Circulation and Evolution of SARS-CoV-2 in India: Let the Data Speak

The COVID-19 pandemic is a global challenge that impacted 200+ countries. India ranks in the second and third positions in terms of number of reported cases and deaths. Being a populous country with densely packed cities, SARS-CoV-2 spread exponentially. India sequenced ≈0.14% isolates from confirmed cases for pandemic surveillance and contributed ≈1.58% of complete genomes sequenced globally. This study was designed to map the circulating lineage diversity and to understand the evolution of SARS-CoV-2 in India using comparative genomics and population genetics approaches. Despite varied sequencing coverage across Indian States and Union Territories, isolates belonging to variants of concern (VoC) and variants of interest (VoI) circulated, persisted, and diversified during the first seventeen months of the pandemic. Delta and Kappa lineages emerged in India and spread globally. The phylogenetic tree shows lineage-wise monophyletic clusters of VoCs/VoIs and diversified tree topologies for non-VoC/VoI lineages designated as ‘Others’ in this study. Evolutionary dynamics analyses substantiate a lack of spatio-temporal clustering, which is indicative of multiple global and local introductions. Sites under positive selection and significant variations in spike protein corroborate with the constellation of mutations to be monitored for VoC/VoI as well as substitutions that are characteristic of functions with implications in virus–host interactions, differential glycosylation, immune evasion, and escape from neutralization.

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

Science ◽

10.1126/science.abf2946 ◽

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.

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Spatio-temporal ecological and evolutionary dynamics in natural butterfly populations

The UW National Parks Service Research Station Annual Reports ◽

10.13001/uwnpsrc.2017.5563 ◽

2017 ◽

Vol 40 ◽

pp. 31-36

Author(s):

Zachariah Gompert ◽

Lauren Lucas

Keyword(s):

Evolutionary Dynamics ◽

Natural Populations ◽

Distance Sampling ◽

Spatial And Temporal Variation ◽

Insect Community ◽

Long Term Study ◽

Greater Yellowstone Area ◽

Genome Wide ◽

Spatio Temporal

Long term studies of wild populations indicate that natural selection can cause rapid and dramatic changes in traits, with spatial and temporal variation in the strength of selection a critical driver of genetic variation in natural populations. In 2012, we began a long term study of genome-wide molecular evolution in populations of the butterfly Lycaeides ideas in the Greater Yellowstone Area (GYA). We aimed to quantify the role of environment-dependent selection on evolution in these populations. Building on previous work, in 2017 we collected new samples, incorporated distance sampling, and surveyed the insect community at each site. We also defined the habitat boundary at anew, eleventh site. Our preliminary analyses suggest that both genetic drift and selection are important drivers in this system. Featured photo from Figure 1 in report.

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Recognizing Human Actions in Basketball Video Sequences on the Basis of Global and Local Pairwise Representation

Computer Vision ◽

10.4018/978-1-5225-5204-8.ch091 ◽

2018 ◽

pp. 2083-2101

Author(s):

Masaki Takahashi ◽

Masahide Naemura ◽

Mahito Fujii ◽

James J. Little

Keyword(s):

Feature Representation ◽

Video Sequences ◽

Human Actions ◽

The Public ◽

Motion Features ◽

Spatio Temporal ◽

Representation Method ◽

Global And Local ◽

The Relationship ◽

Local Representations

A feature-representation method for recognizing actions in sports videos on the basis of the relationship between human actions and camera motions is proposed. The method involves the following steps: First, keypoint trajectories are extracted as motion features in spatio-temporal sub-regions called “spatio-temporal multiscale bags” (STMBs). Global representations and local representations from one sub-region in the STMBs are then combined to create a “glocal pairwise representation” (GPR). The GPR considers the co-occurrence of camera motions and human actions. Finally, two-stage SVM classifiers are trained with STMB-based GPRs, and specified human actions in video sequences are identified. An experimental evaluation of the recognition accuracy of the proposed method (by using the public OSUPEL basketball video dataset and broadcast videos) demonstrated that the method can robustly detect specific human actions in both public and broadcast basketball video sequences.

