Plasmonic Fluorescence Sensors in Diagnosis of Infectious Diseases

The increasing demand for rapid, cost-effective, and reliable diagnostic tools in personalized and point-of-care medicine is driving scientists to enhance existing technology platforms and develop new methods for detecting and measuring clinically significant biomarkers. Humanity is confronted with growing risks from emerging and recurring infectious diseases, including the influenza virus, dengue virus (DENV), human immunodeficiency virus (HIV), Ebola virus, tuberculosis, cholera, and, most notably, SARS coronavirus-2 (SARS-CoV-2; COVID-19), among others. Timely diagnosis of infections and effective disease control have always been of paramount importance. Plasmonic-based biosensing holds the potential to address the threat posed by infectious diseases by enabling prompt disease monitoring. In recent years, numerous plasmonic platforms have risen to the challenge of offering on-site strategies to complement traditional diagnostic methods like polymerase chain reaction (PCR) and enzyme-linked immunosorbent assays (ELISA). Disease detection can be accomplished through the utilization of diverse plasmonic phenomena, such as propagating surface plasmon resonance (SPR), localized SPR (LSPR), surface-enhanced Raman scattering (SERS), surface-enhanced fluorescence (SEF), surface-enhanced infrared absorption spectroscopy, and plasmonic fluorescence sensors. This review focuses on diagnostic methods employing plasmonic fluorescence sensors, highlighting their pivotal role in swift disease detection with remarkable sensitivity. It underscores the necessity for continued research to expand the scope and capabilities of plasmonic fluorescence sensors in the field of diagnostics.

SARS-CoV-2 detecting rapid metasurface-based sensor

We have proposed a novel approach to detect COVID-19 by detecting the ethyl butanoate which high volume ratio is present in the exhaled breath of a COVID-19 infected person. We have employed a refractive index sensor (RIS) with the help of a metasurface-based slotted T-shape perfect absorber that can detect ethyl butanoate present in exhaled breath of COVID-19 infected person with high sensitivity and in-process SARS-CoV-2. The optimized structure of the sensor is obtained by varying several structure parameters including structure length and thickness, slotted T-shape resonator length, width, and thickness. Sensor's performance is evaluated based on numerous factors comprising of sensitivity, Q factor, detection limit, a figure of merit (FOM), detection accuracy, and other performance defining parameters. The proposed slotted T-shape RIS achieved the largest sensitivity of 2500 nm/RIU, Q factor of 131.06, a FOM of 131.58 RIU^-1, detection limit of 0.0224 RIU.

Recent Advances in Biosensors for Detection of COVID-19 and Other Viruses

This century has introduced very deadly, dangerous, and infectious diseases to humankind such as the influenza virus, Ebola virus, Zika virus, and the most infectious SARS-CoV-2 commonly known as COVID-19 and have caused epidemics and pandemics across the globe. For some of these diseases, proper medications, and vaccinations are missing and the early detection of these viruses will be critical to saving the patients. And even the vaccines are available for COVID-19, the new variants of COVID-19 such as Delta, and Omicron are spreading at large. The available virus detection techniques take a long time, are costly, and complex and some of them generates false negative or false positive that might cost patients their lives. The biosensor technique is one of the best qualified to address this difficult challenge. In this systematic review, we have summarized recent advancements in biosensor-based detection of these pandemic viruses including COVID-19. Biosensors are emerging as efficient and economical analytical diagnostic instruments for early-stage illness detection. They are highly suitable for applications related to healthcare, wearable electronics, safety, environment, military, and agriculture. We strongly believe that these insights will aid in the study and development of a new generation of adaptable virus biosensors for fellow researchers.

An overview of advancement in aptasensors for influenza detection

INTRODUCTION

The platforms for early identification of infectious diseases such as influenza has seen a surge in recent years as delayed diagnosis of such infections can lead to dreadful effects causing large numbers of deaths. The time taken in detection of an infectious disease may vary from a few days to a few weeks depending upon the choice of the techniques. So, there is an urgent need for advanced methodologies for early diagnosis of the influenza.

AREAS COVERED

The emergence of "Aptasensor" synergistically with biosensors for diagnosis has opened a new era for sensitive, selective and early detection approaches. This review described various conventional as well as advanced methods based on artificial immunogenic nucleotide sequences complementing a part of the virus, i.e., aptamers based aptasensors for influenza diagnosis and the challenges faced in their commercialization.

EXPERT OPINION

Although numerous traditional methods are available for influenza detection but mostly associated with low sensitivity, specificity, high cost, trained personnel, and animals required for virus culture/ antibody raising as the major drawbacks. Aptamers can be manufactured invitro as 'chemical antibodies' at commercial level, no animal required. Following these advantages, aptamers can pave the way for an efficient diagnostic technique as compared to other existing conventional methods..

A microfluidic cell chip for virus isolation via rapid screening for permissive cells

Virus identification is a prerequisite not only for the early diagnosis of viral infectious diseases but also for the effective prevention of epidemics. Successful cultivation is the gold standard for identifying a virus, according to the Koch postulates. However, this requires screening for a permissive cell line, which is traditionally time-, reagent- and labor-intensive. Here, a simple and easy-to-operate microfluidic chip, formed by seeding a variety of cell lines and culturing them in parallel, is reported for use in virus cultivation and virus-permissive host-cell screening. The chip was tested by infection with two known viruses, enterovirus 71 (EV71) and influenza virus H1N1. Infection with EV71 and H1N1 caused significant cytopathic effects (CPE) in RD and MDCK cells, respectively, demonstrating that virus cultivation based on this microfluidic cell chip can be used as a substitute for the traditional plate-based culture method and reproduce the typical CPE caused by virus infection. Using this microfluidic cell chip method for virus cultivation could make it possible to identify an emerging virus in a high-throughput, automatic, and unprecedentedly fast way.

