In action—an early warning system for the detection of unexpected or novel pathogens

Abstract

Pro-active approaches in preventing future epidemics include pathogen discovery prior to their emergence in human and/or animal populations. Playing an important role in pathogen discovery, high-throughput sequencing (HTS) enables the characterization of microbial and viral genetic diversity within a given sample. In particular, metagenomic HTS allows the unbiased taxonomic profiling of sequences; hence, it can identify novel and highly divergent pathogens such as viruses. Newly discovered viral sequences must be further investigated using genomic characterization, molecular and serological screening, and/or in-vitro and in-vivo characterization. Several outbreak and surveillance studies apply unbiased generic HTS to characterize whole genome sequences of suspected pathogens. In contrast, this study aimed to screen for novel and unexpected pathogens in previously generated HTS datasets and use this information as a starting point for the establishment of an early warning system (EWS). As a proof of concept, the EWS was applied to HTS datasets and archived samples from the 2018-19 West Nile virus (WNV) epidemic in Germany. A metagenomics read classifier detected sequences related to genome sequences of various members of Riboviria. We focused the further EWS investigation on viruses belonging to the families Peribunyaviridae and Reoviridae, under suspicion of causing co-infections in WNV-infected birds. Phylogenetic analyses revealed that the reovirus genome sequences clustered with sequences assigned to the species Umatilla virus, whereas a new peribunyavirid, tentatively named “Hedwig virus” belonged to a putative novel genus of the family Peribunyaviridae. In follow up studies, newly developed molecular diagnostic assays detected fifteen Umatilla virus-positive wild birds from different German cities and eight Hedwig virus-positive captive birds from two zoological gardens. Umatilla virus was successfully cultivated in mosquito C6/36 cells inoculated with a blackbird liver. In conclusion, this study demonstrates the power of the applied EWS for the discovery and characterization of unexpected viruses in repurposed sequence datasets, followed by virus screening and cultivation using archived sample material. The EWS enhances the strategies for pathogen recognition before causing sporadic cases and massive outbreaks and proves to be a reliable tool for modern outbreak preparedness.

Novel Virus Identification through Metagenomics: A Systematic Review

“…mNGS is characterized by a constant and ultra-rapid development of new analytical methods, both biological and bioinformatics, that seem better suited to follow the dynamic of pandemic events and in general viral outbreaks. This suggests the opportunity to implement these technologies to establish early warning systems [74] and to design effective disease control and prevention strategies.…”

Metagenomic Analysis of Togaviridae in Mosquito Viromes Isolated From Yunnan Province in China Reveals Genes from Chikungunya and Ross River Viruses

“…In addition, the component of mosquito virome and the high abundance of viruses in mosquitoes can be revealed using metagenomic sequencing (Metsky et al, 2019;Ramıŕez et al, 2020). Moreover, metagenomic sequencing is also of great significance for the discovery and identification of novel viruses (Sadeghi et al, 2018;Santos et al, 2021). Many mosquito species virome studies applying NGS tools identified new viruses and described their diversity, which led to the discovery of insect-specific viruses (Romo et al, 2018;Chenyan et al, 2020).…”

Multiple Novel Mosquito-Borne Zoonotic Viruses Revealed in Pangolin Virome

“…Illumina sequencing combined with bioinformatics analysis is more likely to be effective than traditional methods ( Zhang et al., 2018 ; Marzoli et al, 2021 ; Thannesberger et al., 2021 ). Moreover, a lot of viruses derived from numerous species have been detected using this approach ( Sadeghi et al., 2018 ; Santos et al., 2021 ). Therefore, the composition of the pangolin virome can be revealed using Illumina sequencing.…”