scholarly journals VGsim: scalable viral genealogy simulator for global pandemic

2021 ◽  
Author(s):  
Vladimir Shchur ◽  
Vadim Spirin ◽  
Victor Pokrovskii ◽  
Evgeni Burovski ◽  
Nicola De Maio ◽  
...  
Keyword(s):  
Gillespie Algorithm ◽  
Global Pandemic ◽  
Large Numbers ◽  
Model Complex ◽  
Complex Population ◽  
Selection For ◽  
Two Phases ◽  
A Chain ◽  
Viral Sequences ◽  
Source Of Information

AbstractAs an effort to help contain the COVID-19 pandemic, large numbers of SARS-CoV-2 genomes have been sequenced from all continents. More than one million viral sequences are publicly available as of April 2021. Many studies estimate viral genealogies from these sequences, as these can provide valuable information about the spread of the pandemic across time and space. Additionally such data are a rich source of information about molecular evolutionary processes including natural selection, for example allowing the identification and investigating the spread of new variants conferring transmissibility and immunity evasion advantages to the virus. To validate new methods and to verify results resulting from these vast datasets, one needs an efficient simulator able to simulate the pandemic to approximate world-scale scenarios and generate viral genealogies of millions of samples. Here, we introduce a new fast simulatorVGsimwhich addresses this problem. The simulation process is split into two phases. During the forward run the algorithm generates a chain of events reflecting the dynamics of the pandemic using an hierarchical version of the Gillespie algorithm. During the backward run a coalescent-like approach generates a tree genealogy of samples conditioning on the events chain generated during the forward run. Our software can model complex population structure, epistasis and immunity escape. The code is freely available athttps://github.com/Genomics-HSE/VGsim.

scholarly journals The Impact of Armed Conflict on the Epidemiological Situation of COVID-19 in Libya, Syria and Yemen

2021 ◽  
Vol 9 ◽  
Author(s):  
Mohamed A. Daw
Keyword(s):  
Armed Conflict ◽  
Early Stage ◽  
Armed Conflicts ◽  
Cumulative Number ◽  
The Novel ◽  
Global Pandemic ◽  
Large Numbers ◽  
Public Data ◽  
Novel Coronavirus ◽  
The Impact

Background: Since the Arab uprising in 2011, Libya, Syria and Yemen have gone through major internal armed conflicts. This resulted in large numbers of deaths, injuries, and population displacements, with collapse of the healthcare systems. Furthermore, the situation was complicated by the emergence of COVID-19 as a global pandemic, which made the populations of these countries struggle under unusual conditions to deal with both the pandemic and the ongoing wars. This study aimed to determine the impact of the armed conflicts on the epidemiology of the novel coronavirus (SARS-CoV-2) within these war-torn countries and highlight the strategies needed to combat the spread of the pandemic and its consequences.Methods: Official and public data concerning the dynamics of the armed conflicts and the spread of SARS-COV-2 in Libya, Syria and Yemen were collected from all available sources, starting from the emergence of COVID-19 in each country until the end of December 2020. Datasets were analyzed by a set of statistical techniques and the weekly resolved data were used to probe the link between the intensity levels of the conflict and the prevalence of COVID-19.Results: The data indicated that there was an increase in the intensity of the violence at an early stage from March to August 2020, when it approximately doubled in the three countries, particularly in Libya. During that period, few cases of COVID-19 were reported, ranging from 5 to 53 cases/day. From September to December 2020, a significant decline in the intensity of the armed conflicts was accompanied by steep upsurges in the rate of COVID-19 cases, which reached up to 500 cases/day. The accumulative cases vary from one country to another during the armed conflict. The highest cumulative number of cases were reported in Libya, Syria and Yemen.Conclusions: Our analysis demonstrates that the armed conflict provided an opportunity for SARS-CoV-2 to spread. The early weeks of the pandemic coincided with the most intense period of the armed conflicts, and few cases were officially reported. This indicates undercounting and hidden spread during the early stage of the pandemic. The pandemic then spread dramatically as the armed conflict declined, reaching its greatest spread by December 2020. Full-blown transmission of the COVID-19 pandemic in these countries is expected. Therefore, urgent national and international strategies should be implemented to combat the pandemic and its consequences.

