Related Experiment Video
Updated: Oct 20, 2025

Isolation of Fidelity Variants of RNA Viruses and Characterization of Virus Mutation Frequency
Published on: June 16, 2011
Stepwise Evolution and Exceptional Conservation of ORF1a/b Overlap in Coronaviruses
Han Mei1, Sergei Kosakovsky Pond2, Anton Nekrutenko1
1Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, PA, USA.
Abstract:
The programmed frameshift element (PFE) rerouting translation from ORF1a to ORF1b is essential for the propagation of coronaviruses. The combination of genomic features that make up PFE-the overlap between the two reading frames, a slippery sequence, as well as an ensemble of complex secondary structure elements-places severe constraints on this region as most possible nucleotide substitution may disrupt one or more of these elements. The vast amount of SARS-CoV-2 sequencing data generated within the past year provides an opportunity to assess the evolutionary dynamics of PFE in great detail. Here, we performed a comparative analysis of all available coronaviral genomic data available to date. We show that the overlap between ORF1a and ORF1b evolved as a set of discrete 7, 16, 22, 25, and 31 nucleotide stretches with a well-defined phylogenetic specificity. We further examined sequencing data from over 1,500,000 complete genomes and 55,000 raw read data sets to demonstrate exceptional conservation and detect signatures of selection within the PFE region.
Related Concept Videos
Gene Duplication and Divergence
The duplicated copies of the gene are called Paralogs. Paralogs with similar sequences and functions form a gene family. Across several species, a large number of gene families are...
Convergent Evolution
Eukaryotic Evolution
Contrary to the endosymbiont theory, the eukaryote-first hypothesis proposes that the simpler prokaryotic and...
Viral Mutations
Gene Evolution - Fast or Slow?
In contrast, regions which code...
Evolutionary Relationships through Genome Comparisons

