A duplex real-time RT-PCR assay for detecting H5N1 avian influenza virus and pandemic H1N1 influenza virus

Testing and diagnosis of SARS-CoV-2 infection

The recent outbreak of the coronavirus disease 2019 (COVID-19) has rapidly spread around the world since its discovery in China, in December 2019. The current standard method for determining whether a patient is infected with the SARS-CoV-2 virus involves taking a nasal or throat swab sample, which is then sent to laboratories for testing. The laboratories then use polymerase chain reaction (PCR)-based technology on respiratory specimens remain the gold standard to determine if the genetic material of the virus is present in the sample and use this information to diagnose the patient. However, serologic immunoassays and point-of-care technologies are rapidly emerging with high specificity and sensitivity as well. Even if there are excellent techniques for diagnosing symptomatic patients with COVID-19 in equipped laboratories, critical gaps still exist in the screening of asymptomatic individuals who are in the incubation phase of the virus, as well as in the accurate determination of live virus shedding during convalescence to inform decisions for ending isolation.

Establishment of a cell-based quantitative reverse transcription-polymerase chain reaction (RT-qPCR) assay for detection of multivalent rotavirus vaccine

Because of deficiencies of traditional potency tests in rotavirus detection, a one-step TaqMan probe-based quantitative reverse transcription-polymerase chain reaction (RT-qPCR) assay combined with cell-based method was established to determine the infectious potency of the target virus in multivalent live rotavirus vaccines in vitro. Series dilutions of rotavirus samples were inoculated into Vero cells and cultured for 24 hours. The cells were lysed and the potency was detected by RT-qPCR. The reference standards with a known titer (lgCCID50 /mL) were assayed in parallel, and the potencies of each sample were determined using parallel line method. The specificity, precision and accuracy of the assay were evaluated, respectively. The results showed that messenger RNA produced during rotavirus replication was the primary template of RT-qPCR and the primers and probes were specific to each strain. The coefficient of variation of different wells and different working days did not exceed 6% and the results of the assay were proved to be concordant with those of cell culture infective dose 50% with a relative deviation less than 5%. This assay is a more rapid, cost-effective and high-throughput way for detecting multivalent rotavirus vaccine, and will be a valuable tool in the quality control and stability monitoring of live multivalent rotavirus vaccine.

Simple, rapid detection of influenza A (H1N1) viruses using a highly sensitive peptide-based molecular beacon

A peptide-based molecular beacon (PEP-MB) was prepared for the simple, rapid, and specific detection of H1N1 viruses using a fluorescence resonance energy transfer (FRET) system. The PEP-MB exhibited minimal fluorescence in its "closed" hairpin structure. However, in the presence of H1N1 viruses, the specific recognition of the hemagglutinin (HA) protein of H1 strains by the PEP-MB causes the beacon to assume an "open" structure that emits strong fluorescence. The PEP-MB could detect H1N1 viruses within 15 min or even 5 min and can exhibit strong fluorescence even at low viral concentrations, with a detection limit of 4 copies.

Detection and typing of human-infecting influenza viruses in China by using a multiplex DNA biochip assay

Rapid identification of the infections of specific subtypes of influenza viruses is critical for patient treatment and pandemic control. Here we report the application of multiplex reverse transcription polymerase chain reaction (RT-PCR) coupled with membrane-based DNA biochip to the detection and discrimination of the type (A and B) and subtype (human H1N1, human H3N2, avian H5N1 and avian H7N9) of influenza viruses in circulation in China. A multiplex one-step RT-PCR assay was designed to simultaneously amplify the HA and NA genes of the four subtypes of influenza A viruses and NS genes to discriminate type A and B viruses. PCR products were analyzed by a membrane-based biochip. The analytical sensitivity of the assay was determined at a range of 2-100 copies/reactions for each of the gene transcripts. Eighty one clinical samples, containing 66 positive samples with evident seasonal influenza virus infections, were tested, which gives the clinical sensitivity and specificity of 95.5% and 100% respectively. For the avian influenza samples, 3 out of 4 H5N1 samples and 2 out of 2 H7N9 avian samples were correctly identified. We argue this method could allow a rapid, reliable and inexpensive detection and differentiation of human-infecting influenza viruses.

