Characterization of oseltamivir-resistant influenza virus populations in immunosuppressed patients using digital-droplet PCR: Comparison with qPCR and next generation sequencing analysis

CRISPR-Based Assays for Point-of-Need Detection and Subtyping of Influenza

The high disease burden of influenza virus poses a significant threat to human health. Optimized diagnostic technologies that combine speed, sensitivity, and specificity with minimal equipment requirements are urgently needed to detect the many circulating species, subtypes, and variants of influenza at the point of need. Here, we introduce such a method using Streamlined Highlighting of Infections to Navigate Epidemics (SHINE), a clustered regularly interspaced short palindromic repeats (CRISPR)-based RNA detection platform. Four SHINE assays were designed and validated for the detection and differentiation of clinically relevant influenza species (A and B) and subtypes (H1N1 and H3N2). When tested on clinical samples, these optimized assays achieved 100% concordance with quantitative RT-PCR. Duplex Cas12a/Cas13a SHINE assays were also developed to detect two targets simultaneously. This study demonstrates the utility of this duplex assay in discriminating two alleles of an oseltamivir resistance (H275Y) mutation as well as in simultaneously detecting influenza A and human RNAse P in patient samples. These assays have the potential to expand influenza detection outside of clinical laboratories for enhanced influenza diagnosis and surveillance.

Design of new chemical entities targeting both native and H275Y mutant influenza a virus by deep reinforcement learning

Influenza virus remains a major public health challenge due to its high morbidity and mortality and seasonal surge. Although antiviral drugs against the influenza virus are widely used as a first-line defense, the virus undergoes rapid genetic changes, resulting in the emergence of drug-resistant strains. Thus, new antiviral drugs that can outwit resistant strains are of significant importance. Herein, we used deep reinforcement learning (RL) algorithm to design new chemical entities (NCEs) that are able to bind to the native and H275Y mutant (oseltamivir-resistant) neuraminidases (NAs) of influenza A virus with better binding energy than oseltamivir. We generated more than 66211 NCEs, which were prioritized based on the filtering rules, structural alerts, and synthetic accessibility. Then, 18 NCEs with better MM/PBSA scores than oseltamivir were further analyzed in molecular dynamics (MD) simulations conducted for 100 ns. The MD experiments showed that 8 NCEs formed very stable complexes with the binding pocket of both native and H275Y mutant NAs of H1N1. Furthermore, most NCEs demonstrated much better binding affinity to group 2 (N2, N3, and N9) and influenza B virus NAs than oseltamivir. Although all 8 NCEs have non-sialic acid-like structures, they showed a similar binding mode as oseltamivir, indicating that it is possible to find new scaffolds with better binding and antiviral properties than sialic acid-like inhibitors. In conclusion, we have designed potential compounds as antiviral candidates for further synthesis and testing against wild and mutant influenza virus.Communicated by Ramaswamy H. Sarma.

Development of Digital Droplet PCR Targeting the Influenza H3N2 Oseltamivir-Resistant E119V Mutation and Its Performance through the Use of Reverse Genetics Mutants

The monitoring of antiviral-resistant influenza virus strains is important for public health given the availability and use of neuraminidase inhibitors and other antivirals to treat infected patients. Naturally occurring oseltamivir-resistant seasonal H3N2 influenza virus strains often carry a glutamate-to-valine substitution at position 119 in the neuraminidase (E119V-NA). Early detection of resistant influenza viruses is important for patient management and for the rapid containment of antiviral resistance. The neuraminidase inhibition assay allows the phenotypical identification of resistant strains; however, this test often has limited sensitivity with high variability depending on the virus strain, drugs and assays. Once a mutation such as E119V-NA is known, highly sensitive PCR-based genotypic assays can be used to identify the prevalence of such mutant influenza viruses in clinical samples. In this study, based on an existing reverse transcriptase real-time PCR (RT-qPCR) assay, we developed a reverse transcriptase droplet digital PCR assay (RT-ddPCR) to detect and quantify the frequency of the E119V-NA mutation. Furthermore, reverse genetics viruses carrying this mutation were created to test the performance of the RT-ddPCR assay and compare it to the standard phenotypic NA assay. We also discuss the advantage of using an RT-ddPCR instead of qPCR method in the context of viral diagnostics and surveillance.

