Hepatitis E virus (HEV) genotype 3 is the most common linked to HEV infections in Europe and America. Three major clades (HEV-3.1, HEV-3.2, HEV-3.3) have been identified but overlaps between intra-subtype inter-subtype p-distances make subtype classification inconsistent. Reference sequences proposed facilitate communication researchers new putative subtypes recently. We used full or near full-length HEV-3 genome available Genbank database (April 2020; n = 503) distance analyses of HEV-3.1...

Hepatitis E virus is a single-strand, positive-sense RNA that can lead to chronic infection in immunocompromised patients. Virus-host recombinant variants (VHRVs) have been described such These integrate part of human genes into the polyproline-rich region could introduce new post-translational modifications (PTMs), as ubiquitination. The aim this study was characterize replication capacity different VHRVs, namely, RNF19A, ZNF787, KIF1B, EEF1A1, RNA18, RPS17, and RPL6. We used plasmid...

Abstract New variants and genetic mutations of the severe acute respiratory syndrome coronavirus 2 (SARS‐CoV‐2) genome can only be identified using accurate sequencing methods. Single molecule real‐time (SMRT) has been used to characterize Alpha Delta variants, but not Omicron harboring numerous in SARS‐CoV‐2 genome. This study assesses performance a target capture SMRT protocol for whole (WGS) compared it that an amplicon optimized variants. The failure rate (6%) was lower than (34%, p <...

Comparisons of mammalian gut microbiota across different environmental conditions shed light on the diversity and composition bacteriome suggest consequences for human animal health. Gut comparisons environments diverge in their results, showing no generalizable patterns linking habitat dietary degradation with bacterial diversity. The challenge drawing general conclusions from such studies lies broad terms describing diverse habitats ("wild", "captive", "pristine"). We conducted 16S...

Human adenovirus (HAdV) represents a major cause of mortality and morbidity in pediatric recipients allogeneic hematopoietic stem cell transplants (HSCT). HAdV species F type 41 (HAdV-F41) infections HSCT patients are scarce, whereas HAdV-F41 circulates commonly healthy individuals. Between March July 2018, were identified four children (A, B, C, E) who received one child before (D) at Robert Debré Hospital, Paris, France. We report here the clinical course infection phylogenetic...

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is the causal agent of COVID-19 pandemic that emerged in late 2019. outbreak variants with mutations region encoding spike protein S1 sub-unit can make them more resistant to neutralizing or monoclonal antibodies main point current monitoring. This study examines feasibility predicting variant lineage and monitoring appearance reported by sequencing only domain Pacific Bioscience Single Molecule Real-Time (PacBio SMRT). Using...

We used variant typing polymerase chain reaction to describe the evolution of severe acute respiratory syndrome coronavirus 2 Omicron sublineages between December 2021 and mid-March 2022. The selective advantage BA.2 over BA.1 is not due greater nasopharyngeal viral loads.

Fast, accurate sequencing methods are needed to identify new variants and genetic mutations of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) genome. Single-molecule real-time (SMRT) Pacific Biosciences (PacBio) provides long, highly sequences by circular consensus reads. This study compares performance a target capture SMRT PacBio protocol for whole-genome (WGS) SARS-CoV-2 that an amplicon protocol. The median genome coverage was higher (p < 0.05) with (99.3%...

Co-infection with at least 2 strains of virus is the prerequisite for recombination, one means genetic diversification. Little known about prevalence these events in SARS-CoV-2, partly because it difficult to detect them. We used long-read PacBio single-molecule real-time (SMRT) sequencing technology sequence whole genomes and targeted regions haplotyping. identified 17 co-infections SARS-CoV-2 belonging different clades 6829 samples sequenced between January October, 2022 (prevalence...

Abstract Human-animal pathogenic transmissions threaten both human and animal health, the processes catalyzing zoonotic spillover spillback are complex. Prior field studies offer partial insight into these but overlook ecologies perceptions practices facilitating human-animal contact. Conducted in Cameroon a European zoo, this integrative study elucidates processes, incorporating metagenomic, historical, anthropological great ape ecological analyses, real-time evaluation of human-great...

