title: Subtype-specific structural constraints in the evolution of influenza A virus hemagglutinin genes.
abstract: The influenza A virus genome consists of eight RNA segments. RNA structures within these segments and complementary (cRNA) and protein-coding mRNAs may play a role in virus replication. Here, conserved putative secondary structures that impose significant evolutionary constraints on the gene segment encoding the surface glycoprotein hemagglutinin (HA) were investigated using available sequence data on tens of thousands of virus strains. Structural constraints were identified by analysis of covariations of nucleotides suggested to be paired by structure prediction algorithms. The significance of covariations was estimated by mutual information calculations and tracing multiple covariation events during virus evolution. Covariation patterns demonstrated that structured domains in HA RNAs were mostly subtype-specific, whereas some structures were conserved in several subtypes. The influence of RNA folding on virus replication was studied by plaque assays of mutant viruses with disrupted structures. The results suggest that over the whole length of the HA segment there are local structured domains which contribute to the virus fitness but individually are not essential for the virus. Existence of subtype-specific structured regions in the segments of the influenza A virus genome is apparently an important factor in virus evolution and reassortment of its genes.
authors.affiliation: Department of Viroscience, Erasmus Medical Centre, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands.|Group Imaging and Bioinformatics, Leiden Institute of Advanced Computer Science, Leiden University, P.O. Box 9512, 2300 RA Leiden, The Netherlands.
authors.forename: Alexander P
authors.initials: AP
authors.lastname: Gultyaev
authors.affiliation: Department of Viroscience, Erasmus Medical Centre, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands.
authors.forename: Monique I
authors.initials: MI
authors.lastname: Spronken
authors.affiliation: Department of Viroscience, Erasmus Medical Centre, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands.
authors.forename: Mathilde
authors.initials: M
authors.lastname: Richard
authors.affiliation: Department of Viroscience, Erasmus Medical Centre, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands.
authors.forename: Eefje J A
authors.initials: EJ
authors.lastname: Schrauwen
authors.affiliation: Leiden Institute of Chemistry, Leiden University, P.O. Box 9502, 2300 RA Leiden, The Netherlands.
authors.forename: René C L
authors.initials: RC
authors.lastname: Olsthoorn
authors.affiliation: Department of Viroscience, Erasmus Medical Centre, P.O. Box 2040, 3000 CA Rotterdam, The Netherlands.
authors.forename: Ron A M
authors.initials: RA
authors.lastname: Fouchier
mesh_terms: D019143:Evolution, Molecular; D016679:Genome, Viral; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics*; D009980:Influenza A virus / Q000235:genetics*
chemical_list: D019267:Hemagglutinin Glycoproteins, Influenza Virus; C483468:hemagglutinin, human influenza A virus