Spatio-Temporal Mutational Profile Appearances of Swedish SARS-CoV-2 during the Early Pandemic

Background: During the COVID-19 pandemic, the virus evolved, and we therefore aimed to provide an insight into which genetic variants were enriched, and how they spread in Sweden. Methods: We analyzed 348 Swedish SARS-CoV-2 sequences freely available from GISAID obtained from 7 February 2020 until 14 May 2020. Results: We identified 14 variant sites ≥5% frequency in the population. Among those sites, the D936Y substitution in the viral Spike protein was under positive selection. The variant sites can distinguish 11 mutational profiles in Sweden. Nine of the profiles appeared in Stockholm in March 2020. Mutational profiles 3 (B.1.1) and 6 (B.1), which contain the D936Y mutation, became the predominant profiles over time, spreading from Stockholm to other Swedish regions during April and the beginning of May. Furthermore, Bayesian phylogenetic analysis indicated that SARS-CoV-2 could have emerged in Sweden on 27 December 2019, and community transmission started on February 1st with an evolutionary rate of 1.5425 × 10−3 substitutions per year. Conclusions: Our study provides novel knowledge on the spatio-temporal dynamics of Swedish SARS-CoV-2 variants during the early pandemic. Characterization of these viral variants can provide precious insights on viral pathogenesis and can be valuable for diagnostic and drug development approaches.

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TMOD-15. IDENTIFYING THE SPATIAL AND TEMPORAL DYNAMICS OF GLIOBLASTOMA SUBPOPULATIONS WITHIN INDIVIDUAL PATIENTS

Neuro-Oncology ◽

10.1093/neuonc/noz175.1114 ◽

2019 ◽

Vol 21 (Supplement_6) ◽

pp. vi265-vi266

Author(s):

Bethan Morris ◽

Lee Curtin ◽

Andrea Hawkins-Daarud ◽

Bernard Bendok ◽

Maciej Mrugala ◽

...

Keyword(s):

Treatment Response ◽

Temporal Dynamics ◽

Dynamic Information ◽

Treatment Regimes ◽

Spatially Resolved ◽

Spatial And Temporal Dynamics ◽

Genetic Features ◽

Spatio Temporal ◽

Insight Into

Abstract Glioblastomas (GBMs) are known to be complex tumors comprising multiple subpopulations of genetically-distinct cancer cells; it is thought that this genetic variation is a major factor in the lack of observed survival benefit of treatment regimes that target one of these subpopulations. The field of radiogenomics seeks to study correlations between MRI patterns and genetic features of GBM tumors. Spatial radiogenomic maps produced using machine-learning (ML) methods that are trained against information from image-localized patient biopsies identify regions where particular cancer sub-populations are predicted to occur within a GBM, thus non-invasively characterizing the regional genetic variability of these tumors. These tumor subpopulations may also interact with one another, in ways which may be of a competitive or cooperative nature to varying degrees. It is important to ascertain the nature of these interactions, as they may have implications for treatment response to targeted therapies, and characterization of the spatio-temporal dynamics of these co-evolving sub-populations will shed light on why some therapies fail. Here we combine mathematical modeling techniques and spatially-resolved radiogenomic maps to study the nature of these interactions between molecularly-distinct GBM subpopulations. We model the interactions between cell populations using a partial differential equation based formalism. The model is parameterized using radiogenomic ML maps from which we infer the nature of interactions between subpopulations. Furthermore, using maps as inputs, the model turns static maps into dynamic information, thus providing insight into how these subpopulations composing the tumor change over time and the effect this has on observed treatment response for individual patients.

