scholarly journals Establishment and lineage dynamics of the SARS-CoV-2 epidemic in the UK

Science ◽  
2021 ◽  
pp. eabf2946
Author(s):  
Louis du Plessis ◽  
John T. McCrone ◽  
Alexander E. Zarebski ◽  
Verity Hill ◽  
Christopher Ruis ◽  
...  
Keyword(s):  
Large Scale ◽  
Phylogenetic Analyses ◽  
Transmission Dynamics ◽  
Genetic Lineage ◽  
Size Dependent ◽  
Spatio Temporal ◽  
The Uk ◽  
Lineage Structure ◽  
And Control ◽  
Lineage Diversity

The UK’s COVID-19 epidemic during early 2020 was one of world’s largest and unusually well represented by virus genomic sampling. Here we reveal the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 SARS-CoV-2 genomes, including 26,181 from the UK sampled throughout the country’s first wave of infection. Using large-scale phylogenetic analyses, combined with epidemiological and travel data, we quantify the size, spatio-temporal origins and persistence of genetically-distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown tended to be larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, while lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.

scholarly journals Establishment & lineage dynamics of the SARS-CoV-2 epidemic in the UK

2020 ◽  
Author(s):  
Louis du Plessis ◽  
John T. McCrone ◽  
Alexander E. Zarebski ◽  
Verity Hill ◽  
Christopher Ruis ◽  
...  
Keyword(s):  
Large Scale ◽  
Phylogenetic Analyses ◽  
Transmission Dynamics ◽  
Genetic Lineage ◽  
Size Dependent ◽  
Spatio Temporal ◽  
The Uk ◽  
Lineage Structure ◽  
And Control ◽  
Lineage Diversity

AbstractThe UK’s COVID-19 epidemic during early 2020 was one of world’s largest and unusually well represented by virus genomic sampling. Here we reveal the fine-scale genetic lineage structure of this epidemic through analysis of 50,887 SARS-CoV-2 genomes, including 26,181 from the UK sampled throughout the country’s first wave of infection. Using large-scale phylogenetic analyses, combined with epidemiological and travel data, we quantify the size, spatio-temporal origins and persistence of genetically-distinct UK transmission lineages. Rapid fluctuations in virus importation rates resulted in >1000 lineages; those introduced prior to national lockdown were larger and more dispersed. Lineage importation and regional lineage diversity declined after lockdown, whilst lineage elimination was size-dependent. We discuss the implications of our genetic perspective on transmission dynamics for COVID-19 epidemiology and control.

scholarly journals Reconstructing the emergence of a lethal infectious disease of wildlife supports a key role for spread through translocations by humans

2016 ◽  
Vol 283 (1839) ◽  
pp. 20160952 ◽  
Author(s):  
Stephen J. Price ◽  
Trenton W. J. Garner ◽  
Andrew A. Cunningham ◽  
Tom E. S. Langton ◽  
Richard A. Nichols
Keyword(s):  
Phylogenetic Analyses ◽  
Control Measures ◽  
Spatial Spread ◽  
Potential Control ◽  
Temporal Models ◽  
Spatio Temporal ◽  
Using Data ◽  
Impact On Biodiversity ◽  
The Uk ◽  
Citizen Science Project

There have been few reconstructions of wildlife disease emergences, despite their extensive impact on biodiversity and human health. This is in large part attributable to the lack of structured and robust spatio-temporal datasets. We overcame logistical problems of obtaining suitable information by using data from a citizen science project and formulating spatio-temporal models of the spread of a wildlife pathogen (genus Ranavirus , infecting amphibians). We evaluated three main hypotheses for the rapid increase in disease reports in the UK: that outbreaks were being reported more frequently, that climate change had altered the interaction between hosts and a previously widespread pathogen, and that disease was emerging due to spatial spread of a novel pathogen. Our analysis characterized localized spread from nearby ponds, consistent with amphibian dispersal, but also revealed a highly significant trend for elevated rates of additional outbreaks in localities with higher human population density—pointing to human activities in also spreading the virus. Phylogenetic analyses of pathogen genomes support the inference of at least two independent introductions into the UK. Together these results point strongly to humans repeatedly translocating ranaviruses into the UK from other countries and between UK ponds, and therefore suggest potential control measures.