scholarly journals Insights into circovirus host range from the genomic fossil record

2018 ◽  
Author(s):  
Tristan P.W. Dennis ◽  
Peter J. Flynn ◽  
William Marciel de Souza ◽  
Joshua B. Singer ◽  
Corrie S. Moreau ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Animal Species ◽  
Diverse Range ◽  
Pathological Conditions ◽  
Host Relationships ◽  
Genome Assemblies ◽  
Viral Sequences ◽  
Source Of Information ◽  
Animal Genomes

AbstractA diverse range of DNA sequences derived from circoviruses (family Circoviridae) have been identified in samples obtained from humans and domestic animals, often in association with pathological conditions. In the majority of cases, however, little is known about the natural biology of the viruses from which these sequences are derived. Endogenous circoviral elements (CVe) are DNA sequences derived from circoviruses that occur in animal genomes and provide a useful source of information about circovirus-host relationships. In this study we screened genome assemblies of 675 animal species and identified numerous circovirus-related sequences, including the first examples of CVe derived from cycloviruses. We confirmed the presence of these CVe in the germline of the elongate twig ant (Pseudomyrmex gracilis), thereby establishing that cycloviruses infect insects. We examined the evolutionary relationships between CVe and contemporary circoviruses, showing that CVe from ants and mites group relatively closely with cycloviruses in phylogenies. Furthermore, the relatively random interspersal of CVe from insect genomes with cyclovirus sequences recovered from vertebrate samples, suggested that contamination might be an important consideration in studies reporting these viruses. Our study demonstrates how endogenous viral sequences can inform metagenomics-based virus discovery. In addition, it raises doubts about the role of cycloviruses as pathogens of humans and other vertebrates.

scholarly journals The Structure-Based Design of SARS-CoV-2 Nsp14 Methyltransferase Ligands Yields Nanomolar Inhibitors

2021 ◽  
Author(s):  
Tomáš Otava ◽  
Michal Šála ◽  
Fengling Li ◽  
Jindřich Fanfrlík ◽  
Kanchan Devkota ◽  
...  
Keyword(s):  
Subsequent Development ◽  
Homology Model ◽  
Docking Studies ◽  
Viral Rna ◽  
Research Priority ◽  
Global Pandemic ◽  
Viral Target ◽  
Biotechnology Sector ◽  
Source Of Information

COVID-19, caused by the SARS-CoV-2 virus, is responsible for a global pandemic that has paralyzed the normal life in many countries around the globe. Therefore, the preparation of both effective vaccines and potential therapeutics has become a major research priority in the biotechnology sector. Both viral proteins and selected host factors are important targets for the treatment of this disease. Suitable targets for antiviral therapy include i.a. viral methyltransferases, which allow the viral mRNA to be efficiently translated and protect the viral RNA from the innate immune system. In this study, we have focused on the structure-based design of the inhibitors of one of the two SARS-CoV-2 methyltransferases, nsp14. This methyltransferase catalyzes the transfer of the methyl group from <i>S</i>-adenosyl-<i>L</i>-methionine (SAM) to cap the guanosine triphosphate moiety of the newly synthesized viral RNA, yielding the methylated capped RNA and <i>S</i>-adenosyl-<i>L</i>-homocysteine (SAH). The crystal structure of SARS-CoV-2 nsp14 is unknown; we have taken advantage of its high homology to SARS-CoV nsp14 and prepared its homology model, which has allowed us to identify novel SAH derivatives modified at the adenine nucleobase as inhibitors of this important viral target. We have synthesized and tested the designed compounds <i>in vitro</i> and shown that these derivatives exert unprecedented inhibitory activity against this crucial enzyme. The docking studies nicely explain the contribution of an aromatic part attached by a linker to the position 7 of the 7-deaza analogues of SAH. Our results will serve as an important source of information for the subsequent development of new antivirals to combat COVID-19.