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Real-time characterization of the spatio-temporal dynamics of deformable mirrors

10.1117/12.2238431 ◽

2016 ◽

Author(s):

James Kilpatrick ◽

Adela Apostol ◽

Anatoliy Khizhnya ◽

Vladimir Markov ◽

Leonid Beresnev

Keyword(s):

Real Time ◽

Temporal Dynamics ◽

Deformable Mirrors ◽

Spatio Temporal

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Hot spot detection and spatio-temporal dynamics of dengue in Queensland, Australia

ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences ◽

10.5194/isprsarchives-xl-8-197-2014 ◽

2014 ◽

Vol XL-8 ◽

pp. 197-204 ◽

Cited By ~ 6

Author(s):

S. Naish ◽

S. Tong

Keyword(s):

Temporal Variation ◽

Temporal Dynamics ◽

Hot Spot ◽

Seasonal Pattern ◽

Temporal Distribution ◽

Health Concern ◽

Spatial And Temporal Variation ◽

Dengue Case ◽

Spatio Temporal ◽

Over Time

Dengue has been a major public health concern in Australia since it re-emerged in Queensland in 1992–1993. This study explored spatio-temporal distribution and clustering of locally-acquired dengue cases in Queensland State, Australia and identified target areas for effective interventions. A computerised locally-acquired dengue case dataset was collected from Queensland Health for Queensland from 1993 to 2012. Descriptive spatial and temporal analyses were conducted using geographic information system tools and geostatistical techniques. Dengue hot spots were detected using SatScan method. Descriptive spatial analysis showed that a total of 2,398 locally-acquired dengue cases were recorded in central and northern regions of tropical Queensland. A seasonal pattern was observed with most of the cases occurring in autumn. Spatial and temporal variation of dengue cases was observed in the geographic areas affected by dengue over time. Tropical areas are potential high-risk areas for mosquito-borne diseases such as dengue. This study demonstrated that the locally-acquired dengue cases have exhibited a spatial and temporal variation over the past twenty years in tropical Queensland, Australia. There is a clear evidence for the existence of statistically significant clusters of dengue and these clusters varied over time. These findings enabled us to detect and target dengue clusters suggesting that the use of geospatial information can assist the health authority in planning dengue control activities and it would allow for better design and implementation of dengue management programs.

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Temporal dynamics of SARS-CoV-2 mutation accumulation within and across infected hosts

10.1101/2021.01.19.427330 ◽

2021 ◽

Author(s):

Andrew L. Valesano ◽

Kalee E. Rumfelt ◽

Derek E. Dimcheff ◽

Christopher N. Blair ◽

William J. Fitzsimmons ◽

...

Keyword(s):

Genetic Variants ◽

Temporal Dynamics ◽

Medical Center ◽

Variant Calling ◽

Global Consensus ◽

Temporal Aspects ◽

Host Genetic ◽

Insight Into ◽

High Depth ◽

Shared Variation

AbstractAnalysis of SARS-CoV-2 genetic diversity within infected hosts can provide insight into the generation and spread of new viral variants and may enable high resolution inference of transmission chains. However, little is known about temporal aspects of SARS-CoV-2 intrahost diversity and the extent to which shared diversity reflects convergent evolution as opposed to transmission linkage. Here we use high depth of coverage sequencing to identify within-host genetic variants in 325 specimens from hospitalized COVID-19 patients and infected employees at a single medical center. We validated our variant calling by sequencing defined RNA mixtures and identified a viral load threshold that minimizes false positives. By leveraging clinical metadata, we found that intrahost diversity is low and does not vary by time from symptom onset. This suggests that variants will only rarely rise to appreciable frequency prior to transmission. Although there was generally little shared variation across the sequenced cohort, we identified intrahost variants shared across individuals who were unlikely to be related by transmission. These variants did not precede a rise in frequency in global consensus genomes, suggesting that intrahost variants may have limited utility for predicting future lineages. These results provide important context for sequence-based inference in SARS-CoV-2 evolution and epidemiology.

