Recent infectious disease outbreaks highlight the importance of timely genomic surveillance in affected areas to guide public health responses. In the context of the largest known outbreak of mpox virus (MPXV), which included over 86,000 notifications in more than 110 countries, genomic surveillance has efforts have primarily focused on high-incidence nations in Europe and the Americas. However, there has been a paucity of genomic data collected and analysed from South-East Asia and the Western Pacific regions, including Australia.
In this study, we provide genomic characterisation of MPXV from a well-sampled cohort in Victoria, Australia. We include sampling from common body sites and at varied stages of infection for these individuals. Additionally, de-identified information about individuals from which samples were collected, including suspected country of acquisition is provided by the Victorian Department of Health. Comparative genomic and phylogenetic methods are applied to explore viral genetic diversity, both within and between individuals, integrated with patient travel history with findings at the intersection of evolutionary biology and epidemiology.
In total, we use Illumina and Oxford Nanopore Technology to present 102 MPXV whole genomes sampled from fifty-six Australian individuals. All individuals were male and 50.0% (28/56) acquired these infections in Australia. We found all genomes fell within the 2022 MPXV outbreak lineage (B.1), with onward transmission and evolution in Victoria evidenced by local clades where local acquisition was more common than international acquisition. Additionally, we analysed low-frequency sequence variation within samples, highlighting the potential of APOBEC-associated within-host evolution, and show that this can be differentiated from co-infection from multiple strains.
These data expand our view of MPXV genetic diversity within and between individuals, as well as the distribution of predefined lineages globally. Our findings highlight further examples of structural variation and other forms of evolution in the current MPXV outbreak. Regularly updating our understanding of MPXV dispersal and diversification will guide public health measures and containment, as well as allowing for global surveillance and monitoring of viral evolutionary trajectory throughout the outbreak. These findings underscore the significance of within-host factors in the ongoing evolution and transmission of mpox to be considered in future studies.