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A simple microfluidic chip for tandem culture of different cell lines is achieved.

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The cell chip has been used for permissive cell screening and culture of viruses.

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The cell chip has advantages of being sample-, reagent-, and time-saving.

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The cell chip system holds potential for high-throughput and automated screening.

Evaluating an app-guided self-test for influenza: lessons learned for improving the feasibility of study designs to evaluate self-tests for respiratory viruses

Background

Seasonal influenza leads to significant morbidity and mortality. Rapid self-tests could improve access to influenza testing in community settings. We aimed to evaluate the diagnostic accuracy of a mobile app-guided influenza rapid self-test for adults with influenza like illness (ILI), and identify optimal methods for conducting accuracy studies for home-based assays for influenza and other respiratory viruses.

Methods

This cross-sectional study recruited adults who self-reported ILI online. Participants downloaded a mobile app, which guided them through two low nasal swab self-samples. Participants tested the index swab using a lateral flow assay. Test accuracy results were compared to the reference swab tested in a research laboratory for influenza A/B using a molecular assay.

Results

Analysis included 739 participants, 80% were 25–64 years of age, 79% female, and 73% white. Influenza positivity was 5.9% based on the laboratory reference test. Of those who started their test, 92% reported a self-test result. The sensitivity and specificity of participants’ interpretation of the test result compared to the laboratory reference standard were 14% (95%CI 5–28%) and 90% (95%CI 87–92%), respectively.

Conclusions

A mobile app facilitated study procedures to determine the accuracy of a home based test for influenza, however, test sensitivity was low. Recruiting individuals outside clinical settings who self-report ILI symptoms may lead to lower rates of influenza and/or less severe disease. Earlier identification of study subjects within 48 h of symptom onset through inclusion criteria and rapid shipping of tests or pre-positioning tests is needed to allow self-testing earlier in the course of illness, when viral load is higher.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12879-021-06314-1.

Fabrication of Electrochemical Influenza Virus (H1N1) Biosensor Composed of Multifunctional DNA Four-Way Junction and Molybdenum Disulfide Hybrid Material

The outbreak of the influenza virus (H1N1) has symptoms such as coughing, fever, and a sore throat, and due to its high contagious power, it is fatal to humans. To detect H1N1 precisely, the present study proposed an electrochemical biosensor composed of a multifunctional DNA four-way junction (4WJ) and carboxyl molybdenum disulfide (carboxyl-MoS2) hybrid material. The DNA 4WJ was constructed to have the hemagglutinin aptamer on the head group (recognition part); each of the two arms has four silver ions (signal amplification part), and the tail group has an amine group (anchor). This fabricated multifunctional DNA 4WJ can specifically and selectively bind to hemagglutinin. Moreover, the carboxyl-MoS2 provides an increase in the sensitivity of this biosensor. Carboxyl-MoS2 was immobilized using a linker on the electrode, followed by the immobilization of the multifunctional 4WJ on the electrode. The synthesis of carboxyl-MoS2 was confirmed by field emission scanning electron microscopy (FE-SEM), and the surface of the electrode was confirmed by atomic force microscopy. When H1N1 was placed in the immobilized electrode, the presence of H1N1 was confirmed by electrochemical analysis (cyclic voltammetry, electrochemical impedance spectroscopy). Through selectivity tests, it was also possible to determine whether this sensor responds specifically and selectively to H1N1. We confirmed that the biosensor showed a linear response to H1N1, and that H1N1 could be detected from 100 nM to 10 pM. Finally, clinical tests, in which hemagglutinin was diluted with human serum, showed a similar tendency to those diluted with water. This study showed that the multi-functional DNA 4WJ and carboxyl-MoS2 hybrid material can be applied to a electrochemical H1N1 biosensor.

Discrimination between target and non-target interactions on the viral surface by merging fluorescence emission into Rayleigh scattering

Direct and quantitative determination of antibodies or cellular receptors dynamically binding to the surface of viral particles is the key issue for predicting the efficacy of therapeutic materials or host susceptibility to a new emerging pathogen. However, targeted visualization of infectious viruses is still highly challenging owing to their nanoscopic sizes and uncontrollable nonspecific interactions with loading molecules responsible for false signals. Here we present a multimodal single-molecule and single-particle (SMSP) visualization capable of simultaneously yet independently tracking Rayleigh scattering and fluorescence that, respectively, are generated from viruses (approximately 100 nm) and labeled interacting molecules. By analyzing real-time trajectories of fluorescent antibodies against a virus surface protein with reference to single virus-derived Rayleigh scattering, we determined heterogeneous binding stoichiometry of virus-antibody couplings irrespective of the nonspecific binder population. Therefore, our multimodal (or multi-level) SMSP assay visually identifies and selectively quantifies specific interactions between them with single binding event accuracy. As a 'specific-binding quantifier' to assess variable host susceptibility to a virus, it was further applied for distinguishing ratiometric bindings and spontaneous dissociation kinetics of synthesized isomeric receptors to influenza virus. The present framework could offer a solid analytical foundation for the development of a direct-acting antiviral agent inhibiting an integral viral enveloped protein and for nanobiological investigation for dissecting spatiotemporal nanoparticle-molecule interactions, which have been scarcely explored compared to those among plasmonic nanoparticles or among molecules only.

