RESUMO
Recombination is a driving force for the emergence, evolution and virulence/epidemics of viruses, comprising the Enterovirus genus of the Picornaviridae family, important for human and animal health. By analyzing 2949 complete genomes/coding sequences, we provide a thorough and up-to-date overview of the genome-wide patterns and hotspots of intertypic recombination between the genogroups of this genus. Two prominent recombination hotspots are identified/verified, at the 5'UTR-capsid region junction, and at the beginning of the P2 region. In general, P2 was enriched in recombination events. Key phylogenetic groups implicated in recombination events are E71 and CVA6 in Enterovirus A species, E30 and E6 in Enterovirus B species, polioviruses 1 and 2 in Enterovirus C species. In addition, many events involve recombination partners that have not been sequenced yet, thus strongly suggesting a large environmental reservoir of genetic variation with a high potential for the emergence of new modified pathogens by recombination.
Assuntos
Enterovirus/genética , Evolução Molecular , Genoma Viral/genética , Recombinação Genética , Regiões 5' não Traduzidas/genética , Proteínas do Capsídeo/genética , Bases de Dados Genéticas , Enterovirus/classificação , Genótipo , Humanos , Filogenia , Rhinovirus/classificação , Rhinovirus/genética , Proteínas não Estruturais Virais/genéticaRESUMO
BACKGROUND: Many computational tools that detect recombination in viruses are not adapted for the ongoing genomic revolution. A computational tool is needed, that will rapidly scan hundreds/thousands of genomes or sequence fragments and detect candidate recombination events that may later be further analyzed with more sensitive and specialized methods. RESULTS: T-RECs, a Windows based graphical tool, employs pairwise alignment of sliding windows and can perform (i) genotyping, (ii) clustering of new genomes, (iii) detect recent recombination events among different evolutionary lineages, (iv) manual inspection of detected recombination events by similarity plots and (v) annotation of genomic regions. CONCLUSIONS: T-RECs is very effective, as demonstrated by an analysis of 555 Norovirus complete genomes and 2500 sequence fragments, where a recombination hotspot was identified at the ORF1-ORF2 junction.
