MpoxRadar: a worldwide MPXV genomic surveillance dashboard

Abstract

The mpox virus (MPXV) is mutating at an exceptional rate for a DNA virus and its global spread is concerning, making genomic surveillance a necessity. With MpoxRadar, we provide an interactive dashboard to track virus variants on mutation level worldwide. MpoxRadar allows users to select among different genomes as reference for comparison. The occurrence of mutation profiles based on the selected reference is indicated on an interactive world map that shows the respective geographic sampling site in customizable time ranges to easily follow the frequency or trend of defined mutations. Furthermore, the user can filter for specific mutations, genes, countries, genome types, and sequencing protocols and download the filtered data directly from MpoxRadar. On the server, we automatically download all MPXV genomes and metadata from the National Center for Biotechnology Information (NCBI) on a daily basis, align them to the different reference genomes, generate mutation profiles, which are stored and linked to the available metainformation in a database. This makes MpoxRadar a practical tool for the genomic survaillance of MPXV, supporting users with limited computational resources. MpoxRadar is open-source and freely accessible at https://MpoxRadar.net.

Graphical Abstract

MpoxRadar: a worldwide genomic surveillance dashboard for MPXV.

Figure 1.

Simplified overview of the processes and steps taken to obtain, process, store and visualise the data on MpoxRadar. The first steps (top right corner) include retrieving data from NCBI, pre-processing, and aligning sequences, followed by variant calling, all done by our analytical tool, MpoxSonar. The data is then stored in a database. Visualisations and interactive maps are presented based on this data on MpoxRadar, while also allowing direct user interaction to the database via the website.

Figure 2.

Resulting visualisation from the explore tool, after filtering for the genes ‘MPXV-UK_P2-076’, ‘MPXV-UK_P2-133’, ‘MPXV-UK_P2-157’, ‘MPXV-UK_P2-182’, and using the pre-selected amino-acid mutation list with the reference genome ‘MT903344.1’. We changed the interval to 300 days to get a wider coverage of time and evolution of these mutations. The results can be viewed as two sections (marked as 1 and 2). Section 1) The world map with mutation counts provides a quick overview of the presence and frequency of the chosen mutations. (A) The colours on the map represent the number of sequences. One has to keep in mind that some countries sample and publish more MPXV sequences than other countries, corollary having higher mutation numbers. (B) Users can move the time duration the map is based on by moving this circle. (C) By clicking on a certain country on this map, the users will get detailed information on the mutations in the sequences from that country in section 2 of the output figures. In this case, we click on the United Kingdom, which is also printed to enable a more intuitive understanding of this function for the user at point (D). The first plot shows the number of sequences with chosen mutations on chosen genes. (E) For example, for the gene ‘MPXV-UK_P2-076’, there are two mutations appearing in the United Kingdom: ‘D88K’ and ‘S30F’ with equally high frequencies. On the mutation development plot below, the user can see the trend of the mutation frequency over time. To increase visual intuition, we colour code each gene with a certain colour starting from the filter input for the gene and its mutations to the plots for sequences including that gene and the mutation development. (F) Here, you can see the colour green used for the gene ‘MPXV-UK_P2-076’ which shows a steady increase in the two mutation frequencies on the plot.