Rapid detection of respiratory tract viral infections and coinfections in patients with influenza-like illnesses by use of reverse transcription-PCR DNA microarray systems

Multiplexed detection of eight respiratory viruses based on nanozyme colorimetric microfluidic immunoassay

Pandemics caused by respiratory viruses, such as the SARS-CoV-1/2, influenza virus, and respiratory syncytial virus, have resulted in serious consequences to humans and a large number of deaths. The detection of such respiratory viruses in the early stages of infection can help control diseases by preventing the spread of viruses. However, the diversity of respiratory virus species and subtypes, their rapid antigenic mutations, and the limited viral release during the early stages of infection pose challenges to their detection. This work reports a multiplexed microfluidic immunoassay chip for simultaneous detection of eight respiratory viruses with noticeable infection population, namely, influenza A virus, influenza B virus, respiratory syncytial virus, SARS-CoV-2, human bocavirus, human metapneumovirus, adenovirus, and human parainfluenza viruses. The nanomaterial of the nanozyme (Au@Pt nanoparticles) was optimized to improve labeling efficiency and enhance the detection sensitivity significantly. Nanozyme-binding antibodies were used to detect viral proteins with a limit of detection of 0.1 pg/mL with the naked eye and a microplate reader within 40 min. Furthermore, specific antibodies were screened against the conserved proteins of each virus in the immunoassay, and the clinical sample detection showed high specificity without cross reactivity among the eight pathogens. In addition, the microfluidic chip immunoassay showed high accuracy, as compared with the RT-PCR assay for clinical sample detection, with 97.2%/94.3% positive/negative coincidence rates. This proposed approach thus provides a convenient, rapid, and sensitive method for simultaneous detection of eight respiratory viruses, which is meaningful for the early diagnosis of viral infections. Significantly, it can be widely used to detect pathogens and biomarkers by replacing only the antigen-specific antibodies.

ADLM Guidance Document on Laboratory Diagnosis of Respiratory Viruses

Respiratory viral infections are among the most frequent infections experienced worldwide. The COVID-19 pandemic has highlighted the need for testing and currently several tests are available for the detection of a wide range of viruses. These tests vary widely in terms of the number of viral pathogens included, viral markers targeted, regulatory status, and turnaround time to results, as well as their analytical and clinical performance. Given these many variables, selection and interpretation of testing requires thoughtful consideration. The current guidance document is the authors' expert opinion based on the preponderance of available evidence to address key questions related to best practices for laboratory diagnosis of respiratory viral infections including who to test, when to test, and what tests to use. An algorithm is proposed to help laboratories decide on the most appropriate tests to use for the diagnosis of respiratory viral infections.

Targeted metagenomics reveals association between severity and pathogen co-detection in infants with respiratory syncytial virus

Respiratory syncytial virus (RSV) is the leading cause of hospitalisation for respiratory infection in young children. RSV disease severity is known to be age-dependent and highest in young infants, but other correlates of severity, particularly the presence of additional respiratory pathogens, are less well understood. In this study, nasopharyngeal swabs were collected from two cohorts of RSV-positive infants <12 months in Spain, the UK, and the Netherlands during 2017-20. We show, using targeted metagenomic sequencing of >100 pathogens, including all common respiratory viruses and bacteria, from samples collected from 433 infants, that burden of additional viruses is common (111/433, 26%) but only modestly correlates with RSV disease severity. In contrast, there is strong evidence in both cohorts and across age groups that presence of Haemophilus bacteria (194/433, 45%) is associated with higher severity, including much higher rates of hospitalisation (odds ratio 4.25, 95% CI 2.03-9.31). There is no evidence for association between higher severity and other detected bacteria, and no difference in severity between RSV genotypes. Our findings reveal the genomic diversity of additional pathogens during RSV infection in infants, and provide an evidence base for future causal investigations of the impact of co-infection on RSV disease severity.

