Rapid Detection Of Respiratory Viruses Research Articles

Common viral respiratory infections in children with cancer during the COVID-19 pandemic: a multicenter study from Türkiye.

Microbiologic confirmation of respiratory tract infections gained importance during the coronavirus disease 2019 (COVID-19) pandemic. This study retrospectively evaluated seasonal distribution, clinical presentation, and complications of respiratory viral infections (RVIs) other than COVID-19 in children with cancer during and after the pandemic lockdown. Two hundred and sixty-five inpatient and outpatient RVI episodes in 219 pediatric cancer patients confirmed by multiplex reverse transcriptase polymerase chain reaction (RT-PCR) panels from 13 centers were enrolled. Eighty-six (32.5%) of the total 265 episodes occurred in 16 months corresponding to the lockdowns in Türkiye, and the remaining 67.5% in 10 months thereafter. Human rhinovirus/enterovirus (hRE) (48.3%) was the most common agent detected during and after lockdown. Parainfluenza virus (PIV) (23.0%), influenza virus (9.8%), and respiratory syncytial virus (RSV) (9.1%) were the other common agents. The 28.7% of episodes were lower respiratory tract infections (LRTIs), and complications and mortality were higher than upper respiratory tract infections (URTIs) (25.0% vs 5.3%). Bacteremia was identified in 11.5% of culture-drawn episodes. Treatment delay in one-third and death within four weeks after RVI in 4.9% of episodes were observed. During the pandemic, fewer episodes of RVIs occurred during the lockdown period. Respiratory viruses may cause complications, delays in treatment, and even death in children with cancer. Therefore, increased awareness of RVIs and rapid detection of respiratory viruses will benefit the prevention and, in some cases, abrupt supportive and some antiviral treatment of RVI in children with cancer.

Multichannel microfluidic virus sensor for rapid detection of respiratory viruses using virus-imprinted polymer for digital livestock farming

This paper reports a multichannel microfluidic sensor for detecting H1N1 swine influenza A virus (IAV). This device integrates six independent sensing elements, measurement chambers, and passive mixers on a microfluidic platform to enable parallel processing and analysis of multiple samples. The sensing element uses a conducting virus-imprinted polymer (VIP) to recognize, immobilize, and qualify the target H1N1 virus. The VIP is formed via electropolymerization of 2-amino-1,3,4-thiadiazole monomers and template H1N1 virus particles and subsequent removal of the template particles. The formed cavities are complementary to H1N1 virus in shape and size. High selectivity, conductance, and charge transfer characteristics make the VIP suitable for electrochemical detection of H1N1 virus. The sensor demonstrates a linear response to the logarithmic concentration of H1N1 virus in a concentration range of up to 5 × 106 TCID50/mL with a limit of detection of 9 TCID50/mL. The sensor exhibits high selectivity to H1N1 virus in the presence of several non-specific swine pathogens. Further, the sensor can be regenerated and reused by simply washing the sensing surface with acetic acid. The device demonstrates parallel detection of H1N1 virus in nasal swabs, oral fluids, and lung homogenates sampled from swine with low consumption of reagents and samples. Data AvailabilityData will be made available on request

Assay System for Simultaneous Detection of SARS-CoV-2 and Other Respiratory Viruses.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) triggers disease with nonspecific symptoms that overlap those of infections caused by other seasonal respiratory viruses (RVs), such as the influenza virus (Flu) or respiratory syncytial virus (RSV). A molecular assay for accurate and rapid detection of RV and SARS-CoV-2 is crucial to manage these infections. Here, we compared the analytical performance and clinical reliability of Allplex™ SARS-CoV-2/FluA/FluB/RSV (SC2FabR; Seegene Inc., Seoul, South Korea) kit with those of four commercially available RV detection kits. Upon testing five target viral strains (SARS-CoV-2, FluA, FluB, RSV A, and RSV B), the analytical performance of SC2FabR was similar to that of the other kits, with no significant difference (p ≥ 0.78) in z-scores. The efficiency of SC2FabR (E-value, 81–104%) enabled reliable SARS-CoV-2 and seasonal RV detection in 888 nasopharyngeal swab specimens processed using a fully automated nucleic acid extraction platform. Bland–Altman analyses revealed an agreement value of 95.4% (SD ± 1.96) for the kits, indicating statistically similar results for all five. In conclusion, SC2FabR is a rapid and accurate diagnostic tool for both SARS-CoV-2 and seasonal RV detection, allowing for high-throughput RV analysis with efficiency comparable to that of commercially available kits. This can be used to help manage respiratory infections in patients during and after the coronavirus disease 2019 pandemic.

