Inverted repeats in the monkeypox virus genome are hot spots for mutation

Abstract

The current monkeypox virus (MPXV) strain differs from the strain arising in 2018 by 50+ single nucleotide polymorphisms (SNPs) and is mutating much faster than expected. The cytidine deaminase apolipoprotein B messenger RNA editing enzyme, catalytic subunit B (APOBEC3) was hypothesized to be driving this increased mutation. APOBEC has recently been identified to preferentially mutate cruciform DNA secondary structures formed by inverted repeats (IRs). IRs were recently identified as hot spots for mutation in severe acute respiratory syndrome coronavirus 2, and we aimed to identify whether IRs were also hot spots for mutation within MPXV genomes. We found that MPXV genomes were replete with IR sequences. Of the 50+ SNPs identified in the 2022 outbreak strain, 63.9% of these were found to have arisen within IR regions in the 2018 reference strain (MT903344.1). Notably, IR sequences found in the 2018 reference strain were significantly lost over time, with an average of 32.5% of these sequences being conserved in the 2022 MPXV genomes. This evidence was highly indicative that mutations were arising within IRs. This data provides further support to the hypothesis that APOBEC may be driving MPXV mutation and highlights the necessity for greater surveillance of IRs of MPXV genomes to detect new mutations.

Evolutionary potential of the monkeypox genome arising from interactions with human APOBEC3 enzymes

“…As with HIV, this effect may be a result of ITR genes at chromosome ends having a longer exposure time of ssDNA during replication than other genes within the chromosome (46). This finding is consistent with previous publications which found higher gene gain and loss activity at the ends (35) and a higher frequency of recent mutations in the MPXV inverted repeat regions (26).…”

“…Although APOBEC3s have already been strongly implicated in the MPXV outbreak of 2022 (3,7,26,27), the question of how emerging MPXV strains will continue to undergo further APOBEC3-mediated mutations remains open. Thus, we have evaluated the potential for future evolution of the MPXV genome mediated by APOBEC3.…”

“…Vaccinia viruses, for example, have been seen to increase fitness relatively quickly in vitro through a "gene accordion" model (34). While gene duplication and loss in MPXV genomes may be a major component of host evasion (35) and inverted repeats may be mutational hotspots in MPXV (26), we focus part of our analysis on the TC hotspot representation and amino acid replacement of inverted terminal repeats (ITR), since our analysis suggests these genes may have a higher probability of being exposed to APOBEC3 during viral replication. Our results suggest that the prior evolution of the virus has led to a greatly increased present potential for APOBEC3mediated mutations, assuming that other selective forces do not counteract this potential.…”

Sequencing of monkeypox virus from infected patients reveals viral genomes with APOBEC3‐like editing, gene inactivation, and bacterial agents of skin superinfection

“…As previously reported, we identified a strong mutation bias with a large majority of mutations (94%) being G > A (57%) and C > U (37%) in a dinucleotide context suggesting that they could have occurred because of genome editing by human APOBEC3 enzymes. This has been previously highlighted in several studies 5,13,41,42,48,52,67,70 . In addition, such signatures of APOBEC3 activity were prominent among clade IIb whereas not among other MPXV clades.…”

“…This has been previously highlighted in several studies. 5,13,41,42,48,52,67,70 In addition, such signatures of APO-BEC3 activity were prominent among clade IIb whereas not among other MPXV clades. Besides, interestingly, Forni et al 48 reported based on the analysis of 1,624 MKPV genomes and of experimental data for VACV infection that APOBEC3 signatures preferentially implicated highly expressed viral genes.…”