Expanded PCR Panel Testing for Identification of Respiratory Pathogens and Coinfections in Influenza-like Illness

While COVID-19 has dominated Influenza-like illness (ILI) over the past few years, there are many other pathogens responsible for ILI. It is not uncommon to have coinfections with multiple pathogens in patients with ILI. The goal of this study was to identify the different organisms in symptomatic patients presenting with ILI using two different high throughput multiplex real time PCR platforms. Specimens were collected from 381 subjects presenting with ILI symptoms. All samples (nasal and nasopharyngeal swabs) were simultaneously tested on two expanded panel PCR platforms: Applied Biosystems™ TrueMark™ Respiratory Panel 2.0, OpenArray™ plate (OA) (32 viral and bacterial targets); and Applied Biosystems™ TrueMark™ Respiratory Panel 2.0, TaqMan™ Array card (TAC) (41 viral, fungal, and bacterial targets). Results were analyzed for concordance between the platforms and for identification of organisms responsible for the clinical presentation including possible coinfections. Very good agreement was observed between the two PCR platforms with 100% agreement for 12 viral and 3 bacterial pathogens. Of 381 specimens, approximately 58% of the samples showed the presence of at least one organism with an important incidence of co-infections (~36-40% of positive samples tested positive for two and more organisms). S. aureus was the most prevalent detected pathogen (~30%) followed by SARS-CoV-2 (~25%), Rhinovirus (~15%) and HHV6 (~10%). Co-infections between viruses and bacteria were the most common (~69%), followed by viral-viral (~23%) and bacterial-bacterial (~7%) co-infections. These results showed that coinfections are common in RTIs suggesting that syndromic panel based multiplex PCR tests could enable the identification of pathogens contributing to coinfections, help guide patient management thereby improving clinical outcomes and supporting antimicrobial stewardship.

Optical reflectometric measurement of SARS-CoV-2 (COVID-19) RNA based on cationic cysteamine-capped gold nanoparticles

The coronavirus disease (COVID-19) caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) emerged as a major public health outbreak in late 2019 and was proclaimed a global pandemic in March 2020. A reflectometric-based RNA biosensor was developed by using cysteamine-stabilized gold nanoparticles (cysAuNPs) as the colorimetric probe for bioassay of COVID-19 RNA (SARS-CoV-2 RNA) sequence. The cysAuNPs aggregated in the presence of DNA probes via cationic and anionic electrostatic attraction between the positively charged cysteamine ligands and the negatively charged sugar-phosphate backbone of DNA, whilst in the presence of target RNAs, the specific recognition between DNA probes and targets depleted the electrostatic interaction between the DNA probes and cysAuNPs signal probe, leading to dispersed particles. This has rendered a remarkable shifting in the surface plasmon resonance (SPR) on the basis of visual color change of the RNA biosensor from red to purplish hue at the wavelength of 765 nm. Optical evaluation of SARS-CoV-2 RNA by means on reflectance transduction of the RNA biosensor based on cysAuNPs optical sensing probes demonstrated rapid response time of 30 min with high sensitivity, good linearity and high reproducibility across a COVID-19 RNA concentration range of 25 nM to 200 nM, and limit of detection (LOD) at 0.12 nM. qPCR amplification of SARS-CoV-2 viral RNA showed good agreement with the proposed RNA biosensor by using spiked RNA samples of the oropharyngeal swab from COVID-19 patients. Therefore, this assay is useful for rapid and early diagnosis of COVID-19 disease including asymptomatic carriers with low viral load even in the presence of co-infection with other viruses that manifest similar respiratory symptoms.

International Olympic Committee (IOC) consensus statement on acute respiratory illness in athletes part 1: acute respiratory infections

