scholarly journals Estimating the strength of selection for new SARS-CoV-2 variants

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Christiaan H. van Dorp ◽  
Emma E. Goldberg ◽  
Nick Hengartner ◽  
Ruian Ke ◽  
Ethan O. Romero-Severson
Keyword(s):  
Molecular Epidemiology ◽  
Selective Advantage ◽  
Global Perspective ◽  
Detailed Model ◽  
Strong Selection ◽  
Time Horizons ◽  
New Variant ◽  
Selection For ◽  
Global Threat ◽  
Substantial Heterogeneity

AbstractControlling the SARS-CoV-2 pandemic becomes increasingly challenging as the virus adapts to human hosts through the continual emergence of more transmissible variants. Simply observing that a variant is increasing in frequency is relatively straightforward, but more sophisticated methodology is needed to determine whether a new variant is a global threat and the magnitude of its selective advantage. We present two models for quantifying the strength of selection for new and emerging variants of SARS-CoV-2 relative to the background of contemporaneous variants. These methods range from a detailed model of dynamics within one country to a broad analysis across all countries, and they include alternative explanations such as migration and drift. We find evidence for strong selection favoring the D614G spike mutation and B.1.1.7 (Alpha), weaker selection favoring B.1.351 (Beta), and no advantage of R.1 after it spreads beyond Japan. Cutting back data to earlier time horizons reveals that uncertainty is large very soon after emergence, but that estimates of selection stabilize after several weeks. Our results also show substantial heterogeneity among countries, demonstrating the need for a truly global perspective on the molecular epidemiology of SARS-CoV-2.

scholarly journals Estimating the strength of selection for new SARS-CoV-2 variants

2021 ◽  
Author(s):  
Christiaan H van Dorp ◽  
Emma E Goldberg ◽  
Nicolas Hengartner ◽  
Ruian Ke ◽  
Ethan Obie Romero-Severson
Keyword(s):  
Molecular Epidemiology ◽  
Type Strain ◽  
Wild Type Strain ◽  
Sequence Data ◽  
Relative Magnitude ◽  
Global Perspective ◽  
Wild Type ◽  
Country Level ◽  
Selection For ◽  
Selection Of

A challenge to controlling the SARS-CoV-2 pandemic is the ability of the virus to adapt to its new human hosts, with novel and more transmissible strains of the virus being continually identified. Yet there are no generally accepted methods to consistently estimate the relative magnitude of the change in transmissiblity of newly emerging variants. In this paper we consider three methods for examining and quantifying positive selection of new and emerging strains of SARS-CoV-2 over an existing wild-type strain. We consider replication at the level of countries and allow for the action of other processes that can change variants' frequencies, specifically migration and drift. We apply these methods to the D614G spike mutation and the variant designated B.1.1.7, in every country where there is sufficient sequence data. For each of D614G and B.1.1.7, we find evidence for strong selection (greater than 25% increased contagiousness) in more than half of countries analyzed. Our results also shows that the selective advantages of these strains are highly heterogeneous at the country level, suggesting the need for a truly global perspective on the molecular epidemiology of SARS-CoV-2.

scholarly journals Thinking Globally, Acting Locally: Distantly Supervised Global-to-Local Knowledge Selection for Background Based Conversation

2020 ◽  
Vol 34 (05) ◽  
pp. 8697-8704
Author(s):  
Pengjie Ren ◽  
Zhumin Chen ◽  
Christof Monz ◽  
Jun Ma ◽  
Maarten De Rijke
Keyword(s):  
Local Knowledge ◽  
State Of The Art ◽  
Background Knowledge ◽  
Global Perspective ◽  
Conversational Context ◽  
Human Evaluation ◽  
Text Fragment ◽  
Selection For ◽  
High Degree ◽  
Transition Vector

