Stepwise Evolution and Exceptional Conservation of ORF1a/b Overlap in Coronaviruses.
Mol Biol Evol
; 38(12): 5678-5684, 2021 12 09.
Article
in English
| MEDLINE | ID: covidwho-1402409
Preprint
This scientific journal article is probably based on a previously available preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
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This scientific journal article is probably based on a previously available preprint. It has been identified through a machine matching algorithm, human confirmation is still pending.
See preprint
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.
Keywords
Full text:
Available
Collection:
International databases
Database:
MEDLINE
Main subject:
Phylogeny
/
Open Reading Frames
/
Coronavirus
/
SARS-CoV-2
Type of study:
Diagnostic study
/
Randomized controlled trials
Language:
English
Journal:
Mol Biol Evol
Journal subject:
Molecular Biology
Year:
2021
Document Type:
Article
Affiliation country:
Molbev
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