scholarly journals Insights into The Codon Usage Bias of 13 Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) Isolates from Different Geo-locations

2020 ◽  
Author(s):  
Saif M. Khodary ◽  
Ali Mostafa Anwar
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Homo Sapiens ◽  
World Health ◽  
Codon Usage Pattern ◽  
Design Strategies ◽  
Mutation Pressure ◽  
A Genome ◽  
The World

AbstractSevere acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the causative agent of Coronavirus disease 2019 (COVID-19) which is an infectious disease that spread throughout the world and was declared as a pandemic by the World Health Organization (WHO). In this study, we performed a genome-wide analysis on the codon usage bias (CUB) of 13 SARS-CoV-2 isolates from different geo-locations (countries) in an attempt to characterize it, unravel the main force shaping its pattern, and understand its adaptation to Homo sapiens. Overall results revealed that, SARS-CoV-2 codon usage is slightly biased similarly to other RNA viruses. Nucleotide and dinucleotide compositions displayed a bias toward A/U content in all codon positions and CpU-ended codons preference, respectively. Eight common putative preferred codons were identified, and all of them were A/U-ended (U-ended: 7, A-ended: 1). In addition, natural selection was found to be the main force structuring the codon usage pattern of SARS-CoV-2. However, mutation pressure and other factors such as compositional constraints and hydrophobicity had an undeniable contribution. Two adaptation indices were utilized and indicated that SARS-CoV-2 is moderately adapted to Homo sapiens compared to other human viruses. The outcome of this study may help in understanding the underlying factors involved in the evolution of SARS-CoV-2 and may aid in vaccine design strategies.

scholarly journals Codon Usage Bias in Two Hemipteran Insect Species: Bemisia tabaci and Homalodisca coagulata

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Jyotika Sharma ◽  
Supriyo Chakraborty ◽  
Arif Uddin
Keyword(s):  
Codon Usage ◽  
Bemisia Tabaci ◽  
Codon Usage Bias ◽  
Codon Bias ◽  
Insect Species ◽  
Codon Usage Pattern ◽  
Mutation Pressure ◽  
Homalodisca Coagulata ◽  
Highly Expressed Genes ◽  
Hemipteran Insect

Codon bias is the nonuniform use of synonymous codons which encode the same amino acid. Some codons are more frequently used than others in several organisms, particularly in the highly expressed genes. The spectacular diversity of insects makes them a suitable candidate for analyzing the codon usage bias. Recent expansion in genome sequencing of different insect species provides an opportunity for studying the codon usage bias. Several works on patterns of codon usage bias were done on Drosophila and other related species but only few works were found in Hemiptera order. We analyzed codon usage in two Hemipteran insect species namely Bemisia tabaci and Homalodisca coagulata. Most frequent codons end with A or C at the 3rd codon position. The ENC (a measure of codon bias) value ranges from 43 to 60 (52.80) in B. tabaci but from 49 to 60 (56.69) in H. coagulata. In both insect species, a significant positive correlation was observed between A and A3%, C and C3%, and GC and GC3%, respectively. Our findings suggest that codon usage bias in two Hemipteran insect species is not remarkable and that mutation pressure causes the codon usage pattern in two Hemipteran insect species.

scholarly journals Comprehensive Analysis of Codon Usage Patterns in Chinese Porcine Circoviruses Based on Their Major Protein-Coding Sequences

Viruses ◽  
2022 ◽  
Vol 14 (1) ◽  
pp. 81
Author(s):  
Hua Feng ◽  
Joaquim Segalés ◽  
Fangyu Wang ◽  
Qianyue Jin ◽  
Aiping Wang ◽  
...  
Keyword(s):  
Natural Selection ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Large Scale ◽  
Codon Usage Pattern ◽  
Major Protein ◽  
Mutation Pressure ◽  
Coding Sequences ◽  
Usage Patterns ◽  
Porcine Circoviruses

