Comparative Genomic Analysis MERS CoV Isolated from Humans and Camels with Special Reference to Virus Encoded Helicase.
Identifieur interne : 000E55 ( Main/Exploration ); précédent : 000E54; suivant : 000E56Comparative Genomic Analysis MERS CoV Isolated from Humans and Camels with Special Reference to Virus Encoded Helicase.
Auteurs : Mohamed Alnazawi ; Abdallah Altaher ; Mahmoud KandeelSource :
- Biological & pharmaceutical bulletin [ 1347-5215 ] ; 2017.
Descripteurs français
- KwdFr :
- Animaux, Chameaux, Codon, Coronavirus du syndrome respiratoire du Moyen-Orient (génétique), Coronavirus du syndrome respiratoire du Moyen-Orient (isolement et purification), Génome viral, Génomique, Helicase (génétique), Humains, Ilots CpG, Infections à coronavirus (virologie), Modèles moléculaires, Nucléotides, Protéines virales non structurales (génétique).
- MESH :
- génétique : Coronavirus du syndrome respiratoire du Moyen-Orient, Helicase, Protéines virales non structurales.
- isolement et purification : Coronavirus du syndrome respiratoire du Moyen-Orient.
- virologie : Infections à coronavirus.
- Animaux, Chameaux, Codon, Génome viral, Génomique, Humains, Ilots CpG, Modèles moléculaires, Nucléotides.
English descriptors
- KwdEn :
- Animals, Camelus, Codon, Coronavirus Infections (virology), CpG Islands, DNA Helicases (genetics), Genome, Viral, Genomics, Humans, Middle East Respiratory Syndrome Coronavirus (genetics), Middle East Respiratory Syndrome Coronavirus (isolation & purification), Models, Molecular, Nucleotides, Viral Nonstructural Proteins (genetics).
- MESH :
- chemical , genetics : DNA Helicases, Viral Nonstructural Proteins.
- chemical : Codon, Nucleotides.
- genetics : Middle East Respiratory Syndrome Coronavirus.
- isolation & purification : Middle East Respiratory Syndrome Coronavirus.
- virology : Coronavirus Infections.
- Animals, Camelus, CpG Islands, Genome, Viral, Genomics, Humans, Models, Molecular.
Abstract
Middle East Respiratory Syndrome Coronavirus (MERS CoV) is a new emerging viral disease characterized by high fatality rate. Understanding MERS CoV genetic aspects and codon usage pattern is important to understand MERS CoV survival, adaptation, evolution, resistance to innate immunity, and help in finding the unique aspects of the virus for future drug discovery experiments. In this work, we provide comprehensive analysis of 238 MERS CoV full genomes comprised of human (hMERS) and camel (cMERS) isolates of the virus. MERS CoV genome shaping seems to be under compositional and mutational bias, as revealed by preference of A/T over G/C nucleotides, preferred codons, nucleotides at the third position of codons (NT3s), relative synonymous codon usage, hydropathicity (Gravy), and aromaticity (Aromo) indices. Effective number of codons (ENc) analysis reveals a general slight codon usage bias. Codon adaptation index reveals incomplete adaptation to host environment. MERS CoV showed high ability to resist the innate immune response by showing lower CpG frequencies. Neutrality evolution analysis revealed a more significant role of mutation pressure in cMERS over hMERS. Correspondence analysis revealed that MERS CoV genomes have three genetic clusters, which were distinct in their codon usage, host, and geographic distribution. Additionally, virtual screening and binding experiments were able to identify three new virus-encoded helicase binding compounds. These compounds can be used for further optimization of inhibitors.
