Philippe Pérot
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View article: Predominance of <scp> <i>L. monocytogenes</i> </scp> Lineage I Clones in Wastewater, Ruminants, and Natural Environments
Predominance of <span> <i>L. monocytogenes</i> </span> Lineage I Clones in Wastewater, Ruminants, and Natural Environments Open
Listeria monocytogenes is a saprophytic bacterium and a foodborne pathogen of humans and animals. Little is known about its distribution and genetic diversity across different environments within the same geographical region. We conducted …
View article: Molecular detection of hrHPV-induced high-grade squamous intraepithelial lesions of the cervix through a targeted RNA next generation sequencing assay
Molecular detection of hrHPV-induced high-grade squamous intraepithelial lesions of the cervix through a targeted RNA next generation sequencing assay Open
Background Cervical cancer screening programs are increasingly relying on sensitive molecular approaches as primary tests to detect high-risk human papillomaviruses (hrHPV), the causative agents of cervix cancer. Although hrHPV infection i…
View article: Insights into the virome of Hyalomma marginatum in the Danube Delta: a major vector of Crimean-Congo hemorrhagic fever virus in Eastern Europe
Insights into the virome of Hyalomma marginatum in the Danube Delta: a major vector of Crimean-Congo hemorrhagic fever virus in Eastern Europe Open
Background Ticks are significant vectors of pathogens, including viruses, bacteria, and protozoa. With approximately 900 tick species worldwide, many are expanding their geographical range due to changing socioeconomic and climate factors.…
View article: Circovirus Hepatitis in Immunocompromised Patient, Switzerland
Circovirus Hepatitis in Immunocompromised Patient, Switzerland Open
We identified a novel human circovirus in an immunocompromised 66-year-old woman with sudden onset of self-limiting hepatitis. We detected human circovirus 1 (HCirV-1) transcripts in hepatocytes and the HCirV-1 genome long-term in the pati…
View article: A quantitative assay for the assessment of cutaneous human papillomaviruses and polyomaviruses over time: A proof-of-concept in two patients with atopic dermatitis and psoriasis
A quantitative assay for the assessment of cutaneous human papillomaviruses and polyomaviruses over time: A proof-of-concept in two patients with atopic dermatitis and psoriasis Open
The human skin virome, unlike commensal bacteria, is an under investigated component of the human skin microbiome. We developed a sensitive, quantitative assay to detect cutaneous human resident papillomaviruses (HPV) and polyomaviruses (H…
View article: Performance of clinical metagenomics in France: a prospective observational study
Performance of clinical metagenomics in France: a prospective observational study Open
For the French translation of the abstract see Supplementary Materials section.
View article: Human Circovirus is not detected in plasma pools for fractionation
Human Circovirus is not detected in plasma pools for fractionation Open
Background Human Circovirus 1 and 2 were recently described in a French hepatitis case and in two Chinese drug users. Because of its small size and presumable high resistance to both inactivation and removal by nanofilters, such viruses—if…
View article: Virus Pop—Expanding Viral Databases by Protein Sequence Simulation
Virus Pop—Expanding Viral Databases by Protein Sequence Simulation Open
The improvement of our knowledge of the virosphere, which includes unknown viruses, is a key area in virology. Metagenomics tools, which perform taxonomic assignation from high throughput sequencing datasets, are generally evaluated with d…
View article: Acute tubulointerstitial nephritis with or without uveitis: a novel form of post-acute COVID-19 syndrome in children
Acute tubulointerstitial nephritis with or without uveitis: a novel form of post-acute COVID-19 syndrome in children Open
Background COVID-19 is a complex multisystem disease, frequently associated with kidney injury. Since the beginning of the COVID-19 pandemic, we observed a striking increase in the incidence of acute tubulointerstitial nephritis (aTIN) wit…
View article: Golgi localization of SARS-CoV-2 spike protein and interaction with furin in cerebral COVID-19 microangiopathy: a clue to the central nervous system involvement?
Golgi localization of SARS-CoV-2 spike protein and interaction with furin in cerebral COVID-19 microangiopathy: a clue to the central nervous system involvement? Open
In a neuropathological series of 20 COVID-19 cases, we analyzed six cases (three biopsies and three autopsies) with multiple foci predominantly affecting the white matter as shown by MRI. The cases presented with microhemorrhages evocative…
View article: Circovirus Hepatitis Infection in Heart-Lung Transplant Patient, France
Circovirus Hepatitis Infection in Heart-Lung Transplant Patient, France Open
In March 2022, a 61-year-old woman in France who had received a heart-lung transplant sought treatment with chronic hepatitis mainly characterized by increased liver enzymes. After ruling out common etiologies, we used metagenomic next-gen…
View article: Renal arcuate vein thrombosis–induced acute kidney injury: a rare multiple-Hit–mediated disease
Renal arcuate vein thrombosis–induced acute kidney injury: a rare multiple-Hit–mediated disease Open
Background Renal arcuate vein thrombosis (RAVT) is a rare and recently recognized cause of acute kidney injury (AKI) in young adults. However, the precise incidence and underlying pathophysiologic mechanisms leading to AKI in these patient…
View article: Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery
Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery Open
We present Microseek, a pipeline for virus identification and discovery based on RVDB-prot, a comprehensive, curated and regularly updated database of viral proteins. Microseek analyzes metagenomic Next Generation Sequencing (mNGS) raw dat…
View article: Files for publication "Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery"
Files for publication "Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery" Open
Context These files correspond to the article “Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery” submitted to Genes. File content input_data-empty_matrices: 50M-read Tissues and Plasma matrices, no spike; …
View article: Files for publication "Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery"
Files for publication "Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery" Open
Context These files correspond to the article “Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery” submitted to Genes. File content input_data-empty_matrices: 50M-read Tissues and Plasma matrices, no spike; …
View article: Files for publication "Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery"
Files for publication "Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery" Open
Context These files correspond to the article “Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery” submitted to Genes. File content input_data-empty_matrices: 50M-read Tissues and Plasma matrices, no spike; …
View article: Deep Impact of Random Amplification and Library Construction Methods on Viral Metagenomics Results
Deep Impact of Random Amplification and Library Construction Methods on Viral Metagenomics Results Open
Clinical metagenomics is a broad-range agnostic detection method of pathogens, including novel microorganisms. A major limit is the low pathogen load compared to the high background of host nucleic acids. To overcome this issue, several so…
View article: Files for publication "Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery"
Files for publication "Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery" Open
Context These files correspond to the article “Microseek: A Protein-Based Metagenomic Pipeline for Virus Diagnostic and Discovery” submitted to Genes. File content empty_matrices: 50M-read Tissues and Plasma matrices, no spike; matrices_sp…
View article: RVDB-prot, a reference viral protein database and its HMM profiles
RVDB-prot, a reference viral protein database and its HMM profiles Open
We present RVDB-prot, a database corresponding to the protein equivalent of the nucleic acid reference virus database RVDB. Protein databases can be helpful to perform more sensitive protein sequence comparisons. Similarly to its homologou…