de Block, T. | Search bioRxiv

bioRxiv2025

High genetic diversity of mpox virus (MPXV) in three different rodent species in the Democratic Republic of the Congo (DRC)

Altough zoonotic spillover events continue to drive human mpox outbreaks in the Democratic Republic of the Congo (DRC), the wildlife reservoir of mpox virus (MPXV) remains unkown. To address this gap, we screened samples from 2,701 wild mammals, mainly rodents (59.7%), bats (26.4%) and shrews (12.1%). Only six (0.2%) animals were Orthopoxvirus (OPV) PCR positive. Near full-length MPXV sequences were obtained from two squirrels (Funisciurus anerythrus and Paraxerus sp.) and one soft furred mouse (Praomys jacksoni). A novel Taterapox virus was identified in a shrew (Crocidura cf. denti). All newly identified MPXV strains belong to clade Ia, but they cluster into different groups or subgroups, despite being collected from geographically close locations, and all are closely related to human MPXV strainsfrom the same regions. Our study provides for the first time clear evidence that MPXV diversity is not restricted to a single rodent host species nor confined to a geographic area. Importantly, MPXV positive Paraxerus and Praomys specimens were sampled close to Kisangani, a city with more than one million inhabitants, highlighting that spillover events can als ooccur in or near major cities, with more favorable conditions for interhuman transmissions and potential emergence of new lineages.

microbiology↗

bioRxiv2025

SquiDBase: a community resource of raw nanopore data from microbes

Experimental data-driven research relies on raw data, which consist of unprocessed experimental outputs, whereas derived data are transformed through a number of processing steps to reveal specific insights. Such processing, however, can potentially introduce biases or information loss, compromising transparency and reproducibility. In nucleic acid sequencing, nucleotide sequences stored in the FASTQ format are widely shared, but FASTQ files are generated from platform-specific raw data outputs, which vary depending on the sequencing platform used. The raw data produced by Oxford Nanopore Technologies (ONT) sequencing devices contain valuable biological information and are also useful to improve data processing methods, which includes basecaller optimisation and modification detection. Increasing attention goes to exploring these raw signals to develop algorithms that could improve ONT device portability and enhance target enrichment efficiency through adaptive sampling. Despite these benefits, the storage and sharing of raw nanopore data remain limited due to technical constraints and the lack of appropriate, standardised and centralised infrastructure. To address this challenge, we developed SquiDBase (https://squidbase.org), a dedicated repository to collect raw microbial nanopore sequencing data. To maximise the utility of SquiDBase from its inception, we built SquiDPipe, a Nextflow pipeline for the automated removal of human or unwanted reads from raw nanopore data. Additionally, we sequenced 24 clinically relevant viruses and incorporated them into SquiDBase, significantly expanding the diversity of publicly available reference datasets. By offering a centralised, open-access raw data collection platform, SquiDBase facilitates data sharing, enhances reproducibility, and supports the development and benchmarking of novel computational tools, reinforcing open science in nanopore sequencing research.

bioinformatics↗