Background Based Conversation (BBCs) have been introduced to help conversational systems avoid generating overly generic responses. In a BBC, the conversation is grounded in a knowledge source. A key challenge in BBCs is Knowledge Selection (KS): given a conversational context, try to find the appropriate background knowledge (a text fragment containing related facts or comments, etc.) based on which to generate the next response. Previous work addresses KS by employing attention and/or pointer mechanisms. These mechanisms use a local perspective, i.e., they select a token at a time based solely on the current decoding state. We argue for the adoption of a global perspective, i.e., pre-selecting some text fragments from the background knowledge that could help determine the topic of the next response. We enhance KS in BBCs by introducing a Global-to-Local Knowledge Selection (GLKS) mechanism. Given a conversational context and background knowledge, we first learn a topic transition vector to encode the most likely text fragments to be used in the next response, which is then used to guide the local KS at each decoding timestamp. In order to effectively learn the topic transition vector, we propose a distantly supervised learning schema. Experimental results show that the GLKS model significantly outperforms state-of-the-art methods in terms of both automatic and human evaluation. More importantly, GLKS achieves this without requiring any extra annotations, which demonstrates its high degree of scalability.

scholarly journals Z-Curve

2017 ◽  
Author(s):  
Ulrich Schimmack ◽  
Jerry Brunner
Keyword(s):  
Selection Bias ◽  
Statistical Power ◽  
False Negative ◽  
Simulation Studies ◽  
Replication Studies ◽  
Negative Results ◽  
False Negative Results ◽  
Selection For ◽  
Z Curve ◽  
Substantial Heterogeneity

In recent years, the replicability of original findings published in psychology journals has been questioned. A key concern is that selection for significance inflates observed effect sizes and observed power. If selection bias is severe, replication studies are unlikely to reproduce a significant result. We introduce z-curve as a new method that can estimate the average true power for sets of studies that are selected for significance. We compare this method with p-curve, which has been used for the same purpose. Simulation studies show that both methods perform well when all studies have the same power, but p-curve overestimates power if power varies across studies. Based on these findings, we recommend z-curve to estimate power for sets of studies that are heterogeneous and selected for significance. Application of z-curve to various datasets suggests that the average replicability of published results in psychology is approximately 50%, but there is substantial heterogeneity and many psychological studies remain underpowered and are likely to produce false negative results. To increase replicability and credibility of published results it is important to reduce selection bias and to increase statistical power.

A note on the voluntary intake of Andropogon gayanus hay by cattle, as affected by level of feeding

1972 ◽  
Vol 15 (1) ◽  
pp. 85-88 ◽  
Author(s):  
G. Zemmelink ◽  
R. J. Haggar ◽  
J. H. Davies
Keyword(s):  
Protein Content ◽  
Feed Intake ◽  
Linear Effect ◽  
Low Level ◽  
Strong Selection ◽  
Andropogon Gayanus ◽  
The Mean ◽  
Voluntary Intake ◽  
Selection For ◽  
White Fulani

SUMMARYUnchaffed Andropogon gayanus hays, harvested in July, September, early-October, late-October and November, and the July to November regrowth, were offered to White Fulani heifers at three levels of feeding.Animals on all hays selected for protein and the mean intake of the different hays was closely related to the protein content of the consumed forage. At the low level of feeding all animals, except those on the July hay, left more than 15% residue. Nevertheless, higher levels of feeding had a marked linear effect on feed intake. This effect was largely independent of the effect of level of feeding on the protein content of the consumed ration and was associated with a strong selection for leaves.

scholarly journals Impact of strong selection for the PrP major gene on genetic variability of four French sheep breeds (Open Access publication)

2008 ◽  
Vol 40 (6) ◽  
pp. 663
Author(s):  
Isabelle Palhiere ◽  
Mickaël Brochard ◽  
Katayoun Moazami-Goudarzi ◽  
Denis Laloë ◽  
Yves Amigues ◽  
...  
Keyword(s):  
Open Access ◽  
Genetic Variability ◽  
Major Gene ◽  
Strong Selection ◽  
Sheep Breeds ◽  
Open Access Publication ◽  
Selection For

Dynamics of Microbial Populations and Strong Selection for Cycloclasticus pugetii following the Nakhodka Oil Spill