A review and comparison of two commercial molecular methods for detection of respiratory viruses in a new tertiary hospital in Perth

Aim: To evaluate the test performance and clinical utility of the GeneXpert flu/RSV XC (GX) and Filmarray Respiratory panel (FRP) for the rapid detection of respiratory viruses.Methods: Between June and October 2015, samples were tested for influenza A, influenza B and RSV at PathWest FSH using GX, FRP and our routine method (RM), an in-house real-time multiplex PCR performed at Pathwest QEII laboratory. Sensitivity and specificity for the GX and FRP was compared to RM. In addition mean test turnaround time (MTT) was determined for GX and RM.Results: GX tested samples (n=54) demonstrated a 95% sensitivity and 100% specificity with a MTT of 3.66 h [interquartile range (IQR)=2.42–10.02 h) compared to 66.21 h (IQR=47.83–93.96 h) (p≤0.001) for RM. FRP (n=34) demonstrated a 92.86% sensitivity and 100% specificity compared to RM. MTT was not assessed for FRP. RM and FRP were able to detect additional respiratory pathogens.Conclusion: The sensitivity and specificity of both commercial methods were similar. The MTT for GX was significantly shorter than RM. FRP and RM have the advantage of detecting a broader range of pathogens than the GX. Cost effectiveness should be assessed and these tests may provide improved outcome for patients in our hospital. Aim: To evaluate the test performance and clinical utility of the GeneXpert flu/RSV XC (GX) and Filmarray Respiratory panel (FRP) for the rapid detection of respiratory viruses. Methods: Between June and October 2015, samples were tested for influenza A, influenza B and RSV at PathWest FSH using GX, FRP and our routine method (RM), an in-house real-time multiplex PCR performed at Pathwest QEII laboratory. Sensitivity and specificity for the GX and FRP was compared to RM. In addition mean test turnaround time (MTT) was determined for GX and RM. Results: GX tested samples (n=54) demonstrated a 95% sensitivity and 100% specificity with a MTT of 3.66 h [interquartile range (IQR)=2.42–10.02 h) compared to 66.21 h (IQR=47.83–93.96 h) (p≤0.001) for RM. FRP (n=34) demonstrated a 92.86% sensitivity and 100% specificity compared to RM. MTT was not assessed for FRP. RM and FRP were able to detect additional respiratory pathogens. Conclusion: The sensitivity and specificity of both commercial methods were similar. The MTT for GX was significantly shorter than RM. FRP and RM have the advantage of detecting a broader range of pathogens than the GX. Cost effectiveness should be assessed and these tests may provide improved outcome for patients in our hospital.

FilmArray® respiratory panel performance in respiratory samples from neonatal care units

FilmArray Respiratory Panel (RP) (Idaho Technology, Inc., Salt Lake City, UT, USA) performance was retrospectively evaluated in respiratory samples collected from neonates in 2 reference neonatology units. Using the FilmArray RP assay, 121/152 (79.6%) samples were positive for at least 1 respiratory virus, while 31/152 (20.4%) were negative. FilmArray RP results were concordant in 68/72 (94.4%) respiratory samples tested with laboratory-developed real-time PCR assays, while in 4/72 (5.6%) samples, the FilmArray RP assay detected an additional virus (2 human rhinovirus/enterovirus and 2 bocavirus). In addition, FilmArray RP results for 70 of 80 (87.5%) respiratory samples tested were concordant with the Seegene Seeplex RV15® detection assay (Seegene, Inc., Seoul, South Korea), while 10/80 (12.5%) were discordant. The advantages of the FilmArray RP are the rapid detection of respiratory viruses (1 hour), the wide number of pathogens detectable in a single assay, and the reduced hands-on time.

Reverse transcription polymerase chain reaction and electrospray ionization mass spectrometry for identifying acute viral upper respiratory tract infections

Diagnosis of respiratory viruses traditionally relies on culture or antigen detection. We aimed to demonstrate capacity of the reverse transcription polymerase chain reaction/electrospray ionization mass spectrometry (RT-PCR/ESI-MS) platform to identify clinical relevant respiratory viruses in nasopharyngeal aspirate (NPA) samples and compare the diagnostic performance characteristics relative to conventional culture- and antigen-based methods. An RT-PCR/ESI-MS respiratory virus surveillance kit designed to detect respiratory syncytial virus, influenza A and B, parainfluenza types 1–4, Adenoviridae types A–F, Coronaviridae, human bocavirus, and human metapneumovirus was evaluated using both mock-ups and frozen archived NPA ( N = 280), 95 of which were positive by clinical virology methods. RT-PCR/ESI-MS detected 74/95 (77.9%) known positive samples and identified an additional 13/185 (7%) from culture-negative samples. Viruses that are nondetectable with conventional methods were also identified. Viral load was semiquantifiable and ranged from 2400 to >320 000 copies/mL. Time to results was 8 h. RT-PCR/ESI-MS showed promise in rapid detection of respiratory viruses and merits further evaluation for use in clinical settings.