Magnetic Particle Spectroscopy for Detection of Influenza A Virus Subtype H1N1

Magnetic nanoparticles (MNPs) with proper surface functionalization have been extensively applied as labels for magnetic immunoassays, carriers for controlled drug/gene delivery, tracers and contrasts for magnetic imaging, etc. Here, we introduce a new biosensing scheme based on magnetic particle spectroscopy (MPS) and the self-assembly of MNPs to quantitatively detect H1N1 nucleoprotein molecules. MPS monitors the harmonics of oscillating MNPs as a metric for the freedom of rotational process, thus indicating the bound states of MNPs. These harmonics can be readily collected from nanogram quantities of iron oxide nanoparticles within 10 s. The H1N1 nucleoprotein molecule hosts multiple different epitopes that forms binding sites for many IgG polyclonal antibodies. Anchoring IgG polyclonal antibodies onto MNPs triggers the cross-linking between MNPs and H1N1 nucleoprotein molecules, thereby forming MNP self-assemblies. Using MPS and the self-assembly of MNPs, we were able to detect as low as 44 nM (4.4 pmole) H1N1 nucleoprotein. In addition, the morphologies and the hydrodynamic sizes of the MNP self-assemblies are characterized to verify the MPS results. Different MNP self-assembly models such as classical cluster, open ring tetramer, and chain model as well as multimers (from dimer to pentamer) are proposed in this paper. Herein, we claim the feasibility of using MPS and the self-assembly of MNPs as a new biosensing scheme for detecting ultralow concentrations of target biomolecules, which can be employed as rapid, sensitive, and wash-free magnetic immunoassays.

Comparison of the performance of the Panther Fusion respiratory virus panel to R-Gene and laboratory developed tests for diagnostic and hygiene screening specimens from the upper and lower respiratory tract

Introduction. Diagnosis of acute respiratory infections (ARIs) can be facilitated by the Panther Fusion (PF) automatic, random access PCR system for the detection of influenzavirus A (Flu A) and B (Flu B), parainfluenzavirus (Paraflu), respiratory syncytial virus (RSV), human metapneumovirus (hMPV), rhinovirus (RV) and human adenovirus (AdV) in nasopharyngeal swabs.

Aim. To evaluate the performance of PF in comparison with established methods, including subsets of (1) lower respiratory tract (LRT) specimens and (2) upper respiratory tract (URT) hygiene screening specimens of patients without ARI symptoms.

Methodology. The performance characteristics of PF were compared with bioMérieux R-Gene and laboratory-developed PCR tests (LDTs). Overall, 1544 specimens with 6658 individual diagnostic requests were analysed.

Results. The overall concordances of PF and LDTs for Flu A, Flu B and AdV were 98.4, 99.9 and 96.1%, respectively; by re-testing of discrepant specimens concordances increased to 99.4, 99.9 and 98.0%, respectively. Initial concordances of PF and R-Gene assays for RSV, Paraflu, hMPV and RV were 98.4, 96.3, 99.3 and 96.0%, respectively, and retest concordances were 99.7, 97.9, 99.9 and 98.9%, respectively. No differences to the overall performance were found for the subgroups of LRT and hygiene screening specimens. PCR cycle threshold (Ct) values correlated very well between methods, indicating that a semi-quantitative diagnostic approach using Ct values (e.g. highly vs. weakly positive) could augment the diagnostic information.

Conclusion. PF performed similar to R-Gene and LDTs not only for its intended use but also for LRT and hygiene screening specimens with shorter hands-on and turnaround times.

Molecular characteristics and successful management of a respiratory syncytial virus outbreak among pediatric patients with hemato-oncological disease

Background

Respiratory syncytial virus (RSV) is responsible for upper and lower respiratory tract infection in adults and children. Especially immunocompromised patients are at high risk for a severe course of infection, and mortality is increased. Moreover RSV can spread in healthcare settings and can cause outbreaks. Herein we demonstrate the successful control and characteristics of a RSV outbreak that included 8 patients in our Department of Pediatric Hematology and Oncology.

Methods

We performed an epidemiologic investigation and a molecular analysis of the outbreak strains. Moreover we present the outbreak control bundle and our concept for RSV screening in the winter season.

Results

RSV A and B strains caused the outbreak. RSV B strains affected 3 patients, 2 of whom were co-infected with RSV A. Exactly this RSV A strain was detected in another 5 patients. Our multimodal infection control bundle including prophylactic RSV screening was able to rapidly stop the outbreak.

Conclusion

An infection control bundle in RSV outbreaks should address all potential transmission pathways. In pediatric settings the restriction of social activities might have a temporal negative impact on quality of life but helps to limit transmission opportunities. Molecular analysis allows better understanding of RSV outbreaks and, if done in a timely manner, might be helpful for guidance of infection control measures.

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.

Sensitive Detection and Simultaneous Discrimination of Influenza A and B Viruses in Nasopharyngeal Swabs in a Single Assay Using Next-Generation Sequencing-Based Diagnostics

Reassortment of 2009 (H1N1) pandemic influenza virus (pdH1N1) with other strains may produce more virulent and pathogenic forms, detection and their rapid characterization is critical. In this study, we reported a “one-size-fits-all” approach using a next-generation sequencing (NGS) detection platform to extensively identify influenza viral genomes for diagnosis and determination of novel virulence and drug resistance markers. A de novo module and other bioinformatics tools were used to generate contiguous sequence and identify influenza types/subtypes. Of 162 archived influenza-positive patient specimens, 161(99.4%) were positive for either influenza A or B viruses determined using the NGS assay. Among these, 135(83.3%) were A(H3N2), 14(8.6%) were A(pdH1N1), 2(1.2%) were A(H3N2) and A(pdH1N1) virus co-infections and 10(6.2%) were influenza B viruses. Of the influenza A viruses, 66.7% of A(H3N2) viruses tested had a E627K mutation in the PB2 protein, and 87.8% of the influenza A viruses contained the S31N mutation in the M2 protein. Further studies demonstrated that the NGS assay could achieve a high level of sensitivity and reveal adequate genetic information for final laboratory confirmation. The current diagnostic platform allows for simultaneous identification of a broad range of influenza viruses, monitoring emerging influenza strains with pandemic potential that facilitating diagnostics and antiviral treatment in the clinical setting and protection of the public health.