Acute illnesses affecting the respiratory tract are common and form a significant component of the work of Sport and Exercise Medicine (SEM) clinicians. Acute respiratory illness (ARill) can broadly be classified as non-infective ARill and acute respiratory infections (ARinf). The aim of this consensus is to provide the SEM clinician with an overview and practical clinical approach to ARinf in athletes. The International Olympic Committee (IOC) Medical and Scientific Commission appointed an international consensus group to review ARill (non-infective ARill and ARinf) in athletes. Six subgroups of the IOC Consensus group were initially established to review the following key areas of ARill in athletes: (1) epidemiology/risk factors for ARill, (2) ARinf, (3) non-infective ARill including ARill due to environmental exposure, (4) acute asthma and related conditions, (5) effects of ARill on exercise/sports performance, medical complications/return-to-sport and (6) acute nasal/vocal cord dysfunction presenting as ARill. Several systematic and narrative reviews were conducted by IOC consensus subgroups, and these then formed the basis of sections in the consensus documents. Drafting and internal review of sections were allocated to 'core' members of the consensus group, and an advanced draft of the consensus document was discussed during a meeting of the main consensus core group in Lausanne, Switzerland on 11 to 12 October 2021. Final edits were completed after the meeting. This consensus document (part 1) focusses on ARinf, which accounts for the majority of ARill in athletes. The first section of this consensus proposes a set of definitions and classifications of ARinf in athletes to standardise future data collection and reporting. The remainder of the consensus paper examines a wide range of clinical considerations related to ARinf in athletes: epidemiology, risk factors, pathology/pathophysiology, clinical presentation and diagnosis, management, prevention, medical considerations, risks of infection during exercise, effects of infection on exercise/sports performance and return-to-sport guidelines.

Viral etiology of acute respiratory infections during 2014–16 in Riyadh, Saudi Arabia

Aim: Viral etiology of respiratory infections is not well understood in Saudi Arabia. This study was conceptualized to understand viral etiology in children with acute respiratory tract infections (ARTI) from Riyadh. Patients and methods: Respiratory viruses were detected by real-time PCR in nasopharyngeal aspirates or swab from 580 children aged ≤5 years. Results: Respiratory viruses were detected in 64% of the samples with 6% mixed viral infections. Respiratory syncytial virus, adenovirus, influenza, parainfluenza and human metapneumovirus infections accounted for 42, 20, 16, 12 and 10%, respectively. Maximum prevalence (37%) was among the lowest age group followed by 30% among the 7- to 12-month age group. Conclusion: The prevalence and determinants of viral etiology are in line with the previous report from the region. No major shift in the viral etiologies was observed in the 2-year study period.

Microfluidic-based approaches for COVID-19 diagnosis

Novel coronavirus, COVID-19, erupted in Wuhan, China, in 2019 and has now spread to almost all countries in the world. Until the end of November 2020, there were over 50 × 10⁶ people diagnosed with COVID-19 worldwide and it caused at least 1 × 10⁶ deaths. These numbers are still increasing. To control the spread of the pandemic and to choose a suitable treatment plan, a fast, accurate, effective, and ready-to-use diagnostic method has become an important prerequisite. In this Review, we introduce the principles of multiple off-site and on-site detection methods for virus diagnosis, including qPCR-based, ELISA-based, CRISPR-based methods, etc. All of these methods have been successfully implanted on the microfluidic platform for rapid screening. We also summarize currently available diagnostic methods for the detection of SARS, MERS, and COVID-19. Some of them not only can be used to analyze the SARS and MERS but also have the potential for COVID-19 detection after modifications. Finally, we hope that understanding of current microfluidic-based detection approaches can help physicians and researchers to develop advanced, rapid, and appropriate clinical detection techniques that reduce the financial expenditure of the society, accelerate the examination process, increase the accuracy of diagnosis, and eventually suppress the worldwide pandemic.

Respiratory viruses in pediatric emergency department patients and their family members

Background

Respiratory viral infections account for a substantial fraction of pediatric emergency department (ED) visits. We examined the epidemiological patterns of seven common respiratory viruses in children presenting to EDs with influenza‐like illness (ILI). Additionally, we examined the co‐occurrence of viral infections in the accompanying adults and risk factors associated with the acquisition of these viruses.

Methods

Nasopharyngeal swab were collected from children seeking medical care for ILI and their accompanying adults (Total N = 1315). Study sites included New York Presbyterian, Bellevue, and Tisch hospitals in New York City. PCR using a respiratory viral panel was conducted, and data on symptoms and medical history were collected.

