background mutations rates for Gag, protease, and RT p66 at 4.71 × 10−5, 6.03 × 10−5, and 7.09 × 10−5 mutations/bp, respectively. Gag and p66 genes showed a large number of ‘A to G’ mutations. Comparisons with silently mutated p66 sequences showed an increase in mutation rates (1.88 × 10−4 mutations/bp) and that ‘A to G’ mutations occurred in regions reminiscent of ADAR neighbor sequence preferences. Mutational free energies of the ‘A to G’ mutations revealed an avoidance of destabilizing effects, with the natural p66 gene codon usage providing barriers to disruptive amino acid changes. Our study demonstrates the importance of studying mutation emergence in HIV genes in a RT-PCR in vitro selection pressure free system to understand how fast drug resistance can emerge, providing transferable applications to how new viral diseases and drug resistances can emerge.

scholarly journals Stability of Murine Cytomegalovirus Genome after In Vitro and In Vivo Passage

2009 ◽  
Vol 84 (5) ◽  
pp. 2623-2628 ◽  
Author(s):  
Tammy P. Cheng ◽  
Mark C. Valentine ◽  
Jian Gao ◽  
Jeanette T. Pingel ◽  
Wayne M. Yokoyama
Keyword(s):  
Selection Pressure ◽  
Genome Stability ◽  
Murine Cytomegalovirus ◽  
Mutation Rates ◽  
Nucleotide Level ◽  
Single Nucleotide ◽  
Dna Viruses ◽  
Single Base Pair

ABSTRACT While large DNA viruses are thought to have low mutation rates, only a small fraction of their genomes have been analyzed at the single-nucleotide level. Here, we defined the genetic stability of murine cytomegalovirus (MCMV) by whole-genome sequencing. Independently assembled sequences of three sister plaques showed only two single-base-pair substitutions after in vitro passage. In vivo-passaged MCMV likewise demonstrated low mutation rates, comparable to those after in vitro passage, indicating high genome stability of MCMV at the single-nucleotide level in the absence of obvious selection pressure.

scholarly journals NICHE EXPANSION IN BACTERIA: CAN INFECTIOUS GENE EXCHANGE AFFECT THE RATE OF EVOLUTION?

Genetics ◽  
1986 ◽  
Vol 113 (3) ◽  
pp. 775-795
Author(s):  
Ralph Evans
Keyword(s):  
Gene Transfer ◽  
Natural Populations ◽  
Mutation Rates ◽  
Gene Exchange ◽  
Growth Inhibitors ◽  
Triple Mutant ◽  
Accelerated Evolution ◽  
Evolution Of Resistance ◽  
Selection For ◽  
Accelerate Evolution

ABSTRACT Recombination occurs by infectious gene transfer in bacteria, at rates much lower than recombination by sexual reproduction in other organisms. Thus, recombination may accelerate evolution in bacteria only under restricted conditions, such as occur when mutations at several loci are required for the evolution of an expanded ecological niche. Mathematical ("chemostat") models of several such cases—evolution of independence from three limiting essential or "interactive-essential" resources; evolution of the ability to use three new substitutable resources; and evolution of resistance to three growth inhibitors—were analyzed by computer simulation. All combinations of three mutation rates (U) and four values for the "infectious gene transfer rate parameter" (χ) were considered. Recombination accelerated evolution most when U was low and χ was high, but was unlikely to have large effects when χ was low enough to be realistic for natural populations of Escherichia coli. Recombination had the largest effects when resources were substitutable, and in that case could have substantially reduced the chance of random loss of the favored "triple mutant" while it was still rare. The simulations also revealed some interesting features of selection for an expanded niche. Evolution of independence from essential resources occurred more rapidly when the resources were weakly complementary than when they did not interact. Selection for the ability to use all substitutable resources was weak after all intermediate types that used only one or two of the resources had arisen.

scholarly journals (Sör) Forradalmi helyzetkép: Gyümölcsös sörök a magyar sörpiacon

2019 ◽  
Vol 13 (2) ◽  
pp. 9-18
Author(s):  
Anita Major
Keyword(s):  
Scientific Research ◽  
Future Trends ◽  
New Wave ◽  
The Usa ◽  
Craft Beers

„Beer revolution” started in the USa during the years after the economical crisis, which reached hungary in the the last few years as well. Thanks to this gastrotrend, the already wide choice of beer was increased further by numerous so called new-wave beers. among these special – mainly craft beers – several fruity beers and fruit flavoured beers appeared on the hungarian beer market, too. a comprehensive scientific research and review of their role and weight, furthermore the consumers’ opinion about them on the hungarian beer sector has not happened up till now, however it could be useful to consider the expected changes in future trends, which would result in an increase of these beer products’ meaning on the prospective beer market in hungary.

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