HIV-1 resistance testing is recommended in clinical management and next-generation sequencing (NGS) methods are now available many virology laboratories.

The spread of SARS-CoV-2 and the resulting disease COVID-19 has killed over 2.6 million people as 18 March 2021. We have used a modified susceptible, infected, recovered (SIR) epidemiological model to predict how virus in regions France will vary depending on proportions variants public health strategies adopted, including anti-COVID-19 vaccination. proportion variant B.1.1.7, which was not detected early January, increased become 60% forms circulating Toulouse urban area at beginning...

The increasing use of monoclonal antibodies (mAbs) to treat coronavirus disease 2019 raises questions about their impact on the emergence severe acute respiratory syndrome 2 (SARS-CoV-2) mAb-resistant variants. We assessed Casirivimab-Imdevimab SARS-CoV-2 mutations associated with reduced mAb activity in treated patients.We measured nasopharyngeal (NP) viral load and sequenced haplotypes spike gene 50 patients infected delta variant using single-molecule real-time sequencing.The NP decreased...

Characterization of the respiratory tract bacterial microbiome is in its infancy when compared to gut microbiota. To limit bias mandates a robust methodology. Specific amplification hypervariable (V) region 16SrRNA gene crucial step. Differences accuracy exist for one V another depending on sampled environment. We aimed assess impact primer sequences targeting V4 currently used microbiota studies samples. Materials and methods: The original 515 F-806R pair targets gene. two different pairs...

Human papillomavirus (HPV) genotyping is widely used, particularly in combination with high-risk (HR) HPV tests for cervical cancer screening. We developed a method using sequences of approximately 800 bp the E6/E7 region obtained by PacBio single molecule real-time sequencing (SMRT) and evaluated its performance against MY09-11 L1 after APTIMA assay. The levels concordance SMRT were 100% 90.8%, respectively. sensitivity E6/EA7 was slightly greater than that and, as expected, lower HR-HPV...

Accurate HIV-1 genome sequencing is necessary to identify drug resistance mutations (DRMs) in people with (PWH). Next-generation-sequencing (NGS) allows the detection of minor variants and now available many laboratories. Our study aimed compare two NGS approaches, a "short read" protocol using DeepChek® Whole Genome Assay on Illumina, "long pol env single-molecule real-time (SMRT) Pacific Biosciences (PacBio). We analyzed 16 plasma samples 13 cellular from PWH. whole was amplified into five...

To evaluate the routine use of Sentosa ultra-deep sequencing (UDS) system for HIV-1 polymerase resistance genotyping in treatment-naïve individuals and to analyse virological response (VR) first-line antiretroviral treatment.HIV drug was determined on 237 consecutive samples from using UDS platform with two mutation detection thresholds (3% 20%). VR defined as a plasma virus load <50 copies/mL after 6 months treatment.Resistance at least one threshold 3% identified 29% 16% according ANRS...

Abstract Background Characterization of the respiratory tract bacterial microbiota is in its infancy when compared to gut knowledge. As key methodological steps can directly affect accuracy results, it crucial determine a robust methodology order limit bias.Two different pairs primers 515F-806R targeting V4 hypervariable region 16SrRNA gene, “S-V4” for “Stringent V4” primer pair and “R-V4” “Relaxed pair, are respectively used two ongoing international projects “the Human microbiome project”...

Abstract Human-animal pathogenic transmissions threaten both human and animal health, the processes catalyzing zoonotic spillover spillback are complex. Prior field studies offer partial insight into these but overlook ecologies perceptions practices facilitating human-animal contact. Conducted in Cameroon a European zoo, this holistic study elucidates processes, integrating metagenomic, historical, anthropological great ape ecological analyses, real-time evaluation of human-great contact...

<ns4:p><ns4:bold>Background:</ns4:bold> The lung microbiome is composed of bacteria, viruses and fungi that interplay with each other participate in mucosal defense protecting the lungs from colonization infection by pathogenic microorganisms. In intensive care, a change composition microbiome, called dysbiosis, could be associated to occurrence ventilator-associated pneumonia. objective study was test method assess virome.</ns4:p><ns4:p> <ns4:bold>Methods:</ns4:bold> We applied protocol...