Higher Levels of SARS-CoV-2 Genetic Variation in Immunocompromised Patients: A Retrospective Case-Control Study

BACKGROUND

A severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection lasts longer in immunocompromised hosts than in immunocompetent patients. Prolonged infection is associated with a higher probability of selection for novel SARS-CoV-2 mutations, particularly in the spike protein, a critical target for vaccines and therapeutics.

METHODS

From December 2020 to September 2022, respiratory samples from 444 immunocompromised patients and 234 health care workers positive for SARS-CoV-2, diagnosed at 2 hospitals in Paris, France, were analyzed using whole-genome sequencing using Nanopore technology. Custom scripts were developed to assess the SARS-CoV-2 genetic diversity between the 2 groups and within the host.

RESULTS

Most infections were SARS-CoV-2 Delta or Omicron lineages. Viral genetic diversity was significantly higher in infections of immunocompromised patients than those of controls. Minor mutations were identified in viruses sequenced from immunocompromised individuals, which became signature mutations for newer SARS-CoV-2 variants as the epidemic progressed. Two patients were coinfected with Delta and Omicron variants. The follow-up of immunocompromised patients revealed that the SARS-CoV-2 genome evolution differed in the upper and lower respiratory tracts.

CONCLUSIONS

This study found that SARS-CoV-2 infection in immunocompromised patients is associated with higher genetic diversity, which could lead to the emergence of new SARS-CoV-2 variants with possible immune evasion or different virulence characteristics.

RSV-GenoScan: An automated pipeline for whole-genome human respiratory syncytial virus (RSV) sequence analysis

BACKGROUND

Advances in high-throughput sequencing (HTS) technologies and reductions in sequencing costs have revolutionised the study of genomics and molecular biology by making whole-genome sequencing (WGS) accessible to many laboratories. However, the analysis of WGS data requires significant computational effort, which is the major drawback in implementing WGS as a routine laboratory technique.

OBJECTIVE

Automated pipelines have been developed to overcome this issue, but they do not exist for all organisms. This is the case for human respiratory syncytial virus (RSV), which is a leading cause of lower respiratory tract infections in infants, the elderly, and immunocompromised adults.

RESULTS

We present RSV-GenoScan, a fast and easy-to-use pipeline for WGS analysis of RSV generated by HTS on Illumina or Nanopore platforms. RSV-GenoScan automates the WGS analysis steps directly from the raw sequence data. The pipeline filters the sequence data, maps the reads to the RSV reference genomes, generates a consensus sequence, identifies the RSV subgroup, and lists amino acid mutations, insertions and deletions in the F and G viral genes. This enables the rapid identification of mutations in these coding genes that are known to confer resistance to monoclonal antibodies.

AVAILABILITY

RSV-GenoScan is freely available at https://github.com/AlexandreD-bio/RSV-GenoScan.

BA.2.86 variant emergence and spread dynamics through wastewater monitoring in Paris, France

Numerous SARS-CoV-2 variants are emerging as the epidemic continues, inducing new waves of contamination. In July 2023, a new variant named BA.2.86 was identified, raising concerns about its potential for viral escape, even in an immune population. The reduction in patient-centered testing and the identification of variants by sequencing means that we are now blind to the spread of this new variant. The aim of this study was to track the signature of this variant in wastewater in Paris, France. This variant showed a very rapid spread, highly correlated with national flash studies involving sequencing of clinical samples, but with a moderate impact on virus circulation. This easy-to-implement approach enabled us to monitor the emergence and spread of this new variant in real time at low cost.

Oxford Nanopore and Bionano Genomics technologies evaluation for plant structural variation detection

Background

Structural Variations (SVs) are genomic rearrangements derived from duplication, deletion, insertion, inversion, and translocation events. In the past, SVs detection was limited to cytological approaches, then to Next-Generation Sequencing (NGS) short reads and partitioned assemblies. Nowadays, technologies such as DNA long read sequencing and optical mapping have revolutionized the understanding of SVs in genomes, due to the enhancement of the power of SVs detection.

This study aims to investigate performance of two techniques, 1) long-read sequencing obtained with the MinION device (Oxford Nanopore Technologies) and 2) optical mapping obtained with Saphyr device (Bionano Genomics) to detect and characterize SVs in the genomes of the two ecotypes of Arabidopsis thaliana, Columbia-0 (Col-0) and Landsberg erecta 1 (Ler-1).

Results

We described the SVs detected from the alignment of the best ONT assembly and DLE-1 optical maps of A. thaliana Ler-1 against the public reference genome Col-0 TAIR10.1. After filtering (SV > 1 kb), 1184 and 591 Ler-1 SVs were retained from ONT and Bionano technologies respectively. A total of 948 Ler-1 ONT SVs (80.1%) corresponded to 563 Bionano SVs (95.3%) leading to 563 common locations. The specific locations were scrutinized to assess improvement in SV detection by either technology. The ONT SVs were mostly detected near TE and gene features, and resistance genes seemed particularly impacted.

Conclusions

Structural variations linked to ONT sequencing error were removed and false positives limited, with high quality Bionano SVs being conserved. When compared with the Col-0 TAIR10.1 reference genome, most of the detected SVs discovered by both technologies were found in the same locations. ONT assembly sequence leads to more specific SVs than Bionano one, the latter being more efficient to characterize large SVs. Even if both technologies are complementary approaches, ONT data appears to be more adapted to large scale populations studies, while Bionano performs better in improving assembly and describing specificity of a genome compared to a reference.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08499-4.