Detection of Avian Influenza Virus of H9 Subtype in the Faeces of Experimentally and Naturally Infected Chickens by Reverse Transcription-Polymerase Chain Reaction

Avian Influenza (AI) is a viral, highly contagious disease of domestic and wild birds. In an avian diagnostic laboratory, it is essential to have methods for rapid detection of respiratory viruses. In the present study, cloacal swabs collected from chickens experimentally and naturally infected with mild pathogenicity AI virus subtype H9, used in a reverse transcription-polymerase chain reaction (RTPCR) assay for detection of AI. On cloacal swabs collected from experimentally infected chickens, AI virus was detected most frequently between days 3 and 7 post infection (p.i.) and the relative sensitivity, specificity, correlation rate, positive predictive value and negative predictive value of the RT-PCR compared to virus isolation (VI) assay were 84%, 80%, 82%, 83% and 81%, respectively. On pooled cloacal swabs collected from flocks suspected of AI, these results were 96%, 100%, 97%, 83% and 100%, respectively. The results proved that the RT-PCR assay could be a reliable and rapid alternative to VI assay for detection of AI virus subtype H9 in faecal specimens.

Use of monoclonal antibodies for rapid diagnosis of respiratory viruses in a community hospital.

An indirect fluorescence antibody (IFA) procedure was used for the rapid detection of respiratory viruses in direct clinical specimens and for determining the epidemiology of viruses in a community hospital setting. Viral respiratory diseases were monitored for 10 consecutive respiratory seasons. The Bartels Viral Respiratory Screening and Identification Kit is an IFA method that contains pooled and individual monoclonal antibodies for seven common respiratory viruses. Compared with 8,670 conventional tube cell cultures, IFA staining of direct patient specimens had an overall sensitivity of 84.2% and a specificity of 87.7%. Yearly epidemics of respiratory syncytial virus were seen with alternating short and long intervals between successive periods when virus was isolated. Epidemics following short intervals were more severe. Influenza A virus epidemics occurred yearly, and influenza B virus activity was seen generally every other year. When influenza A and influenza B viruses were cocirculating in a given season, the months of peak activity of one virus were always within 1 month of the peak activity of the other virus. Parainfluenza virus type 1 was detected in the autumn of odd-numbered years, and parainfluenza type 2 virus was seen usually in the autumn of even-numbered years. Parainfluenza type 3 virus and adenovirus were the most ubiquitous agents, with peak incidence occurring in the late winter to spring.

Rapid detection of respiratory viruses by centrifugation enhanced cultures from children with acute lower respiratory tract infections.

Acute respiratory tract infection (ARI) is the major cause of morbidity and mortality in young children in developing countries. Information on viral aetiology in ARI in India is very limited. The aim of the study was to define the role of viruses in acute lower respiratory tract infections (ALRTI) in children in India using centrifugation enhanced cultures followed by indirect immunofluorescence (IIF). Nasopharyngeal aspirates (NPAs) were collected from children from September 1995 to April 1997, attending paediatric clinic of All India Institute of Medical Sciences (AIIMS) with symptoms of ALRTI. Virus isolation was done by centrifugation enhanced cultures using HEp-2, LLC-MK2 and MDCK cells. The viruses were identified at 24-48 h post inoculation by IIF staining using monoclonal antibodies to respiratory syncytial virus (RSV), parainfluenza virus (PIV), influenza virus and adenovirus. Of 200 NPA samples, 89 (44.5%) were positive for one or more viral pathogens. RSV was detected in 34 (17%) of all ALRTI cases followed by influenza viruses in 29 (14.5%), PIVs in 23 (11.5%) and adenoviruses in three (1.5%). In 79 children with bronchiolitis, RSV was most frequently isolated (25%) pathogen, while in bronchopneumonia cases (101) the most common viral pathogen was influenza virus (17%). In eight cases (4%) of ALRTI dual infections were detected. In 100 NPA specimens IIF staining on direct cell smears was carried out and viruses were detected in only 17%. RSV and influenza virus infection peaked from September to December, where as PIV infections were more frequent from January to April. Respiratory viruses accounted for 44.5% of cases of ALRTI in India and the results of viral aetiology could be given in 24-48 h using centrifugation enhanced cultures. RSV was the most common viral agent associated with ALRTI in children under 5 years of age with greater association with bronchiolitis.

