A nucleotide substitution model with nearest-neighbour interactions

AbstractHuman gammaherpesvirus 8 (HHV-8) consists of six major clades (A–F) based on the genetic sequence of the open reading frame (ORF)-K1. There are a few conflicting reports regarding the global distribution of the different HHV-8 genotypes. This study aimed to determine the global distribution of the different HHV-8 genotypes based on phylogenetic analysis of the ORF-K1 coding region using sequences published in the GenBank during 1997–2020 and construct a phylogenetic tree using the maximum likelihood algorithm with the GTR + I + G nucleotide substitution model. A total of 550 sequences from 38 countries/origins were analysed in this study. Genotypes A and C had similar global distributions and were prevalent in Africa and Europe. Genotype B was prevalent in Africa. Of the rare genotypes, genotype D was reported in East Asia and Oceania and genotype E in South America, while genotype F was prevalent in Africa. The highest genotypic diversity was reported in the American continent, with Brazil housing five HHV-8 genotypes (A, B, C, E, and F). In this study, we present update of the global distribution of HHV-8 genotypes, providing a basis for future epidemiological and evolutionary studies of HHV-8.

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Substitution Model Distance Analysis for SARS-CoV-2 in China, USA, and Europe (Preprint)

10.2196/preprints.20462 ◽

2020 ◽

Author(s):

Hsiuying Wang ◽

Yi-Hau Chen

Keyword(s):

Common Ancestor ◽

Nucleotide Substitution ◽

Virus Transmission ◽

The Other ◽

Substitution Model ◽

Distance Analysis ◽

Study Results ◽

The World ◽

Substitution Models ◽

The Usa

BACKGROUND Coronavirus pandemic has been a wake-up call for the world. A dispute over the origin of SARS-CoV-2 has been raised. Study results showed that all SARS-CoV-2 sequences around the world sharing a common ancestor towards the end of 2019. Nevertheless, it is hard to reach conclusion regarding SARS-CoV-2 origin. OBJECTIVE In this study, we compare the divergence of SARS-CoV-2 sequences from the three areas, China, the USA, and Europe. METHODS We download SARS-CoV-2 sequences of China, USA, and Europe from the National Center for Biotechnology Information (NCBI). To investigate the diversity of these sequences from these three areas, we apply 17 different nucleotide substitution models to compare the diversity of these SARS-CoV-2 sequences. In the three groups of SARS-CoV-2 sequences, we calculate the pairwise nucleotide substitution distance of any two sequences in each group and then compare the distances in these three groups. RESULTS The analyzed results are consistent in most of the 17 substitution models. The outcomes from 14 substitution models show that China has the lowest diversity, followed by Europe and lastly by the USA. For the other 3 models, in one model, China has the lowest diversity, followed by the USA and lastly by Europe; in another model, USA has the lowest diversity, followed by China and lastly by Europe, and in the last one model, Europe has the lowest diversity, followed by China and lastly by the USA. CONCLUSIONS In this study, we compare the diversity of SARS-CoV-2 samples from China, Europe, and the USA. Different substitution models were applied to analyze the data. Our outcome shows that China has the smallest mean distance value, followed by Europe and lastly by the USA, which consists with the virus transmission time order that SARS-CoV-2 starts in China, then outbreaks in Europe and finally in the USA.

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A63 Quantifying the dynamics of evolutionary rates through time

Virus Evolution ◽

10.1093/ve/vez002.062 ◽

2019 ◽

Vol 5 (Supplement_1) ◽

Author(s):

J V Membrebe ◽

G Baele ◽

M A Suchard ◽

P Lemey

Keyword(s):

Evolutionary History ◽

Nucleotide Substitution ◽

Evolutionary Rate ◽

Evolutionary Rates ◽

Dynamic Feature ◽

Substitution Model ◽

Substitution Rates ◽

Divergence Time Estimates ◽

The Past ◽

Codon Substitution

Abstract The availability of evolutionary rate estimates in recent years led to the observation that they may depend on the time-scale on which they are measured. Specifically, RNA virus evolutionary rates are frequently estimated to be low towards the past and high towards the present. This time-dependent rate phenomenon (TDRP) has important implications for evolutionary studies as it could severely bias divergence time estimates. While recent studies are providing insights into the relationship between viral evolutionary rate and time, formal probabilistic models to draw inference under TDRP scenarios remain lacking. Here, we adopt epoch-modelling to develop a Bayesian model of discrete rate changes through time in an unknown evolutionary history and combine this with a log-linear parameterization of rates as a function of times in the past. We provide an implementation for nucleotide substitution rates as well as for nonsynonymous rates change in a codon substitution model. Using a foamy virus dataset for which internal node calibrations can be applied based on host-virus co-divergence, we estimate a significant decline in evolutionary rates as a function of time into the past for nucleotide substitutions as well as for non-synonymous substitutions in a codon model. We also estimate a deep evolutionary history for primate Lentiviruses by combining an HIV-1 group M node calibration and a biogeographic calibration for viruses in drill monkeys in the TDRP model. Our analyses lead to the conclusion that studies of evolutionary timescales require a reconsideration of substitution rates, in either codon and nucleotide substitution model, as a dynamic feature of molecular evolution.

