scholarly journals Genomic diversity of SARS-CoV-2 in Oxford during United Kingdom’s first national lockdown

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Altar M. Munis ◽  
Monique Andersson ◽  
Alexander Mobbs ◽  
Stephen C. Hyde ◽  
Deborah R. Gill
Keyword(s):  
Large Scale ◽  
Genomic Diversity ◽  
Viral Diversity ◽  
Host Immune System ◽  
Infection Rates ◽  
Short Term ◽  
Viral Genomes ◽  
The United Kingdom ◽  
Local Spread ◽  
Term Evolution

AbstractEpidemiological efforts to model the spread of SARS-CoV-2, the virus that causes COVID-19, are crucial to understanding and containing current and future outbreaks and to inform public health responses. Mutations that occur in viral genomes can alter virulence during outbreaks by increasing infection rates and helping the virus evade the host immune system. To understand the changes in viral genomic diversity and molecular epidemiology in Oxford during the first wave of infections in the United Kingdom, we analyzed 563 clinical SARS-CoV-2 samples via whole-genome sequencing using Nanopore MinION sequencing. Large-scale surveillance efforts during viral epidemics are likely to be confounded by the number of independent introductions of the viral strains into a region. To avoid such issues and better understand the selection-based changes occurring in the SARS-CoV-2 genome, we utilized local isolates collected during the UK’s first national lockdown whereby personal interactions, international and national travel were considerably restricted and controlled. We were able to track the short-term evolution of the virus, detect the emergence of several mutations of concern or interest, and capture the viral diversity of the region. Overall, these results demonstrate genomic pathogen surveillance efforts have considerable utility in controlling the local spread of the virus.

scholarly journals Massive expansion of human gut bacteriophage diversity

2020 ◽  
Author(s):  
Luis F. Camarillo-Guerrero ◽  
Alexandre Almeida ◽  
Guillermo Rangel-Pineros ◽  
Robert D. Finn ◽  
Trevor D. Lawley
Keyword(s):  
Gene Flow ◽  
Large Scale ◽  
Bacterial Species ◽  
Single Species ◽  
Viral Diversity ◽  
Evolutionary Analysis ◽  
Flow Networks ◽  
Human Gut ◽  
Viral Genomes ◽  
Globally Distributed

SUMMARYBacteriophages drive evolutionary change in bacterial communities by creating gene flow networks that fuel ecological adaptions. However, the extent of viral diversity and prevalence in the human gut remains largely unknown. Here, we introduce the Gut Phage Database (GPD), a collection of ∼142,000 non-redundant viral genomes (>10 kb) obtained by mining a dataset of 28,060 globally distributed human gut metagenomes and 2,898 reference genomes of cultured gut bacteria. Host assignment revealed that viral diversity is highest in the Firmicutes phyla and that ∼36% of viral clusters (VCs) are not restricted to a single species, creating gene flow networks across phylogenetically distinct bacterial species. Epidemiological analysis uncovered 280 globally distributed VCs found in at least 5 continents and a highly prevalent novel phage clade with features reminiscent of p-crAssphage. This high-quality, large-scale catalogue of phage genomes will improve future virome studies and enable ecological and evolutionary analysis of human gut bacteriophages.

scholarly journals Viral Complexity: Amino acid co-evolution in viral genomes as a possible metric

2017 ◽  
Author(s):  
C. K. Sruthi ◽  
Meher K. Prakash
Keyword(s):  
Amino Acid ◽  
Avian Influenza ◽  
Large Scale ◽  
Host Immune System ◽  
Network Characteristics ◽  
Viral Genomes ◽  
Richter Scale ◽  
Universality Classes ◽  
Evolutionary Networks ◽  
Hiv 1

ABSTRACTViruses are simultaneously simple and complex. Simple because they have barely around ten types of proteins compared to tens of thousands of proteins in bacteria. Complex because amino acid mutation rates are very high, challenging host immune system and drugs. In this work we use the co-evolution of amino acids and the network characteristics that arise out of it to describe the complexity hidden in the multitude of variations in a viral genome. Using large-scale genomic data, the complexity in several viruses was compared. Interestingly, the co-evolutionary relations were primarily intra-protein in avian influenza and inter-protein in HIV-1. The network degree distributions showed two universality classes: a power-law with exponent −1 in HIV-1 and avian-influenza, random co-evolutionary behavior in human flu and dengue, suggesting the co-evolution as one way to statistically classify the complexity in viruses. The observed correlation between the network densities and the strengths on virus Richter scale raises interesting questions on whether it is possible to define the complexity of viruses using their evolutionary networks.