Porcine circoviruses (PCVs) are distributed in swine herds worldwide and represent a threat to the health of domestic pigs and the profits of the swine industry. Currently, four PCV species, including PCV-1, PCV-2, PCV-3 and PCV-4, have been identified in China. Considering the ubiquitous characteristic of PCVs, the new emerged PCV-4 and the large scale of swine breeding in China, an overall analysis on codon usage bias for Chinese PCV sequences was performed by using the major proteins coding sequences (ORF1 and ORF2) to better understand the relationship of these viruses with their host. The data from genome nucleotide frequency composition and relative synonymous codon usage (RSCU) analysis revealed an overrepresentation of AT pair and the existence of a certain codon usage bias in all PCVs. However, the values of an effective number of codons (ENC) revealed that the bias was of low magnitude. Principal component analysis, ENC-plot, parity rule two analysis and correlation analysis suggested that natural selection and mutation pressure were both involved in the shaping of the codon usage patterns of PCVs. However, a neutrality plot revealed a stronger effect of natural selection than mutation pressure on codon usage patterns. Good host adaptation was also shown by the codon adaptation index analysis for all these viruses. Interestingly, obtained data suggest that PCV-4 might be more adapted to its host compared to other PCVs. The present study obtained insights into the codon usage pattern of PCVs based on ORF1 and ORF2, which further helps the understanding the molecular evolution of these swine viruses.

scholarly journals SARS-CoV-2 codon usage bias downregulates host expressed genes with similar codon usage

2020 ◽  
Author(s):  
Andres Mariano Alonso ◽  
Luis Diambra
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
World Health Organisation ◽  
Host Protein ◽  
World Health ◽  
Translation Rate ◽  
Proteomic Data ◽  
The World ◽  
Highly Expressed Genes ◽  
Infected Cells

ABSTRACTSevere acute respiratory syndrome is quickly spreading throughout the world and was declared as a pandemic by the World Health Organisation (WHO). The pathogenic agent is a new coronavirus (SARS-CoV-2) that infects pulmonary cells with great effectiveness. In this study we focus on the codon composition for the viral proteins synthesis and its relationship with the proteins synthesis of the host. Our analysis reveals that SARS-CoV-2 preferred codons have poor representation of G or C nucleotides in the third position, a characteristic which could conduct to an unbalance in the tRNAs pools of the infected cells with serious implications in host protein synthesis. By integrating this observation with proteomic data from infected cells, we observe a reduced translation rate of host proteins associated with highly expressed genes, and that they share the codon usage bias of the virus. The functional analysis of these genes suggests that this mechanism of epistasis contributes to understand some deleterious collateral effect as result of the viral replication. In this manner, our finding contribute to the understanding of the SARS-CoV-2 pathogeny and could be useful for the design of a vaccine based on the live attenuated strategy.

The relevance of dietetic approach of Ayurveda from the perspective of COVID-19 pandemic

2020 ◽  
Vol 11 (SPL1) ◽  
pp. 748-752
Author(s):  
Swapnali Khabade ◽  
Bharat Rathi ◽  
Renu Rathi
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Healthy Person ◽  
World Health ◽  
Physical And Mental Health ◽  
Leading Role ◽  
Global Pandemic ◽  
The People ◽  
The World ◽  
Health Organization ◽  
The Individual

A novel, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), causes severe acute respiratory syndrome and spread globally from Wuhan, China. In March 2020 the World Health Organization declared the SARS-Cov-2 virus as a COVID- 19, a global pandemic. This pandemic happened to be followed by some restrictions, and specially lockdown playing the leading role for the people to get disassociated with their personal and social schedules. And now the food is the most necessary thing to take care of. It seems the new challenge for the individual is self-isolation to maintain themselves on the health basis and fight against the pandemic situation by boosting their immunity. Food organised by proper diet may maintain the physical and mental health of the individual. Ayurveda aims to promote and preserve the health, strength and the longevity of the healthy person and to cure the disease by properly channelling with and without Ahara. In Ayurveda, diet (Ahara) is considered as one of the critical pillars of life, and Langhana plays an important role too. This article will review the relevance of dietetic approach described in Ayurveda with and without food (Asthavidhi visheshaytana & Lanhgan) during COVID-19 like a pandemic.