Pharmacokinetics of lamivudine, zidovudine, and nevirapine administered as a fixed-dose combination formulation versus coadministration of the individual products

The pharmacokinetics of 150 mg lamivudine, 300 mg zidovudine, and 200 mg nevirapine were assessed following single oral administration of a fixed-dose combination tablet and coadministration of the separate innovator products in healthy male subjects (n = 64) under fasting conditions in an open-label, randomized, 2-way crossover study. Multiple blood samples were collected up to 72 hours and plasma concentrations of antiretrovirals were assayed using liquid chromatography/tandem mass spectrometry methods. Pharmacokinetic parameters were calculated using noncompartmental methods, and bioequivalence was assessed using an analysis of variance model. The ratio of the least squares mean (fixed-dose combination to individual products) and 90% confidence intervals of AUC(0-t), AUC(0-infinity), and C(max) for lamivudine, zidovudine, and nevirapine were all within 80.0% to 125.0%, suggesting a similar rate and extent of antiretroviral exposure in the bloodstream. Mean oral clearance (CL/F) values of lamivudine, zidovudine, and nevirapine for the fixed-dose combination were 23.7, 127, and 1.65 L/h, respectively. The fixed-dose combination and individual products were equally safe and well tolerated, with only a few subjects experiencing drug-related adverse events. The current fixed-dose combination of lamivudine, zidovudine, and nevirapine is expected to provide a similar efficacy/safety profile as coadministration of the individual products, a better adherence to treatment, and considerable cost savings in the treatment of HIV.

Study of the drug-drug interaction between simvastatin and cisapride in man

OBJECTIVE

The objective of our study was to evaluate in humans the drug-drug interaction occurring during the concomitant administration of cisapride and simvastatin, two well-known substrates of CYP3A4.

METHODS

Eleven healthy men aged between 20 years and 35 years gave their written informed consent to participate in the study. Each participant received repeated doses of cisapride and/or simvastatin. At first, subjects received cisapride alone, 10 mg every 8 h, for 3 days. Then, the drug was given at the same regimen during concomitant administration of simvastatin, 20 mg every 12 h for 4 days, starting on the night of day 3. Finally, cisapride was stopped and subjects received simvastatin (20 mg every 12 h) for four additional days.

RESULTS

Simvastatin administration caused a 14 +/- 20% increase in the AUC0-8 of cisapride. In contrast, plasma concentrations of simvastatin were unaltered by the coadministration of cisapride, whereas plasma concentrations of simvastatin acid, its active metabolite, were decreased by 33 +/- 24%.

CONCLUSION

The concomitant administration of the prokinetic agent cisapride and the 3-hydroxy-3-methylgluaryl CoA reductase inhibitor simvastatin resulted in altered pharmacokinetics of both drugs. Increased plasma concentrations of cisapride suggest that some patients may be at risk of toxicity while receiving both drugs, whereas the decrease in simvastatin acid plasma concentrations suggests that cholesterol lowering effects of simvastatin treatment may be blunted.

Absence of in vivo lipid peroxidation in CdCl2-treated rats as measured by exhaled pentane

We have used a new sensitive and non-invasive method, measuring exhaled pentane production, to evaluate in vivo lipid peroxidation (LP) in rats treated i.p. with CdCl2. Pentane, a by-product of LP, was measured 2, 6, 12, 24, 72 h and 8, 15, 22 days after treatment. No increase in pentane production was detected at these time periods for cadmium (Cd) doses reported to increase malondialdehyde (MDA) in major organs such as liver and lungs. This suggests that Cd cannot induce LP in vivo, but a prooxidant state which fragilized the tissues. Cd could also cause changes either in the production or in the metabolism of LP by-products (e.g. pentane).

The COOH-domain of the product of the Saccharomyces cerevisiae SCD25 gene elicits activation of p21-ras proteins in mammalian cells

The evidence presented here indicates that the domain containing the COOH-terminal part of the Saccharomyces cerevisiae SCD25 gene product (C-domain), which is homologous to the COOH-terminal part of CDC25 protein, can elicit activation of mammalian ras proteins in CHO cells. Transfection of expression vectors carrying the C-domain of SCD25, but not of CDC25, promotes the GTP-bound form of ras proteins as determined by analysis of the guanine nucleotides bound to ras proteins immunoprecipitated by Y13-259 mAb, and enhances transcription of a HIV-LTR-CAT construct. This is the first demonstration of the activation of ras proteins by transfection of a single heterologous gene.

Sequence analysis of the DdPYR5-6 gene coding for UMP synthase in Dictyostelium discoideum and comparison with orotate phosphoribosyl transferases and OMP decarboxylases

A Dictyostelium discoideum DNA fragment that complements the ura3 and the ura5 mutants of Saccharomyces cerevisiae has been sequenced. It contains an open reading frame of 478 codons capable of encoding a polypeptide of molecular weight 52475. This gene, named DdPYR5-6, encodes a bifunctional protein composed of the orotate phosphoribosyl transferase (OPRTase) and the orotidine-5'-phosphate decarboxylase (OMPdecase) domains described for UMP synthase in mammals. The existence of separate domains for the two activities was suspected because deletion of the N-terminal coding segment of the gene eliminated the ura5 but not the ura3 complementing activity. We have now confirmed that the two parts of the open reading frame share homology with known OPRTase and OMPdecase sequences. Several blocks of sequence are conserved among OPRTase from bacteria, fungi and slime mold and one of them corresponds to the consensus sequence for phosphoribosylbinding sites. The OMPdecase domain shows extensive similarity with the yeast and Neurospora crassa enzymes, suggesting that they have evolved from an ancestral gene which was fused to the OPRTase gene in D. discoideum. It is less related to the bacterial enzyme but all these sequences present conserved blocks of homology which could identify the active site. The codon usage is strongly biased in a manner similar to that found for other D. discoideum genes. The flanking DNA contains homopolymers of A and T and alternating sequences that are characteristic of the gene organization in D. discoideum.