Unbiased Virus Detection in a Danish Zoo Using a Portable Metagenomic Sequencing System

A safety and absolute activity measurement method for Phi29 DNA polymerase based on chemiluminescent detection of dATP consumption

BACKGROUND

Phi29 DNA polymerase serves as a cornerstone enzyme in molecular biology, enabling critical applications such as rolling-circle amplification, multiple strand-displacement amplification, and single-molecule real-time sequencing. Despite its widespread use, traditional methods for assessing its activity-including radioactive labeling and fluorescence-based quantification-suffer from limitations such as operational complexity, low precision, and safety risks. These challenges have hindered standardized quality control in both academic and industrial settings.

RESULTS

To address these limitations, we developed a chemiluminescence-based absolute quantitation method that directly measures dATP consumption during polymerization. This method streamlines operational workflows by eliminating the need for multi-step purification procedures or specialized equipment, enabling the quantification of Phi29 DNA polymerase activity within 2 h. It demonstrates robust linearity and sensitivity across a broad dynamic range (25-200 μg/mL), while employing chemiluminescence-based detection of dATP to replace 3H-labeled dTTP, thereby eliminating biohazard risks associated with radioactive materials and enhancing feasibility for routine laboratory implementation.

SIGNIFICANCE

This method introduces a novel approach for determining DNA polymerase activity by pioneering the correlation between dATP stoichiometry and enzymatic activity. It expands the applicability of activity assays to routine molecular biology laboratories, enabling rapid inter-batch consistency testing in commercial enzyme production. This advancement establishes a new benchmark for polymerase quality control.

INSaFLU-TELEVIR: an open web-based bioinformatics suite for viral metagenomic detection and routine genomic surveillance

BACKGROUND

Implementation of clinical metagenomics and pathogen genomic surveillance can be particularly challenging due to the lack of bioinformatics tools and/or expertise. In order to face this challenge, we have previously developed INSaFLU, a free web-based bioinformatics platform for virus next-generation sequencing data analysis. Here, we considerably expanded its genomic surveillance component and developed a new module (TELEVIR) for metagenomic virus identification.

RESULTS

The routine genomic surveillance component was strengthened with new workflows and functionalities, including (i) a reference-based genome assembly pipeline for Oxford Nanopore technologies (ONT) data; (ii) automated SARS-CoV-2 lineage classification; (iii) Nextclade analysis; (iv) Nextstrain phylogeographic and temporal analysis (SARS-CoV-2, human and avian influenza, monkeypox, respiratory syncytial virus (RSV A/B), as well as a "generic" build for other viruses); and (v) algn2pheno for screening mutations of interest. Both INSaFLU pipelines for reference-based consensus generation (Illumina and ONT) were benchmarked against commonly used command line bioinformatics workflows for SARS-CoV-2, and an INSaFLU snakemake version was released. In parallel, a new module (TELEVIR) for virus detection was developed, after extensive benchmarking of state-of-the-art metagenomics software and following up-to-date recommendations and practices in the field. TELEVIR allows running complex workflows, covering several combinations of steps (e.g., with/without viral enrichment or host depletion), classification software (e.g., Kaiju, Kraken2, Centrifuge, FastViromeExplorer), and databases (RefSeq viral genome, Virosaurus, etc.), while culminating in user- and diagnosis-oriented reports. Finally, to potentiate real-time virus detection during ONT runs, we developed findONTime, a tool aimed at reducing costs and the time between sample reception and diagnosis.

CONCLUSIONS

The accessibility, versatility, and functionality of INSaFLU-TELEVIR are expected to supply public and animal health laboratories and researchers with a user-oriented and pan-viral bioinformatics framework that promotes a strengthened and timely viral metagenomic detection and routine genomics surveillance. INSaFLU-TELEVIR is compatible with Illumina, Ion Torrent, and ONT data and is freely available at https://insaflu.insa.pt/ (online tool) and https://github.com/INSaFLU (code).