Novel UL23 and UL30 substitutions in HSV1 and HSV2 viruses related to polymorphism or drug resistance.

Data on herpes simplex virus (HSV) polymorphism as well as acyclovir (ACV) and foscarnet (FOS) resistance mutations are not exhaustive and may hinder accurate diagnosis by next-generation sequencing (NGS). Here, we report novel UL23 and UL30 substitutions for HSV1 and HSV2 identified in immunocompromised patients treated for hematological malignancies during the last 6 years of HSV resistance surveillance at the University Hospital of Lyon. For HSV1, 35 novel UL23 substitutions and 52 novel UL30 substitutions were identified. For HSV2, 2 novel UL23 substitutions and 12 novel UL30 substitutions were identified. These results allow to complete the database of HSV1 and HSV2 substitutions, related either to polymorphism or to ACV and FOS resistance.

Quality control implementation for universal characterization of DNA and RNA viruses in clinical respiratory samples using single metagenomic next-generation sequencing workflow.

BACKGROUND: In recent years, metagenomic Next-Generation Sequencing (mNGS) has increasingly been used for an accurate assumption-free virological diagnosis. However, the systematic workflow evaluation on clinical respiratory samples and implementation of quality controls (QCs) is still lacking. METHODS: A total of 3 QCs were implemented and processed through the whole mNGS workflow: a no-template-control to evaluate contamination issues during the process; an internal and an external QC to check the integrity of the reagents, equipment, the presence of inhibitors, and to allow the validation of results for each sample. The workflow was then evaluated on 37 clinical respiratory samples from patients with acute respiratory infections previously tested for a broad panel of viruses using semi-quantitative real-time PCR assays (28 positive samples including 6 multiple viral infections; 9 negative samples). Selected specimens included nasopharyngeal swabs (n = 20), aspirates (n = 10), or sputums (n = 7). RESULTS: The optimal spiking level of the internal QC was first determined in order to be sufficiently detected without overconsumption of sequencing reads. According to QC validation criteria, mNGS results were validated for 34/37 selected samples. For valid samples, viral genotypes were accurately determined for 36/36 viruses detected with PCR (viral genome coverage ranged from 0.6 to 100%, median = 67.7%). This mNGS workflow allowed the detection of DNA and RNA viruses up to a semi-quantitative PCR Ct value of 36. The six multiple viral infections involving 2 to 4 viruses were also fully characterized. A strong correlation between results of mNGS and real-time PCR was obtained for each type of viral genome (R2 ranged from 0.72 for linear single-stranded (ss) RNA viruses to 0.98 for linear ssDNA viruses). CONCLUSIONS: Although the potential of mNGS technology is very promising, further evaluation studies are urgently needed for its routine clinical use within a reasonable timeframe. The approach described herein is crucial to bring standardization and to ensure the quality of the generated sequences in clinical setting. We provide an easy-to-use single protocol successfully evaluated for the characterization of a broad and representative panel of DNA and RNA respiratory viruses in various types of clinical samples.

[Neonatal enterovirus infections reported in France in 2012]. / Infections néonatales à entérovirus en France en 2012.

Enteroviruses (EVs) are among the most common viruses infecting humans. One-third of EV infections affect children under 1 year of age. Neonatal EV infections lead to a wide range of clinical manifestations, from mild febrile illness to severe, potentially fatal sepsis-like conditions with multiorgan failure. EV detections by serotype are reported by the National Reference Centre for EV Infections Lyon on a monthly basis. Demographic, clinical, and biological data were also collected in neonates hospitalized in 2012 for EV infection. Two subgroups were identified according to the beginning of symptoms: until 8 days of life (D8) or strictly after D8. There were 120 neonatal EV infections. Before D8, children with severe infection were born more prematurely with a low birth weight. The EVs most commonly detected in neonates were CV-B4 and E-11. Risk factors for severe EV infections included liver (73% before D8) and hematological damage (thrombocytopenia, 82%; coagulopathy, 64% before D8). This study suggests that systematic serotyping of neonatal EV infections and biological monitoring of liver function could be useful for early identification of children at high risk of clinical severity and fatality.

Influenza A replication and host nuclear compartments: many changes and many questions.

It is over 40 years since investigations showed that influenza A, one of the rare nuclear replicating RNA viruses, induces marked remodeling of the host nuclear architecture. Influenza modifies and/or hijacks host nuclear machinery in order to replicate, express viral proteins and interfere with host antiviral response. Numerous interactions between constitutive nuclear proteins and viral factors are now characterized but less is known concerning their functional significance and their connection with viral-induced modifications of nuclear ultrastructure. Therefore, the purpose of this review is to summarize data and hypotheses about functional interplays between host nuclear compartments and influenza A during viral replication.