2003 ◽  
Vol 46 (4) ◽  
pp. 442-453 ◽  
Author(s):  
A. Maruyama ◽  
H. Ishiwata ◽  
K. Kitamura ◽  
M. Sunamura ◽  
T. Fujita ◽  
...  
Keyword(s):  
Oil Spill ◽  
Microbial Populations ◽  
Strong Selection ◽  
Selection For

scholarly journals New insights on equid locomotor evolution from the lumbar region of fossil horses

2016 ◽  
Vol 283 (1829) ◽  
pp. 20152947 ◽  
Author(s):  
Katrina Elizabeth Jones
Keyword(s):  
Body Size ◽  
Adaptive Evolution ◽  
Axial Skeleton ◽  
Lumbar Region ◽  
Scaling Effects ◽  
Classic Case ◽  
Strong Selection ◽  
Selection For ◽  
Joint Shape

The specialization of equid limbs for cursoriality is a classic case of adaptive evolution, but the role of the axial skeleton in this famous transition is not well understood. Extant horses are extremely fast and efficient runners, which use a stiff-backed gallop with reduced bending of the lumbar region relative to other mammals. This study tests the hypothesis that stiff-backed running in horses evolved in response to evolutionary increases in body size by examining lumbar joint shape from a broad sample of fossil equids in a phylogenetic context. Lumbar joint shape scaling suggests that stability of the lumbar region does correlate with size through equid evolution. However, scaling effects were dampened in the posterior lumbar region, near the sacrum, which suggests strong selection for sagittal mobility in association with locomotor–respiratory coupling near the lumbosacral joint. I hypothesize that small-bodied fossil horses may have used a speed-dependent running gait, switching between stiff-backed and flex-backed galloping as speed increased.

scholarly journals Clonal yeast biofilms can reap competitive advantages through cell differentiation without being obligatorily multicellular

2016 ◽  
Vol 283 (1842) ◽  
pp. 20161303 ◽  
Author(s):  
Birgitte Regenberg ◽  
Kristian Ebbesen Hanghøj ◽  
Kaj Scherz Andersen ◽  
Jacobus J. Boomsma
Keyword(s):  
Cell Differentiation ◽  
Single Gene ◽  
Cell Types ◽  
Selective Advantage ◽  
Division Of Labour ◽  
Competitive Advantages ◽  
Epigenetic Switch ◽  
Organizational Complexity ◽  
Switch Mechanism ◽  
Selection For

How differentiation between cell types evolved is a fundamental question in biology, but few studies have explored single-gene phenotypes that mediate first steps towards division of labour with selective advantage for groups of cells. Here, we show that differential expression of the FLO11 gene produces stable fractions of Flo11 + and Flo11 − cells in clonal Saccharomyces cerevisiae biofilm colonies on medium with intermediate viscosity. Differentiated Flo11 +/− colonies, consisting of adhesive and non-adhesive cells, obtain a fourfold growth advantage over undifferentiated colonies by overgrowing glucose resources before depleting them, rather than depleting them while they grow as undifferentiated Flo11 − colonies do. Flo11 +/− colonies maintain their structure and differentiated state by switching non-adhesive cells to adhesive cells with predictable probability. Mixtures of Flo11 + and Flo11 − cells from mutant strains that are unable to use this epigenetic switch mechanism produced neither integrated colonies nor growth advantages, so the condition-dependent selective advantages of differentiated FLO11 expression can only be reaped by clone-mate cells. Our results show that selection for cell differentiation in clonal eukaryotes can evolve before the establishment of obligate undifferentiated multicellularity, and without necessarily leading to more advanced organizational complexity.

scholarly journals Typing of Neisseria gonorrhoeae Isolates in Shenzhen, China, from 2014 to 2018 Reveals the Shift of Genotypes Significantly Associated with Antimicrobial Resistance