Results

Respiratory viruses were detected in 399 children (62.25%) and 118 (17.5%) accompanying adults. The most frequent pathogen detected was human rhinovirus (HRV) (28.81%). Co‐infection rates were 14.79% in children and 8.47% in adults. Respiratory syncytial virus (RSV) and parainfluenza infections occurred more often in younger children. Influenza and HRV occurred more often in older children. Influenza and coronavirus were mostly isolated in winter and spring, RSV in fall and winter and HRV in fall and spring. Children with HRV were more likely to have history of asthma. Adults with the same virus as their child often accompanied ≤ 2‐year‐old‐positive children and were more likely to be symptomatic compared to adults with different viruses.

Conclusions

Respiratory viruses, while presenting the same suite of symptoms, possess distinct seasonal cycles and affect individuals differently based on a number of identifiable factors, including age and history of asthma.

Influenza-like illness is associated with high pneumococcal carriage density in Malawian children

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Influenza-like illness (ILI) in children is associated with high pneumococcal carriage density.

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Children with ILI harboured more viral organisms than asymptomatic healthy children.

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Children with ILI patients had higher IL-8 levels in nasal aspirates than asymptomatic healthy children.

Background

High pneumococcal carriage density is a risk factor for invasive pneumococcal disease (IPD) and transmission, but factors that increase pneumococcal carriage density are still unclear.

Methods

We undertook a cross-sectional study to evaluate the microbial composition, cytokine levels and pneumococcal carriage densities in samples from children presenting with an influenza-like illness (ILI) and asymptomatic healthy controls (HC).

Results

The proportion of children harbouring viral organisms (Relative risk (RR) 1.4, p = 0.0222) or ≥ 4 microbes at a time (RR 1.9, p < 0.0001), was higher in ILI patients than HC. ILI patients had higher IL-8 levels in nasal aspirates than HC (median [IQR], 265.7 [0 – 452.3] vs. 0 [0 – 127.3] pg/ml; p = 0.0154). Having an ILI was associated with higher pneumococcal carriage densities compared to HC (RR 4.2, p < 0.0001).

Conclusion

These findings suggest that children with an ILI have an increased propensity for high pneumococcal carriage density. This could in part contribute to increased susceptibility to IPD and transmission in the community.

Systematic Review of the Respiratory Syncytial Virus (RSV) Prevalence, Genotype Distribution, and Seasonality in Children from the Middle East and North Africa (MENA) Region

Respiratory syncytial virus (RSV) is one of the most common viruses to infect children worldwide and is the leading cause of lower respiratory tract illness (LRI) in infants. This study aimed to conduct a systematic review by collecting and reviewing all the published knowledge about the epidemiology of RSV in the Middle East and North Africa (MENA) region. Therefore, we systematically searched four databases; Embase, Medline, Scopus, and Cochrane databases from 2001 to 2019 to collect all the information related to the RSV prevalence, genotype distribution, and seasonality in children in MENA region. Our search strategy identified 598 studies, of which 83 met our inclusion criteria, which cover the past 19 years (2000–2019). Odds ratio (OR) and confidence interval (CI) were calculated to measure the association between RSV prevalence, gender, and age distribution. An overall prevalence of 24.4% (n = 17,106/69,981) of respiratory infections was recorded for RSV. The highest RSV prevalence was reported in Jordan (64%, during 2006–2007) and Israel (56%, 2005–2006). RSV A subgroup was more prevalent (62.9%; OR = 2.9, 95%CI = 2.64–3.13) than RSV B. RSV was most prevalent in children who were less than 12 months old (68.6%; OR = 4.7, 95%CI = 2.6–8.6) and was higher in males (59.6%; OR = 2.17, 95%CI = 1.2–3.8) than in female infants. Finally, the highest prevalence was recorded during winter seasons in all countries, except for Pakistan. RSV prevalence in the MENA region is comparable with the global one (24.4% vs. 22%). This first comprehensive report about RSV prevalence in the MENA region and our data should be important to guide vaccine introduction decisions and future evaluation.

Is multiple viral infection a predictor of severity in children with acute bronchiolitis?

Background:

Acute bronchiolitis is a common cause of pediatric emergency department admissions in children younger than 2.

