scholarly journals Novel Coronavirus (COVID-19): Molecular Evolutionary Analysis, Global Burden and Possible Threat to Bangladesh

2020 ◽  
Author(s):  
Md Bashir Uddin ◽  
Mahmudul Hasan ◽  
Ahmed Harun-Al-Rashid ◽  
Md. Irtija Ahsan ◽  
Md. Abdus Shukur Imran ◽  
...  
Keyword(s):  
Viral Proteins ◽  
Molecular Characteristics ◽  
Evolutionary Analysis ◽  
Genomic Information ◽  
Wuhan City ◽  
Membrane Envelope ◽  
Open Datasets ◽  
Novel Coronavirus ◽  
Molecular Evolutionary Analysis ◽  
Antigenic Epitopes

Abstract Recently a new coronavirus strain, COVID-19 has emerged in Wuhan City, China which cause disease and in many cases deaths to humans. Considering its severity a number of works are working on it and full genomic sequences has already released in the last few weeks to understand the evolutionary origin and molecular characteristics of this virus. Based on currently available genomic information a phylogenetic tree was constructed from four types of representative viral proteins (Spike, Membrane, Envelope and Nucleoproetin) of COVID-19, HCoV-229E, HCoV-OC43, SARS-CoV, HCoV-NL63, HKU1, MERS-CoV, HKU4, HKU5 and BufCoV-HKU26 clearly demonstrated that the ancestral origin and distant evolutionary relation of newly epidemic novel coronavirus (COVID-19). It had been found that COVID-19 was evolutionary related to SARS-CoV. It was also found that COVID-19 proteins were almost more than ninety (90%) similar and identical with SARS-CoV proteins. The cross-checked conservancy analysis of COVID-19 antigenic epitopes showed significant conservancy with SARS-CoV proteins. VaxiJen server reveal almost 100% immunogenic potential of four viral proteins with COVID-19. In this article, we present an effort on molecular evolutionary analysis, temperature comparison and compile and analyze epidemiological outbreak information on the 2019 novel coronavirus based on the several open datasets on COVID-19 (SARS-COV-2) and possible threat to Bangladesh.Authors Md Bashir Uddin and Mahmudul Hasan contributed equally to this work

scholarly journals Ancestral origin, antigenic resemblance and epidemiological insights of novel coronavirus (SARS-CoV-2): Global burden and Bangladesh perspective

2020 ◽  
Author(s):  
Md Bashir Uddin ◽  
Mahmudul Hasan ◽  
Ahmed Harun-Al-Rashid ◽  
Md. Irtija Ahsan ◽  
Md. Abdus Shukur Imran ◽  
...  
Keyword(s):  
Viral Proteins ◽  
Molecular Characteristics ◽  
Evolutionary Analysis ◽  
Wuhan City ◽  
Ancestral Origin ◽  
Membrane Envelope ◽  
Open Datasets ◽  
Novel Coronavirus ◽  
Molecular Evolutionary Analysis ◽  
Antigenic Epitopes

Abstract Recently a new coronavirus strain, COVID-19 has emerged in Wuhan City, China which cause disease and in many cases deaths to humans. Considering its severity a number of works are working on it and full genomic sequences has already released in the last few weeks to understand the evolutionary origin and molecular characteristics of this virus. Based on currently available genomic information a phylogenetic tree was constructed from four types of representative viral proteins (Spike, Membrane, Envelope and Nucleoproetin) of COVID-19, HCoV-229E, HCoV-OC43, SARS-CoV, HCoV-NL63, HKU1, MERS-CoV, HKU4, HKU5 and BufCoV-HKU26 clearly demonstrated that the ancestral origin and distant evolutionary relation of newly epidemic novel coronavirus (COVID-19). It had been found that COVID-19 was evolutionary related to SARS-CoV. It was also found that COVID-19 proteins were almost more than ninety (90%) similar and identical with SARS-CoV proteins. The cross-checked conservancy analysis of COVID-19 antigenic epitopes showed significant conservancy with SARS-CoV proteins. VaxiJen server reveal almost 100% immunogenic potential of four viral proteins with COVID-19. In this article, we present an effort on molecular evolutionary analysis, temperature comparison and compile and analyze epidemiological outbreak information on the 2019 novel coronavirus based on the several open datasets on COVID-19 (SARS-COV-2) and possible threat to Bangladesh.Authors Md Bashir Uddin and Mahmudul Hasan contributed equally to this work

scholarly journals Features of smaller ribosomes in Candidate Phyla Radiation (CPR) bacteria revealed with a molecular evolutionary analysis

2022 ◽  
Author(s):  
Megumi Tsurumaki ◽  
Motofumi Saito ◽  
Masaru Tomita ◽  
Akio Kanai
Keyword(s):  
Amino Acids ◽  
Ribosomal Proteins ◽  
Surface Structures ◽  
Small Cells ◽  
Evolutionary Analysis ◽  
Genomic Information ◽  
Free Living ◽  
Specific Manner ◽  
Molecular Evolutionary Analysis ◽  
Candidate Phyla Radiation

