Translation-associated mutational U-pressure in the first ORF of SARS-CoV-2 and other coronaviruses

Abstract

Within four months of the ongoing COVID-19 pandemic caused by SARS-CoV-2, more than 250 nucleotide mutations have been detected in the ORF1 of the virus isolated from different parts of the globe. These observations open up an obvious question about the rate and direction of mutational pressure for further vaccine and therapeutics designing. In this study, we did a comparative analysis of ORF1a and ORF1b by using the first isolate (Wuhan strain) as the parent sequence. We observed that most of the nucleotide mutations are C to U transitions. The rate of synonymous C to U transitions is significantly higher than the rate of nonsynonymous ones, indicating negative selection on amino acid substitutions. Further, trends in nucleotide usage bias have been investigated in 49 coronaviruses species. A strong bias in nucleotide usage in fourfold degenerated sites towards uracil residues is seen in ORF1 of all the studied coronaviruses. A more substantial mutational U pressure is observed in ORF1a than in ORF1b owing to the translation of ORF1ab via programmed ribosomal frameshifting. Unlike other nucleotide mutations, mutational U pressure caused by cytosine deamination, mostly occurring in the RNAplus strand, cannot be corrected by the proof-reading machinery of coronaviruses. The knowledge generated on the direction of mutational pressure during translation of viral RNAplus strands has implications for vaccine and nucleoside analogue development for treating covid-19 and other coronavirus infections.

Stability of SARS-CoV-2 Phylogenies

“…Hypermutation rather than positive selection may explain many remaining highly recurrent sites. Previous analyses showed that the rate of C>U mutation is exceptionally high relative to other mutation types in the viral genome [10,25,43,47] . This class of mutations should show increased evidence of recurring multiple times because they experience elevated mutation rates [25] .…”

“…Extremely rapid whole genome sequencing has enabled nearly real-time tracing of the evolution of the SARS-CoV-2 pandemic [1][2][3][4][5] . By leveraging sequence data produced by labs throughout the world, researchers can trace transmission of the virus across human populations [6][7][8][9][10][11][12][13][14] . Typically, viral evolution is encapsulated by a phylogenetic tree relating all of the virus samples in a large set to one another [5,[15][16][17][18][19] .…”

Implications of SARS-CoV-2 Mutations for Genomic RNA Structure and Host microRNA Targeting

“…These mutations are mostly limited to point mutations, with little evidence for recombination events mediating the simultaneous transfer of multiple mutations. Although mutations may be due to RdRP/Nsp12 infidelity, the predominance of C → U and G → A mutations is consistent with base-editing defence (e.g., APOBEC/ADAR) [42,73]. The Nsp14 exonuclease-based proof-reader is a critical counter-defence against host base-editor attack on the coronavirus genome [1].…”

“…The Nsp14 exonuclease-based proof-reader is a critical counter-defence against host base-editor attack on the coronavirus genome [1]. It is also possible that the position of mutations within the genome could reflect accessibility of host base-editors to the SARS-CoV-2 genome upon uncoating, or during genome translation [42].…”

“…Most of these mutations are substitutions of C/G to U. The high A/U content (U = 32.1%; A = 29.9%; G = 19.6%; C = 18.4%) and enrichment of codons in pyrimidines is likely due to APOBEC editing of viral RNA and the fact that the proof-reading Nsp14 does not remove U (the product of cytosine deamination) [42]. Two mutations at 241 and 29742, are in the 5 and 3 untranslated regions (UTRs).…”