Objectives:

The study aimed to compare the outcomes and the severity of bronchiolitis in young children with multiple simultaneous respiratory virus infections to those with single virus infection and no virus identified group.

Methods:

Patients with moderate and severe bronchiolitis who visited our emergency department between November 2016 and May 2017 had nasopharyngeal swab samples results tested by multiplex polymerase chain reaction were included in the study. Patients’ characteristics, clinical severity of illness, and outcome (pediatric emergency department discharge, admission to ward or pediatric intensive care unit) were compared with the detected viral agents.

Results:

A total of 241 patients were included in the study. The mean age was 7.8 ± 2.6 months and 147 (61%) were male. Respiratory syncytial virus was the most common detected viral agent in 108 (39%) cases followed by human rhinoviruses in 67 (24%). Respiratory syncytial virus was found more frequently in February and March (p = 0.002). Leukocytosis and pneumonia were more likely observed in patients with only human rhinoviruses (+) subjects (p = 0.010 and p = 0.015, respectively). Intensive care hospitalization rate (16%) was higher in patients with multiple viral agents (p = 0.004).

Conclusions:

Respiratory syncytial virus remains the most common detected viral agent in acute bronchiolitis patients. While the pathogens detected were seasonally different, there was a significant relationship between leukocytosis, bacterial pneumonia, and detected viral agents. The disease was more severe in patients with multiple viral agents.

Unreliable usage of a single influenza virus IgM antibody assay in influenza-like illness: A retrospective study of the 2016-2018 flu epidemic

We retrospectively analyzed serum IgM antibodies (Abs) to influenza viruses from two tertiary hospitals in Beijing from December 2016 to February 2018. Samples from 36,792 patients, aged 0–98 years, were collected and tested. Among the patients, 923 children from two winter flu seasons were assayed with both antigens and IgM Abs to Flu A and Flu B and assigned as paired groups. Another 2,340 adults and 1,978 children with only antigen tested in the 2016 and 2017 winter flu seasons were named as unpaired groups. IgM Abs-positivity rates in children were 0.80% and 36.57% for Flu A and Flu B, respectively, peaking at 4–5 years of age. For adults, the Flu A and Flu B IgM Abs-positivity rates were 10.34% and 21.49%, respectively, peaking at 18–35 years of age. The trend of temporal distribution between the children and the adults was significantly correlated for IgM Abs to Flu B, but not for Flu A. Compared with unpaired groups, the detection rate of Flu A antigen was significantly higher than IgM Abs in children, whereas frequencies of IgM Abs were higher than antigen in adults. Incidence of Flu B antigen was sharply increased in 2017 winter than in the 2016 winter in both children and adults, but no concomitant increase was observed in IgM Abs to Flu B. For paired children groups, incidence of Flu B antigen in the 2017 flu season was significantly higher than that in the 2016 flu season; in contrast, positive rates of IgM Abs in the 2017 flu season were even lower than those in 2016. Considering antigen detection may reflect the Flu A/Flu B epidemic, our results indicate single-assayed IgM Abs were less effective in the diagnosis of acute influenza virus infection, and the use of this assay for epidemiology evaluations was not supported by these findings.

Clinical characteristics and viral etiologies of outpatients with acute respiratory infections in Huzhou of China: a retrospective study

BACKGROUND

Viruses are commonly found in patients with acute respiratory infections (ARIs). However, the viral etiologies and clinical characteristics of outpatients with ARIs are poorly understood in China. Here, we identified the viral etiologies in outpatients with ARIs in Huzhou, China.

RESULTS

Our results indicated that of 426 outpatients, 246 were positive for viruses. Of them, 221 were positive for a single virus, including influenza A, which comprised H3N2 (28.5%) and pandemic H1N1 (2009) (19.0%), enterovirus (10.4%), and influenza B (8.6%). Other single viruses were detected at less than 8.0%. Twenty-five patients were positively coinfected with two viruses. The prevalent viruses in coinfections were rhinovirus and H3N2 virus (28.0%). Viruses were major pathogens in young children (< 5 years) (75.0%). Coinfections were prevalent in older adults (11.9%) and young children (9.5%). Virus-positive outpatients presented higher temperatures and more sore throat, fatigue and shortness of breath than virus-negative outpatients. ARIs and most virus detections peaked during the winter, but enteroviruses emerged between April and September.

