Ana da Silva Filipe

The potential of H5N1 viruses to adapt to bovine cells varies throughout evolution

This study shows that H5N1 viruses' ability to adapt to bovine cells varies across genotypes and time, with key mutations in PB2 playing a role.

Quantifying virus load and characterising virus diversity in wildlife samples with target enrichment sequencing

This study uses target enrichment sequencing to assess viral load and diversity in wildlife samples, showing a log-linear relationship between spike-in concentration and read depth.

Comparative study of two Rift Valley fever virus field strains circulating in Mauritania in 2010 and 2013 reveals the high virulence of the MRU25010-30 strain isolated from camel

This study compares two Rift Valley fever virus strains from Mauritania, showing that MRU25010-30 is more virulent and replicates more efficiently than MRU2687-3.

Mosquito virus diversity in Western and North-western Uganda

This study uses metagenomic sequencing to identify a diverse range of viruses in Ugandan mosquitoes, revealing many novel species with potential human and animal pathogenicity.

Genomic and phenotypic comparisons reveal distinct variants of Wolbachia strain wAlbB

The paper identifies two genomic variants of Wolbachia strain wAlbB, showing differences in gene content and density that correlate with environmental tolerance and stability in mosquito populations.

Genome sequencing and comparative analysis of Wolbachia strain wAlbA reveals Wolbachia-associated plasmids are common

The paper sequenced the Wolbachia strain wAlbA and found it associated with plasmids, revealing that such plasmids are common in Wolbachia and may contribute to host-symbiont interactions.

periscope: Sub-Genomic RNA Identification in SARS-CoV-2 Genomic Sequencing Data

Periscope identifies and quantifies sub-genomic RNAs in SARS-CoV-2 genomic data, detecting canonical and non-canonical sgRNAs with high fidelity.

Within-host genomics of SARS-CoV-2

This study analyzes within-host SARS-CoV-2 diversity and transmission patterns using 1390 UK clinical samples, finding low within-host diversity and a narrow transmission bottleneck.

Interferon lambda 4 impacts broadly on hepatitis C virus diversity.

The paper examines the impact of IFN-lambda4 on HCV diversity using host and viral genetic data from 485 patients, finding that IFN-lambda4 variants influence viral amino acid diversity and load.