Airborne virus detection by a sensing system using a disposable integrated impaction device

There are many respiratory infections such as influenza that cause epidemics. These respiratory infection epidemics can be effectively prevented by determining the presence or absence of infections in patients using frequent tests. We think that self-diagnosis may be possible using a system that can collect and detect biological aerosol particles in the patient's breath because breath sampling is easy work requiring no examiner. In this paper, we report a sensing system for biological aerosol particles (SSBAP) with a disposable device. Using the system and the device, someone with no medical knowledge or skills can safely, easily, and rapidly detect infectious biological aerosol particles. The disposable device, which is the core of the SSBAP, can be an impactor for biological aerosol particles, a flow-cell for reagents, and an optical window for the fluorescent detection of collected particles. Furthermore, to detect the fluorescence of very small collected particles, this disposable device is covered with a light-blocking film that lets only fluorescence of particles pass through a fluorescence detector of the SSBAP. The SSBAP using the device can automatically detect biological aerosol particles by the following process: collecting biological aerosol particles from a patient's breath in a sampling bag by the impaction method, labeling the collected biological aerosol particles with fluorescent dyes by the antigen-antibody reaction, removing free fluorescent dyes, and detecting the fluorescence of the biological aerosol particles. The collection efficiency of the device for microspheres aerosolized in the sampling bag was more than 97%, and the SSBAP with the device could detect more than 8.3  ×  10(3) particles l(-1) of aerosolized influenza virus particles within 10 min.

Current Approaches for Diagnosis of Influenza Virus Infections in Humans

Despite significant advancement in vaccine and virus research, influenza continues to be a major public health concern. Each year in the United States of America, influenza viruses are responsible for seasonal epidemics resulting in over 200,000 hospitalizations and 30,000–50,000 deaths. Accurate and early diagnosis of influenza viral infections are critical for rapid initiation of antiviral therapy to reduce influenza related morbidity and mortality both during seasonal epidemics and pandemics. Several different approaches are currently available for diagnosis of influenza infections in humans. These include viral isolation in cell culture, immunofluorescence assays, nucleic acid amplification tests, immunochromatography-based rapid diagnostic tests, etc. Newer diagnostic approaches are being developed to overcome the limitations associated with some of the conventional detection methods. This review discusses diagnostic approaches currently available for detection of influenza viruses in humans.

Accuracy of rapid influenza detection test in diagnosis of influenza A and B viruses in children less than 59 months old

Influenza burden among children is underestimated. Rapid influenza diagnostic tests (RIDTs) may be helpful in the early diagnosis of the disease, but their results should be interpreted cautiously. The aim of our study was to estimate the accuracy of the rapid influenza detection test BD Directigen™ EZ Flu A+B (Becton, Dickinson and Company, Sparks, MD) used among children with influenza-like illness (ILI) consulted in the ambulatory care clinics. A total number of 150 patients were enrolled into the study. The inclusion criteria were: age of the child less than 59 months, presentation of ILI according to CDC definition (fever >37.8 °C, cough, and/or sore throat in the absence of another known cause of illness), and duration of symptoms shorter than 96 h. In all patients two nasal and one pharyngeal swab were obtained and tested by RIDT, RT-PCR, and real time RT-PCR. For or influenza A(H1N1)pdm09, virus sensitivity of RIDT was 62.2 % (95 %CI 53.4-66.5 %), specificity 97.1 % (95 %CI 93.4-99 %), positive predictive value (PPV) 90.3 % (95 %CI 77.5-96.5 %), and negative predictive value (NPV) 85.7 % (95 %CI 82.4-87.3 %). For influenza B, virus sensitivity was 36.8 % (95 %CI 23.3-41.1 %), specificity 99.2 % (95 %CI 97.3-99.9 %), PPV 87.5 % (95 %CI 55.4-97.7 %), and NPV 91.5 % (95 % CI 89.7-92.1 %). We conclude that the RIDT immunoassay is a specific, but moderately sensitive, method in the diagnosis of influenza type A and is of low sensitivity in the diagnosis of influenza B infections in infants and children.

Comparison of the detection of influenza A and B viruses by different methods

OBJECTIVE

To investigate the detection of influenza viruses by three different methods.

METHODS

Nasopharyngeal swabs were collected from patients with influenza symptoms and examined for influenza A and B viruses using a rapid antigen test, a multiplex polymerase chain reaction (PCR) test and a shell vial cell culture test.

RESULTS

Using the shell vial cell culture test, the rapid antigen test and the multiplex PCR test in 130 patients, 31 (23.8%), 24 (18.5%) and 24 (18.5%) samples, respectively, were positive for influenza A and 10 (7.7%), nine (6.9%) and four (3.1%) samples, respectively, were positive for influenza B. Compared with the shell vial test, the sensitivity, specificity, and positive and negative predictive values of the rapid antigen test were 77.4%, 93.3%, 80.0% and 93.1%, respectively, for influenza A, and 90.0%, 95.8%, 64.2% and 99.1%, respectively, for influenza B. The corresponding values for the multiplex PCR test were 77.4%, 95.9%, 85.7% and 93.1%, respectively, for influenza A, and 40.0%, 97.5%, 57.1% and 95.1%, respectively, for influenza B.

CONCLUSIONS

The multiplex PCR test and the rapid antigen test are both effective in the detection of influenza A and B viruses.