CONCLUSION

Viruses are major agents of ARIs among outpatients in Huzhou, China. There was a variation in the distribution of viruses across different age groups and seasons. These findings are beneficial for planning prevention and treatment services for outpatients with ARIs.

Influenza-like illness in healthcare personnel at a paediatric referral hospital: Clinical picture and impact of the disease

INTRODUCTION

Healthcare personnel (HP) are frequently exposed to influenza and can be a source of transmission to patients and other workers, resulting in high-cost outbreaks for healthcare institutions.

OBJECTIVES

To analyse the presentation of HP with influenza-like illness (ILI) and the differences between individuals with influenza confirmed by polymerase chain reaction (PCR) and those with a negative test. The secondary objective was to evaluate the duration of symptomatology and work absenteeism as well as the vaccination rate of HP at a paediatric referral hospital.

METHODS

A cross-sectional, descriptive study was conducted at a paediatric referral hospital. Clinical and epidemiological data on HP with ILI were collected between January and April 2016. Nasopharyngeal swab for influenza PCR was obtained from one in every three workers with ILI. Telephone follow-up was conducted to document duration of symptoms, complications and absenteeism.

RESULTS

A total of 164 ILI episodes were evaluated in 162 HP. A swab was obtained in 59 cases, and influenza was detected in 30 cases. The clinical picture of HP with confirmed influenza was similar to that of HP with a negative PCR. Arthralgia was more common in those with influenza (90% vs 58%), with a tendency towards statistical significance. No HP required hospitalization, and 78.5% were absent from work at least 1 day.

CONCLUSIONS

Influenza causes significant morbidity and absenteeism among HP. Influenza infection was confirmed in only half of HP with an ILI on whom a PCR was performed, suggesting that other respiratory viruses can cause a similar pattern.

Viruses causing severe acute respiratory infections (SARI) in children ≤5 years of age at a tertiary care hospital in Rajasthan, India

BACKGROUND & OBJECTIVES

Severe acute respiratory infection (SARI) is one of the leading causes of death among children worldwide. As different respiratory viruses exhibit similar symptoms, simultaneous detection of these viruses in a single reaction mixture can save time and cost. The present study was done in a tertiary care children's hospital for rapid identification of viruses causing SARI among children less than or equal to five years of age using multiplex real-time reverse transcription polymerase chain reaction (RT-PCR) kit.

METHODS

A total of 155 throat swabs were collected from equal number of children suspected to have SARI and processed for extraction of nucleic acids using automated extraction system. Multiplex real-time RT-PCR was done to identify the viruses in the samples.

RESULTS

The overall positivity for viruses in the study was found to be 72.9 per cent with a co-infection rate of 19.5 per cent. Human metapneumovirus (HMPV) was the predominant virus detected in 25.7 per cent children followed by influenza A (H1N1)pdm09, human rhinovirus (HRV) and human adenovirus (HAdV) in 19.9, 11.0 and 8.8 per cent children, respectively. The HMPV was at its peak in February 2013, HAdV showed two peaks in March-April, 2012 and November 2012-March 2013 while HRV was detected throughout the year.

INTERPRETATION & CONCLUSIONS

Multiplex real-time PCR helped in rapid identification of viruses. Seventeen viruses were detected in SARI cases with overall positivity of 72.9 per cent. HMPV was the most predominant virus. However, for better clinico-virological correlation, studies are required with complete work up of all the aetiological agents, clinical profile of patients and treatment outcome.