scholarly journals Molecular Detection and Phylogeny of Tick-Borne Pathogens in Ticks Collected from Dogs in the Republic of Korea

Pathogens ◽  
2021 ◽  
Vol 10 (5) ◽  
pp. 613
Author(s):  
A-Tai Truong ◽  
Jinhyeong Noh ◽  
Yeojin Park ◽  
Hyun-Ji Seo ◽  
Keun-Ho Kim ◽  
...  
Keyword(s):  
Disease Surveillance ◽  
Large Scale ◽  
Phylogenetic Analyses ◽  
Republic Of Korea ◽  
16S Rrna Genes ◽  
Rrna Genes ◽  
Haemaphysalis Longicornis ◽  
Babesia Gibsoni ◽  
The Republic ◽  
And Control

Ticks are important vectors of various pathogens that result in clinical illnesses in humans and domestic and wild animals. Information regarding tick infestations and pathogens transmitted by ticks is important for the identification and prevention of disease. This study was a large-scale investigation of ticks collected from dogs and their associated environments in the Republic of Korea (ROK). It included detecting six prevalent tick-borne pathogens (Anaplasma spp., A. platys, Borrelia spp., Babesia gibsoni, Ehrlichia canis, and E. chaffeensis). A total of 2293 ticks (1110 pools) were collected. Haemaphysalis longicornis (98.60%) was the most frequently collected tick species, followed by Ixodes nipponensis (0.96%) and H. flava (0.44%). Anaplasma spp. (24/1110 tick pools; 2.16%) and Borrelia spp. (4/1110 tick pools; 0.36%) were detected. The phylogenetic analyses using 16S rRNA genes revealed that the Anaplasma spp. detected in this study were closely associated with A. phagocytophilum reported in humans and rodents in the ROK. Borrelia spp. showed phylogenetic relationships with B. theileri and B. miyamotoi in ticks and humans in Mali and Russia. These results demonstrate the importance of tick-borne disease surveillance and control in dogs in the ROK.

scholarly journals A Syndromic Surveillance Tool to Detect Anomalous Clusters of COVID-19 Symptoms in the United States

2020 ◽  
Author(s):  
Amparo Güemes ◽  
Soumyajit Ray ◽  
Khaled Aboumerhi ◽  
Michael Richard Desjardins ◽  
Anton Kvit ◽  
...  
Keyword(s):  
Correlation Analysis ◽  
Syndromic Surveillance ◽  
Large Scale ◽  
Cross Correlation ◽  
Warning System ◽  
The United States ◽  
Johns Hopkins University ◽  
Cross Correlation Analysis ◽  
Spatio Temporal ◽  
And Control

Coronavirus SARS-COV-2 infections continue to spread across the world, yet effective large-scale disease detection and prediction remain limited. COVID Control: A Johns Hopkins University Study, is a novel syndromic surveillance approach, which collects body temperature and COVID-like illness (CLI) symptoms across the US using a smartphone app and applies spatio-temporal clustering techniques and cross-correlation analysis to create maps of abnormal symptomatology incidence that are made publicly available. The results of the cross-correlation analysis identify optimal temporal lags between symptoms and a range of COVID-19 outcomes, with new taste/smell loss showing the highest correlations. We also identified temporal clusters of change in taste/smell entries and confirmed COVID-19 incidence in Baltimore City and County. Further, we utilized an extended simulated dataset to showcase our analytics in Maryland. The resulting clusters can serve as indicators of emerging COVID-19 outbreaks, and support syndromic surveillance as an early warning system for disease prevention and control.

scholarly journals High frequency of horizontal transfer in Jockey families (LINE order) of drosophilids

Mobile DNA ◽  
2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Izabella L. Tambones ◽  
Annabelle Haudry ◽  
Maryanna C. Simão ◽  
Claudia M. A. Carareto
Keyword(s):  
Transposable Element ◽  
Horizontal Transfer ◽  
Large Scale ◽  
Evolutionary Dynamics ◽  
Phylogenetic Analyses ◽  
Genetic Material ◽  
Long Terminal Repeat Retrotransposons ◽  
Spatio Temporal ◽  
Line Elements ◽  
Horizontal Transfers