Multiplexed detection of influenza A virus subtype H5 and H9 via quantum dot-based immunoassay

A quantum dot-based lateral flow immunoassay system (QD-LFIAS) was developed to simultaneously detect both influenza A virus subtypes H5 and H9. Water-soluble carboxyl-functionalized quantum dots (QDs) were used as fluorescent tags. The QDs were conjugated to specific influenza A virus subtype H5 and H9 antibodies via an amide bond. When influenza A virus subtype H5 or H9 was added to the QD-LFIAS, the QD-labeled antibodies specifically bound to the H5 or H9 subtype viruses and were then captured by the coating antibodies at test line 1 or 2 to form a sandwich complex. This complex produced a bright fluorescent band in response to 365 nm ultraviolet excitation. The intensity of fluorescence can be detected using an inexpensive, low-maintenance instrument, and the virus concentration directly correlates with the fluorescence intensity. The detection limit of the QD-LFIAS for influenza A virus subtype H5 was 0.016 HAU, and the detection limit of the QD-LFIAS for influenza A virus subtype H9 was 0.25 HAU. The specificity and reproducibility were good. The simple analysis step and objective results that can be obtained within 15 min indicate that this QD-LFIAS is a highly efficient test that can be used to monitor and prevent both Influenza A virus subtypes H5 and H9.

Comprehensive molecular screening: from the RT-PCR to the RNA-seq

Up to now, the analysis of the mRNA expression in tumoral and non-tumoral has been conducted via RT-PCR. It is considered to be the gold standard for measuring the number of copies of specific cDNA targets. The application of RT-PCR has demonstrated that levels of RNA transcripts stratify patients and predict outcomes in a variety of diseases, providing the basis for several important clinical tests. However, the inherent variability in the quality of any quantitative PCR data makes it difficult to replicate and the analysis is time consuming in the laboratory for the analysis of one gene. Moreover, comparing expression levels across different experiments is often difficult and can require complicated normalization methods. Many techniques have been developed over the years but without good clinical applications. A new, simple and effective way to measure transcriptome composition and to discover new exons or genes is by the RNA-seq. Some advantages of this technique are high reproducibility, the large dynamic range, requirement of less sample RNA, and the ability to detect novel transcripts, alternative splicing, even in the absence of a sequenced genome. However, this RNA-Seq technique will not likely replace current RT-PCR methods, but will be complementary depending on the needs and the resources of the clinic and the laboratory as the results of the RNA-Seq will identify those genes that need to then be examined using RT-PCR methods. The application of the two complementary technologies in the routine analysis of cancer laboratories would be useful in characterizing patients and would assist oncologists in making clinical decisions, as it allows us to identify all molecular characteristics of the tumor.

Development of a Specific and Rapid Diagnostic Method for Detecting Influenza A (H1N1) pdm09 Virus Infection Using Immunochromatographic Assay

Objectives

The aim of this study was to develop an immunochromatographic assay (ICA) for the detection of influenza A (H1N1) pdm09 virus infection.

Materials and methods

Several monoclonal antibodies against influenza A (H1N1) pdm09 virus were generated and an ICA (pdm09-ICA) was developed for the rapid and specific detection of influenza A (H1N1) pdm09 virus infection. The specificity and sensitivity of the developed assay were compared with that of hemagglutination assay and real-time reverse-transcription polymerase chain reaction (rRT-PCR).

Results

The detection limit was estimated to be 1/2 (8) hemagglutinating unit; the sensitivity and specificity rates of pdm09-ICA were 75.86% (110/145) and 100% (43/43), respectively, compared with rRT-PCR. The cross-reactivity for 20 influenza viruses, including seasonal H1N1 viruses, was found to be negative except for the H1N1 virus (A/Swine/Korea/GC0503/2005).

Conclusion

These results indicate that the proposed method can be easily used for rapid and specific detection of the pdm09 infection. The assay developed in this study would be a useful tool for distinguishing the pdm09 infection from seasonal influenza A and B infections.

Molecular diagnosis of respiratory virus infections

The appearance of eight new respiratory viruses, including the SARS coronavirus in 2003 and swine-origin influenza A/H1N1 in 2009, in the human population in the past nine years has tested the ability of virology laboratories to develop diagnostic tests to identify these viruses. Nucleic acid based amplification tests (NATs) for respiratory viruses were first introduced two decades ago and today are utilized for the detection of both conventional and emerging viruses. These tests are more sensitive than other diagnostic approaches, including virus isolation in cell culture, shell vial culture (SVC), antigen detection by direct fluorescent antibody (DFA) staining, and rapid enzyme immunoassay (EIA), and now form the backbone of clinical virology laboratory testing around the world. NATs not only provide fast, accurate and sensitive detection of respiratory viruses in clinical specimens but also have increased our understanding of the epidemiology of both new emerging viruses such as the pandemic H1N1 influenza virus of 2009, and conventional viruses such as the common cold viruses, including rhinovirus and coronavirus. Multiplex polymerase chain reaction (PCR) assays introduced in the last five years detect up to 19 different viruses in a single test. Several multiplex PCR tests are now commercially available and tests are working their way into clinical laboratories. The final chapter in the evolution of respiratory virus diagnostics has been the addition of allelic discrimination and detection of single nucleotide polymorphisms associated with antiviral resistance. These assays are now being multiplexed with primary detection and subtyping assays, especially in the case of influenza virus. These resistance assays, together with viral load assays, will enable clinical laboratories to provide physicians with new and important information for optimal treatment of respiratory virus infections.

