VODKA2: a fast and accurate method to detect non-standard viral genomes from large RNA-seq data sets

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.

VODKA2: A fast and accurate method to detect non-standard viral genomes from large RNA-seq datasets

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 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.

Accumulation of copy-back viral genomes during respiratory syncytial virus infection is preceded by diversification of the copy-back viral genome population followed by selection

RNA 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. As cbVGs are dependent on the virus replication machinery to be generated and replicated, we hypothesized that host factors that affect virus replication exert selective pressure on cbVGs and drive their evolution within a virus population. To test this hypothesis, we used respiratory syncytial virus (RSV) as a model and took an experimental evolution approach by serially passaging RSV in immune-competent human lung adenocarcinoma A549 control and immune-deficient A549 Signal transducer and activator of transcription 1 (STAT1) KO cells, which allow higher levels of virus replication. As predicted, we observed that virus populations accumulated higher amounts of cbVGs in the more permissive A549 STAT1 KO cells over time; however, unexpectedly, the predominant cbVG species after passages in the two conditions were different. While A549 STAT1 KO cells accumulated relatively short cbVGs, A549 control cells mainly contained cbVGs of much longer predicted size, which have not been described previously. These long cbVGs were predominant at first in both cell lines in vitro and the predominant ones observed in samples from RSV-infected patients. Although sustained high replication levels are associated with cbVG generation and accumulation, our data show that sustained high levels of virus replication are critical for cbVG population diversification, a process that precedes the generation of shorter cbVGs that selectively accumulate over time. Taken together, we show that selection and evolution of cbVGs within a virus population are shaped by how resistant or permissive a host is to RSV.

Detection of respiratory syncytial virus defective genomes in nasal secretions is associated with distinct clinical outcomes

Respiratory syncytial virus (RSV) causes respiratory illness in children, immunosuppressed individuals and the elderly. However, the viral factors influencing the clinical outcome of RSV infections remain poorly defined. Defective viral genomes (DVGs) can suppress virus replication by competing for viral proteins and by stimulating antiviral immunity. We studied the association between detection of DVGs of the copy-back type and disease severity in three RSV A-confirmed cohorts. In hospitalized children, detection of DVGs in respiratory samples at or around the time of admission associated strongly with more severe disease, higher viral load and a stronger pro-inflammatory response. Interestingly, in experimentally infected adults, the presence of DVGs in respiratory secretions differentially associated with RSV disease severity depending on when DVGs were detected. Detection of DVGs early after infection associated with low viral loads and mild disease, whereas detection of DVGs late after infection, especially if DVGs were present for prolonged periods, associated with high viral loads and severe disease. Taken together, we demonstrate that the kinetics of DVG accumulation and duration could predict clinical outcome of RSV A infection in humans, and thus could be used as a prognostic tool to identify patients at risk of worse clinical disease.

RNA-seq accuracy and reproducibility for the mapping and quantification of influenza defective viral genomes

Like most RNA viruses, influenza viruses generate defective viral genomes (DVGs) with large internal deletions during replication. There is accumulating evidence supporting a biological relevance of such DVGs. However, further understanding of the molecular mechanisms that underlie the production and biological activity of DVGs is conditioned upon the sensitivity and accuracy of detection methods, that is, next-generation sequencing (NGS) technologies and related bioinformatics algorithms. Although many algorithms were developed, their sensitivity and reproducibility were mostly assessed on simulated data. Here, we introduce DG-seq, a time-efficient pipeline for DVG detection and quantification, and a set of biological controls to assess the performance of not only our bioinformatics algorithm but also the upstream NGS steps. Using these tools, we provide the first rigorous comparison of the two commonly used sample processing methods for RNA-seq, with or without a PCR preamplification step. Our data show that preamplification confers a limited advantage in terms of sensitivity and introduces size- but also sequence-dependent biases in DVG quantification, thereby providing a strong rationale to favor preamplification-free methods. We further examine the features of DVGs produced by wild-type and transcription-defective (PA-K635A or PA-R638A) influenza viruses, and show an increased diversity and frequency of DVGs produced by the PA mutants compared to the wild-type virus. Finally, we demonstrate a significant enrichment in DVGs showing direct, A/T-rich sequence repeats at the deletion breakpoint sites. Our findings provide novel insights into the mechanisms of influenza virus DVG production.

Genome analysis of coxsackievirus B1 isolates during the consecutive alternating administration course of triple antiviral combination in newborn mice

Background

We developed a new approach for the treatment of enterovirus infections, the consecutive alternating administration (CAA) of a combination of enterovirus inhibitors. On the model of coxsackievirus B1 (CVB1) in mice, two phenomena were observed: absence of drug resistance and increased susceptibility to the antivirals. This study aims to clarify the genetic basis of these phenomena.

Methods

Brain samples from CVB1-infected mice subjected to a CAA course with the combination pleconaril/MDL-860/oxoglaucine were used for viral RNA extraction and next generation sequencing. In parallel, samples from monotherapeutic courses of the three substances included in the combination were studied. Whole genome sequence analysis was carried out on all samples.

Results

Samples of pleconaril monotherapy showed mutations in 5′untranslated region, VP3, 2C, 3C and 2A regions of viral RNA, translated in amino acid substitution of the 2A protein. The MDL-860 course induced changes in CVB1 RNA in the VP3 and 2C regions. The oxoglaucine monotherapy samples showed RNA mutation and amino acid substitution in the VP1 region and nucleotide substitution in the 3D region. In the specimens taken from mice subjected to the CAA course with pleconaril/MDL-860/oxoglaucine, the following RNA mutations were established: 5′ untranslated region, 2A, and 2B, and amino acids substitutions in VP3 and 2A, which differ from those mentioned above. These changes could be the reason for the prevention of drug resistance development and also to be considered as the basis for the phenomenon of increased drug susceptibility.

Conclusions

The results reveal that the high anti-enteroviral efficacy of the CAA course is substantiated by the appearance of specific changes in the viral genome.

[Visceral leishmaniasis in children. A study of hospitalized cases from 1974 to 1988 at the Children's Hospital in Tunis]

The authors reported 122 cases of kala-azar admitted at Tunisian Children's hospital between 1974 and 1988. This affection was concerned male child and 78% of cases were aged less than 3 years old. The clinical feature was pallor, fever and splenomegaly. The diagnosis of kala-azar was established by serological test. The death rate was 8%.

[Severe forms of liver involvement in visceral leishmaniasis. Apropos of 7 cases]

In a series of 180 cases of Kala-azar, hepatic involvement was found in 16 patients. The authors report 7 cases of severe hepatitis with cytolysis, cholestasis and liver failure. These patients presented with high triglyceride, low cholesterol and low alpha-lipoprotein blood levels. The authors suggest that an activation of the mononuclear phagocyte system might explain these abnormalities.

[Thrombosis of the right ventricle in 2 infants with myocardiopathy]

We report two cases of left ventricular thrombosis in infants with myocardiopathy. Patients were aged ten and twelve months respectively. Two-dimensional echocardiography, performed because of the development of heart failure, evidenced an echogenic image within the left ventricle and significant dilatation of the left ventricular chamber. One patient developed a peripheral arterial thrombosis that resolved under anticoagulant therapy. The intracardiac thrombus disappeared under anticoagulant therapy after one month in one patient and six months in the other. Pathophysiology of the left ventricular thrombosis is discussed; the dilatation of the left ventricle apparently played a significant role. We emphasize the value of early initiation of preventive anticoagulant therapy in patients with myocardiopathy.