scholarly journals Rates of Molecular Evolution in a Marine Synechococcus Phage Lineage

Viruses ◽  
2019 ◽  
Vol 11 (8) ◽  
pp. 720
Author(s):  
Anne Kupczok ◽  
Tal Dagan
Keyword(s):  
Time Series Data ◽  
Evolutionary Rates ◽  
Genomic Diversity ◽  
Series Data ◽  
Short Term ◽  
Metabolic Genes ◽  
Term Evolution ◽  
Genome Wide ◽  
Auxiliary Metabolic Genes ◽  
Rates Of Molecular Evolution

Cyanophages are characterized by vast genomic diversity and the formation of stable ecotypes over time. The evolution of phage diversity includes vertical processes, such as mutation, and horizontal processes, such as recombination and gene transfer. Here, we study the contribution of vertical and horizontal processes to short-term evolution of marine cyanophages. Analyzing time series data of Synechococcus-infecting Myoviridae ecotypes spanning up to 17 years, we found a high contribution of recombination relative to mutation (r/m) in all ecotypes. Additionally, we found a molecular clock of substitution and recombination in one ecotype, RIM8. The estimated RIM8 evolutionary rates are 2.2 genome-wide substitutions per year (1.275 × 10−5 substitutions/site/year) and 29 genome-wide nucleotide alterations due to recombination per year. We found 26 variable protein families, of which only two families have a predicted functional annotation, suggesting that they are auxiliary metabolic genes with bacterial homologs. A comparison of our rate estimates to other phage evolutionary rate estimates in the literature reveals a negative correlation of phage substitution rates with their genome size. A comparison to evolutionary rates in bacterial organisms further shows that phages have high rates of mutation and recombination compared to their bacterial hosts. We conclude that the increased recombination rate in phages likely contributes to their vast genomic diversity.

More about Diamonds

2019 ◽  
pp. 115-119
Author(s):  
Vladimir Shubin
Keyword(s):  
United Kingdom ◽  
South African ◽  
Personal Experience ◽  
African Studies ◽  
Short Term ◽  
Soviet State ◽  
The United Kingdom ◽  
De Beers

The article is a rejoinder to the work of Yury S. Skubko, previously published in the Journal of the Institute for African Studies, on Moscow’s relations with De Beers. It is based not only on the available literature but also on the author’s personal experience. The author shows that under the monopoly of this South African company in the field of diamond sales, Soviet organizations, even in the conditions of a South African boycott, were forced to deal with its subordinate structures and the attempts to sideline them were in vain. In particular the article analyses the attitude to a controversial agreement signed by the Soviet state-owned “Glavalmalmazzoloto” and De Beers Centenary in 1990, when, like in many other cases in the “Gorbachev’s era” Moscow’s principle stand was eroded for short-term results even personal gains. The author comes to the conclusion that the responsibility for Moscow’s dealings with De Beers must be borne not by our country, but above all by the United Kingdom, which allowed De Beers have the headquarters of its Central Selling Organisation (CСO) in London.

SHORT-TERM EVOLUTION OF FLOW & MORPHOLOGY IN AN ERODIBLE MEANDERING CHANNEL WITH & WITHOUT GROYNES

2018 ◽  
Vol 74 (4) ◽  
pp. I_1147-I_1152
Author(s):  
Saroj KARKI ◽  
Yuji HASEGAWA ◽  
Masakazu HASHIMOTO ◽  
Hajime NAKAGAWA ◽  
Kenji KAWAIKE
Keyword(s):  
Short Term ◽  
Meandering Channel ◽  
Term Evolution ◽  
Flow Morphology

scholarly journals BattleNet: Capturing Advantageous Battlefield in RTS Games (Student Abstract)

2020 ◽  
Vol 34 (10) ◽  
pp. 13849-13850
Author(s):  
Donghyeon Lee ◽  
Man-Je Kim ◽  
Chang Wook Ahn
Keyword(s):  
Artificial Intelligence ◽  
Decision Making ◽  
Real Time ◽  
Large Scale ◽  
Outcome Predictor ◽  
Short Term ◽  
Rts Game

In a real-time strategy (RTS) game, StarCraft II, players need to know the consequences before making a decision in combat. We propose a combat outcome predictor which utilizes terrain information as well as squad information. For training the model, we generated a StarCraft II combat dataset by simulating diverse and large-scale combat situations. The overall accuracy of our model was 89.7%. Our predictor can be integrated into the artificial intelligence agent for RTS games as a short-term decision-making module.