Advances in droplet digital polymerase chain reaction on microfluidic chips

The PCR technique has been known to the general public since the pandemic outbreak of COVID-19. This technique has progressed through three stages: from simple PCR to real-time fluorescence PCR to digital PCR. Among them, the microfluidic-based droplet digital PCR technique has attracted much attention and has been widely applied due to its advantages of high throughput, high sensitivity, low reagent consumption, low cross-contamination, and absolute quantification ability. In this review, we introduce various designs of microfluidic-based ddPCR developed within the last decade. The microfluidic-based droplet generation methods, thermal cycle strategies, and signal counting approaches are described, and the applications in the fields of single-cell analysis, disease diagnosis, and pathogen detection are introduced. Further, the challenges and prospects of microfluidic-based ddPCR are discussed. We hope that this review can contribute to the further development of the microfluidic-based ddPCR technique.

Cys-SH based quantitative redox proteomics of salt induced response in sugar beet monosomic addition line M14

BACKGROUND

Salt stress is a major abiotic stress that limits plant growth, development and productivity. Studying the molecular mechanisms of salt stress tolerance may help to enhance crop productivity. Sugar beet monosomic addition line M14 exhibits tolerance to salt stress.

RESULTS

In this work, the changes in the BvM14 proteome and redox proteome induced by salt stress were analyzed using a multiplex iodoTMTRAQ double labeling quantitative proteomics approach. A total of 80 proteins were differentially expressed under salt stress. Interestingly, A total of 48 redoxed peptides were identified for 42 potential redox-regulated proteins showed differential redox change under salt stress. A large proportion of the redox proteins were involved in photosynthesis, ROS homeostasis and other pathways. For example, ribulose bisphosphate carboxylase/oxygenase activase changed in its redox state after salt treatments. In addition, three redox proteins involved in regulation of ROS homeostasis were also changed in redox states. Transcription levels of eighteen differential proteins and redox proteins were profiled. (The proteomics data generated in this study have been submitted to the ProteomeXchange and can be accessed via username: reviewer_pxd027550@ebi.ac.uk, password: q9YNM1Pe and proteomeXchange# PXD027550.) CONCLUSIONS: The results showed involvement of protein redox modifications in BvM14 salt stress response and revealed the short-term salt responsive mechanisms. The knowledge may inform marker-based breeding effort of sugar beet and other crops for stress resilience and high yield.

Droplet digital PCR as an emerging tool in detecting pathogens nucleic acids in infectious diseases

The microbial infectious diseases (infectious diseases) represent the leading global public health problem, and the effective treatment depends on rapid and accurate detection of pathogens. Droplet digital PCR (ddPCR), a new assay that combines microfluidics technology with TaqMan-based PCR, provides absolute quantification without the need of the standard curves. With the development of ddPCR, it has become an ideal tool for microorganism detection. In this review, we summarized the major literature with regard to the application of ddPCR in detecting the pathogenic microorganisms of infectious diseases, including bacteria, fungi, and virus. The ddPCR method has the advantages of detecting the targeted DNA of infectious microorganisms, with high sensitivity, high precision, and absolute quantification. Thus, ddPCR has emerged as a promising and reliable tool in detecting pathogenicmicroorganisms.

[Virological diagnosis of lower respiratory tract infections]

INTRODUCTION

The etiological diagnosis of bronchopulmonary infections cannot be assessed with clinical, radiological and epidemiological data alone. Viruses have been demonstrated to cause a large proportion of these infections, both in children and adults.

BACKGROUND

The diagnosis of viral bronchopulmonary infections is based on the analysis of secretions, collected from the lower respiratory tract when possible, by techniques that detect either influenza and respiratory syncytial viruses, or a large panel of viruses that can be responsible for respiratory disease. The latter, called multiplex PCR assays, allow a syndromic approach to respiratory infection. Their high cost for the laboratory raises the question of their place in the management of patients in terms of antibiotic economy and isolation. In the absence of clear recommendations, the strategy and equipment are very unevenly distributed in France.

OUTLOOK

Medico-economic analyses need to be performed in France to evaluate the place of these tests in the management of patients. The evaluation of the role of the different viruses often detected in co-infection, especially in children, also deserves the attention of virologists and clinicians.

CONCLUSIONS

The availability of new diagnostic technologies, the recent emergence of SARS-CoV-2, together with the availability of new antiviral drugs are likely to impact future recommendations for the management of viral bronchopulmonary infections.