Phage displayed peptides to avian H5N1 virus distinguished the virus from other viruses

The purpose of the current study was to identify potential ligands and develop a novel diagnostic test to highly pathogenic avian influenza A virus (HPAI), subtype H5N1 viruses using phage display technology. The H5N1 viruses were used as an immobilized target in a biopanning process using a 12-mer phage display random peptide library. After five rounds of panning, three phages expressing peptides HAWDPIPARDPF, AAWHLIVALAPN or ATSHLHVRLPSK had a specific binding activity to H5N1 viruses were isolated. Putative binding motifs to H5N1 viruses were identified by DNA sequencing. In terms of the minimum quantity of viruses, the phage-based ELISA was better than antiserum-based ELISA and a manual, semi-quantitative endpoint RT-PCR for detecting H5N1 viruses. More importantly, the selected phages bearing the specific peptides to H5N1 viruses were capable of differentiating this virus from other avian viruses in enzyme-linked immunosorbent assays.

Salivary Detection of H1N1 Virus: A Clinical Feasibility Investigation

The fast and efficient transportation among continents will continue to play a role in the spread of airborne pandemics. The objective of this study was to detect H1N1 virus in the saliva of individuals who visited the emergency department and were diagnosed as having H1N1 influenza. Nasopharyngeal swabs and saliva samples from those who presented to the emergency department with flu-like symptoms were sent to the laboratory. RNA was extracted from both samples. Real-time RT-PCR tests were performed, and the saliva and nasopharyngeal swab tests were compared. Samples were drawn from 26 individuals. A positive nasopharyngeal swab test and salivary test was found in 14 persons, and negative tests were found in 12 persons. Saliva sampling for H1N1 has excellent predictive value, is highly accurate and reliable, and is more convenient than the nasopharyngeal swab. Clinical trial with the Helsinki Committee at Rambam Health Care Campus, registration number 036309-RMB.

A duplex real-time reverse transcriptase polymerase chain reaction assay for detecting western equine and eastern equine encephalitis viruses

In order to establish an accurate, ready-to-use assay for simultaneous detection of Eastern equine encephalitis virus (EEEV) and Western equine encephalitis virus (WEEV), we developed one duplex TaqMan real-time reverse transcriptase polymerase chain reaction (RT-PCR) assay, which can be used in human and vector surveillance. First, we selected the primers and FAM-labeled TaqMan-probe specific for WEEV from the consensus sequence of NSP3 and the primers and HEX-labeled TaqMan-probe specific for EEEV from the consensus sequence of E3, respectively. Then we constructed and optimized the duplex real-time RT-PCR assay by adjusting the concentrations of primers and probes. Using a series of dilutions of transcripts containing target genes as template, we showed that the sensitivity of the assay reached 1 copy/reaction for EEEV and WEEV, and the performance was linear within the range of at least 106 transcript copies. Moreover, we evaluated the specificity of the duplex system using other encephalitis virus RNA as template, and found no cross-reactivity. Compared with virus isolation, the gold standard, the duplex real time RT-PCR assay we developed was 10-fold more sensitive for both WEEV and EEEV detection.

Evaluation of a rapid diagnostic test, NanoSign® Influenza A/B Antigen, for detection of the 2009 pandemic influenza A/H1N1 viruses

Background

This study evaluated the clinical accuracy and analytical sensitivity of the NanoSign^® Influenza A/B antigen kit in detecting 2009 pandemic influenza A/H1N1 viruses. The kit is one of the most popular rapid diagnostic tests for detecting influenza in Republic of Korea.

Results

The NanoSign^® Influenza A/B kit resulted in 79.4% sensitivity and 97.2% specificity compared to RT-PCR in the detection of the viruses from 1,023 specimens. In addition, the kit was able to detect two strains of novel influenza viruses, Influenza A/California/12/2009(H1N1) and clinically isolated wild-type novel influenza A/H1N1, both of which are spreading epidemically throughout the world. In addition, the correlation between NanoSign^® Influenza A/B test and conventional RT-PCR was approximately 94%, indicating a high concordance rate. Analytical sensitivity of the kit was approximately 73 ± 3.65 ng/mL of the purified viral proteins and 1.13 ± 0.11 hemagglutination units for the cultured virus.

Conclusions

As the NanoSign^® Influenza A/B kit showed relatively high sensitivity and specificity and the good correlation with RT-PCR, it will be very useful in the early control of influenza infection and in helping physicians in making early treatment decisions.