Rapid Detection of Respiratory Viruses by Shell Vial Assay Using Simultaneous Culture of HEp-2, LLC-MK2, and MDCK Cells in a Single Vial

Rapid Detection of Respiratory Viruses by Shell Vial Assay Using Simultaneous Culture of HEp-2, LLC-MK2, and MDCK Cells in a Single Vial

Rapid detection of respiratory viruses by shell vial assay using simultaneous culture of HEp-2, LLC-MK2, and MDCK cells in a single vial.

A shell vial assay with simultaneous culture of HEp-2, LLC-MK2, and MDCK cell lines in a single tube (CoHLM SV assay) was compared with traditional tube culture (TC) for the detection of the main respiratory viruses in 358 nasal wash specimens. A total of 170 strains were isolated from 168 virus-positive samples. A total of 94. 1% of the strains (160 strains; 128 respiratory syncytial viruses and 32 other viruses) were detected by the CoHLM SV assay in 48 h, whereas 98.2% of the strains (167 strains; 132 respiratory syncytial viruses and 35 other viruses) were detected by TC in a mean time of 6 days. The CoHLM SV assay may be useful for the rapid detection of respiratory viruses.

Rapid detection of respiratory viruses using mixtures of monoclonal antibodies on shell vial cultures.

Eleven hundred and thirty-three clinical specimens submitted to the laboratory for diagnosis of respiratory virus infections were tested by direct immunofluorescence (DIF) for respiratory syncytial virus (RSV), by shell vial culture, and by conventional cell culture. The shell vial cultures were stained with 8 different monoclonal antibodies both 1 day and 3-7 days after inoculation. In order to limit the cost and the workload, mixtures of monoclonal antibodies were used. Coverslips with HEp-2 cells were incubated with a mixture of FITC-labeled monoclonal antibody to RSV and nonlabeled monoclonal antibody to adenovirus. When no RSV positive IF staining was observed after the first incubation step, the same coverslip was incubated once more with FITC-labeled anti-mouse antibody. A positive reaction at this stage indicated the presence of adenovirus. Similarly, cultures of tertiary monkey kidney cells were investigated with a mixture of two FITC-labeled monoclonals to the influenza viruses A and B and three nonlabeled monoclonals to the parainfluenza viruses 1, 2 and 3. If influenza virus or parainfluenza virus was detected, the exact type was determined by staining different parts of a duplicate coverslip. Shell vial cultures for cytomegalovirus (CMV) were always performed separately on human embryonic lung fibroblasts. Using this approach, we detected RSV (n = 248), CMV (n = 42), parainfluenza virus (n = 31), influenza virus (n = 28), and adenovirus (n = 6), in most cases after only one day of culture. For RSV, the sensitivity of the shell vial method was too low (74%) to allow omission of DIF (sensitivity 95%).(ABSTRACT TRUNCATED AT 250 WORDS)

Detection of respiratory syncytial, parainfluenza type 2, and adenovirus antigens by radioimmunoassay and enzyme immunoassay on nasopharyngeal specimens from children with acute respiratory disease.

Four-layer antispecies radioimmunoassay (RIA) and enzyme immunoassay (EIA) procedures were developed for the detection of respiratory syncytial virus (RSV), parainfluenza type 2 virus, and adenovirus antigens in nasopharyngeal specimens from children hospitalized for acute respiratory disease. Polystyrene beads (RIA) or flat-bottomed polystyrene microtiter plates (EIA) were used as the solid phases, guinea pig anti-virus immunoglobulins were used as the captive antibodies, rabbit anti-virus immunoglobulins were used as the secondary antibodies, and 125I-labeled sheep anti-rabbit (RIA) or horseradish peroxidase-labeled swine anti-rabbit (EIA) immunoglobulins were used as the indicator antibodies. A comparison of the EIAs and RIAs with routinely used immunofluorescence (IF) techniques was made with 164 nasopharyngeal specimens collected from children with acute respiratory disease. Only 3 of 66 RSV IF-positive specimens were negative in RSV RIA, and of 83 RSV, parainfluenza type 2 virus, and adenovirus IF-negative specimens, 1 was positive in RSV RIA. Of 4 parainfluenza type 2 virus IF-positive and 11 adenovirus IF-positive specimens, each was positive in corresponding RIAs, and all 83 IF-negative specimens were negative in parainfluenza type 2 virus and adenovirus RIAs. The results of the RSV, parainfluenza type 2, and adenovirus EIAs confirmed the results of corresponding RIAs in each selected case tested. The RIAs and EIAs were found to be as specific and sensitive as IF techniques, and more practical in the rapid detection of respiratory viruses in nasopharyngeal secretions.