Abstract Background The use of large-scale genomic analyses has resulted in an improvement of transposable element sampling and a significant increase in the number of reported HTT (horizontal transfer of transposable elements) events by expanding the sampling of transposable element sequences in general and of specific families of these elements in particular, which were previously poorly sampled. In this study, we investigated the occurrence of HTT events in a group of elements that, until recently, were uncommon among the HTT records in Drosophila – the Jockey elements, members of the LINE (long interspersed nuclear element) order of non-LTR (long terminal repeat) retrotransposons. The sequences of 111 Jockey families deposited in Repbase that met the criteria of the analysis were used to identify Jockey sequences in 48 genomes of Drosophilidae (genus Drosophila, subgenus Sophophora: melanogaster, obscura and willistoni groups; subgenus Drosophila: immigrans, melanica, repleta, robusta, virilis and grimshawi groups; subgenus Dorsilopha: busckii group; genus/subgenus Zaprionus and genus Scaptodrosophila). Results Phylogenetic analyses revealed 72 Jockey families in 41 genomes. Combined analyses revealed 15 potential HTT events between species belonging to different genera and species groups of Drosophilidae, providing evidence for the flow of genetic material favoured by the spatio-temporal sharing of these species present in the Palaeartic or Afrotropical region. Conclusions Our results provide phylogenetic, biogeographic and temporal evidence of horizontal transfers of the Jockey elements, increase the number of rare records of HTT in specific families of LINE elements, increase the number of known occurrences of these events, and enable a broad understanding of the evolutionary dynamics of these elements and the host species.

scholarly journals A syndromic surveillance tool to detect anomalous clusters of COVID-19 symptoms in the United States

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Amparo Güemes ◽  
Soumyajit Ray ◽  
Khaled Aboumerhi ◽  
Michael R. Desjardins ◽  
Anton Kvit ◽  
...  
Keyword(s):  
Correlation Analysis ◽  
Syndromic Surveillance ◽  
Large Scale ◽  
Cross Correlation ◽  
Warning System ◽  
The United States ◽  
Johns Hopkins University ◽  
Cross Correlation Analysis ◽  
Spatio Temporal ◽  
And Control

AbstractCoronavirus SARS-COV-2 infections continue to spread across the world, yet effective large-scale disease detection and prediction remain limited. COVID Control: A Johns Hopkins University Study, is a novel syndromic surveillance approach, which collects body temperature and COVID-like illness (CLI) symptoms across the US using a smartphone app and applies spatio-temporal clustering techniques and cross-correlation analysis to create maps of abnormal symptomatology incidence that are made publicly available. The results of the cross-correlation analysis identify optimal temporal lags between symptoms and a range of COVID-19 outcomes, with new taste/smell loss showing the highest correlations. We also identified temporal clusters of change in taste/smell entries and confirmed COVID-19 incidence in Baltimore City and County. Further, we utilized an extended simulated dataset to showcase our analytics in Maryland. The resulting clusters can serve as indicators of emerging COVID-19 outbreaks, and support syndromic surveillance as an early warning system for disease prevention and control.

scholarly journals Cnidaria in UK coastal waters: description of spatio-temporal patterns and inter-annual variability

2014 ◽  
Vol 94 (7) ◽  
pp. 1401-1408 ◽  
Author(s):  
Stephen K. Pikesley ◽  
Brendan J. Godley ◽  
Sue Ranger ◽  
Peter B. Richardson ◽  
Matthew J. Witt
Keyword(s):  
Coastal Waters ◽  
Large Scale ◽  
Temporal Patterns ◽  
Spatial And Temporal Patterns ◽  
Annual Variability ◽  
Corrected Data ◽  
Spatio Temporal ◽  
Analyse Data ◽  
The Uk ◽  
Temporal Coverage

