Rapid genotypic assay for detection of oseltamivir-resistant influenza A (H1N1) viruses

Favipiravir Analogues as Inhibitors of SARS-CoV-2 RNA-Dependent RNA Polymerase, Combined Quantum Chemical Modeling, Quantitative Structure-Property Relationship, and Molecular Docking Study

Our study was motivated by the urgent need to develop or improve antivirals for effective therapy targeting RNA viruses. We hypothesized that analogues of favipiravir (FVP), an inhibitor of RNA-dependent RNA polymerase (RdRp), could provide more effective nucleic acid recognition and binding processes while reducing side effects such as cardiotoxicity, hepatotoxicity, teratogenicity, and embryotoxicity. We proposed a set of FVP analogues together with their forms of triphosphate as new SARS-CoV-2 RdRp inhibitors. The main aim of our study was to investigate changes in the mechanism and binding capacity resulting from these modifications. Using three different approaches, QTAIM, QSPR, and MD, the differences in the reactivity, toxicity, binding efficiency, and ability to be incorporated by RdRp were assessed. Two new quantum chemical reactivity descriptors, the relative electro-donating and electro-accepting power, were defined and successfully applied. Moreover, a new quantitative method for comparing binding modes was developed based on mathematical metrics and an atypical radar plot. These methods provide deep insight into the set of desirable properties responsible for inhibiting RdRp, allowing ligands to be conveniently screened. The proposed modification of the FVP structure seems to improve its binding ability and enhance the productive mode of binding. In particular, two of the FVP analogues (the trifluoro- and cyano-) bind very strongly to the RNA template, RNA primer, cofactors, and RdRp, and thus may constitute a very good alternative to FVP.

[Oseltamivir resistance depends on the position 273 amino acid of neuraminidase of the type A influenza virus (H1N1), circulating in human population]

The structure of neuraminidase of the type A influenza virus (H1N1) spreading in the human population was analyzed. The obtained results indicate a significant correlation between the oseltamivir sensitivity and the nature of the amino acid localized not only to neuraminidase position 274, but also to position 273 of this protein. Phenylalanine at position 273 in neuraminidase indicates a higher propensity to influenza virus mutation H274Y, leading to the appearance of resistant strains. It is suggested that the mutation at position 273 may be one of the characteristics allowing type A influenza virus to be ascribed to a pandemic or a seasonal type.

Reverse-transcription polymerase chain reaction/pyrosequencing to characterize neuraminidase H275 residue of influenza A 2009 H1N1 virus for rapid and specific detection of the viral oseltamivir resistance marker in a clinical laboratory

Pandemic 2009 H1N1 is normally susceptible to oseltamivir, but variants harboring the H275Y (CAC → TAC) mutation exhibit resistance. We describe the use of a combined reverse-transcription polymerase chain reaction (RT-PCR)/pyrosequencing approach to identify the H275 residue. A total of 223 specimens were tested with this method: 216 randomly selected clinical specimens positive for 2009 H1N1 and 7 cell-culture supernatants from the Centers for Disease Control and Prevention (CDC; 4 resistant, 3 susceptible 2009 H1N1 strains). The assay detected H275Y in 1 clinical respiratory sample (0.5%) and all 4 oseltamivir-resistant strains from the CDC; the remaining 215 clinical and 3 susceptible CDC specimens were wild-type. Sanger sequencing confirmed the results for 50 of 50 selected isolates. The RT-PCR/pyrosequencing method was highly specific, producing no amplicons or valid sequences from samples containing non-H1N1 viruses or bacteria. Our findings suggest that this method provides a rapid tool for H275Y detection, with high sensitivity and potential benefit for patient care.

Rapid detection of the H275Y oseltamivir resistance mutation in influenza A/H1N1 2009 by single base pair RT-PCR and high-resolution melting

Introduction

We aimed to design a real-time reverse-transcriptase-PCR (rRT-PCR), high-resolution melting (HRM) assay to detect the H275Y mutation that confers oseltamivir resistance in influenza A/H1N1 2009 viruses.

Findings

A novel strategy of amplifying a single base pair, the relevant SNP at position 823 of the neuraminidase gene, was chosen to maintain specificity of the assay. Wildtype and mutant virus were differentiated when using known reference samples of cell-cultured virus. However, when dilutions of these reference samples were assayed, amplification of non-specific primer-dimer was evident and affected the overall melting temperature (T_m) of the amplified products. Due to primer-dimer appearance at >30 cycles we found that if the cycle threshold (C_T) for a dilution was >30, the HRM assay did not consistently discriminate mutant from wildtype. Where the C_T was <30 we noted an inverse relationship between C_T and T_m and fitted quadratic curves allowed the discrimination of wildtype, mutant and 30∶70 mutant∶wildtype virus mixtures. We compared the C_T values for a TaqMan H1N1 09 detection assay with those for the HRM assay using 59 clinical samples and demonstrated that samples with a TaqMan detection assay C_T>32.98 would have an H275Y assay C_T>30. Analysis of the TaqMan C_T values for 609 consecutive clinical samples predicted that 207 (34%) of the samples would result in an HRM assay C_T>30 and therefore not be amenable to the HRM assay.

Conclusions

The use of single base pair PCR and HRM can be useful for specifically interrogating SNPs. When applied to H1N1 09, the constraints this placed on primer design resulted in amplification of primer-dimer products. The impact primer-dimer had on HRM curves was adjusted for by plotting T_m against C_T. Although less sensitive than TaqMan assays, the HRM assay can rapidly, and at low cost, screen samples with moderate viral concentrations.

Emerging oseltamivir resistance in seasonal and pandemic influenza A/H1N1

The emergence of oseltamivir resistance in seasonal and pandemic influenza A/H1N1 has created challenges for diagnosis and clinical management. This review discusses how clinical virology laboratories have handled diagnosis of oseltamivir-resistant H1N1 and what we have learned from clinical studies and case series. Immunocompetent patients infected with oseltamivir-resistant H1N1 have similar outcomes as patients infected with oseltamivir-susceptible H1N1. However, immunocompromised patients infected with oseltamivir-resistant H1N1 experience potentially more risks of complication and transmissibility with few therapeutic options.