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EvoFreq: visualization of the Evolutionary Frequencies of sequence and model data

BMC Bioinformatics ◽

10.1186/s12859-019-3173-y ◽

2019 ◽

Vol 20 (1) ◽

Cited By ~ 4

Author(s):

Chandler D. Gatenbee ◽

Ryan O. Schenck ◽

Rafael R. Bravo ◽

Alexander R. A. Anderson

Keyword(s):

High Throughput ◽

Evolutionary Dynamics ◽

Temporal Dynamics ◽

Sequence Data ◽

Single Point ◽

Model Data ◽

Genotype Frequencies ◽

Tool Set ◽

Over Time

Abstract Background High throughput sequence data has provided in depth means of molecular characterization of populations. When recorded at numerous time steps, such data can reveal the evolutionary dynamics of the population under study by tracking the changes in genotype frequencies over time. This necessitates a simple and flexible means of visualizing an increasingly complex set of data. Results Here we offer EvoFreq as a comprehensive tool set to visualize the evolutionary and population frequency dynamics of clones at a single point in time or as population frequencies over time using a variety of informative methods. EvoFreq expands substantially on previous means of visualizing the clonal, temporal dynamics and offers users a range of options for displaying their sequence or model data. Conclusions EvoFreq, implemented in R with robust user options and few dependencies, offers a high-throughput means of quickly building, and interrogating the temporal dynamics of hereditary information across many systems. EvoFreq is freely available via https://github.com/MathOnco/EvoFreq.

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Large scale spatio-temporal patterns of road development in the Amazon rainforest

Environmental Conservation ◽

10.1017/s0376892913000520 ◽

2013 ◽

Vol 41 (3) ◽

pp. 253-264 ◽

Cited By ~ 4

Author(s):

SADIA E. AHMED ◽

ROBERT M. EWERS ◽

MATTHEW J. SMITH

Keyword(s):

Large Scale ◽

Temporal Dynamics ◽

Temporal Patterns ◽

Biodiversity Loss ◽

Road Density ◽

Road Development ◽

Spatio Temporal ◽

Dominant Direction ◽

Dynamics Of Populations

SUMMARYThere is burgeoning interest in predicting road development because of the wide ranging important socioeconomic and environmental issues that roads present, including the close links between road development, deforestation and biodiversity loss. This is especially the case in developing nations, which are high in natural resources, where road development is rapid and often not centrally managed. Characterization of large scale spatio-temporal patterns in road network development has been greatly overlooked to date. This paper examines the spatio-temporal dynamics of road density across the Brazilian Amazon and assesses the relative contributions of local versus neighbourhood effects for temporal changes in road density at regional scales. To achieve this, a combination of statistical analyses and model-data fusion techniques inspired by studies of spatio-temporal dynamics of populations in ecology and epidemiology were used. The emergent development may be approximated by local growth that is logistic through time and directional dispersal. The current rates and dominant direction of development may be inferred, by assuming that roads develop at a rate of 55 km per year. Large areas of the Amazon will be subject to extensive anthropogenic change should the observed patterns of road development continue.

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Characterization of In Vivo Function(s) of Members of the Plant Mitochondrial Carrier Family

Biomolecules ◽

10.3390/biom10091226 ◽

2020 ◽

Vol 10 (9) ◽

pp. 1226

Author(s):

Adriano Nunes-Nesi ◽

João Henrique F. Cavalcanti ◽

Alisdair R. Fernie

Keyword(s):

Endoplasmic Reticulum ◽

Plasma Membrane ◽

Genetic Variants ◽

Mitochondrial Carrier ◽

Wide Range ◽

Mitochondrial Carrier Family ◽

Insight Into ◽

Green Lineage

Although structurally related, mitochondrial carrier family (MCF) proteins catalyze the specific transport of a range of diverse substrates including nucleotides, amino acids, dicarboxylates, tricarboxylates, cofactors, vitamins, phosphate and H+. Despite their name, they do not, however, always localize to the mitochondria, with plasma membrane, peroxisomal, chloroplast and thylakoid and endoplasmic reticulum localizations also being reported. The existence of plastid-specific MCF proteins is suggestive that the evolution of these proteins occurred after the separation of the green lineage. That said, plant-specific MCF proteins are not all plastid-localized, with members also situated at the endoplasmic reticulum and plasma membrane. While by no means yet comprehensive, the in vivo function of a wide range of these transporters is carried out here, and we discuss the employment of genetic variants of the MCF as a means to provide insight into their in vivo function complementary to that obtained from studies following their reconstitution into liposomes.