Asymptotic final size distribution of the multitype Reed–Frost process

1986 ◽  
Vol 23 (03) ◽  
pp. 563-584
Author(s):  
Gianpaolo Scalia-Tomba
Keyword(s):  
Size Distribution ◽  
Total Population ◽  
Large Population ◽  
Asymptotic Distributions ◽  
Reproduction Rate ◽  
Final Size ◽  
Basic Reproduction Rate ◽  
Infection Pattern ◽  
Large Numbers ◽  
A Chain

The asymptotic final size distribution of a multitype Reed–Frost process, a chain-binomial model for the spread of an infectious disease in a finite, closed multitype population, is derived, as the total population size grows large. When all subgroups are of comparable size, the infection pattern irreducible and the epidemic started by a small number of initial infectives, the classical threshold behaviour is obtained, depending on the basic reproduction rate of the disease in the population, and the asymptotic distributions for small and large outbreaks can be found. The same techniques can then be used to study other asymptotic situations, e.g. small groups in an otherwise large population, large numbers of initial infectives and reducible infection patterns.

‘March Separately, But Strike Together!’ The Communist Party’s United-Front Policy in the Weimar Republic

2020 ◽  
pp. 1-28
Author(s):  
Marcel Bois
Keyword(s):  
Communist Party ◽  
Weimar Republic ◽  
New Members ◽  
Large Numbers ◽  
United Front ◽  
Two Phases

Abstract The Communist Party of Germany (KPD) first coined the united-front policy in 1921, representing a promising effort to bolster Communist influence in the workers’ movement of that country. As the first part of the article shows, the KPD recruited large numbers of new members and significantly improved its electoral returns as a result. Despite this success, however, the party only pursued the united-front policy in two phases (1921–3 and 1926). As illustrated in the second part of the article, the KPD bid farewell to the united front as ‘Stalinisation’ began to set in during the Weimar Republic’s final years – with lethal consequences, as its abandonment decisively abetted the victory of German fascism.

scholarly journals Selection for a threshold character in Drosophila II. Homeostatic behaviour on relaxation of selection

1966 ◽  
Vol 8 (2) ◽  
pp. 205-218 ◽  
Author(s):  
B. D. H. Latter
Keyword(s):  
Natural Selection ◽  
Artificial Selection ◽  
Competitive Ability ◽  
Reproductive Capacity ◽  
Correlated Responses ◽  
Genetic Sampling ◽  
Bristle Number ◽  
Large Populations ◽  
Selection For ◽  
Two Phases

This paper is concerned with three related aspects of the behaviour of populations under artificial selection for increased scutellar bristle number: (i) the pattern of response on the probit scale; (ii) the homeostatic behaviour of the selection lines on relaxation of artificial selection; and (iii) correlated responses in generation interval, reproductive capacity and competitive ability. The study was designed so that linkage would be a comparatively unimportant factor in promoting correlated responses to selection, and the effects of genetic sampling from generation to generation were also reduced to a low level.Progress from the base mean of 4·05 bristles in females to a level of almost 8 bristles has been shown to involve two distinct phases with realized heritabilities of 0·34 and 0·10 respectively, the zone of transition corresponding closely to the position of the 6/7 threshold on the underlying scale. In addition to an apparent average reduction of about 25% in the additive genetic standard deviation in phase II by comparison with phase I, the loss in response due to the opposition of natural selection has been shown to reach a maximum near the zone of separation of the two phases.The pattern of behaviour of the populations under artificial and natural selection has suggested the presence in the base population of genes of large effect on both bristle number and reproductive fitness. There is also evidence of additional genetic variation in bristle number which is effectively neutral with respect to fitness. Continued selection for increased scutellar bristle number in large populations has been shown to reduce mean competitive ability by more than 80%.