scholarly journals Optimizing COVID-19 testing capabilities and clinical management using pathology informatics

JAMIA Open ◽  
2020 ◽  
Author(s):  
Srikar Chamala ◽  
Sherri Flax ◽  
Petr Starostik ◽  
Kartikeya Cherabuddi ◽  
Nicole M Iovine ◽  
...  
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
Clinical Management ◽  
World Health ◽  
University Of Florida ◽  
Pathology Informatics ◽  
Large Numbers ◽  
The World ◽  
Health Organization ◽  
The University ◽  
Reporting Data

Abstract Coronavirus disease 2019, first reported in China in late 2019, has quickly spread across the world. The outbreak was declared a pandemic by the World Health Organization on March 11, 2020. Here, we describe our initial efforts at the University of Florida Health for processing of large numbers of tests, streamlining data collection, and reporting data for optimizing testing capabilities and superior clinical management. Specifically, we discuss clinical and pathology informatics workflows and informatics instruments which we designed to meet the unique challenges of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing. We hope these results benefit institutions preparing to implement SARS-CoV-2 testing.

scholarly journals Genome-Wide Analysis of Codon Usage Patterns of SARS-CoV-2 Virus Reveals Global Heterogeneity of COVID-19

Biomolecules ◽  
2021 ◽  
Vol 11 (6) ◽  
pp. 912
Author(s):  
Saadullah Khattak ◽  
Mohd Ahmar Rauf ◽  
Qamar Zaman ◽  
Yasir Ali ◽  
Shabeen Fatima ◽  
...  
Keyword(s):  
Standard Deviation ◽  
Codon Usage ◽  
Codon Usage Bias ◽  
Geographic Location ◽  
Mutation Pressure ◽  
Genome Wide ◽  
Margin Of Error ◽  
Usage Patterns ◽  
Causative Agents ◽  
Virus Genomes

The ongoing outbreak of coronavirus disease COVID-19 is significantly implicated by global heterogeneity in the genome organization of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The causative agents of global heterogeneity in the whole genome of SARS-CoV-2 are not well characterized due to the lack of comparative study of a large enough sample size from around the globe to reduce the standard deviation to the acceptable margin of error. To better understand the SARS-CoV-2 genome architecture, we have performed a comprehensive analysis of codon usage bias of sixty (60) strains to get a snapshot of its global heterogeneity. Our study shows a relatively low codon usage bias in the SARS-CoV-2 viral genome globally, with nearly all the over-preferred codons’ A.U. ended. We concluded that the SARS-CoV-2 genome is primarily shaped by mutation pressure; however, marginal selection pressure cannot be overlooked. Within the A/U rich virus genomes of SARS-CoV-2, the standard deviation in G.C. (42.91% ± 5.84%) and the GC3 value (30.14% ± 6.93%) points towards global heterogeneity of the virus. Several SARS-CoV-2 viral strains were originated from different viral lineages at the exact geographic location also supports this fact. Taking all together, these findings suggest that the general root ancestry of the global genomes are different with different genome’s level adaptation to host. This research may provide new insights into the codon patterns, host adaptation, and global heterogeneity of SARS-CoV-2.