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Spatio-temporal variations in agricultural diversification in India

Journal of Agribusiness in Developing and Emerging Economies ◽

10.1108/jadee-11-2018-0161 ◽

2019 ◽

Vol 9 (5) ◽

pp. 476-502 ◽

Cited By ~ 1

Author(s):

Md Ejaz Anwer ◽

Bimal Kishore Sahoo ◽

Simantini Mohapatra

Keyword(s):

Capita Income ◽

Temporal Variations ◽

Primary Study ◽

Per Capita Income ◽

Indian States ◽

Price Inflation ◽

Content Type ◽

Agricultural Diversification ◽

Per Capita ◽

Spatio Temporal

Purpose Agriculture diversification acts as income enhancing as well as distress mitigating strategy. India has witnessed rise in per-capita income which in turn has increased the demand for food particularly high-valued food items but agricultural production has failed to keep pace with the growing demand. The purpose of this paper is to examine spatio-temporal variations in agricultural diversification (AD) in India. Second, the authors try to identify the determinants of AD. Third, the authors examine the convergence hypothesis with reference to agriculture diversification across Indian states. Design/methodology/approach The study is based on the panel data constituting 20 major states of India during 1990–1991 to 2013–2014. It uses Simpson Diversification Index to measure AD. The heteroskedasticity-corrected panel regression model is applied to find out the determinants of AD. The fixed-effects model is used to examine β-convergence in AD across the sample states. Alternative time series models are applied to examine σ-convergence in AD. Findings The rising per-capita income and urbanization are driving dietary diversity towards high-valued crops and providing ample opportunity for AD. But poor and inadequate cold storage facility and rising cost of cultivation are posing major hindrance to it. Small land holding and road length have negatively influenced AD which is contrary to the traditional wisdom. The study found divergence in diversification and rising inequality in diversification. Research limitations/implications The study is based on secondary data. A primary study to complement this could have been better. It is only based on one country. Social implications Food inflation has serious adverse effect on the society at large. It is necessary to promote AD for controlling food price inflation. Minimum support price provided by the government should be extended to all crops; otherwise, it will fuel inflation. Given the fact fragmentation of land holding is adversely affecting AD, community based farming and consolidation of farm land should be the way forward to improve farmers’ income as well as reduce risk. Originality/value To best of the authors’ study, this is the first study that examines determinants of AD and convergence in AD during the high growth period of India.

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Phylogeography and evolutionary dynamics analysis of porcine delta-coronavirus with host expansion to humans

10.22541/au.163255668.83590934/v1 ◽

2021 ◽

Author(s):

Gen Li ◽

Shao-Lun Zhai ◽

Xia Zhou ◽

Tianbao Chen ◽

Jiawei Niu ◽

...

Keyword(s):

Evolutionary Dynamics ◽

Molecular Genetic ◽

Molecular Genetic Analysis ◽

Amino Acid Sequences ◽

Interspecies Transmission ◽

Protein Membrane ◽

Red Flag ◽

Spatio Temporal ◽

Comprehensive Surveillance ◽

Insight Into

From 2003 onwards, three pandemics have been caused by coronaviruses: severe acute respiratory syndrome coronavirus (SARS-CoV); middle east respiratory syndrome coronavirus (MERS-CoV); and, most recently, SARS-CoV-2. Notably, all three were transmitted from animals to humans. This would suggest that animals are potential sources of epidemics for humans. The emerging porcine delta-coronavirus was reported to infect children. This is a red flag that marks the ability of PDCoV to break barriers of cross-species transmission to humans. Therefore, we conducted molecular genetic analysis of global clade PDCoV to characterize spatio-temporal patterns of viral diffusion and genetic diversity. PDCoV was classified into three major lineages, according to distribution and phylogenetic analysis of PDCoV. It can be determined that PDCoV originated in Asia—most likely in Southeast Asia—through inference of migration rate and transmission routes. We also selected six special spike amino acid sequences to align and analyze to find seven significant mutation sites. The accumulation of these mutations may enhance dynamic movements, accelerating spike protein membrane fusion events and transmission. Altogether, our study offers a novel insight into the diversification, evolution, and interspecies transmission and origin of PDCoV and emphasizes the need to study the zoonotic potential of the PDCoV and comprehensive surveillance and enhanced biosecurity precautions for PDCoV.

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Drosophila Evolution over Space and Time (DEST) - A New Population Genomics Resource

Molecular Biology and Evolution ◽

10.1093/molbev/msab259 ◽

2021 ◽

Author(s):

Martin Kapun ◽

Joaquin C B Nunez ◽

María Bogaerts-Márquez ◽

Jesús Murga-Moreno ◽

Margot Paris ◽

...

