Singleplex real-time RT-PCR for detection of influenza A virus and simultaneous differentiation of A/H1N1v and evaluation of the RealStar influenza kit

UPLC-MS-Based Non-targeted Analysis of Endogenous Metabolite Changes in the Leaves of Scabiosa tschiliensis Grüning Induced by 6-Benzylaminopurine and Kinetin

In vitro propagation technology with plant growth regulators (PGRs) is generally applied in the cultivation of Scabiosa tschiliensis, which can solve collection difficulties and limited resources of S. tschiliensis. Nevertheless, comprehensive metabolomic evaluation on S. tschiliensis with PGR effects is still lacking. In this work, a non-targeted metabolomics approach, coupled with statistical and pathway enrichment analysis, was used to assess the regulatory influences of 6-benzylaminopurine (6-BA) and kinetin (KT) applied in S. tschiliensis. The results showed that the PGRs affect metabolism differentially, and the addition of 6-BA and KT can increase different secondary metabolites. In the two PGR groups, some primary metabolites such as L-phenylalanine, L-tyrosine, L-arginine, L-asparagine, and D-proline were significantly reduced. We suspect that under the action of PGRs, these decreased amino acids are derived into secondary metabolites such as umbelliferone, chlorogenic acid, and glutathione. Additionally, some of those secondary metabolites have a biological activity and can also promote the plant growth. Our results provide a basis for the targeted cultivation and utilization of S. tschiliensis, especially the expression of metabolites related to PGR application.

A Rapid On-Site Assay for the Detection of Influenza A by Capillary Convective PCR

BACKGROUND

Morbidity and mortality from influenza A (Flu A) have increased in recent years. Timely diagnosis and management are critical for disease control. Therefore, the development of a rapid, accurate, and portable analytical method for on-site analysis is imperative.

OBJECTIVES

The aim of this work was to develop a rapid, on-site, automated assay for the detection of Flu A and to evaluate the assay.

METHODS

A handheld instrument (TD-01) based on capillary convective polymerase chain reaction (PCR) was developed for rapid on-site detection of Flu A. Since a previous version of the instrument, an automated motion mechanism has been introduced to TD-01 to achieve RNA automated testing. The primers and probe used for Flu A detection were designed according to the Flu A gene sequence of matrix proteins. Finally, we evaluated the detection spectra, sensitivity, specificity, and diagnostic performance of the assay.

RESULTS

The TD-01 was able to successfully automatically detect Flu A RNA within 30 min. Results for serially diluted viruses indicated that the lower limit of detection for Flu A was 0.1 TCID₅₀/ml (50% tissue culture infective dose). After evaluating known virus stocks, including 15 strains of Flu A, four strains of Flu B, and two strains of respiratory syncytial virus (RSV), the assay had a favorable detection spectrum and no obvious cross-reactivity. Method verification based on 554 clinical samples indicated that the sensitivity and specificity of TD-01 were 98.30% (231/235) and 98.75% (315/319), respectively.

CONCLUSIONS

The results indicate that Flu A detection by TD-01 is particularly suitable for on-site testing and has the potential for application in point-of-care testing.

A diagnostic one-step real-time reverse transcription polymerase chain reaction method for accurate detection of influenza virus type A

INTRODUCTION

Influenza A is known as a public health concern worldwide. In this study, a novel one-step real-time reverse transcription polymerase chain reaction (rtRT-PCR) assay was designed and optimized for the detection of influenza A viruses.

MATERIAL AND METHODS

The primers and probe were designed based on the analysis of 90 matrix nucleotide sequence data of influenza type A subtypes from the GenBank database of the National Center for Biotechnology Information (NCBI). The influenza virus A/Tehran/5652/2010 (H1N1 pdm09) was used as a reference. The rtRT-PCR assay was optimized, compared with that of the World Health Organization (WHO), and its analytical sensitivity, specificity and reproducibility were evaluated. In total, 64 nasopharyngeal swabs from patients with influenza-like illness (ILI) and 41 samples without ILI symptoms were tested for the virus, using conventional cell culture, direct immunofluorescence antibody (DFA) methods, and one-step rtRT-PCR with the designed primer set and probe and the WHO's.

