Distinct monkeypox virus lineages co-circulating in humans before 2022

Abstract

The 2022 global mpox outbreak raises questions about how this zoonotic disease established effective human-to-human transmission and its potential for further adaptation. The 2022 outbreak virus is related to an ongoing outbreak in Nigeria originally reported in 2017, but the evolutionary path linking the two remains unclear due to a lack of genomic data between 2018, when virus exportations from Nigeria were first recorded, and 2022, when the global mpox outbreak began. Here, 18 viral genomes obtained from patients across southern Nigeria in 2019-2020 reveal multiple lineages of monkeypox virus (MPXV) co-circulated in humans for several years before 2022, with progressive accumulation of mutations consistent with APOBEC3 activity over time. We identify Nigerian A.2 lineage isolates, confirming the lineage that has been multiply exported to North America independently of the 2022 outbreak originated in Nigeria, and that it has persisted by human-to-human transmission in Nigeria for more than 2 years before its latest exportation. Finally, we identify a lineage-defining APOBEC3-style mutation in all A.2 isolates that disrupts gene A46R, encoding a viral innate immune modulator. Collectively, our data demonstrate MPXV capacity for sustained diversification within humans, including mutations that may be consistent with established mechanisms of poxvirus adaptation.

Fig. 1. Phylogenetic analysis and geographic distribution MPXV genomes.

a, Phylogenetic tree of clade II MPXV genomes. Genomes described in this study are highlighted in red and those with a disrupted A46R gene (lineage A.2) are marked with a red square. Published lineage B.1 genomes from the current international outbreak are depicted in a single cluster in gray. The cutoff date for inclusion of newly published genomes was 18 June 2022. b, Expanded map created with Datawrapper software (https://www.datawrapper.de/) showing the distribution of cases from which the genomes described in the study were isolated, across southern states of Nigeria. Geographic metadata were not available for OP612691.

Fig. 2. Frequency of APOBEC3-style mutations in clade II genomes.

a,b, APOBEC3-style mutation frequency in clade II genomes isolated since 2019, using the UK 2018 MT903345 isolate as a baseline (a), and in clade II genomes isolated since 2017 using the Nigeria 1971 KJ642617 as a baseline (b). Genomes are placed in temporal groups by year of isolation except for OP612691, which is included in the 2019 group but was isolated in January 2020. ‘Other’ refers to lineage A.2 genomes isolated in 2022 in the United States, which are phylogenetically separated from the majority of sequences in the international outbreak and arise from a separate lineage within clade II.

Fig. 3. Distribution of APOBEC3-style mutations across the genome.

The linear position of all APOBEC3-style mutations for all 18 isolates described in this study is plotted, with the number of isolates with a given mutation shown on the vertical axis. Genome length is 195 kb.

Fig. 4. Phylogenetic tree of lineage A MPXV genomes.

The tree is generated using concatenated nucleotide ORF sequences extracted from complete genomes with a limited number of unknown bases in their sequence, after genes with any ambiguous nucleotides in their sequence have been excluded for all sequences. Genomes described in this study are highlighted in red, and those with a disrupted A46R gene (lineage A.2) are marked with a red square. Genomes from an additional potential lineage are marked with a brown square.