Evolutionary analysis of mumps viruses of genotype F collected in mainland China in 2001–2015

Cui, Ai‐Li; Rivailler, Pierre; Zhu, Zhen; Deng, Xin; Hu, Ying; Wang, Yan; Li, Fangcai; Sun, Zhaodan; He, Jun; Yuan, Shu; Tian, Xiaoling; Zhou, Shujie; Lei, Yake; Zheng, Huanying; Rota, Paul A.; Xu, Wenbo

doi:10.1038/s41598-017-17474-z

Cited by 19 publications

(22 citation statements)

References 35 publications

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“…Much effort has been devoted to pin down the CEP position, both from the theoretical and the experimental fronts. On the theory side, a large number of techniques has been employed, including the sum rules method, Schwinger-Dyson equations, holography, functional renormalization and effective models [39][40][41][42][43][44][45][46][47][48][49][50][51][52][53][54][55][56]. A wide spread for the CEP location has been obtained (for a recent summary of theoretically computed CEP positions see Ref.…”

Section: Introductionmentioning

confidence: 99%

On the critical end point in a two-flavor linear sigma model coupled to quarks

et al. 2020

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We use the linear sigma model coupled to quarks to explore the location of the phase transition lines in the QCD phase diagram from the point of view of chiral symmetry restoration at high temperature and baryon chemical potential. We compute analytically the effective potential in the high-and low-temperature approximations up to sixth order, including the contribution of the ring diagrams to account for the plasma screening properties. We determine the model parameters, namely, the couplings and massparameter, from conditions valid at the first order phase transition at vanishing temperature and, using the Hagedorn limiting temperature concept applied to finite baryon density, for a critical baryochemical potential of order of the nucleon mass. We show that when using the set of parameters thus determined, the second order phase transition line (our proxy for the crossover transition) that starts at finite temperature and zero baryon chemical potential converges to the line of first order phase transitions that starts at zero temperature and finite baryon chemical potential to determine the critical end point to lie in the region 5.02 < µ CEP B /T c < 5.18, 0.14 < T CEP /T c < 0.23, where T c is the critical transition temperature at zero baryon chemical potential.

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Section: Introductionmentioning

confidence: 99%

On the critical end point in a two-flavor linear sigma model coupled to quarks

et al. 2020

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“…Imposing the inflection condition d 2 B/dT 2 = 0 and upon plugging (50) into (51), we arrive at the following condition certainly fall within the group of lower temperatures and larger chemical potentials.…”

Section: B Euclidean Localizationmentioning

confidence: 88%

Localized rainbows in the QCD phase diagram

2020

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We study the phase diagram of strongly interacting matter with light quarks using a recently proposed, small parameter approach to infrared QCD in the Landau gauge. This is based on an expansion with respect to both the inverse number of colors and the pure Yang-Mills coupling in the presence of a Curci-Ferrari mass term. At leading order, this leads to the well-known rainbow equation for the quark propagator with a massive gluon propagator. We solve the latter at nonzero temperature and chemical potential using a simple semi-analytic approximation known to capture the essence of chiral symmetry breaking in the vacuum. In the chiral limit, we find a tricritical point which becomes a critical endpoint in the presence of a nonzero bare quark mass, in agreement with the results of nonperturbative functional methods and model calculations. This supports the view that the present approach allows for a systematic study of the QCD phase diagram in a controlled expansion scheme.

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“…Subgenomic alignments shown in Fig. 6 include the small hydrophobic (SH) gene of mumps virus [22] and glycoprotein (GP) sequences of Ebola virus analysed in this study as well as sequences of two human influenza A viruses: genome of subtype H1N1/09 [23], and haemagglutinin sequences of subtypes H1N1/09 [4] and H3N2 [24], sequences of two commonly studied bloodborne pathogens: pol, env, and coding regions of HIV-1M [25] and nonstructural protein 5B (NS5B) region of hepatitis C virus [26]. With respect to temporal resolution influenza A virus haemagglutinin gene (HA) is expected to acquire a mutation every one to two months on average compared to around three to six months for Ebola virus GP and over a year for mumps virus SH.…”

Section: Temporal Resolutionmentioning

confidence: 99%

The ability of single genes vs full genomes to resolve time and space in outbreak analysis

Dudas

Bedford

2019

BMC Evol Biol

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BackgroundInexpensive pathogen genome sequencing has had a transformative effect on the field of phylodynamics, where ever increasing volumes of data have promised real-time insight into outbreaks of infectious disease. As well as the sheer volume of pathogen isolates being sequenced, the sequencing of whole pathogen genomes, rather than select loci, has allowed phylogenetic analyses to be carried out at finer time scales, often approaching serial intervals for infections caused by rapidly evolving RNA viruses. Despite its utility, whole genome sequencing of pathogens has not been adopted universally and targeted sequencing of loci is common in some pathogen-specific fields.ResultsIn this study we highlighted the utility of sequencing whole genomes of pathogens by re-analysing a well-characterised collection of Ebola virus sequences in the form of complete viral genomes (≈19 kb long) or the rapidly evolving glycoprotein (GP, ≈2 kb long) gene. We have quantified changes in phylogenetic, temporal, and spatial inference resolution as a result of this reduction in data and compared these to theoretical expectations.ConclusionsWe propose a simple intuitive metric for quantifying temporal resolution, i.e. the time scale over which sequence data might be informative of various processes as a quick back-of-the-envelope calculation of statistical power available to molecular clock analyses.

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Evolutionary analysis of mumps viruses of genotype F collected in mainland China in 2001–2015

Cited by 19 publications

References 35 publications

On the critical end point in a two-flavor linear sigma model coupled to quarks

On the critical end point in a two-flavor linear sigma model coupled to quarks

Localized rainbows in the QCD phase diagram

The ability of single genes vs full genomes to resolve time and space in outbreak analysis

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