Tarja A. Sironen

EMtrace: offline nanopore metagenomics on a laptop for rapid viral diagnostics, genome recovery and 16S profiling

A rational design strategy and validation for protease-resistant fusion-inhibitor antiviral peptides

This study designs and validates protease-resistant antiviral peptides that inhibit SARS-CoV-2 fusion, showing improved efficacy in vitro and in vivo.

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.

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.

Drivers of host-pathogen community assemblies in European forests and urban green spaces

The paper investigates how biodiversity and habitat changes affect pathogen communities in European forests and urban areas, finding that host diversity increases pathogen richness but urbanization reduces certain pathogens.

Egyptian rousette bat humoral immunity to H9 influenza hemagglutinin

The paper develops a yeast surface display library of bat antibodies to study humoral immunity to H9 influenza hemagglutinin, revealing structural and functional characteristics of bat antibodies.

Bartonella and hemotropic Mycoplasma species in synanthropic bats in Kenya

The paper identifies Bartonella and hemotropic Mycoplasma species in synanthropic bats in Kenya and assesses their potential to infect humans.

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.

Age-dependent effects of infection on survival of a wild rodent reservoir host

This study shows that PUUV infection reduces survival of bank voles, especially young ones, in a natural setting, contradicting the expectation that reservoir hosts are unaffected.

Surveillance of zoonotic pathogens in small mammals across a gradient of forest anthropization in Eastern France

The paper surveys zoonotic pathogens in small mammals across a forest anthropization gradient, finding pathogen richness and community structure vary with host species, site, and urban adaptation traits.

American mink as an animal model to study SARS-CoV-2 and vaccine response

The paper develops a SARS-CoV-2 vaccine in mink and evaluates its immune response and efficacy against Alpha and Omicron variants, showing reduced severity and virus presence in vaccinated animals.

Time-series sewage metagenomics can separate the seasonal, human-derived and environmental microbial communities, holding promise for source-attributed surveillance

This study uses sewage metagenomics to distinguish seasonal, human-derived, and environmental microbial communities, offering potential for improved AMR surveillance.

Ecological factors alter how spatial overlap predicts viral infection dynamics in wild rodent populations

The paper examines how ecological factors modify the relationship between spatial overlap and hantavirus infection likelihood in wild bank voles.

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.