Concern has been expressed over future biogeographical expansion and habitat capitalization by species of the phylum Cnidaria, as this may have negative implications on human activities and ecosystems. There is, however, a paucity of knowledge and understanding of jellyfish ecology, in particular species distribution and seasonality. Recent studies in the UK have principally focused on the Celtic, Irish and North Seas, but all in isolation. In this study we analyse data from a publicly-driven sightings scheme across UK coastal waters (2003–2011; 9 years), with the aim of increasing knowledge on spatial and temporal patterns and trends. We describe inter-annual variability, seasonality and patterns of spatial distribution, and compare these with existing historic literature. Although incidentally-collected data lack quantification of effort, we suggest that with appropriate data management and interpretation, publicly-driven, citizen-science-based, recording schemes can provide for large-scale (spatial and temporal) coverage that would otherwise be logistically and financially unattainable. These schemes may also contribute to baseline data from which future changes in patterns or trends might be identified. We further suggest that findings from such schemes may be strengthened by the inclusion of some element of effort-corrected data collection.

scholarly journals Epidemic Dynamics of a Fractional-Order SIS Infectious Network Model

2021 ◽  
Vol 2021 ◽  
pp. 1-8
Author(s):  
Na Liu ◽  
Yunliu Li ◽  
Junwei Sun ◽  
Jie Fang ◽  
Peng Liu
Keyword(s):  
Fractional Order ◽  
Network Model ◽  
Large Scale ◽  
Equilibrium Points ◽  
Transmission Dynamics ◽  
Economic Losses ◽  
Epidemic Dynamics ◽  
Order Coefficient ◽  
The Stability ◽  
And Control

Outbreak and large-scale of the infectious diseases have caused enormous economic losses to all countries in the world. Constructing a network model which could reflect the transmission dynamics of the epidemics and investigating their transmission laws have a significant meaning in the precaution and control of the epidemics. In this article, a fractional-order SIS epidemic network model is proposed. First, an expression of the basic reproduction number is deduced. Second, applying the Lyapunov function, the stability of the equilibrium points about the infectious model is analyzed in detail. Finally, an example is present to verify the theoretical analysis. Furthermore, on account of the fractional-order coefficient, its influence on the transmission dynamics is also exhibited.

Collaboration, Power, Participation and Control on a Large Scale Research Team: Multiple Perspectives from the Oxford House Research Project

2001 ◽  
Author(s):  
Bradley Olson ◽  
Leonard Jason ◽  
Joseph R. Ferrari ◽  
Leon Venable ◽  
Bertel F. Williams ◽  
...  
Keyword(s):  
Large Scale ◽  
Research Team ◽  
Multiple Perspectives ◽  
Research Project ◽  
Oxford House ◽  
And Control

Interference mitigation in point to point wireless sensor networks using LSP protocol and time division multiplexing approach

2020 ◽  
Vol 39 (4) ◽  
pp. 5449-5458
Author(s):  
A. Arokiaraj Jovith ◽  
S.V. Kasmir Raja ◽  
A. Razia Sulthana
Keyword(s):  
Energy Consumption ◽  
Large Scale ◽  
Control Parameter ◽  
Interference Mitigation ◽  
Wireless Sensor ◽  
Point To Point ◽  
A Minor ◽  
Two Stages ◽  
Time Division ◽  
And Control

Interference in Wireless Sensor Network (WSN) predominantly affects the performance of the WSN. Energy consumption in WSN is one of the greatest concerns in the current generation. This work presents an approach for interference measurement and interference mitigation in point to point network. The nodes are distributed in the network and interference is measured by grouping the nodes in the region of a specific diameter. Hence this approach is scalable and isextended to large scale WSN. Interference is measured in two stages. In the first stage, interference is overcome by allocating time slots to the node stations in Time Division Multiple Access (TDMA) fashion. The node area is split into larger regions and smaller regions. The time slots are allocated to smaller regions in TDMA fashion. A TDMA based time slot allocation algorithm is proposed in this paper to enable reuse of timeslots with minimal interference between smaller regions. In the second stage, the network density and control parameter is introduced to reduce interference in a minor level within smaller node regions. The algorithm issimulated and the system is tested with varying control parameter. The node-level interference and the energy dissipation at nodes are captured by varying the node density of the network. The results indicate that the proposed approach measures the interference and mitigates with minimal energy consumption at nodes and with less overhead transmission.

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