RESULTS

The optimized assay results were similar to the WHO's. The optimized assay results were similar to WHO's, with non-significant differences for 10-10³ copies of viral RNA/reaction (p > 0.05). It detected 10 copies of viral RNA/reaction with high reproducibility and no cross reactivity with other respiratory viruses. A specific cytopathic effect was observed in 6/64 (9.37%) of the ILI group using conventional culture and DFA staining methods; however, it was not seen in non-ILI. Also, the results of our assay and the WHO's were similar to those of viral isolation and DFA staining.

CONCLUSIONS

Given the high specificity, sensitivity and reproducibility of this novel assay, it can serve as a reliable diagnostic tool for the detection of influenza A viruses in clinical specimens and lab experiments.

Influenza A virus drift variants reduced the detection sensitivity of a commercial multiplex nucleic acid amplification assay in the season 2014/15

The influenza season 2014/15 was dominated by drift variants of influenza A(H3N2), which resulted in a reduced vaccine effectiveness. It was not clear if the performance of commercial nucleic-acid-based amplification (NAT) assays for the detection of influenza was affected. The purpose of this study was to perform a real-life evaluation of two commercial NAT assays. During January-April 2015, we tested a total of 665 samples from patients with influenza-like illness using the Fast Track Diagnostics Respiratory pathogens 21, a commercial multiplex kit, (cohorts 1 and 2, n = 563 patients) and the Xpert Flu/RSV XC assay (cohort 3, n = 102 patients), a single-use cartridge system. An in-house influenza real-time RT-PCR (cohort 1) and the RealStar Influenza RT-PCR 1.0 Kit (cohort 2 and 3) served as reference tests. Compared to the reference assay, an overall agreement of 95.9 % (cohort 1), 95 % (cohort 2), and 98 % (cohort 3) was achieved. A total of 24 false-negative results were observed using the Fast Track Diagnostics Respiratory pathogens 21 kit. No false-negative results occurred using the Xpert Flu/RSV XC assay. The Fast Track Diagnostics Respiratory pathogens 21 kit and the Xpert Flu/RSV XC assay had sensitivities of 90.7 % and 100 % and specificities of 100 % and 94.1 %, respectively, compared to the RealStar 1.0 kit. Upon modification of the Fast Track Diagnostics Respiratory pathogens 21 kit, the sensitivity increased to 97.3 %. Influenza virus strains circulating during the 2014/15 season reduced the detection sensitivity of a commercial NAT assay, and continuous monitoring of test performance is therefore necessary.

Viral etiology and seasonality of influenza-like illness in Gabon, March 2010 to June 2011

Background

Surveillance of influenza-like illness (ILI) in Central Africa began only recently, and few data are therefore available on the circulation of influenza virus and other respiratory viruses. In Gabon, a Central African country, we established a surveillance network in four major towns in order to analyze cases of ILI among patients who visited health centers between March 2010 and June 2011, and to determine the viral etiology.

Methods

Nasal swabs were sent for analysis to the Centre International de Recherches Médicales de Franceville, where they were screened for 17 respiratory viruses in a multiplex real-time reverse transcription polymerase chain reaction for all pathogens according the following pairs: adenovirus/parainfluenza virus 4, respiratory syncytial virus/human metapneumovirus, parainfluenza virus 1/parainfluenza virus 2, pandemic influenza virus A/seasonal influenza virus A (H1N1, H3N2)/seasonal influenza virus B, human coronaviruses 229E/OC43, human coronaviruses NL63/HKU1, rhinovirus/human parechovirus, and enterovirus/parainfluenza virus 3.

Results

We analyzed a total of 1041 specimens, of which 639 (61%) were positive for at least one virus. Three-quarters of the patients were children under five years old. We therefore focused on this age group, in which 68.1% of patients were positive for at least one virus. The most common viruses were adenoviruses (17.5%), followed by parainfluenza viruses (PIVs) 1–4 (16.8%), enteroviruses (EV) (14.7%), respiratory syncytial virus (RSV) (13.5%), and influenza virus (11.9%). The prevalence of some viruses was subject to geographic and seasonal variations. One-third of positive samples contained more than one virus.

Conclusions

Like most studies in the world, the virus PIVs, EV, RSV, Influenza virus, HRV were predominant among children under five years old in Gabon. An exception is made for adenoviruses which have a high prevalence in our study. However adenoviruses can be detected in asymptomatic persons. These finding gave a better knowledge of the circulation and the seasonality of the viruses involved in ILI in Gabon.