Probability of detecting influenza A virus subtypes H1N1 and H3N2 in individual pig nasal swabs and pen-based oral fluid specimens over time

The probability of detecting influenza A virus (IAV) by virus isolation (VI), point-of-care (POC) antigen detection, and real-time reverse-transcription polymerase chain reaction (rRT-PCR) was estimated for pen-based oral fluid (OF) and individual pig nasal swab (NS) specimens. Piglets (n=82) were isolated for 30 days and confirmed negative for porcine reproductive and respiratory syndrome virus, Mycoplasma hyopneumoniae, and IAV infections. A subset (n=28) was vaccinated on day post inoculation (DPI) -42 and -21 with a commercial multivalent vaccine. On DPI 0, pigs were intratracheally inoculated with contemporary isolates of H1N1 (n=35) or H3N2 (n=35) or served as negative controls (n=12). OF (n=370) was collected DPI 0-16 and NS (n=924) DPI 0-6, 8, 10, 12, 14, 16. The association between IAV detection and variables of interest (specimen, virus subtype, assay, vaccination status, and DPI) was analyzed by mixed-effect repeated measures logistic regression and the results used to calculate the probability (pˆ) of detecting IAV in OF and NS over DPI by assay. Vaccination (p-value<0.0001), DPI (p-value<0.0001), and specimen-assay interaction (p-value<0.0001) were significant to IAV detection, but virus subtype was not (p-value=0.89). Vaccination and/or increasing DPI reduced pˆ for all assays. VI was more successful using NS than OF, but both VI and POC were generally unsuccessful after DPI 6. Overall, rRT-PCR on OF specimens provided the highest pˆ for the most DPIs, yet significantly different results were observed between the two laboratories independently performing rRT-PCR testing.

Secondary bacterial infections in patients with seasonal influenza A and pandemic H1N1

The aim of the present study is to analyse the secondary bacterial infections in a large group of patients with seasonal influenza A and influenza A(H1N1) pdm09. Patients diagnosed with seasonal influenza A and influenza A(H1N1) pdm09 between 2005 and 2009 were enrolled in the study. Data was retrieved from medical records and laboratory information systems (LIS). In total, 1094 patients with laboratory confirmed influenza were studied. There were 352 patients with seasonal influenza A and 742 patients with influenza A(H1N1) pdm09. The patients with influenza A were older and had higher comorbidity than patients with influenza A(H1N1) pdm09 (P < 0.001 and P < 0.05, resp.). Hospital admission was higher in influenza A group (P = 0.01). In contrast, ICU admission was higher in patients with influenza A(H1N1) pdm09 than influenza A patients (P < 0.05). There were higher numbers of bacterial samples taken and culture positivity in patients with influenza A than patients with influenza A(H1N1) pdm09 (P < 0.0001 and P = 0.01, resp.). In both groups, the majority of the patients with positive bacterial cultures had underlying diseases. The present study shows that the patient characteristics and the frequency of secondary bacterial infections were different in patients with seasonal influenza A and in patients with influenza A(H1N1) pdm09.

Influenza diagnosis and vaccination in Poland

In Poland between several thousand and several million cases of influenza and suspected influenza cases are registered, depending on the epidemic season. A variety of methods are available for the detection of the influenza viruses responsible for respiratory infection starting with the isolation of the virus in chick embryos or in cell lines such as MDCK, VERO, etc., and finishing with a variety of modifications of the classical PCR molecular biology such as PCR multiplex and Real-Time. The most effective way to combat influenza is through vaccination. Regular vaccination is one of the few steps that may be taken to protect individuals, especially in high-risk groups, from the potential and serious complications of influenza. In many countries, including Poland, despite the recommendations, the rate of vaccination against influenza is still low in all age groups. In the epidemic season 2011/2012, the level of distribution of the seasonal influenza vaccines was 4.5% of the population.

Tools to detect influenza virus

In 2009, pandemic influenza A (H1N1) virus (H1N1 09) started to spread quickly in many countries. It causes respiratory infection with signs and symptoms of common infectious agents. Thus, clinicians sometimes may miss the H1N1 patient. Clinical laboratory tests are important for the diagnosis of the H1N1 infection. There are several tests available, however, the rapid test and direct fluorescence antigen test are unable to rule out the influenza virus infection and viral culture test is time consuming. Therefore, nucleic acid amplification techniques based on reverse transcription polymerase chain reaction assays are regarded as a specific diagnosis to confirm the influenza virus infection. Although the nucleic acid-based techniques are highly sensitive and specific, the high mutation rate of the influenza RNA-dependent RNA polymerase could limit the utility of the techniques. In addition, their use depends on the availability, cost and throughput of the diagnostic techniques. To overcome these drawbacks, evaluation and development of the techniques should be continued. This review provides an overview of various techniques for specific diagnosis of influenza infection.

Comparison of four multiplex PCR assays for the detection of viral pathogens in respiratory specimens

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This study will compare 4 different multiplex PCR assays.

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The xTAG RVP, Fast-track RP, Easyplex and an in-house rt-PCR assay were included.

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The performance of the assays was similar, with 93–100% agreement for comparisons.

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Non-performance aspects are key to deciding which of these assays to use.

Multiplex PCR has become the test of choice for the detection of multiple respiratory viruses in clinical specimens. However, there are few direct comparisons of different PCR assays. This study compares 4 different multiplex PCR assays for the recovery of common respiratory viruses. We tested 213 respiratory specimens using four different multiplex PCR assays: the xTAG respiratory viral panel fast (Abbott Molecular Laboratories), Fast-track Respiratory Pathogen assay (Fast-track Diagnostics), Easyplex respiratory pathogen 12 kit (Ausdiagnostics), and an in-house multiplex real-time PCR assay. The performance of the four assays was very similar, with 93–100% agreement for all comparisons. Other issues, such as through-put, technical requirements and cost, are likely to be as important for making a decision about which of these assays to use given their comparative performance.