Analysis of synonymous codon usage inShigella flexneri2a strain 301 and otherShigellaandEscherichia colistrains

2011 ◽  
Vol 57 (12) ◽  
pp. 1016-1023 ◽  
Author(s):  
Xue Lian Luo ◽  
Jian Guo Xu ◽  
Chang Yun Ye
Keyword(s):  
Codon Usage ◽  
Codon Usage Bias ◽  
Synonymous Codon ◽  
Shigella Flexneri ◽  
Synonymous Codon Usage ◽  
Codon Usage Pattern ◽  
Mutational Pressure ◽  
E Coli ◽  
Shigella Flexneri 2A ◽  
Usage Patterns

In this study, we analysed synonymous codon usage in Shigella flexneri 2a strain 301 (Sf301) and performed a comparative analysis of synonymous codon usage patterns in Sf301 and other strains of Shigella and Escherichia coli . Although there was a significant variety in codon usage bias among different Sf301 genes, there was a slight but observable codon usage bias that could primarily be attributable to mutational pressure and translational selection. In addition, the relative abundance of dinucleotides in Sf301 was observed to be independent of the overall base composition but was still caused by differential mutational pressure; this also shaped codon usage. By comparing the relative synonymous codon usage values across different Shigella and E. coli strains, we suggested that the synonymous codon usage pattern in the Shigella genomes was strain specific. This study represents a comprehensive analysis of Shigella codon usage patterns and provides a basic understanding of the mechanisms underlying codon usage bias.

scholarly journals SARS-CoV-2-Cholesterol Interaction: A Lot of Food for Thought

Pathogens ◽  
2021 ◽  
Vol 10 (1) ◽  
pp. 32
Author(s):  
Giovanni Di Guardo
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
World Health Organization ◽  
World Health ◽  
The World ◽  
Global Catastrophe ◽  
Health Organization

With over 80 million cases, and 1,800,000 deaths reported at the end of 2020 by the World Health Organization, the “CoronaVirus Disease-2019” (CoViD-19) pandemic, caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), should be viewed as a global catastrophe [...]

Impact OF Covid-19 on Several Industries in Context with the Dialysis Industry

2021 ◽  
Vol 8 (2) ◽  
pp. 01-03
Author(s):  
Ashish Gujrathi
Keyword(s):  
Severe Acute Respiratory Syndrome ◽  
World Health Organization ◽  
World Health ◽  
Healthcare Sector ◽  
Growth Opportunities ◽  
Wuhan City ◽  
First Case ◽  
The World ◽  
New Challenges ◽  
Health Organization

Coronavirus (COVID-19) was recognized in late December in Hubei province of Wuhan city in China. This highly contagious disease, caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is transmitted from humans to humans. After the first case in Wuhan, the disease rapidly spread to other parts of the globe. On March 11, 2020, the World Health Organization (WHO) made an assessment that COVID-19 can be characterized as a pandemic. Thus, social-distancing became an important measure to stop the spread of this disease. Various countries across the world adopted nationwide lockdowns. This led to a completely new scenario for the world, where every business in each industry faced new challenges and witnessed new opportunities. Similarly, the medical personal protective industry, a vital part of the healthcare sector, also witnessed new growth opportunities.

OBESITY IN SARS-COV-2 INFECTION: LITERATURE REVIEW

2021 ◽  
pp. 19-23
Author(s):  
Donizete Tavares Da Silva ◽  
Priscila De Sousa Barros Lima ◽  
Renato Sampaio Mello Neto ◽  
Gustavo Magalhães Valente ◽  
Débora Dias Cabral ◽  
...  
Keyword(s):  
Public Health ◽  
Acute Respiratory Distress Syndrome ◽  
Gastrointestinal Tract ◽  
Severe Acute Respiratory Syndrome ◽  
Distress Syndrome ◽  
Circulatory System ◽  
World Health ◽  
Global Public Health ◽  
The World ◽  
Health Organization

In March 2020, the World Health Organization (1) declared COVID-19 as a pandemic and a threat to global public health (2). The virus mainly affects the lungs and can cause acute respiratory distress syndrome (ARDS). In addition, coronavirus 2 severe acute respiratory syndrome (SARSCOV2) also has devastating effects on other important organs, including the circulatory system, brain, gastrointestinal tract, kidneys and liver

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