Teemu Smura

Detection and characterisation of alpha- and betacoronaviruses in rodents and bats from Germany, France, Belgium and Ireland

This study detects and characterizes coronaviruses in rodents and bats from four European countries, identifying new viral lineages and highlighting potential zoonotic risks.

LazypipeX: Customizable Virome Analysis Pipeline Enabling Fast and Sensitive Virus Discovery from NGS data

LazypipeX improves virus discovery in mNGS data by offering customizable and efficient annotation strategies that reduce execution time while maintaining accuracy.

Co-circulating TBEV lineages and evidence for vertical transmission in wild bank voles from Poland

The paper investigates TBEV circulation and vertical transmission in bank voles in Poland, finding co-circulating viral lineages and evidence of vertical transmission.

Rat hepatitis E virus and novel paramyxoviruses in synanthropic rodents and shrews in Kenya

This study identifies zoonotic viruses in Kenyan rodents and shrews, including rat hepatitis E virus and novel paramyxoviruses, highlighting the need for genomic surveillance.

Addressing pandemic-wide systematic errors in the SARS-CoV-2 phylogeny

The paper reprocesses SARS-CoV-2 genomic data to correct systematic errors in phylogenies using a novel assembly tool, resulting in a cleaner global tree of 4.47 million samples.

JAK inhibitors remove innate immune barriers facilitating viral propagation

This study shows JAK inhibitors like baricitinib suppress IFN-stimulated genes, aiding viral propagation by reducing antiviral defenses.

Enhanced Viral Metagenomics with Lazypipe 2

This paper introduces Lazypipe2, an improved metagenomic pipeline for virus detection, showing enhanced performance in identifying eukaryotic viruses and handling divergent sequences.

ClusTRace, a bioinformatic pipeline for analyzing clusters in virus phylogenies

ClusTRace is a bioinformatic pipeline for analyzing clusters in SARS-CoV-2 phylogenies to detect super-spreading events and novel mutations.

High prevalence of an alpha variant lineage with a premature stop codon in ORF7a in Iraq, winter 2020-2021

The paper analyzes SARS-CoV-2 genomic data from Iraq during 2020-2021, identifying a high prevalence of the B.1.1.7 lineage with a stop codon mutation in ORF7a.

HaVoC, a bioinformatic pipeline for reference-based consensus assembly and lineage assignment for SARS-CoV-2 sequences

HaVoC is a bioinformatic pipeline that assembles SARS-CoV-2 sequences and identifies lineages to detect variants of concern.

Novel NGS Pipeline for Virus Discovery from a Wide Spectrum of Hosts and Sample Types

The paper introduces a novel NGS pipeline called LAZYPIPE for virus discovery across diverse hosts and samples, demonstrating its ability to identify both known and novel viruses.