A Phylogenomic and Evolutionary Perspectives of COVID-19

From the time immemorial, all drastic pandemics and associated pathogens have been under the spotlight of research in our attempts to identify, characterise, control and trace back their origin. Quite often such attempts have enabled mankind to find effective solutions to overcome such pathogen outbreaks and turn them to pages of history. In the wake of repeated infections in different corners of the world, its quite essential to evaluate if they are the cruel aftermaths of nature or any manmade error. In such as scenario, recent developments in the molecular evolutionary analysis offer us more information in-depth regarding the virus emergence, molecular epidemiology, virulence and evolutionary concepts, adding to the conventional strategies in viral epidemiology. The nucleotide sequences were retrieved from NCBI. The present study revealed the genetic variability of CoV, 2019-nCoV against previously reported corona viruses. Moreover, the genetic variability of COVID-19 from different affected corners of the globe are evaluated to get a better understanding of their modes and routes of spread across our planet.Such nucleotide sequence-analyzed information gathered from this investigation will definitely assist the intention and implementation of effective pandemic control measures.

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The Location of Substitutions and Bacterial Genome Arrangements

Genome Biology and Evolution ◽

10.1093/gbe/evaa260 ◽

2020 ◽

Author(s):

Daniella F Lato ◽

G Brian Golding

Keyword(s):

Sinorhizobium Meliloti ◽

Bacterial Genome ◽

Evolutionary Analysis ◽

Origin Of Replication ◽

Ancestral Reconstruction ◽

Molecular Change ◽

E Coli ◽

A Genome ◽

The Impact ◽

Molecular Evolutionary Analysis

Abstract Increasing evidence supports the notion that different regions of a genome have unique rates of molecular change. This variation is particularly evident in bacterial genomes where previous studies have reported gene expression and essentiality tend to decrease, while substitution rates usually increases with increasing distance from the origin of replication. Genomic reorganization such as rearrangements occur frequently in bacteria and allow for the introduction and restructuring of genetic content, creating gradients of molecular traits along genomes. Here, we explore the interplay of these phenomena by mapping substitutions to the genomes of Escherichia coli, Bacillus subtilis, Streptomyces, and Sinorhizobium meliloti, quantifying how many substitutions have occurred at each position in the genome. Preceding work indicates that substitution rate significantly increases with distance from the origin. Using a larger sample size and accounting for genome rearrangements through ancestral reconstruction, our analysis demonstrates that the correlation between the number of substitutions and distance from the origin of replication is often significant but small and inconsistent in direction. Some replicons had a significantly decreasing trend (E. coli and the chromosome of S. meliloti), while others showed the opposite significant trend (B. subtilis, Streptomyces, pSymA and pSymB in S. meliloti). dN, dS and ω were examined across all genes and there was no significant correlation between those values and distance from the origin. This study highlights the impact that genomic rearrangements and location have on molecular trends in some bacteria, illustrating the importance of considering spatial trends in molecular evolutionary analysis. Assuming that molecular trends are exclusively in one direction can be problematic.

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Classification of hepatitis C virus into major types and subtypes based on molecular evolutionary analysis

Virus Research ◽

10.1016/0168-1702(95)00007-d ◽

1995 ◽

Vol 36 (2-3) ◽

pp. 201-214 ◽

Cited By ~ 21

Author(s):

Ken-ichi Ohba ◽

Masashi Mizokami ◽

Tomoyoshi Ohno ◽

Kaoru Suzuki ◽

Etsuro Orito ◽

...

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Evolutionary Analysis ◽

Molecular Evolutionary Analysis

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Molecular evolutionary analysis of decapentaplegic (dpp) gene in Drosophilidae

The Nucleus ◽

10.1007/s13237-014-0104-1 ◽

2014 ◽

Vol 57 (1) ◽

pp. 61-65

Author(s):

Arpita Rakshit ◽

Rabindra Nath Chatterjee

Keyword(s):

Evolutionary Analysis ◽

Molecular Evolutionary Analysis

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Protocols for the Molecular Evolutionary Analysis of Membrane Protein Gene Duplicates

Methods in Molecular Biology - Computational Methods in Protein Evolution ◽

10.1007/978-1-4939-8736-8_3 ◽

2018 ◽

pp. 49-62 ◽

Cited By ~ 5

Author(s):

Laurel R. Yohe ◽

Liang Liu ◽

Liliana M. Dávalos ◽

David A. Liberles

Keyword(s):

