Global genomic surveillance of monkeypox virus

Abstract

Monkeypox virus (MPXV) is endemic in western and Central Africa, and in May 2022, a clade IIb lineage (B.1) caused a global outbreak outside Africa, resulting in its detection in 116 countries and territories. To understand the global phylogenetics of MPXV, we analyzed all available MPXV sequences, including 10,670 sequences from 65 countries collected between 1958 and 2024. Our analysis reveals high mobility of clade I viruses within Central Africa, sustained human-to-human transmission of clade IIb lineage A viruses within the Eastern Mediterranean region and distinct mutational signatures that can distinguish sustained human-to-human from animal-to-animal transmission. Moreover, distinct clade I sequences from Sudan suggest local MPXV circulation in areas of eastern Africa over the past four decades. Our study underscores the importance of genomic surveillance in tracking spatiotemporal dynamics of MXPV clades and the need to strengthen such surveillance, including in some parts of eastern Africa.

Fig. 1. Spatiotemporal and host species distributions of MPXV sequences (worldwide, 1958–2024).

a, Maximum likelihood phylogenetic tree highlighting the major clades of MPXV. The branches are colored by clade. Lineage B.1 clusters within clade IIb and caused the 2022 global MPXV outbreak; this lineage is therefore separated from the remainder of clade IIb. The scale bar shows the expected number of nucleotide substitutions per site. A subset of clades are collapsed for clarity. b, The temporal and regional distribution of MPXV sequences is shown for each clade. The n numbers show the total number of sequences from the clade. c, Distributions of the number of sequences from each host species.

Fig. 2. Regular international and inter-province transmission of clade I.

a,b, Maximum likelihood phylogenetic tree of 113 high-quality clade I sequences. a, The tips are colored by country to match the map, and the shapes show the host species from which the sequence was isolated. The Sudan sequence cluster is highlighted. The 2024 South Kivu outbreak clade has been collapsed for clarity. The asterisks show phylogenetic nodes with bootstrap support of 70 or higher. The map shows sampling locations with points proportional to the number of sequences from the location. b, The tips are colored by province within the Democratic Republic of the Congo to match the map. Tips collected outside of the Democratic Republic of the Congo are colored gray and tips sampled within the Democratic Republic of the Congo but without a recorded province are colored black. c, We calculated the mutation distance between all possible pairs of clade I sequences (that is, each sequence was compared against all other sequences); the number of mutations is plotted stratified by whether the pairs are from the same (purple) or different (green) provinces.

Fig. 3. Temporal evolutionary history of clade I.

The temporal maximum clade credibility phylogenetic tree is shown. The tips are colored by country of isolation. The red bars show the 95% HPD on the date of the corresponding node. The asterisks show nodes with posterior support of 70 or higher.

Fig. 4. Spatial distributions of clades IIa and IIb A.

a, Maximum likelihood phylogenetic tree of 25 high-quality clade IIa isolates. The tips are colored by host species and the shapes show sampling locations. The asterisks show nodes with bootstrap support of 70 or higher, and the scale bar shows the expected number of nucleotide substitutions per site. b, Maximum likelihood phylogenetic tree of 101 clade IIb A sequences. The tips are colored by country of collection. The red, blue and orange asterisks show samples with travel history. The potential Eastern Mediterranean clade containing samples with travel history to the United Arab Emirates and Saudi Arabia is highlighted. The black asterisks show nodes with bootstrap support of 70 or above, and the scale bar shows the expected number of nucleotide substitutions per site.

Fig. 5. Mutational spectra differ between major MPXV clades.

a, SBS mutational spectra for clade I, clade IIb A and lineage B.1 (clade IIa was not included because of insufficient mutations; Methods). SBS spectra show the proportion of mutations of each mutation type within each surrounding nucleotide context; contexts for an example mutation type are shown in the right-hand panel. The two most prevalent contextual mutations are highlighted for clade I and lineage B.1. Mutational spectra are corrected for genome composition (Methods). Symmetrical mutations (for example, C>T and G>A) are combined as MPXV is a DNA pathogen. b, The proportion of C>T mutations with each nucleotide upstream is shown for each clade. Each bar and dot show the proportion of C>T mutations that occur in the corresponding context within the clade (that is, n = 1 in each case). The error bars represent the Wilson score interval calculated using the corresponding proportion and number of sampled C>T mutations. c, To examine the potential for the clade IIa mutational spectrum to have been generated by the mutational spectra of clade I and lineage B.1, we compared the proportion of each mutation type in the clade IIa spectrum with that in 1,000 subsamplings of the other clade spectrum to the number of mutations in the clade IIa spectrum (Methods). Each gray point represents the mutation type proportion in one subsample of the respective mutational spectrum while each red point shows the mutation type proportion in clade IIa. The clade IIa mutation type proportions are within that expected from clade I but often outside that expected from lineage B.1. The boxplot center lines show median values; the upper and lower bounds show the 25th and 75th quantiles, respectively; the upper and lower whiskers show the largest and smallest values within 1.5 times the interquartile range above the 75th percentile and below the 25th percentile, respectively.

Extended Data Fig. 1. Distribution of MXPV genetic sequences.

(a) The number of high-quality MXPV genetic sequences (see Methods) is shown for each major clade. (b) The number of MXPV sequences from each year is shown. Due to the large number of sequences in 2022 compared to other years, we extract the years before 2022 in the upper panel. (c) The proportion of sequences belonging to each major MPXV clade in each year is shown, colours match those in panel A.

Extended Data Fig. 2. Geographic distribution of MPXV clades across WHO regions.

The map was generated from 10,670 sequences obtained from GenBank and GISAID, 1958- February 2024. Clade I is red, clade IIa is green, and clade IIb is blue.

Extended Data Fig. 3. Duplication of the genome from Sudan 2005 and 2022 (KC257459, OQ621553).

A 10591 bp region directly downstream the left ITR is duplicated to the right site of the genome, resulting in ITRs of 16969 bp and a genome length of 204,808 bp). Three genes (R1, N1R and N3R) are deleted at the site of duplication.

Extended Data Fig. 4. Geographical distribution of laboratory confirmed cases of mpox in Sudan in 2022.

Confirmed cases were reported in Sudan states neighbouring Chad, Central African Republic, Ethiopia and Eritrea, while cases in 2005 were reported from a region that now belong to South Sudan.

Extended Data Fig. 5. Identification of lineage B.1 outliers.

(a) The distribution of residuals around the best fit line shown in B. The red vertical line shows five median absolute deviations above the median residual which was used as a cutoff to identify outliers. (b) The collection date of each lineage B.1 sequence is plotted against the number of mutations between the sequence and sample ON676708.1 which clusters immediately upstream of lineage B.1. Sequences shown in red contain greater diversity than expected given their sampling data so were excluded from further analyses.

Extended Data Fig. 6. Most included MPXV sequences contain close to the complete genome.

The proportion of the total genome covered is plotted for each sequence retained after filtering, split by major clade. Note that due to masking of ITR regions during alignment, no sequence will contain the complete genome.