Biology subjects

Lagier, J.-C.

Publications and source records attributed to Lagier, J.-C..

4 recordsLinked to original sources

bioRxiv2026

Sarrella massiliensis gen. nov. sp. nov., a new gut genus isolated from the stool of a healthy donor

Strain Marseille-QA0792 (=CSUR QA0792, CECT 31199) was isolated from the feces of a healthy person using the culturomics method. The fecal sample originated from leftover material collected for a fecal microbiota transplantation (FMT) procedure, obtained during a routine screening in accordance with the guidelines of the French National Agency for Medicines and Health Products Safety (ANSM). This strain is Gram-stain-negative, rod-shaped, non-motile, and non-spore-forming. It is strictly anaerobic, with optimal growth at 37{degrees}C. Strain Marseille-QA0792 presented its highest 16S rRNA identity, 96.2%, with ''Merdibacter massiliensis'' strain Marseille-P3254 (not validly published) (accession number LT598590) and ANI similarity of 75.0% with the same species. Among validly published species, strain Marseille-QA0792 showed its highest 16S rRNA gene sequence similarity (91.5%) with Faecalicoccus acidiformans strain 37-2a (accession number HQ452864), whereas all computed average nucleotide identity (ANI) values were below 75%. Genome sequencing revealed a genome size of 2.67 Mb and a G+C content of 50.01%. This species is classified within the Erysipelotrichaceae family in the Bacillota phylum. Thus, we isolated for the first time a novel genus named Sarrella massiliensis gen. nov., sp. nov., strain Marseille-QA0792. This discovery highlights the importance of continuing culturomics efforts to explore the human microbiome.

microbiology↗

bioRxiv2025

Long-Term Intra-Host Evolution of SARS-CoV-2 in an Immunocompromised Patient: Recombination and Within-Host Mutations Driving Viral Adaptation

An immuno-compromised patient with lymphoma experienced a prolonged SARS-CoV-2 infection lasting 14 months, initially infected with B.1.160, followed by B.1.1.7. This study focused on intra-host single nucleotide variants (iSNVs) and single nucleotide polymorphisms (SNPs), distinguishing their origin as either within-host mutations or parental. The whole genome analysis revealed accelerated evolution, with positive selection detected in key genes such as Spike, N, ORF9b, and nsp13, all involved in viral replication and immune evasion. Of the two evolutionary mechanisms involved, host-driven mutation has played a dominant role in this evolutionary story. C>T transitions emerged as the most widespread mutational signature, consistent with host-driven RNA editing mechanisms. Two host-internal mutations, A28271T in the translation initiation region of the N Kozak gene and C26858T in the M gene, were highly shared among the deposited SARS-CoV-2 sequences. Recombination with parental lineages played a major role particularly in Spike, ORF3a and M genes. In Spike, the B.1.1.7 sequence was selected, wild-type ORF3a and M were restored, suggesting a selective advantage in returning to an ancestral sequence. In addition, the temporary emergence of intra-host convergent mutations in Spike, notably L5F, D796H and T572I, underlines the strong selective pressures exerted on this gene. A 126-nucleotide deletion in ORF8 resulted in a truncated protein, reinforcing its uselessness for viral replication, as observed in circulating variants such as B.1.1.7. The present case highlights the complex interplay between viral recombination and mutations within the host in chronic infections and further underscores the remarkable evolutionary plasticity of SARS-CoV-2 and its potential to generate highly adapted viral strains.

evolutionary biology↗

bioRxiv2022

Sequencing of Monkeypox virus from infected patients reveals viral genomes with APOBEC3-like editing, gene inactivation, and bacterial agents of skin superinfection

An epidemic of Monkeypox virus (MPX virus) infections has arisen in May 2022 in non-endemic countries particularly in Europe among men having sex with men, whose extent is unprecedented. Since May 2022 we implemented MPX virus diagnosis by real-time PCR at university hospitals of Marseille, southern France. Here, we performed DNA metagenomic analyses of clinical samples from MPX virus-infected patients between June and July 2022, using next-generation sequencing with Illumina or Nanopore technologies. Twenty-five samples from 25 patients were studied. This allowed obtaining a MPX virus genome for 18 patients, essentially from genital skin lesions and rectal swabbing. All 18 genomes were classified in the MPX virus B.1 lineage, and we delineated five sublineages (A-E). We detected a high number of mutations (66-73) scattered along the MPX virus genomes relatively to the genome obtained from a human in Nigeria in 2018. Some non-synonymous mutations occurred in genes encoding central proteins, among which transcription factors and core and envelope proteins. They included two mutations that truncate RNA polymerase subunit RPO132 and a phospholipase D-like protein, which suggests gene inactivation. In addition, we identified that a large majority of nucleotide substitutions (94%) in the 18 MPX virus genomes were G>A or C>T, suggesting the action of human APOBEC3 enzymes. Finally, while we did not detect reads matching with main bacterial agents of sexually transmitted infections, >1,000 reads identified Staphylococcus aureus and Streptococcus pyogenes for 7 and 17 samples, respectively. These findings warrant a close genomic monitoring of MPX virus to get a better picture of this virus genetic evolution and mutational patterns, and they point out the common presence in monkeypox lesions of bacterial agents of skin superinfection, which warrants a close clinical monitoring in monkeypox patients.

microbiology↗

bioRxiv2020

Genomic diversity and evolution of coronavirus (SARS-CoV-2) in France from 309 COVID-19-infected patients

The novel coronavirus (SARS-CoV-2) causes pandemic of viral pneumonia. The evolution and mutational events of the SARS-CoV-2 genomes are critical for controlling virulence, transmissibility, infectivity, severity of symptoms and mortality associated to this infectious disease. We collected and investigated 309 SARS-CoV-2 genomes from patients infected in France. Detailed genome cartography of all mutational events (SNPs, indels) was reported and correlated to clinical features of patients. A comparative analysis between our 309 SARS-CoV-2 genomes from French patients and the reference Wuhan coronavirus genome revealed 315 substitution mutations and six deletion events: ten were in 5/3 UTR, 178 were nonsynonymous, 126 were synonymous and one generated a stop codon. Six different deleted areas were also identified in nine viral variants. In particular, 30 substitution mutations (18 nonsynonymous) and one deletion ({Delta}21765-21770) concerned the spike S glycoprotein. An average of 7.8 mutational events (+/- 1.7 SD) and a median of 8 (range, 7-9) were reported per viral isolate. Comparative analyses and clustering of specific mutational signatures in 309 genomes disclose several divisions in groups and subgroups combining their geographical and phylogenetic origin. Clinical outcomes of the 309 COVID-19-infected patients were investigated according to the mutational signatures of viral variants. These findings highlight the genome dynamics of the coronavirus 2019-20 and shed light on the mutational landscape and evolution of this virus. Inclusion of the French cohort enabled us to identify 161 novel mutations never reported in SARS-CoV-2 genomes collected worldwide. These results support a global and continuing surveillance of the emerging variants of the coronavirus SARS-CoV-2.

genomics↗