Scientists develop new bioinformatics pipeline to identify viruses in environmental samples

Researchers from the University of Helsinki have developed a novel bioinformatics pipeline called Lazy pipe for identifying viruses in host-associated or environmental samples.

The pipeline was developed in close collaboration between virologists and bioinformaticians. The researchers believe they have succeeded to address many challenges typically encountered in viral metagenomics.

Previously, the Viral Zoonooses Research Unit, led by Professor Olli Vapalahti, has published two examples of novel and potentially zoonotic viral agents that were identified with Lazypipe from wild animals that can serve as vectors.

A new ebolavirus was identified from faeces and organ samples of Mops condylurusbats in Kenya, and a new tick-borne pathogen Alongshan virus from ticks in Northeast Europe.

These examples demonstrate the efficacy of Lazy pipe data analysis for NGS libraries with very different DNA/RNA backgrounds, ranging from mammalian tissues to pooled and crushed arthropods."

Dr Teemu Smura, University of Helsinki

Covid-19 heightens the need to detect new viruses rapidly

The current Coronavirus pandemic heightens the need to rapidly detect previously unknown viruses in an unbiased way.

"The detection of SARS-CoV-2 without reference genome demonstrates the utility of Lazy pipe for scenarios in which novel zoonotic viral agents emerge and can be quickly detected by NGS sequencing from clinical samples," says Dr. Ravi Kant.

In early April, the research group tested libraries of SARS-CoV-2 positive samples with Lazy pipe.

"We confirmed that the pipeline detected SARS-CoV-2in 9 out of 10libraries with default settings and without SARS-CoV-2 reference genome," says Dr. Ilja Pljusnin.

"Lazy pipe could play a crucial role in prediction of emerging infectious diseases," adds Assoc. Prof. Tarja Sironen.