Implementation of filmarray respiratory viral panel in a core laboratory improves testing turnaround time and patient care

The FilmArray respiratory virus panel detects 15 viral agents in respiratory specimens using polymerase chain reaction. We performed FilmArray respiratory viral testing in a core laboratory at a regional children’s hospital that provides service 24 hours a day 7 days a week. The average and median turnaround time were 1.6 and 1.4 hours, respectively, in contrast to 7 and 6.5 hours documented 1 year previously at an on-site reference laboratory using a direct fluorescence assay (DFA) that detected 8 viral agents. During the study period, rhinovirus was detected in 20% and coronavirus in 6% of samples using FilmArray; these viruses would not have been detected with DFA. We followed 97 patients with influenza A or influenza B who received care at the emergency department (ED). Overall, 79 patients (81%) were given oseltamivir in a timely manner defined as receiving the drug in the ED, a prescription in the ED, or a prescription within 3 hours of ED discharge. Our results demonstrate that molecular technology can be successfully deployed in a nonspecialty, high-volume, multidisciplinary core laboratory.

Evaluation of a new immunochromatographic assay for rapid identification of influenza A, B, and A(H1N1)2009 viruses

We evaluated Clearline Influenza A/B/(H1N1)2009, a new multi-line immunochromatographic assay for rapid detection of antigens of influenza A (Flu A), B (Flu B), and A(H1N1)2009 viruses. Clearline detected Flu A, Flu B, and A(H1N1)2009 viruses with a detection limit of 4.6 × 10³ to 7.5 × 10⁴ pfu/assay. The sensitivity and specificity of detection of influenza virus by Clearline, using RT-PCR as reference standard, were determined for A(H1N1)2009, Flu A, and Flu B, in nasopharyngeal aspirate, nasopharyngeal swab, and self-blown nasal discharge specimens. Sensitivity for nasopharyngeal aspirate specimens was: A(H1N1)2009 = 97.3 %, Flu A = 94.5 %, and Flu B = 96.8 %, and specificity was Flu A = 99.1 % and Flu B = 100 %. Sensitivity for nasopharyngeal swab specimens was: A(H1N1)2009 = 91.9 %, Flu A = 92.8 %, and Flu B = 100 %, and specificity was Flu A = 98.2 % and Flu B = 100 %. Sensitivity for self-blown nasal discharge specimens was: A(H1N1)2009 = 75.7 %, Flu A = 86.5 %, and Flu B = 76.2 %, and specificity was Flu A = 98.4 % and Flu B = 100 %. Sensitivity and specificity of Clearline were sufficient for nasopharyngeal aspirate and swab specimens. For self-blown nasal discharge specimens, sensitivity was lower than for nasopharyngeal aspirates and nasopharyngeal swabs. The sensitivity of Clearline for A(H1N1)2009 was good even 6 h after the onset of symptoms. These findings suggest that Clearline may be useful for early clinical diagnosis of influenza.

A distinct influenza infection signature in the blood transcriptome of patients with severe community-acquired pneumonia

INTRODUCTION

Diagnosis of severe influenza pneumonia remains challenging because of a lack of correlation between the presence of influenza virus and clinical status. We conducted gene-expression profiling in the whole blood of critically ill patients to identify a gene signature that would allow clinicians to distinguish influenza infection from other causes of severe respiratory failure, such as bacterial pneumonia, and noninfective systemic inflammatory response syndrome.

METHODS

Whole-blood samples were collected from critically ill individuals and assayed on Illumina HT-12 gene-expression beadarrays. Differentially expressed genes were determined by linear mixed-model analysis and overrepresented biological pathways determined by using GeneGo MetaCore.

RESULTS

The gene-expression profile of H1N1 influenza A pneumonia was distinctly different from those of bacterial pneumonia and systemic inflammatory response syndrome. The influenza gene-expression profile is characterized by upregulation of genes from cell-cycle regulation, apoptosis, and DNA-damage-response pathways. In contrast, no distinctive gene-expression signature was found in patients with bacterial pneumonia or systemic inflammatory response syndrome. The gene-expression profile of influenza infection persisted through 5 days of follow-up. Furthermore, in patients with primary H1N1 influenza A infection in whom bacterial co-infection subsequently developed, the influenza gene-expression signature remained unaltered, despite the presence of a superimposed bacterial infection.

CONCLUSIONS

The whole-blood expression-profiling data indicate that the host response to influenza pneumonia is distinctly different from that caused by bacterial pathogens. This information may speed the identification of the cause of infection in patients presenting with severe respiratory failure, allowing appropriate patient care to be undertaken more rapidly.

Two years after pandemic influenza A/2009/H1N1: what have we learned?

The world had been anticipating another influenza pandemic since the last one in 1968. The pandemic influenza A H1N1 2009 virus (A/2009/H1N1) finally arrived, causing the first pandemic influenza of the new millennium, which has affected over 214 countries and caused over 18,449 deaths. Because of the persistent threat from the A/H5N1 virus since 1997 and the outbreak of the severe acute respiratory syndrome (SARS) coronavirus in 2003, medical and scientific communities have been more prepared in mindset and infrastructure. This preparedness has allowed for rapid and effective research on the epidemiological, clinical, pathological, immunological, virological, and other basic scientific aspects of the disease, with impacts on its control. A PubMed search using the keywords "pandemic influenza virus H1N1 2009" yielded over 2,500 publications, which markedly exceeded the number published on previous pandemics. Only representative works with relevance to clinical microbiology and infectious diseases are reviewed in this article. A significant increase in the understanding of this virus and the disease within such a short amount of time has allowed for the timely development of diagnostic tests, treatments, and preventive measures. These findings could prove useful for future randomized controlled clinical trials and the epidemiological control of future pandemics.