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The structure of amorphous and polycrystalline materials using energy-filtered RDF analysis

Proceedings, annual meeting, Electron Microscopy Society of America ◽

10.1017/s0424820100130584 ◽

1992 ◽

Vol 50 (2) ◽

pp. 1190-1191

Author(s):

David Cockayne ◽

David McKenzie

Keyword(s):

Electron Diffraction ◽

Diffraction Pattern ◽

Density Function ◽

Electron Diffraction Pattern ◽

Polycrystalline Materials ◽

Nearest Neighbour ◽

X Ray ◽

Selected Area Electron Diffraction ◽

Reduced Density ◽

System F

The technique of Electron Reduced Density Function (RDF) analysis has ben developed into a rapid analytical tool for the analysis of small volumes of amorphous or polycrystalline materials. The energy filtered electron diffraction pattern is collected to high scattering angles (currendy to s = 2 sinθ/λ = 6.5 Å-1) by scanning the selected area electron diffraction pattern across the entrance aperture to a GATAN parallel energy loss spectrometer. The diffraction pattern is then converted to a reduced density function, G(r), using mathematical procedures equivalent to those used in X-ray and neutron diffraction studies.Nearest neighbour distances accurate to 0.01 Å are obtained routinely, and bond distortions of molecules can be determined from the ratio of first to second nearest neighbour distances. The accuracy of coordination number determinations from polycrystalline monatomic materials (eg Pt) is high (5%). In amorphous systems (eg carbon, silicon) it is reasonable (10%), but in multi-element systems there are a number of problems to be overcome; to reduce the diffraction pattern to G(r), the approximation must be made that for all elements i,j in the system, fj(s) = Kji fi,(s) where Kji is independent of s.

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Percolation models of free and bound water under the influence of nearest neighbour interactions

Journal de Physique ◽

10.1051/jphys:01987004805087700 ◽

1987 ◽

Vol 48 (5) ◽

pp. 877-883 ◽

Cited By ~ 6

Author(s):

W. Weiss

Keyword(s):

Bound Water ◽

Nearest Neighbour ◽

Free And Bound Water

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Characterization of the Original Christmas Disease Mutation (Cysteine 206 → Serine): From Clinical Recognition to Molecular Pathogenesis

Thrombosis and Haemostasis ◽

10.1055/s-0038-1648381 ◽

1992 ◽

Vol 67 (01) ◽

pp. 063-065 ◽

Cited By ~ 6

Author(s):

Sherryl A M Taylor ◽

Jacalyn Duffin ◽

Cherie Cameron ◽

Jerome Teitel ◽

Bernadette Garvey ◽

...

Keyword(s):

Nucleotide Substitution ◽

Novel Mutation ◽

Factor Ix ◽

Causative Mutation ◽

Coding Region ◽

Body Of Knowledge ◽

Polymerase Chain ◽

Splice Junctions

SummaryChristmas disease was first reported as a distinct clinical entity in two manuscripts published in 1952 (1, 2). The eponym associated with this disorder, is the surname of the first patient examined in detail and reported by Biggs and colleagues in a paper describing the clinical and laboratory features of seven affected individuals (3). This patient has severe factor IX coagulant deficiency (less than 0.01 units/ml) and no detectable circulating factor IX antigen (less than 0.01 units/ml). Coding sequence and splice junctions of the factor IX gene from this patient have been amplified in vitro through the polymerase chain reaction (PCR). One nucleotide substitution was identified at nucleotide 30,070 where a guanine was replaced by a cytosine. This mutation alters the amino acid encoded at position 206 in the factor IX protein from cysteine to serine. The non conservative nature of this substitution, the absence of this change in more than 200 previously sequenced factor IX genes and the fact that the remainder of the coding region of this gene was normal, all provide strong circumstantial evidence in favour of this change being the causative mutation in this patient. The molecular characterization of this novel mutation in the index case of Christmas disease, contributes to the rapidly expanding body of knowledge pertaining to Christmas disease pathogenesis.

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