Fast on-site diagnosis of influenza A virus by Palm PCR and portable capillary electrophoresis

A method combining Palm polymerase chain reaction (PCR) and portable capillary electrophoresis (CE) was developed for rapid on-site analysis of influenza A (H1N1) virus. The portable CE system was suitable for rapid diagnosis which was able to detect a sample in ∼4 min after sample loading, while the 'Palm PCR' system allowed for high-speed nucleic acid amplification in ∼16 min. The analysis time from DNA sample to analysis of amplified target DNA molecule was only ∼20 min, which was significantly less than slab gel electrophoresis with other commercially available PCR machine. When the 100-bp DNA ladder was separated, the relative standard deviation values (n=5) for the migration times and peak areas of the 100 and 200-bp DNA molecules were 0.26 and 8.9%. The detection limits were 6.3 and 7.2 pg/μL, respectively. The combined method was also able to identify two influenza A-associated genes (the HA and NP genes of the novel H1N1 influenza). CE separation was achieved with a sieving matrix of 1% poly(vinylpyrrolidone) (Mr=1,300,000) in 1× TBE buffer (pH 8.45). The combined Palm PCR-portable CE system should provide an improved, fast on-site molecular genetic diagnostic method.

Detection of respiratory viruses using a multiplex real-time PCR assay in Germany, 2009/10

The aim of this study was to determine the prevalence of respiratory viruses and to prospectively evaluate the performance of the fast-track diagnostics (FTD) respiratory pathogens multiplex PCR assay shortly after the 2009/10 influenza pandemic. Highly sensitive monoplex real-time PCR assays served as references. Discrepant results were further analyzed by the xTAG RVP Fast assay. A total of 369 respiratory samples from children and adults were collected prospectively in Germany from December 2009 until June 2010. The sensitivity and specificity of the FTD assay after resolution of discrepant results was 92.2 % and 99.5 %, respectively. Lowest specificity of the FTD assay was observed for human bocavirus. Multiple detections were recorded in 33/369 (8.9 %) of the samples by monoplex PCR and in 43/369 (11.7 %) using the FTD assay. The most prevalent viruses were respiratory syncytial virus and human metapneumovirus. Only pandemic influenza virus A/H1N1 (2009), and not seasonal influenza virus, was detected. Viruses other than influenza virus accounted for the majority of acute respiratory infections. The FTD assay can be easily implemented in general diagnostic laboratories and facilitate the optimization of patient-management schemes.

[Influenza today and in the future]

Every year, influenza causes seasonal epidemics and is responsible for increased morbidity and mortality worldwide. In general, clinical signs include fever, respiratory symptoms and myalgia. Human influenza viruses include influenza viruses A/H1N1, A/H3N2, A/H1N1pdm09, influenza virus B and influenza virus C. Wild waterfowl are the natural reservoir of influenza A virus. On a sporadic basis novel viruses can emerge from the zoonotic reservoir and cross the species barrier. In such events clinical presentation in humans can range from mild (e.g. conjunctivitis) to severe pneumonia and acute respiratory distress syndrome (ARDS). In early 2013, a novel avian influenza A virus H7N9 emerged in China and the clinical presentation included bilateral pneumonia with ARDS and a high case fatality rate. In this article a summary is given on diagnosis, therapy and prophylaxis of influenza and on future developments.

Acute fibrinous and organizing pneumonia associated with influenza A/H1N1 pneumonia after lung transplantation

BACKGROUND

Immunocompromised patients, particularly after lung transplantation, are at high risk to develop atypical forms of pulmonary infections including influenza A/H1N1. Acute Fibrinous and Organizing Pneumonia (AFOP) is a special histological pattern in acute respiratory failure with high mortality.

CASE PRESENTATION

We describe a 66-year-old woman with double lung transplantation in August 2009 due to end stage pulmonary fibrosis. After prolonged weaning and subsequent promising course, she developed atypical pneumonia with diffuse pulmonary infiltrates in both lungs in January 2010. Infection with influenza A/H1N1 virus was verified. The patient rapidly suffered from respiratory insufficiency and died eight days after this diagnosis. The post-mortem revealed especially in the lower parts of the lungs the classical histological pattern of pure AFOP. Molecular analyses of lung tissue were positive for influenza A/H1N1.

CONCLUSION

To our knowledge we present the first case of AFOP triggered by viral infection, here proven to be influenza virus A/H1N1. Thus, also in the setting of viral infection the highly deadly differential diagnosis of AFOP must be considered.