The genomic signature of human rhinoviruses A, B and C.

Human rhinoviruses are single stranded positive sense RNA viruses that are presented in more than 50% of acute upper respiratory tract infections. Despite extensive studies on the genetic diversity of the virus, little is known about the forces driving it. In order to explain this diversity, many re...

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Autores principales:	Spyridon Megremis, Philippos Demetriou, Heidi Makrinioti, Alkistis E Manoussaki, Nikolaos G Papadopoulos
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2012
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/dfa6a3e9329d4240870b4d649771265c
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spelling	oai:doaj.org-article:dfa6a3e9329d4240870b4d649771265c2021-11-18T07:05:43ZThe genomic signature of human rhinoviruses A, B and C.1932-620310.1371/journal.pone.0044557https://doaj.org/article/dfa6a3e9329d4240870b4d649771265c2012-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/23028561/pdf/?tool=EBIhttps://doaj.org/toc/1932-6203Human rhinoviruses are single stranded positive sense RNA viruses that are presented in more than 50% of acute upper respiratory tract infections. Despite extensive studies on the genetic diversity of the virus, little is known about the forces driving it. In order to explain this diversity, many research groups have focused on protein sequence requirements for viable, functional and transmissible virus but have missed out an important aspect of viral evolution such as the genomic ontology of the virus. This study presents for the first time the genomic signature of 111 fully sequenced HRV strains from all three groups HRV-A, HRV-B and HRV-C. We observed an HRV genome tendency to eliminate CpG and UpA dinucleotides, coupling with over-representation of UpG and CpA. We propose a specific mechanism which describes how rapid changes in the HRV genomic sequence can take place under the strict control of conservation of the polypeptide backbone. Moreover, the distribution of the observed under- and over-represented dinucleotides along the HRV genome is presented. Distance matrice tables based on CpG and UpA odds ratios were constructed and viewed as heatmaps and distance trees. None of the suppressions can be attributed to codon usage or in RNA secondary structure requirements. Since viral recognition is dependent on RNA motifs rich in CpG and UpA, it is possible that the overall described genome evolution mechanism acts in order to protect the virus from host recognition.Spyridon MegremisPhilippos DemetriouHeidi MakriniotiAlkistis E ManoussakiNikolaos G PapadopoulosNikolaos G PapadopoulosPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 7, Iss 9, p e44557 (2012)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Spyridon Megremis Philippos Demetriou Heidi Makrinioti Alkistis E Manoussaki Nikolaos G Papadopoulos Nikolaos G Papadopoulos The genomic signature of human rhinoviruses A, B and C.
description	Human rhinoviruses are single stranded positive sense RNA viruses that are presented in more than 50% of acute upper respiratory tract infections. Despite extensive studies on the genetic diversity of the virus, little is known about the forces driving it. In order to explain this diversity, many research groups have focused on protein sequence requirements for viable, functional and transmissible virus but have missed out an important aspect of viral evolution such as the genomic ontology of the virus. This study presents for the first time the genomic signature of 111 fully sequenced HRV strains from all three groups HRV-A, HRV-B and HRV-C. We observed an HRV genome tendency to eliminate CpG and UpA dinucleotides, coupling with over-representation of UpG and CpA. We propose a specific mechanism which describes how rapid changes in the HRV genomic sequence can take place under the strict control of conservation of the polypeptide backbone. Moreover, the distribution of the observed under- and over-represented dinucleotides along the HRV genome is presented. Distance matrice tables based on CpG and UpA odds ratios were constructed and viewed as heatmaps and distance trees. None of the suppressions can be attributed to codon usage or in RNA secondary structure requirements. Since viral recognition is dependent on RNA motifs rich in CpG and UpA, it is possible that the overall described genome evolution mechanism acts in order to protect the virus from host recognition.
format	article
author	Spyridon Megremis Philippos Demetriou Heidi Makrinioti Alkistis E Manoussaki Nikolaos G Papadopoulos Nikolaos G Papadopoulos
author_facet	Spyridon Megremis Philippos Demetriou Heidi Makrinioti Alkistis E Manoussaki Nikolaos G Papadopoulos Nikolaos G Papadopoulos
author_sort	Spyridon Megremis
title	The genomic signature of human rhinoviruses A, B and C.
title_short	The genomic signature of human rhinoviruses A, B and C.
title_full	The genomic signature of human rhinoviruses A, B and C.
title_fullStr	The genomic signature of human rhinoviruses A, B and C.
title_full_unstemmed	The genomic signature of human rhinoviruses A, B and C.
title_sort	genomic signature of human rhinoviruses a, b and c.
publisher	Public Library of Science (PLoS)
publishDate	2012
url	https://doaj.org/article/dfa6a3e9329d4240870b4d649771265c
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The genomic signature of human rhinoviruses A, B and C.

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