Effects of Dipyridamole on the Short-Term Evolution of Glomerulonephritis

Nephron ◽  
1991 ◽  
Vol 58 (1) ◽  
pp. 13-16 ◽  
Author(s):  
S. Camara ◽  
J.P. de la Cruz ◽  
M.A. Frutos ◽  
P. Sanchez ◽  
Lopez de Novales ◽  
...  
Keyword(s):  
Short Term ◽  
Term Evolution

scholarly journals Blastocyst formation, embryo transfer and breed comparison in the first reported large scale cloning of camels

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
P. O. Olsson ◽  
A. H. Tinson ◽  
N. Al Shamsi ◽  
K. S. Kuhad ◽  
R. Singh ◽  
...  
Keyword(s):  
Embryo Transfer ◽  
Nuclear Transfer ◽  
Large Scale ◽  
Donor Cell ◽  
Blastocyst Formation ◽  
Short Term ◽  
Embryo Formation ◽  
Large Expansion ◽  
Breed Differences ◽  
Breed Comparison

AbstractCloning, through somatic cell nuclear transfer (SCNT), has the potential for a large expansion of genetically favorable traits in a population in a relatively short term. In the present study we aimed to produce multiple cloned camels from racing, show and dairy exemplars. We compared several parameters including oocyte source, donor cell and breed differences, transfer methods, embryo formation and pregnancy rates and maintenance following SCNT. We successfully achieved 47 pregnancies, 28 births and 19 cloned offspring who are at present healthy and have developed normally. Here we report cloned camels from surgical embryo transfer and correlate blastocyst formation rates with the ability to achieve pregnancies. We found no difference in the parameters affecting production of clones by camel breed, and show clear differences on oocyte source in cloning outcomes. Taken together we demonstrate that large scale cloning of camels is possible and that further improvements can be achieved.

How to increase customer repeated bookings in the short-term room rental market? A large-scale granular data investigation

2021 ◽  
Vol 143 ◽  
pp. 113495
Author(s):  
Jiang Wu ◽  
Jingxuan Cai ◽  
Xin (Robert) Luo ◽  
Jose Benitez
Keyword(s):  
Large Scale ◽  
Short Term ◽  
Rental Market ◽  
Data Investigation

scholarly journals The Effect of Vaccination Rates on the Infection of COVID-19 under the Vaccination Rate below the Herd Immunity Threshold

2021 ◽  
Vol 18 (14) ◽  
pp. 7491
Author(s):  
Yi-Tui Chen
Keyword(s):  
Infection Rate ◽  
Herd Immunity ◽  
The United States ◽  
Vaccination Rate ◽  
Infection Rates ◽  
Vaccination Rates ◽  
The United Kingdom ◽  
The World ◽  
Almost All ◽  
The Impact

Although vaccination is carried out worldwide, the vaccination rate varies greatly. As of 24 May 2021, in some countries, the proportion of the population fully vaccinated against COVID-19 has exceeded 50%, but in many countries, this proportion is still very low, less than 1%. This article aims to explore the impact of vaccination on the spread of the COVID-19 pandemic. As the herd immunity of almost all countries in the world has not been reached, several countries were selected as sample cases by employing the following criteria: more than 60 vaccine doses per 100 people and a population of more than one million people. In the end, a total of eight countries/regions were selected, including Israel, the UAE, Chile, the United Kingdom, the United States, Hungary, and Qatar. The results find that vaccination has a major impact on reducing infection rates in all countries. However, the infection rate after vaccination showed two trends. One is an inverted U-shaped trend, and the other is an L-shaped trend. For those countries with an inverted U-shaped trend, the infection rate begins to decline when the vaccination rate reaches 1.46–50.91 doses per 100 people.

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