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

Abstract

APOBEC3, an enzyme subfamily that plays a role in virus restriction by generating mutations at particular DNA motifs or mutational 'hotspots', can drive viral mutagenesis with host-specific preferential hotspot mutations contributing to pathogen variation. While previous analysis of viral genomes from the 2022 Mpox (formerly Monkeypox) disease outbreak has shown a high frequency of C>T mutations at TC motifs, suggesting recent mutations are human APOBEC3-mediated, how emerging monkeypox virus (MPXV) strains will evolve as a consequence of APOBEC3-mediated mutations remains unknown. By measuring hotspot under-representation, depletion at synonymous sites, and a combination of the two, we analyzed APOBEC3-driven evolution in human poxvirus genomes, finding varying hotspot under-representation patterns. While the native poxvirus molluscum contagiosum exhibits a signature consistent with extensive coevolution with human APOBEC3, including depletion of TC hotspots, variola virus shows an intermediate effect consistent with ongoing evolution at the time of eradication. MPXV, likely the result of recent zoonosis, showed many genes with more TC hotspots than expected by chance (over-representation) and fewer GC hotspots than expected (under-representation). These results suggest the MPXV genome: (1) may have evolved in a host with a particular APOBEC GC hotspot preference, (2) has inverted terminal repeat (ITR) regions-which may be exposed to APOBEC3 for longer during viral replication-and longer genes likely to evolve faster, and therefore (3) has a heightened potential for future human APOBEC3-meditated evolution as the virus spreads in the human population. Our predictions of MPXV mutational potential can both help guide future vaccine development and identification of putative drug targets and add urgency to the task of containing human Mpox disease transmission and uncovering the ecology of the virus in its reservoir host.

Keywords: APOBEC; computational biology; evolution; mokeypox; virus.

Figure 1.

Plots of CDUR statistics (CDUR plots) for TC hotspot under representation (horizontal axis) and amino acid replacement (vertical axis) for genes of human poxviruses. (A) Molluscum contagiosum virus (MCV), (B) Monkeypox virus (MPXV), (C) Vaccinia virus (VACV), and (D) Variola virus (VARV). Red dot indicates the mean.

Figure 2.

CDUR plots for non-TC hotspots in Monkeypox virus, showing, for each gene, the hotspot under representation (horizontal axis) and amino acid replacement (vertical axis). Each plot shows results for a different hotspot: (A) GC hotspots, (B) CC hotspots, and (C) AC hotspots. Red dot indicates the mean.

Figure 3.

On the left are plots of Monkeypox gene length (log10) vs (A1) the CDUR plot ‘distance from the top left corner’ measure of evolutionary potential for TC hotspots, (B1) TC hotspot under representation, and (C1) amino acid replacement. One the right are equivalent plots for GC hotspots, showing Monkeypox gene length (log10) vs (A2) the CDUR plot ‘distance from the top left corner’, (B2) GC hotspot under representation, and (C2) amino acid replacement.

Figure 4.

(A) CDUR plot of TC hotspot under representation (horizontal axis) and amino acid replacement (vertical axis) for MPXV-UK_P2. Triangles are genes within the repeat regions (ITR) and red points are mutated genes. (B) Rolling average of mutations from MPXV-UK_P2 over nucleotide position with a window of 1k nb. Red lines indicate end of repeat regions.

Figure 5.

G+C content histograms and averages of (A) Molluscum contagiosum virus, (B) Vaccinia virus, (C) Variola virus, (D) Monkeypox virus, and (E) MPXV-UK_P2. Red lines indicate the average G+C content.

Figure 6.

Plot of CDUR statistics for CC hotspot under representation (horizontal axis) and amino acid replacement (vertical axis) for genes of Molluscum contagiosum. Red dot indicates the mean.