Feasibility and clinical utility of local rapid Nanopore influenza A virus whole genome sequencing for integrated outbreak management, genotypic resistance detection and timely surveillance

VirDetector: a bioinformatic pipeline for virus surveillance using nanopore sequencing

SUMMARY

Virus surveillance programmes are designed to counter the growing threat of viral outbreaks to human health. Nanopore sequencing, in particular, has proven to be suitable for this purpose, as it is readily available and provides rapid results. However, as special bioinformatic programs are required to extract the relevant information from the sequencing data, applications are needed that allow users without extensive bioinformatics knowledge to carry out the relevant analysis steps. We present VirDetector, a bioinformatic pipeline for virus surveillance using nanopore sequencing. The pipeline automatically installs all required programs and databases and allows all its steps to be executed with a single console command. After preprocessing the samples, including the possibility for basecalling, the pipeline classifies each sample taxonomically and reconstructs the viral consensus genomes, which are then used in phylogenetic analyses. This streamlined workflow provides a user-friendly and efficient solution for monitoring viral pathogens.

AVAILABILITY AND IMPLEMENTATION

VirDetector is freely available at https://github.com/NLKaiser/VirDetector and https://zenodo.org/records/14637302 (10.5281/zenodo.14637302).

The 28S rRNA RT-qPCR assay for host depletion evaluation to enhance avian virus detection in Illumina and Nanopore sequencing

Abundant host and bacterial sequences can obscure the detection of less prevalent viruses in untargeted next-generation sequencing (NGS). Efficient removal of these non-targeted sequences is vital for accurate viral detection. This study presents a novel 28S ribosomal RNA (rRNA) RT-qPCR assay designed to assess the efficiency of avian rRNA depletion before conducting costly NGS for the detection of avian RNA viruses. The comprehensive evaluation of this 28S-test focuses on substituting DNase I with alternative DNases in our established depletion protocols and finetuning essential parameters for reliable host rRNA depletion. To validate the effectiveness of the 28S-test, we compared its performance with NGS results obtained from both Illumina and Nanopore sequencing platforms. This evaluation utilized swab samples from chickens infected with highly pathogenic avian influenza virus, subjected to established and modified depletion protocols. Both methods significantly reduced host rRNA levels, but using the alternative DNase had superior performance. Additionally, utilizing the 28S-test, we explored cost- and time-effective strategies, such as reduced probe concentrations and other alternative DNase usage, assessed the impact of filtration pre-treatment, and evaluated various experimental parameters to further optimize the depletion protocol. Our findings underscore the value of the 28S-test in optimizing depletion methods for advancing improvements in avian disease research through NGS.