Membrane Protein ◽

Protein Gene ◽

Evolutionary Analysis ◽

Gene Duplicates ◽

Molecular Evolutionary Analysis ◽

Membrane Protein Gene

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Phylogenetic and molecular evolutionary analysis of SENV DNA isolated from Iraqi Hepatitis Patients

Bionatura ◽

10.21931/rb/2021.06.04.18 ◽

2021 ◽

Vol 6 (4) ◽

pp. 2251-2255

Author(s):

Arwa Mujahid Al-Shuwaikh ◽

Ealaf Abbas khudair ◽

Dalya Basil Hanna

Keyword(s):

Dna Sequences ◽

Genetic Alterations ◽

Torque Teno Virus ◽

Nucleotide Sequencing ◽

Evolutionary Analysis ◽

Dna Viruses ◽

Post Transfusion Hepatitis ◽

Substitution Mutations ◽

Sen Virus ◽

Molecular Evolutionary Analysis

SEN Virus (SENV) is a newly discovered group of transmissible, hepatotropic, single-stranded, circular, non-enveloped DNA viruses that are distantly linked to the widely distributed Torque Teno Virus (TTV) family. This research aimed to use nucleotide sequencing to identify the genetic alterations of SEN-V and to investigate the similarities between isolates. Seven DNA samples of SENV, which were previously extracted from blood of post transfusion hepatitis, were used to identify the genetic variation of SEN-V by nucleotide sequencing. According to the current analysis results, specific primer pairs were used to detect SENV DNA sequences isolated from Iraqi patients with hepatitis; however, those specific primers can also detect two new variants of SENV that are closely related to the Torque Teno Virus. In addition, four SENV isolates showed several substitution mutations, and one of them revealed the replacement of Proline (P) at position 11 with Serine (S). Only one local isolate of SENV was 100% identical to the Iranian isolate (GenBank acc. no. GQ452051.1) from thalassemia.

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Molecular evolutionary analysis of the widespread piggyBac transposon family and related "domesticated" sequences

Molecular Genetics and Genomics ◽

10.1007/s00438-003-0909-0 ◽

2003 ◽

Vol 270 (2) ◽

pp. 173-180 ◽

Cited By ~ 120

Author(s):

A. Sarkar ◽

C. Sim ◽

Y. S. Hong ◽

J. R. Hogan ◽

M. J. Fraser ◽

...

Keyword(s):

Evolutionary Analysis ◽

Piggybac Transposon ◽

Molecular Evolutionary Analysis

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Molecular Evolutionary Analysis: Its Application in the Study of Hepatitis C Virus

Hepatitis C Protocols ◽

10.1385/0-89603-521-2:147 ◽

2003 ◽

pp. 147-158 ◽

Cited By ~ 3

Author(s):

Masashi Mizokami ◽

Johnson Y. N. Lau

Keyword(s):

Hepatitis C Virus ◽

Hepatitis C ◽

Evolutionary Analysis ◽

Molecular Evolutionary Analysis

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Mathematical models for assessing the role of airflow on the risk of airborne infection in hospital wards

Journal of The Royal Society Interface ◽

10.1098/rsif.2009.0305.focus ◽

2009 ◽

Vol 6 (suppl_6) ◽

Cited By ~ 29

Author(s):

Catherine J. Noakes ◽

P. Andrew Sleigh

Keyword(s):

Environmental Control ◽

Environmental Parameters ◽

Control Measures ◽

Stochastic Version ◽

Airborne Infection ◽

Healthcare Settings ◽

Recent Developments ◽

Original Presentation ◽

Dynamics Simulations ◽

Hospital Wards

Understanding the risk of airborne transmission can provide important information for designing safe healthcare environments with an appropriate level of environmental control for mitigating risks. The most common approach for assessing risk is to use the Wells–Riley equation to relate infectious cases to human and environmental parameters. While it is a simple model that can yield valuable information, the model used as in its original presentation has a number of limitations. This paper reviews recent developments addressing some of the limitations including coupling with epidemic models to evaluate the wider impact of control measures on disease progression, linking with zonal ventilation or computational fluid dynamics simulations to deal with imperfect mixing in real environments and recent work on dose–response modelling to simulate the interaction between pathogens and the host. A stochastic version of the Wells–Riley model is presented that allows consideration of the effects of small populations relevant in healthcare settings and it is demonstrated how this can be linked to a simple zonal ventilation model to simulate the influence of proximity to an infector. The results show how neglecting the stochastic effects present in a real situation could underestimate the risk by 15 per cent or more and that the number and rate of new infections between connected spaces is strongly dependent on the airflow. Results also indicate the potential danger of using fully mixed models for future risk assessments, with quanta values derived from such cases less than half the actual source value.

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