Keyword(s):

Evolutionary Dynamics ◽

Population Genomics ◽

Natural Populations ◽

Easy Access ◽

Data Repository ◽

Bioinformatics Pipeline ◽

Space And Time ◽

Sequencing Technologies ◽

Spatio Temporal ◽

Demographic Inference

Abstract Drosophila melanogaster is a leading model in population genetics and genomics, and a growing number of whole-genome datasets from natural populations of this species have been published over the last years. A major challenge is the integration of disparate datasets, often generated using different sequencing technologies and bioinformatic pipelines, which hampers our ability to address questions about the evolution of this species. Here we address these issues by developing a bioinformatics pipeline that maps pooled sequencing (Pool-Seq) reads from D. melanogaster to a hologenome consisting of fly and symbiont genomes and estimates allele frequencies using either a heuristic (PoolSNP) or a probabilistic variant caller (SNAPE-pooled). We use this pipeline to generate the largest data repository of genomic data available for D. melanogaster to date, encompassing 271 previously published and unpublished population samples from over 100 locations in > 20 countries on four continents. Several of these locations have been sampled at different seasons across multiple years. This dataset, which we call Drosophila Evolution over Space and Time (DEST), is coupled with sampling and environmental meta-data. A web-based genome browser and web portal provide easy access to the SNP dataset. We further provide guidelines on how to use Pool-Seq data for model-based demographic inference. Our aim is to provide this scalable platform as a community resource which can be easily extended via future efforts for an even more extensive cosmopolitan dataset. Our resource will enable population geneticists to analyze spatio-temporal genetic patterns and evolutionary dynamics of D. melanogaster populations in unprecedented detail.

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Plasmid co-infection: linking biological mechanisms to ecological and evolutionary dynamics

Philosophical Transactions of the Royal Society B Biological Sciences ◽

10.1098/rstb.2020.0478 ◽

2021 ◽

Vol 377 (1842) ◽

Cited By ~ 1

Author(s):

Claudia Igler ◽

Jana S. Huisman ◽

Berit Siedentop ◽

Sebastian Bonhoeffer ◽

Sonja Lehtinen

Keyword(s):

Evolutionary Dynamics ◽

Theoretical Work ◽

Plasmid Copy Number ◽

Biological Processes ◽

Ecological Interactions ◽

Biological Mechanisms ◽

Plasmid Copy ◽

Host Interactions ◽

Evolutionary Epidemiology ◽

The Impact

As infectious agents of bacteria and vehicles of horizontal gene transfer, plasmids play a key role in bacterial ecology and evolution. Plasmid dynamics are shaped not only by plasmid–host interactions but also by ecological interactions between plasmid variants. These interactions are complex: plasmids can co-infect the same cell and the consequences for the co-resident plasmid can be either beneficial or detrimental. Many of the biological processes that govern plasmid co-infection—from systems that exclude infection by other plasmids to interactions in the regulation of plasmid copy number—are well characterized at a mechanistic level. Modelling plays a central role in translating such mechanistic insights into predictions about plasmid dynamics and the impact of these dynamics on bacterial evolution. Theoretical work in evolutionary epidemiology has shown that formulating models of co-infection is not trivial, as some modelling choices can introduce unintended ecological assumptions. Here, we review how the biological processes that govern co-infection can be represented in a mathematical model, discuss potential modelling pitfalls, and analyse this model to provide general insights into how co-infection impacts ecological and evolutionary outcomes. In particular, we demonstrate how beneficial and detrimental effects of co-infection give rise to frequency-dependent selection on plasmid variants. This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.

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Phylogeography of hepatitis B: The role of Portugal in the early dissemination of HBV worldwide

10.1101/2022.01.05.22268725 ◽

2022 ◽

Author(s):

Rute Marcelino ◽

Ifeanyi J Ezeonwumelu ◽

Andre Janeiro ◽

Paula Mimoso ◽

Sonia Matos ◽

...