Evaluation of indirect fluorescent antibody assays compared to rapid influenza diagnostic tests for the detection of pandemic influenza A (H1N1) pdm09

Performance of indirect fluorescent antibody (IFA) assays and rapid influenza diagnostic tests (RIDT) during the 2009 H1N1 pandemic was evaluated, along with the relative effects of age and illness severity on test accuracy. Clinicians and laboratories submitted specimens on patients with respiratory illness to public health from April to mid October 2009 for polymerase chain reaction (PCR) testing as part of pandemic H1N1 surveillance efforts in Orange County, CA; IFA and RIDT were performed in clinical settings. Sensitivity and specificity for detection of the 2009 pandemic H1N1 strain, now officially named influenza A(H1N1)pdm09, were calculated for 638 specimens. Overall, approximately 30% of IFA tests and RIDTs tested by PCR were falsely negative (sensitivity 71% and 69%, respectively). Sensitivity of RIDT ranged from 45% to 84% depending on severity and age of patients. In hospitalized children, sensitivity of IFA (75%) was similar to RIDT (84%). Specificity of tests performed on hospitalized children was 94% for IFA and 80% for RIDT. Overall sensitivity of RIDT in this study was comparable to previously published studies on pandemic H1N1 influenza and sensitivity of IFA was similar to what has been reported in children for seasonal influenza. Both diagnostic tests produced a high number of false negatives and should not be used to rule out influenza infection.

Serologic assays for influenza surveillance, diagnosis and vaccine evaluation

Serological techniques play a critical role in various aspects of influenza surveillance, vaccine development and evaluation, and sometimes in diagnosis, particularly for novel influenza virus infections of humans. Because individuals are repeatedly exposed to antigenically and genetically diverse influenza viruses over a lifetime, the gold standard for detection of a recent influenza virus infection or response to current vaccination is the demonstration of a seroconversion, a fourfold or greater rise in antibody titer relative to a baseline sample, to a circulating influenza strain or vaccine component. The hemagglutination-inhibition assay remains the most widely used assay to detect strain-specific serum antibodies to influenza. The hemagglutination-inhibition assay is also used to monitor antigenic changes among influenza viruses which are constantly evolving; such antigenic data is essential for consideration of changes in influenza vaccine composition. The use of the hemagglutinin-specific microneutralization assay has increased, in part, owing to its sensitivity for detection of human antibodies to novel influenza viruses of animal origin. Neutralization assays using replication-incompetent pseudotyped particles may be advantageous in some laboratory settings for detection of antibodies to influenza viruses with heightened biocontainment requirements. The use of standardized protocols and antibody standards are important steps to improve reproducibility and interlaboratory comparability of results of serologic assays for influenza viruses.

Rethinking approaches to improve the utilization of nucleic acid amplification tests for detection and characterization of influenza A in diagnostic and reference laboratories

Influenza A virus (IFVA) is a significant cause of respiratory infections worldwide and was also responsible for a recent pandemic in 2009. Laboratory identification of IFVA can guide antiviral therapy, assist in cohorting of patients and prevent antibiotic use. Characterization of the virus can track the emergence of novel strains, identify resistance and determine how circulating strains match with vaccine components. The gold standard for detection and characterization of IFVA is nucleic acid amplification technology (e.g., reverse transcriptase PCR [RT-PCR]), which must contend with a constantly evolving viral genome. Although molecular technology has been available for over two decades, there is still an operational gap between assay design and utilization of these tests for the diagnosis and characterization of IFVA. This review will discuss issues surrounding the implementation and use of RT-PCR for the identification and characterization of IFVA, and speculate on why RT-PCR has not been used more widely in clinical laboratories or moved closer to the patient. Newer, less widely used technologies that may change our laboratory practices will be identified and the authors will close with an attempt to identify some future applications of RT-PCR-based technologies for the detection and characterization of IFVA.

Distinguishing characteristics between pandemic 2009-2010 influenza A (H1N1) and other viruses in patients hospitalized with respiratory illness

Background

Differences in clinical presentation and outcomes among patients infected with pandemic 2009 influenza A H1N1 (pH1N1) compared to other respiratory viruses have not been fully elucidated.

Methodology/Principal Findings

A retrospective study was performed of all hospitalized patients at the peak of the pH1N1 season in whom a single respiratory virus was detected by a molecular assay targeting 18 viruses/subtypes (RVP, Luminex xTAG). Fifty-two percent (615/1192) of patients from October, 2009 to December, 2009 had a single respiratory virus (291 pH1N1; 207 rhinovirus; 45 RSV A/B; 37 parainfluenza; 27 adenovirus; 6 coronavirus; and 2 metapneumovirus). No seasonal influenza A or B was detected. Individuals with pH1N1, compared to other viruses, were more likely to present with fever (92% & 70%), cough (92% & 86%), sore throat (32% & 16%), nausea (31% & 8%), vomiting (39% & 30%), abdominal pain (14% & 7%), and a lower white blood count (8,500/L & 13,600/L, all p-values<0.05). In patients with cough and gastrointestinal complaints, the presence of subjective fever/chills independently raised the likelihood of pH1N1 (OR 10). Fifty-five percent (336/615) of our cohort received antibacterial agents, 63% (385/615) received oseltamivir, and 41% (252/615) received steroids. The mortality rate of our cohort was 1% (7/615) and was higher in individuals with pH1N1 compared to other viruses (2.1% & 0.3%, respectively; p = 0.04).

Conclusions/Significance

During the peak pandemic 2009–2010 influenza season in Rhode Island, nearly half of patients admitted with influenza-like symptoms had respiratory viruses other than influenza A. A high proportion of patients were treated with antibiotics and pH1N1 infection had higher mortality compared to other respiratory viruses.