Influenza and antiviral resistance: an overview

Influenza affects approximately 1 billion individuals each year resulting in between 290,000 and 650,000 deaths. Young children and immunocompromised individuals are at a particularly high risk of severe illness attributable to influenza and these are also the groups of individuals in which reduced susceptibility to neuraminidase inhibitors is most frequently seen. High levels of resistance emerged with previous adamantane therapy for influenza A and despite no longer being used to treat influenza and therefore lack of selection pressure, high levels of adamantane resistance continue to persist in currently circulating influenza A strains. Resistance to neuraminidase inhibitors has remained at low levels to date and the majority of resistance is seen in influenza A H1N1 pdm09 infected immunocompromised individuals receiving oseltamivir but is also seen less frequently with influenza A H3N2 and B. Rarely, resistance is also seen in the immunocompetent. There is evidence to suggest that these resistant strains (particularly H1N1 pdm09) are able to maintain their replicative fitness and transmissibility, although there is no clear evidence that being infected with a resistant strain is associated with a worse clinical outcome. Should neuraminidase inhibitor resistance become more problematic in the future, there are a small number of  alternative novel agents within the anti-influenza armoury with different mechanisms of action to neuraminidase inhibitors and therefore potentially effective against neuraminidase inhibitor resistant strains. Limited data from use of novel agents such as baloxavir marboxil and favipiravir, does however show that resistance variants can also emerge in the presence of these drugs.

Digital PCR—An Emerging Technology with Broad Applications in Microbiology

BACKGROUND

The PCR and its variant, quantitative PCR (qPCR), have revolutionized the practice of clinical microbiology. Continued advancements in PCR have led to a new derivative, digital PCR (dPCR), which promises to address certain limitations inherent to qPCR.

CONTENT

Here we highlight the important technical differences between qPCR and dPCR, and the potential advantages and disadvantages of each. We then review specific situations in which dPCR has been implemented in clinical microbiology and the results of such applications. Finally, we attempt to place dPCR in the context of other emerging technologies relevant to the clinical laboratory, including next-generation sequencing.

SUMMARY

dPCR offers certain clear advantages over traditional qPCR, but these are to some degree offset by limitations of the technology, at least as currently practiced. Laboratories considering implementation of dPCR should carefully weigh the potential advantages and disadvantages of this powerful technique for each specific application planned.

Neuraminidase inhibitor resistance in influenza: a clinical perspective

PURPOSE OF REVIEW

Neuraminidase inhibitors (NAIs), including oseltamivir, zanamivir, and peramivir, is the main class of antiviral available for clinical use. As such, development of resistance toward these agents is of great clinical and public health concern.

RECENT FINDINGS

At present, NAI resistance remains uncommon among the circulating viruses (oseltamivir <3.5%, zanamivir <1%). Resistance risk is slightly higher in A(H1N1) than A(H3N2) and B viruses. Resistance may emerge during drug exposure, particularly among young children (<5 years), the immunocompromised, and individuals receiving prophylactic regimens. H275Y A(H1N1) variant, showing high-level oseltamivir resistance, is capable of causing outbreaks. R294K A(H7N9) variant shows reduced inhibition across NAIs. Multi-NAI resistance has been reported in the immunocompromised.

SUMMARY

These findings highlight the importance of continuous surveillance, and assessment of viral fitness and transmissibility of resistant virus strains. Detection can be challenging, especially in a mix of resistant and wild-type viruses. Recent advances in molecular techniques (e.g. targeted mutation PCR, iART, ddPCR, pyrosequencing, next-generation sequencing) have improved detection and our understanding of viral dynamics. Treatment options available for oseltamivir-resistant viruses are limited, and susceptibility testing of other NAIs may be required, but non-NAI antivirals (e.g. polymerase inhibitors) that are active against these resistant viruses are in late-stage clinical development.

Seasonal Genetic Drift of Human Influenza A Virus Quasispecies Revealed by Deep Sequencing

After a pandemic wave in 2009 following their introduction in the human population, the H1N1pdm09 viruses replaced the previously circulating, pre-pandemic H1N1 virus and, along with H3N2 viruses, are now responsible for the seasonal influenza type A epidemics. So far, the evolutionary potential of influenza viruses has been mainly documented by consensus sequencing data. However, like other RNA viruses, influenza A viruses exist as a population of diverse, albeit related, viruses, or quasispecies. Interest in this quasispecies nature has increased with the development of next generation sequencing (NGS) technologies that allow a more in-depth study of the genetic variability. NGS deep sequencing methodologies were applied to determine the whole genome genetic heterogeneity of the three categories of influenza A viruses that circulated in humans between 2007 and 2012 in France, directly from clinical respiratory specimens. Mutation frequencies and single nucleotide polymorphisms were used for comparisons to address the level of natural intrinsic heterogeneity of influenza A viruses. Clear differences in single nucleotide polymorphism profiles between seasons for a given subtype also revealed the constant genetic drift that human influenza A virus quasispecies undergo.

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.

Electronic supplementary material

The online version of this article (10.1186/s12879-018-3446-5) contains supplementary material, which is available to authorized users.