2021 ◽  
Vol 65 (5) ◽  
Author(s):  
Yizhun Li ◽  
Yamei Li ◽  
Leshan Xiu ◽  
Yaling Zeng ◽  
Chi Zhang ◽  
...  
Keyword(s):  
Logistic Regression ◽  
Antimicrobial Resistance ◽  
Neisseria Gonorrhoeae ◽  
Molecular Epidemiology ◽  
Important Data ◽  
Content Type ◽  
Future Studies ◽  
Ideal Tool ◽  
Global Threat ◽  
Sequence Types

ABSTRACT The growing antimicrobial resistance (AMR) in Neisseria gonorrhoeae is a serious global threat to gonococcal therapy. Molecular typing is an ideal tool to reveal the association between specific genotypes and resistance phenotypes that provide effective data for tracking the transmission of resistant clones of N. gonorrhoeae. In our study, we aimed to describe the molecular epidemiology of AMR and the distribution of resistance-associated genotypes in Shenzhen, China, during 2014 to 2018. In total, 909 isolates were collected from Shenzhen from 2014 to 2018. Two typing schemes, multilocus sequence typing (MLST) and N. gonorrhoeae sequence typing for antimicrobial resistance (NG-STAR), were performed for all isolates. The distribution of resistance-associated genotypes was described using goeBURST analysis combined with logistic regression data. Among 909 isolates, sequence type 8123 (ST8123), ST7363, ST1901, ST7365, and ST7360 were the most common MLST sequence types, and ST348, ST2473, ST497, and ST199 were the most prevalent NG-STAR STs. Logistic regression analysis showed that NG-STARST497, MLSTST7365, and MLSTST7360 were typically associated with decreased susceptibility to ceftriaxone. Furthermore, the internationally spreading extended-spectrum cephalosporin (ESC)-resistant clone MLSTST1901 has been prevalent since at least 2014 in Shenzhen and showed a significant increase during 2014 to 2018. Additionally, MLSTST7363 owns the potential to become the next internationally spreading ceftriaxone-resistant ST. In conclusion, we performed a comprehensive epidemiological study to explore the correlation between AMR and specific STs, which provided important data for future studies of the molecular epidemiology of AMR in N. gonorrhoeae. Besides, these findings provide insight for adjusting surveillance strategies and therapy management in Shenzhen.

scholarly journals Selection for non-specific adhesion is a driver of FimH evolution increasing Escherichia coli biofilm capacity

2021 ◽  
Author(s):  
Mari YOSHIDA ◽  
Stanislas THIRIET-RUPERT ◽  
Leonie MAYER ◽  
Christophe BELOIN ◽  
Jean-Marc GHIGO
Keyword(s):  
Escherichia Coli ◽  
Selective Advantage ◽  
Coli Strain ◽  
Adhesion Properties ◽  
Lectin Domain ◽  
E Coli ◽  
Type 1 Fimbriae ◽  
Abiotic Surfaces ◽  
Selection For

Bacterial interactions with surfaces rely on the coordinated expression and interplay of surface exposed adhesion factors. However, how bacteria dynamically modulate their vast repertoire of adhesins to achieve surface colonization is not yet well-understood. We used experimental evolution and positive selection for improved adhesion to investigate how an initially poorly adherent Escherichia coli strain increased its adhesion capacities to abiotic surfaces. We showed that all identified evolved clones acquired mutations located almost exclusively in the lectin domain of fimH, the gene coding for the alpha-D-mannose-specific tip adhesin of type 1 fimbriae. While most of these fimH mutants showed reduced mannose-binding ability, they all displayed enhanced binding to abiotic surfaces, indicating a trade-off between FimH-mediated specific and non-specific adhesion properties. Several of the identified mutations were already reported in FimH lectin domain of pathogenic and environmental E. coli, suggesting that, beyond patho-adaptation, FimH microevolution favoring non-specific surface adhesion could constitute a selective advantage for natural E. coli isolates. Consistently, although E. coli deleted for the fim operon still evolves an increased adhesion capacity, mutants selected in the ∆fim background are outcompeted by fimH mutants revealing clonal interference for adhesion. Our study therefore provides insights into the plasticity of E. coli adhesion potential and shows that evolution of type 1 fimbriae is a major driver of the adaptation of natural E. coli to colonization.

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