Keyword(s):

Evolutionary Dynamics ◽

Hbv Genotype ◽

Hbv Genotypes ◽

Molecular Clock Model ◽

Global Spread ◽

History Of ◽

Spatio Temporal ◽

Relaxed Molecular Clock ◽

Nucleotide Substitution Model

In Portugal, the genetic diversity, origin of HBV, and the Portuguese role in the dissemination of HBV worldwide were never investigated. In this work, we studied the epidemic history and transmission dynamics of HBV genotypes that are endemic in Portugal. HBV pol gene was sequenced from 130 patients followed in Lisbon. HBV genotype A (HBV/A) was the most prevalent (n=54, 41.5%), followed by D [HBV/D; (n=44, 33.8%)], and E [HBV/E; (n=32, 24.6%)]. Spatio-temporal evolutionary dynamics was reconstructed in BEAST using a Bayesian Markov Chain Monte Carlo method, with a GTR nucleotide substitution model, an uncorrelated lognormal relaxed molecular clock model, a Bayesian skyline plot, and a continuous diffusion model. HBV/D4 was the first subgenotype to be introduced in Portugal around 1857 (HPD 95% 1699-1931) followed by HBV/D3 and A2 a few decades later. HBV/E and HBV/A1 were introduced in Portugal later, almost simultaneously. Our results also indicate a very important role of Portugal in the exportation of HBV/D4 and A2 to Brazil and Cape Verde, respectively, at the beginning of the XX century. This work clarifies the epidemiological history of HBV in Portugal and shows that Portugal had an important role in the global spread of this virus.

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Evolutionary Dynamics of Viruses or Microbes, but Not Both

Quantitative Viral Ecology ◽

10.23943/princeton/9780691161549.003.0004 ◽

2016 ◽

Author(s):

Joshua S. Weitz

Keyword(s):

Life History ◽

Evolutionary Dynamics ◽

Selective Pressure ◽

Host Interactions ◽

Intermediate Phenotypes ◽

Strong Selective Pressure ◽

Evolution Of Resistance ◽

Resistance To Infection ◽

Host Evolution ◽

Different Levels

This chapter discusses the evolutionary dynamics of viruses. Preexisting variation in host phenotypes include variants with different levels of susceptibility to viruses, including complete resistance. Formative studies of the basis of the mutation rate relied upon virus–host interactions and the possibility of the evolution of resistance to infection. Viruses represent a strong selective pressure and can induce evolution among hosts. Host evolution, as induced by viruses, includes novel forms of ecological dynamics, including cryptic dynamics. Infection of hosts represents a strong selective pressure for viruses. Viruses that differ in their life history traits vary in their fitness and can invade and replace existing viral strains. The latent period represents a model trait for the further study of the evolution of intermediate phenotypes. Evolution among other traits is also possible, including who infects whom.

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The Spatio-Temporal Heterogeneity of Financial Agglomeration on Green Development in China Cities Using GTWR Model

Sustainability ◽

10.3390/su12166660 ◽

2020 ◽

Vol 12 (16) ◽

pp. 6660

Author(s):

Huaxi Yuan ◽

Yidai Feng ◽

Jay Lee ◽

Haimeng Liu

Keyword(s):

Spatial Association ◽

Spatial Clusters ◽

Promoting Effect ◽

Main Cluster ◽

Green Development ◽

Temporal Influence ◽

Spatio Temporal ◽

Global And Local ◽

Local Perspectives ◽

Pressure State

By promoting financial agglomerations to support green development in a region is a keyway for China to resolve the sharp contradiction between economic growth and environmental protection. However, existing research only considered the promotion effect of financial agglomerations on green development, but the spatio-temporal non-stationarity of that effect has been overlooked. Using a panel data of 285 prefecture-level cities in China and based on the evaluation of green development by a Driving-Pressure-State-Impact-Response (DPSIR) model, this paper analyzes the spatial correlation of financial agglomeration on green development. The paper also investigates the differences in the spatio-temporal influence of financial agglomeration on green development from both global and local perspectives by employing a Bivariate Local Indicators of Spatial Association (BLISA) model and a Geographically and Temporally Weighted Regression (GTWR) model. The results indicate that: (1) There exists significant spatial dependency between financial agglomeration and green development from 2003 to 2015, with Low-Low (L-L) and Low-High (L-H) spatial clusters as the main cluster types. (2) From the local perspective, the promoting effect of financial agglomerations on green development has showed significant spatial heterogeneity with a gradually decreasing trend from the southeast coast to the northwest inland of China. This work can help to develop policies for supporting green development by formulating differential strategies for financial agglomerations.

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