Nasri, F. | bioRxiv Science

bioRxiv2023

MpoxRadar: a worldwide Mpox genomic surveillance dashboard

Monkeypox (Mpox) 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 Mpox genomes and metadata from the National Center for Biotechnology Information (NCBI) on a daily basis, align them with 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 Mpox, supporting users with limited computational resources. MpoxRadar is open-source and freely accessible at https://MpoxRadar.net. GRAPHICAL ABSTRACT O_FIG_DISPLAY_L [Figure 1] M_FIG_DISPLAY C_FIG_DISPLAY

bioinformatics↗

bioRxiv2021

Pathogenic potential prediction for novel fungal DNA based on a curated fungi-hosts data collection

BackgroundEmerging pathogens are a growing threat, but large data collections and approaches for predicting the risk associated with novel agents are limited to bacteria and viruses. Pathogenic fungi, which also pose a constant threat to public health, remain understudied. Relevant data remains comparatively scarce and scattered among many different sources, hindering the development of sequencing-based detection workflows for novel fungal pathogens. No prediction method working for agents across all three groups is available, even though the cause of an infection is often difficult to identify from symptoms alone. ResultsWe present a curated collection of fungal host range data, comprising records on human, animal and plant pathogens, as well as other plant-associated fungi, linked to publicly available genomes. We show that it can be used to predict the pathogenic potential of novel fungal species directly from DNA sequences with either sequence homology or deep learning. We develop learned, numerical representations of the collected genomes and visualize the landscape of fungal pathogenicity. Finally, we train multi-class models predicting if next-generation sequencing reads originate from novel fungal, bacterial or viral threats. ConclusionsThe neural networks trained using our data collection enable accurate detection of novel fungal pathogens. A curated set of over 1,400 genomes with host and pathogenicity metadata supports training of machine learning models and sequence comparison, not limited to the pathogen detection task. AvailabilityThe data, models and code are hosted at https://zenodo.org/record/5846345, https://zenodo.org/record/5711877, and https://gitlab.com/dacs-hpi/deepac.

bioinformatics↗