DOI: 10.1248/bpb.b17-00241
PubMed: 28769010
Affiliations:
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University</wicri:noCountry></affiliation></author><author><name sortKey="Altaher, Abdallah" sort="Altaher, Abdallah" uniqKey="Altaher A" first="Abdallah" last="Altaher">Abdallah Altaher</name><affiliation><nlm:affiliation>Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine, King Faisal University.</nlm:affiliation><wicri:noCountry code="subField">King Faisal University</wicri:noCountry></affiliation></author><author><name sortKey="Kandeel, Mahmoud" sort="Kandeel, Mahmoud" uniqKey="Kandeel M" first="Mahmoud" last="Kandeel">Mahmoud Kandeel</name><affiliation><nlm:affiliation>Department of Physiology, Biochemistry and Pharmacology, Faculty of Veterinary Medicine, King Faisal University.</nlm:affiliation><wicri:noCountry code="subField">King Faisal University</wicri:noCountry></affiliation></author></analytic><series><title level="j">Biological & pharmaceutical bulletin</title><idno type="eISSN">1347-5215</idno><imprint><date when="2017" type="published">2017</date></imprint></series></biblStruct></sourceDesc></fileDesc><profileDesc><textClass><keywords scheme="KwdEn" xml:lang="en"><term>Animals</term><term>Camelus</term><term>Codon</term><term>Coronavirus Infections (virology)</term><term>CpG Islands</term><term>DNA Helicases (genetics)</term><term>Genome, Viral</term><term>Genomics</term><term>Humans</term><term>Middle East Respiratory Syndrome Coronavirus (genetics)</term><term>Middle East Respiratory Syndrome Coronavirus (isolation & purification)</term><term>Models, Molecular</term><term>Nucleotides</term><term>Viral Nonstructural Proteins (genetics)</term></keywords><keywords scheme="KwdFr" xml:lang="fr"><term>Animaux</term><term>Chameaux</term><term>Codon</term><term>Coronavirus du syndrome respiratoire du Moyen-Orient (génétique)</term><term>Coronavirus du syndrome respiratoire du Moyen-Orient (isolement et purification)</term><term>Génome viral</term><term>Génomique</term><term>Helicase (génétique)</term><term>Humains</term><term>Ilots CpG</term><term>Infections à coronavirus (virologie)</term><term>Modèles moléculaires</term><term>Nucléotides</term><term>Protéines virales non structurales (génétique)</term></keywords><keywords scheme="MESH" type="chemical" qualifier="genetics" xml:lang="en"><term>DNA Helicases</term><term>Viral Nonstructural Proteins</term></keywords><keywords scheme="MESH" type="chemical" xml:lang="en"><term>Codon</term><term>Nucleotides</term></keywords><keywords scheme="MESH" qualifier="genetics" xml:lang="en"><term>Middle East Respiratory Syndrome Coronavirus</term></keywords><keywords scheme="MESH" qualifier="génétique" xml:lang="fr"><term>Coronavirus du syndrome respiratoire du Moyen-Orient</term><term>Helicase</term><term>Protéines virales non structurales</term></keywords><keywords scheme="MESH" qualifier="isolation & purification" xml:lang="en"><term>Middle East Respiratory Syndrome Coronavirus</term></keywords><keywords scheme="MESH" qualifier="isolement et purification" xml:lang="fr"><term>Coronavirus du syndrome respiratoire du Moyen-Orient</term></keywords><keywords scheme="MESH" qualifier="virologie" xml:lang="fr"><term>Infections à coronavirus</term></keywords><keywords scheme="MESH" qualifier="virology" xml:lang="en"><term>Coronavirus Infections</term></keywords><keywords scheme="MESH" xml:lang="en"><term>Animals</term><term>Camelus</term><term>CpG Islands</term><term>Genome, Viral</term><term>Genomics</term><term>Humans</term><term>Models, Molecular</term></keywords><keywords scheme="MESH" xml:lang="fr"><term>Animaux</term><term>Chameaux</term><term>Codon</term><term>Génome viral</term><term>Génomique</term><term>Humains</term><term>Ilots CpG</term><term>Modèles moléculaires</term><term>Nucléotides</term></keywords></textClass></profileDesc></teiHeader><front><div type="abstract" xml:lang="en">Middle East Respiratory Syndrome Coronavirus (MERS CoV) is a new emerging viral disease characterized by high fatality rate. Understanding MERS CoV genetic aspects and codon usage pattern is important to understand MERS CoV survival, adaptation, evolution, resistance to innate immunity, and help in finding the unique aspects of the virus for future drug discovery experiments. In this work, we provide comprehensive analysis of 238 MERS CoV full genomes comprised of human (hMERS) and camel (cMERS) isolates of the virus. MERS CoV genome shaping seems to be under compositional and mutational bias, as revealed by preference of A/T over G/C nucleotides, preferred codons, nucleotides at the third position of codons (NT3s), relative synonymous codon usage, hydropathicity (Gravy), and aromaticity (Aromo) indices. Effective number of codons (ENc) analysis reveals a general slight codon usage bias. Codon adaptation index reveals incomplete adaptation to host environment. MERS CoV showed high ability to resist the innate immune response by showing lower CpG frequencies. Neutrality evolution analysis revealed a more significant role of mutation pressure in cMERS over hMERS. Correspondence analysis revealed that MERS CoV genomes have three genetic clusters, which were distinct in their codon usage, host, and geographic distribution. Additionally, virtual screening and binding experiments were able to identify three new virus-encoded helicase binding compounds. These compounds can be used for further optimization of inhibitors.</div></front></TEI><affiliations><list></list><tree><noCountry><name sortKey="Alnazawi, Mohamed" sort="Alnazawi, Mohamed" uniqKey="Alnazawi M" first="Mohamed" last="Alnazawi">Mohamed Alnazawi</name><name sortKey="Altaher, Abdallah" sort="Altaher, Abdallah" uniqKey="Altaher A" first="Abdallah" last="Altaher">Abdallah Altaher</name><name sortKey="Kandeel, Mahmoud" sort="Kandeel, Mahmoud" uniqKey="Kandeel M" first="Mahmoud" last="Kandeel">Mahmoud Kandeel</name></noCountry></tree></affiliations></record>Pour manipuler ce document sous Unix (Dilib)
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