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Modeling Spatio-temporal Dynamics of Chromatin Marks

10.1101/239442 ◽

2017 ◽

Author(s):

Petko Fiziev ◽

Jason Ernst

Keyword(s):

Gene Expression ◽

Time Course ◽

Temporal Dynamics ◽

Spatial Dynamics ◽

Computational Method ◽

Time Points ◽

Signal Density ◽

Spatial Changes ◽

Spatio Temporal ◽

Over Time

ABSTRACTTo model spatial changes of chromatin mark peaks over time we developed and applied ChromTime, a computational method that predicts regions for which peaks either expand or contract significantly or hold steady between time points. Predicted expanding and contracting peaks can mark regulatory regions associated with transcription factor binding and gene expression changes. Spatial dynamics of peaks provided information about gene expression changes beyond localized signal density changes. ChromTime detected asymmetric expansions and contractions, which for some marks associated with the direction of transcription. ChromTime facilitates the analysis of time course chromatin data in a range of biological systems.

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Similarity-based fusion of MEG and fMRI reveals spatio-temporal dynamics in human cortex during visual object recognition

10.1101/032656 ◽

2015 ◽

Cited By ~ 5

Author(s):

Radoslaw Cichy ◽

Dimitrios Pantazis ◽

Aude Oliva

Keyword(s):

Object Recognition ◽

Temporal Dynamics ◽

Imaging Techniques ◽

Visual Object ◽

Data Sets ◽

Visual Object Recognition ◽

Occipital Pole ◽

Spatio Temporal ◽

The Brain

Every human cognitive function, such as visual object recognition, is realized in a complex spatio-temporal activity pattern in the brain. Current brain imaging techniques in isolation cannot resolve the brain's spatio-temporal dynamics because they provide either high spatial or temporal resolution but not both. To overcome this limitation, we developed a new integration approach that uses representational similarities to combine measurements from different imaging modalities - magnetoencephalography (MEG) and functional MRI (fMRI) - to yield a spatially and temporally integrated characterization of neuronal activation. Applying this approach to two independent MEG-fMRI data sets, we observed that neural activity first emerged in the occipital pole at 50-80ms, before spreading rapidly and progressively in the anterior direction along the ventral and dorsal visual streams. These results provide a novel and comprehensive, spatio-temporally resolved view of the rapid neural dynamics during the first few hundred milliseconds of object vision. They further demonstrate the feasibility of spatially unbiased representational similarity based fusion of MEG and fMRI, promising new insights into how the brain computes complex cognitive functions.

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Characterization and spatio-temporal dynamics of Cylindrospermopsis raciborski in an Amazonian Lagoon, Ecuador.

Enfoque UTE ◽

10.29019/enfoqueute.v9n2.195 ◽

2018 ◽

Vol 9 (2) ◽

pp. 117-124

Author(s):

Judith Venegas ◽

Pablo Castillejo Pons ◽

Susana Chamorro ◽

Ivonne Carrillo ◽

Eduardo Lobo

Keyword(s):

Fresh Water ◽

Environmental Conditions ◽

Scientific Literature ◽

Temporal Dynamics ◽

Cylindrospermopsis Raciborskii ◽

Human Consumption ◽

Distribution Maps ◽

Spatio Temporal ◽

Recreational Use

The cyanobacteria Cylindrospermopsis raciborskii, is a fresh water ubiquitous species from tropical to temperate weather. It is potentially capable of producing toxins. Thus it is necessary to monitor its presence in fresh waters associated to recreational use activities and human consumption. There are official reports and one thesis reporting the presence of C. raciborskii in Ecuador. Nevertheless, this country does not appear in the latest distribution maps of this species in the scientific literature. In this article, we report the presence of C. raciborskii in Ecuador, together with the characterization of the environmental conditions of one of the habitats where this species is present: the Limoncocha lagoon, province of Sucumbíos.

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