The Candidate Phyla Radiation (CPR) is a large bacterial group consisting mainly of uncultured lineages. They have small cells and small genomes, and often lack ribosomal proteins L1, L9, and/or L30, which are basically ubiquitous in ordinary (non-CPR) bacteria. Here, we comprehensively analyzed the genomic information of CPR bacteria and identified their unique properties. In the distribution of protein lengths in CPR bacteria, the peak was at around 100–150 amino acids, whereas the position of the peak varies in the range of 100–300 amino acids in free-living non-CPR bacteria, and at around 100–200 amino acids in most symbiotic non-CPR bacteria. These results show that CPR bacteria have smaller proteins on average, like symbiotic non-CPR bacteria. We found that ribosomal proteins L28, L29, L32, and L33 are also deleted in CPR bacteria, in a lineage-specific manner. Moreover, the sequences of approximately half of all ribosomal proteins in CPR differ, in part, from those of non-CPR bacteria, with missing regions or specific added region. We also found that several regions of the 16S, 23S, and 5S rRNAs are lacking in CPR bacteria and that the total predicted length of the three rRNAs in CPR bacteria is smaller than that in non-CPR bacteria. The regions missing in the CPR ribosomal proteins and rRNAs are located near the surface of the ribosome, and some are close to one another. These observations suggest that ribosomes are smaller in CPR bacteria than in free-living non-CPR bacteria, with simplified surface structures.

scholarly journals Genomic variance of the 2019-nCoV coronavirus

2020 ◽  
Author(s):  
Carmine Ceraolo ◽  
Federico M. Giorgi
Keyword(s):  
Scientific Community ◽  
Sequence Similarity ◽  
Molecular Characteristics ◽  
Genomic Information ◽  
High Sequence Similarity ◽  
Sequence Identity ◽  
Genomic Variance ◽  
Global Concern ◽  
Novel Coronavirus ◽  
Bat Coronavirus

AbstractThere is rising global concern for the recently emerged novel Coronavirus (2019-nCov). Full genomic sequences have been released by the worldwide scientific community in the last few weeks in order to understand the evolutionary origin and molecular characteristics of this virus. Taking advantage of all the genomic information currently available, we constructed a phylogenetic tree including also representatives of other coronaviridae, such as Bat coronavirus (BCoV) and SARS. We confirm high sequence similarity (>99%) between all sequenced 2019-nCoVs genomes available, with the closest BCoV sequence sharing 96.2% sequence identity, confirming the notion of a zoonotic origin of 2019-nCoV. Despite the low heterogeneity of the 2019-nCoV genomes, we could identify at least two hyper-variable genomic hotspots, one of which is responsible for a Serine/Leucine variation in the viral ORF8-encoded protein. Finally, we perform a full proteomic comparison with other coronaviridae, identifying key aminoacidic differences to be considered for antiviral strategies deriving from previous anti-coronavirus approaches.

Treatment Options in COVID-19: The Role of Bioavailable Antiviral Ribonucleoside Analog on NHC in vitro

2020 ◽  
Author(s):  
Lara Bittmann
Keyword(s):  
World Health Organization ◽  
Clinical Picture ◽  
Treatment Options ◽  
World Health ◽  
Wuhan City ◽  
The World ◽  
Novel Coronavirus ◽  
Health Organization

On December 31, 2019, WHO was informed of cases of pneumonia of unknown cause in Wuhan City, China. A novel coronavirus was identified as the cause by Chinese authorities on January 7, 2020 and was provisionally named "2019-nCoV". This new Coronavirus causes a clinical picture which has received now the name COVID-19. The virus has spread subsequently worldwide and was explained on the 11th of March, 2020 by the World Health Organization to the pandemic.

Can Mandated BCG Vaccine Promote herd Immunity against Novel Coronavirus? A Potential Solution at Hand to Tackle Covid-19 Pandemic

2020 ◽  
Vol 16 (1) ◽  
pp. 6-11
Author(s):  
Ashok Arasu ◽  
Pavithra Balakrishnan ◽  
Thirunavukkarasu Velusamy ◽  
Thiagarajan Ramesh
Keyword(s):  
Protective Factor ◽  
Herd Immunity ◽  
Bcg Vaccine ◽  
Intestinal Cells ◽  
Global Public Health ◽  
Wuhan City ◽  
Live Attenuated Vaccine ◽  
Angiotensin Converting Enzyme 2 ◽  
Lung Epithelial ◽  
Novel Coronavirus

The 2019 novel coronavirus (2019-nCoV) infection is an emerging pandemic that poses a severe threat to global public health. This pandemic started from the Wuhan City of Hubei Province in China, and is speculated to have originated from bats and spread among humans with an unknown intermediate transmitter. The virus binds to angiotensin-converting enzyme 2 (ACE2), which is abundantly expressed on various human cells, including lung epithelial and intestinal cells, thereby entering into these cells and causing infection. It is transmitted to other humans through airborne droplets from infected patients. Presently there are no specific treatments or vaccines that are available to curtail the spread of this disease. There are few indirect reports that explain the potential importance of the mandated BCG vaccine as a protective factor against COVID-19. There is a speculation that a live attenuated vaccine (BCG vaccine) can be beneficial against COVID-19 to develop the initial immune response, and can also spread in the community, thereby boosting herd immunity to fight against COVID-19. This review summarizes the conclusions of various reports on the BCG vaccine, and is an attempt to establish BCG-vaccination mediated herd immunity as an effective instant intermediate approach in curbing COVID-19 spread in highly populous countries.

scholarly journals The Location of Substitutions and Bacterial Genome Arrangements

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.

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

1995 ◽  
Vol 36 (2-3) ◽  
pp. 201-214 ◽  
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

Molecular evolutionary analysis of decapentaplegic (dpp) gene in Drosophilidae

The Nucleus ◽  
2014 ◽  
Vol 57 (1) ◽  
pp. 61-65
Author(s):  
Arpita Rakshit ◽  
Rabindra Nath Chatterjee
Keyword(s):  
Evolutionary Analysis ◽  
Molecular Evolutionary Analysis

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

Bionatura ◽  
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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