Publications by authors named "Emna Achouri"
During viral replication, viruses carrying an RNA genome produce non-standard viral genomes (nsVGs), including copy-back viral genomes (cbVGs) and deletion viral genomes (delVGs), that play a crucial role in regulating viral replication and pathogenesis. Because of their critical roles in determining the outcome of RNA virus infections, the study of nsVGs has flourished in recent years, exposing a need for bioinformatic tools that can accurately identify them within next-generation sequencing data obtained from infected samples. Here, we present our data analysis pipeline, Viral Opensource DVG Key Algorithm 2 (VODKA2), that is optimized to run on a parallel computing environment for fast and accurate detection of nsVGs from large data sets.
View Article and Find Full Text PDFDuring viral replication, viruses carrying an RNA genome produce non-standard viral genomes (nsVGs), including copy-back viral genomes (cbVGs) and deletion viral genomes (delVGs), that play a crucial role in regulating viral replication and pathogenesis. Because of their critical roles in determining the outcome of RNA virus infections, the study of nsVGs has flourished in recent years exposing a need for bioinformatic tools that can accurately identify them within Next-Generation Sequencing data obtained from infected samples. Here, we present our data analysis pipeline, Viral Opensource DVG Key Algorithm2 (VODKA2), that is optimized to run on a High Performance Computing (HPC) environment for fast and accurate detection of nsVGs from large data sets.
View Article and Find Full Text PDFRNA viruses generate nonstandard viral genomes during their replication, including viral genomes of the copy-back (cbVGs) type that cannot replicate in the absence of a standard virus. cbVGs play a crucial role in shaping virus infection outcomes due to their ability to interfere with virus replication and induce strong immune responses. However, despite their critical role during infection, the principles that drive the selection and evolution of cbVGs within a virus population are poorly understood.
View Article and Find Full Text PDFArticle Synopsis
- Respiratory syncytial virus (RSV) can lead to serious respiratory illness, particularly in children and vulnerable populations, but the role of defective viral genomes (DVGs) in influencing disease severity is not well understood.
- In a study involving hospitalized children and experimentally infected adults, the presence of DVGs was linked to disease severity: early detection of DVGs correlated with milder illness whereas late detection was associated with more severe outcomes.
- The findings suggest that monitoring the presence and timing of DVG accumulation can serve as a useful prognostic tool to identify individuals at higher risk for severe RSV infections.
Article Synopsis
- Influenza viruses can create defective versions of themselves called defective viral genomes (DVGs) when they replicate.
- * Researchers have developed a new method called DG-seq to better detect and measure these DVGs, ensuring accurate results.
- * They found that certain ways of preparing samples before testing can make a difference, and some methods actually make it harder to measure DVGs correctly.
Article Synopsis
- A new treatment strategy called consecutive alternating administration (CAA) was developed for enterovirus infections using a combination of antiviral drugs, showing no drug resistance and increased effectiveness in a mouse model infected with coxsackievirus B1 (CVB1).
- Researchers analyzed brain samples from mice treated with CAA and monotherapies for viral RNA mutations using next-generation sequencing, revealing specific genetic changes associated with drug effects.
- The findings suggest that the CAA method leads to distinct mutations in the viral genome, which may contribute to the treatment's high efficacy and prevention of drug resistance.
Gut Microbial Diversity Is Reduced in Smokers with Crohn's Disease.
Inflamm Bowel Dis
September 2016
Background: Smoking has a negative impact on Crohn's disease (CD), but the mechanisms underlying this association are unclear. We compared the gut microbiota composition of smoking with nonsmoking patients with CD using a metagenomic approach.
Methods: Stool samples and clinical data were collected from current smokers and nonsmokers with CD from France and the Netherlands, matched for country, gender, age, disease activity, and body mass index.