Evaluation study of a portable impedance biosensor for detection of avian influenza virus

Current methods for detection of avian influenza virus (AIV) based on virus culture and RT-PCR are well established, but they are either time consuming or require specialized laboratory facilities and highly trained technicians. A simple, rapid, robust, and reliable test, suitable for use in the field or at the patient's bedside, is urgently needed. In this study, the performance of a newly developed portable impedance biosensor was evaluated by comparison with real-time reverse transcriptase PCR (rRT-PCR) and virus culture for detection of AIV in tracheal and cloacal swab samples collected from experimentally H5N2 AIV infected chickens. The impedance biosensor system was based on a combination of magnetic nanobeads, which were coated with AIV subtype-specific antibody for capture (separation and concentration) of a target virus, and a microfluidic chip with an interdigitated array microelectrode for transfer and detection of target virus, and impedance measurement of the bio-nanobeads and AI virus complexes in a buffer solution. A comparison of results obtained from 59 swab samples using virus culture, impedance biosensor and rRT-PCR methods showed that the impedance biosensor technique was comparable in sensitivity and specificity to rRT-PCR. Detection time for the impedance biosensor is less than 1h.

Direct fluorescent-antibody testing followed by culture for diagnosis of 2009 H1N1 influenza A

During the 2009 H1N1 influenza A outbreak, 773 children were tested for influenza by direct fluorescent-antibody testing with PCR confirmation. Direct fluorescent-antibody testing has a specificity of 99.6% but a sensitivity of only 65.0%. Physicians should recognize diagnostic limitations of direct fluorescent-antibody testing, which missed one-third of infected individuals.

Complications and outcomes of pandemic 2009 Influenza A (H1N1) virus infection in hospitalized adults: how do they differ from those in seasonal influenza?

BACKGROUND

It is unclear whether pandemic 2009 influenza A (pH1N1) infection caused more significant disease among hospitalized adults than seasonal influenza.

METHODS

A prospective, observational study was conducted in adults hospitalized with polymerase chain reaction-confirmed pH1N1 infection in 2 acute-care general hospitals from June 2009 to May 2010 (n = 382). Complications and outcomes were described and compared with those in a seasonal influenza cohort (2007-2008, same hospitals; n = 754).

RESULTS

Hospitalized patients with pH1N1 influenza were younger than those with seasonal influenza (mean age ± standard deviation, 47 ± 20 vs 70 ± 19 years) and fewer had comorbid conditions (48% vs 64%). The rate of positive immunofluorescence assay results was low (54% vs 84%), and antiviral use was frequent (96% vs 52%). Most patients in both cohorts developed complicated illnesses (67.8% vs 77.1%), but patients with pH1N1 influenza had higher rates of extrapulmonary complications (23% vs 16%; P = .004) and intensive care unit admission and/or death (patient age <35 years, 2.3% vs 0%; 35-65 years, 12.4% vs 3.2%; >65 years, 13.5% vs 8.5%; adjusted odds ratio [OR] 2.13; 95% confidence interval [CI], 1.25-3.62; P = .005). Patients who received antiviral treatment within 96 h after onset had better survival (log-rank test, P < .001). However, without timely treatment, the mortality risk was higher with pH1N1 infection (9.0% vs 5.8% for seasonal influenza; adjusted OR, 6.85; 95% CI, 1.64-28.65; P = .008]. Bacterial superinfection worsened outcomes.

CONCLUSIONS

Adults hospitalized for pH1N1 influenza had significant complications and mortality despite being younger than patients with seasonal influenza. Antiviral treatment within 96 h may improve survival.

rapidSTRIPE H1N1 test for detection of the pandemic swine origin influenza A (H1N1) virus

The rapidSTRIPE H1N1 test, based on a nucleic acid lateral-flow assay, has been developed for diagnosis of a swine-origin influenza A (H1N1) virus. This test is simple and cost-effective and allows specific detection of the S-OIV A (H1N1) virus from swab sampling to final detection on a lateral-flow stripe within 2 to 3 h.

Detection of Cryptosporidium molnari oocysts from fish by fluorescent-antibody staining assays for cryptosporidium spp. affecting humans

Three direct fluorescent-antibody staining assay kits for the detection of zoonotic Cryptosporidium species were used to detect Cryptosporidium molnari from Murray cod, and the cryptosporidia were characterized by using small-subunit (SSU) ribosomal DNA (rDNA). To facilitate rapid diagnosis of infection, this study demonstrated that all three kits detected fresh C. molnari and two kits detected formalin-fixed oocysts.

Development of two types of rapid diagnostic test kits to detect the hemagglutinin or nucleoprotein of the swine-origin pandemic influenza A virus H1N1

Since its emergence in April 2009, pandemic influenza A virus H1N1 (H1N1 pdm), a new type of influenza A virus with a triple-reassortant genome, has spread throughout the world. Initial attempts to diagnose the infection in patients using immunochromatography (IC) relied on test kits developed for seasonal influenza A and B viruses, many of which proved significantly less sensitive to H1N1 pdm. Here, we prepared monoclonal antibodies that react with H1N1 pdm but not seasonal influenza A (H1N1 and H3N2) or B viruses. Using two of these antibodies, one recognizing viral hemagglutinin (HA) and the other recognizing nucleoprotein (NP), we developed kits for the specific detection of H1N1 pdm and tested them using clinical specimens of nasal wash fluid or nasopharyngeal fluid from patients with influenza-like illnesses. The specificities of both IC test kits were very high (93% for the HA kit, 100% for the NP kit). The test sensitivities for detection of H1N1 pdm were 85.5% with the anti-NP antibody, 49.4% with the anti-HA antibody, and 79.5% with a commercially available influenza A virus detection assay. Use of the anti-NP antibody could allow the rapid and accurate diagnosis of H1N1 pdm infections.

Advances in diagnosis of respiratory virus infections

The diagnosis of respiratory virus infections has evolved substantially in recent years, with the emergence of new pathogens and the development of novel detection methods. While recent advances have improved the sensitivity and turn-around time of diagnostic tests for respiratory viruses, they have also raised important issues such as cost, and the clinical significance of detecting multiple viruses in a single specimen by molecular methods. This article reviews recent advances in specimen collection and detection methods for diagnosis of respiratory virus infections, and discusses the performance characteristics and limitations of these methods.