Stochastic variable selection strategies for zero-inflated models

2017 ◽  
Vol 18 (1) ◽  
pp. 3-23 ◽  
Author(s):  
Eva Cantoni ◽  
Marie Auda
Keyword(s):  
Variable Selection ◽  
Count Data ◽  
Negative Binomial ◽  
Stochastic Search ◽  
Simulation Studies ◽  
Stochastic Variable ◽  
Selection Strategies ◽  
Selection For ◽  
A Chain ◽  
Zero Counts

When count data exhibit excess zero, that is more zero counts than a simpler parametric distribution can model, the zero-inflated Poisson (ZIP) or zero-inflated negative binomial (ZINB) models are often used. Variable selection for these models is even more challenging than for other regression situations because the availability of p covariates implies 4 p possible models. We adapt to zero-inflated models an approach for variable selection that avoids the screening of all possible models. This approach is based on a stochastic search through the space of all possible models, which generates a chain of interesting models. As an additional novelty, we propose three ways of extracting information from this rich chain and we compare them in two simulation studies, where we also contrast our approach with regularization (penalized) techniques available in the literature. The analysis of a typical dataset that has motivated our research is also presented, before concluding with some recommendations.

STRUCTURAL PHASE TRANSITIONS IN A DISCRETE ONE-DIMENSIONAL CHAIN

2009 ◽  
Vol 01 (03) ◽  
pp. 545-556 ◽  
Author(s):  
SRIKANTH VEDANTAM ◽  
S. MOHANRAJ
Keyword(s):  
Phase Transitions ◽  
Interatomic Potential ◽  
Structural Phase ◽  
Structural Phase Transitions ◽  
Temperature Dependent ◽  
One Dimensional ◽  
Nearest Neighbours ◽  
Two Phases ◽  
A Chain ◽  
Exchange Of Stability

We present a lattice dynamics model for describing structural phase transitions in a one-dimensional setting. The model comprises of a chain of discrete masses interacting with nearest neighbours. In order to drive a temperature dependent exchange of stability between two phases, we allow the interatomic potential to be dependent on the temperature. The system exhibits thermal phase transitions accompanied by latent heat.

REFINEMENTS TO MODEL SELECTION FOR NONLINEAR TIME SERIES

2003 ◽  
Vol 13 (05) ◽  
pp. 1263-1274 ◽  
Author(s):  
TOMOMICHI NAKAMURA ◽  
KEVIN JUDD ◽  
ALISTAIR MEES
Keyword(s):  
Time Series ◽  
Real Data ◽  
Nonlinear Time Series ◽  
Basis Functions ◽  
Heuristic Methods ◽  
Hard Problem ◽  
Optimal Subset ◽  
Large Numbers ◽  
Np Hard Problem ◽  
Selection For

Many models of the dynamics of nonlinear time series have large numbers of parameters and tend to overfit. This paper discusses algorithms for selecting the best basis functions from a dictionary for a model of a time series. Selecting the optimal subset of basis functions is typically an NP-hard problem which usually has to be solved by heuristic methods. In this paper, we propose a new heuristic that is a refinement of a previous one. We demonstrate with applications to artificial and real data. The results indicate that the method proposed in this paper is able to obtain better models in most cases.

Carbon Coated Nanoparticle Composites Synthesized in an RF Plasma Torch

1996 ◽  
Vol 457 ◽  
Author(s):  
John Henry J. Scott ◽  
Sara A. Majetich ◽  
Zafer Turgut ◽  
Michael E. Mchenry ◽  
Maher Boulos
Keyword(s):  
Plasma Torch ◽  
Rf Plasma ◽  
Coated Nanoparticles ◽  
Transmission Electron ◽  
Large Numbers ◽  
Carbon Coated ◽  
Carbon Arc ◽  
A Chain ◽  
Nanoparticle Composites ◽  
Encapsulated Nanoparticles

ABSTRACTFeCo alloy nanoparticles are synthesized in an RF plasma torch reactor and characterized using X-ray powder diffraction (XRD) and transmission electron microscopy (XRD). Bare, uncoated particles exhibit a chain-like agglomeration morphology marked by large ring- and bridge-like structures surrounding open voids. Acetylene was used to generate large numbers of carbon-coated nanoparticles similar to those produced in carbon arc reactors. Conventional TEM of this powder revealed numerous particles below 50 nm in diameter embedded in a carbonaceous matrix. These results establish RF plasma torch processing as a well-characterized, scalable alternative to carbon arc synthesis of encapsulated nanoparticles.

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