Mixed viral infections of the respiratory tract; an epidemiological study during consecutive winter seasons

The current study aimed to describe the molecular epidemiology of mixed respiratory viral infections during consecutive winter seasons in a tertiary care hospital. Patients with symptoms of respiratory tract infection were evaluated during the 2009‐2011 and 2013‐15 winter seasons. A clinical microarray technique was used for viral detection. Clinical and epidemiological data were correlated with mixed viral detection and the need for hospitalization. In 332 out of 604 (54.4%) evaluated patients (17.6% children) a respiratory virus was identified. Mixed viral infections were diagnosed in 68/332 (20.5%) patients with virus detection (66.2% mixed Influenza‐RSV infections). Mixed viral infections were more commonly detected in children (OR 3.7; 95%CI 1.9‐5.6, P < 0.01) and patients with comorbidities. In logistic regression analyses, mixed viral infections were associated with younger age (mean age 30.4 years vs. 41.8 years, P ≤ 0.001) and increased rates of fever (OR: 2.7; 95%CI 1.04‐7.2, P < 0.05) but no adverse outcomes or increased rates of hospitalization. High rates of mixed viral infections were noted during all winter seasons (especially Influenza and RSV) and were more common in younger patients. The clinical significance of mixed respiratory viral infection needs further elucidation.

Multiplex PCR system for the rapid diagnosis of respiratory virus infection: systematic review and meta-analysis

OBJECTIVES

To provide a summary of evidence for the diagnostic accuracies of three multiplex PCR systems (mPCRs)-BioFire FilmArray RP (FilmArray), Nanosphere Verigene RV+ test (Verigene RV+) and Hologic Gen-Probe Prodesse assays-on the detection of viral respiratory infections.

METHODS

A comprehensive search up to 1 July 2017 was conducted on Medline and Embase for studies that utilized FilmArray, Verigene RV+ and Prodesse for diagnosis of viral respiratory infections. A summary of diagnostic accuracies for the following five viruses were calculated: influenza A virus (FluA), influenza B virus, respiratory syncytial virus, human metapneumovirus and adenovirus. Hierarchical summary receiver operating curves were used for estimating the viral detection performance per assay.

RESULTS

Twenty studies of 5510 patient samples were eligible for analysis. Multiplex PCRs demonstrated high diagnostic accuracy, with area under the receiver operating characteristic curve (AUROC) equal to or more than 0.98 for all the above viruses except for adenovirus (AUROC 0.89). FilmArray, Verigene RV+ and ProFlu+ (the only Prodesse assay with enough data) demonstrated a summary sensitivity for FluA of 0.911 (95% confidence interval, 0.848-0.949), 0.949 (95% confidence interval, 0.882-0.979) and 0.954 (95% confidence interval, 0.871-0.985), respectively. The three mPCRs were comparable in terms of detection of FluA.

CONCLUSIONS

Point estimates calculated from eligible studies showed that the three mPCRs (FilmArray, Verigene RV+ and ProFlu+) are highly accurate and may provide important diagnostic information for early identification of respiratory virus infections. In patients with low pretest probability for FluA, these three mPCRs can predict a low possibility of infection and may justify withholding empirical antiviral treatments.

An isothermal, label-free, and rapid one-step RNA amplification/detection assay for diagnosis of respiratory viral infections

Recently, RNA viral infections caused by respiratory viruses, such as influenza, parainfluenza, respiratory syncytial virus, coronavirus, and Middle East respiratory syndrome-coronavirus (MERS-CoV), and Zika virus, are a major public health threats in the world. Although myriads of diagnostic methods based on RNA amplification have been developed in the last decades, they continue to lack speed, sensitivity, and specificity for clinical use. A rapid and accurate diagnostic method is needed for appropriate control, including isolation and treatment of the patients. Here, we report an isothermal, label-free, one-step RNA amplification and detection system, termed as iROAD, for the diagnosis of respiratory diseases. It couples a one-step isothermal RNA amplification method and a bio-optical sensor for simultaneous viral RNA amplification/detection in a label-free and real-time manner. The iROAD assay offers a one-step viral RNA amplification/detection example to rapid analysis (<20min). The detection limit of iROAD assay was found to be 10-times more sensitive than that of real-time reverse transcription-PCR method. We confirmed the clinical utility of the iROAD assay by detecting viral RNAs obtained from 63 human respiratory samples. We envision that the iROAD assay will be useful and potentially adaptable for better diagnosis of emerging infectious diseases including respiratory diseases.

Identification of different respiratory viruses, after a cell culture step, by matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS)

In this study matrix assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS), a reliable identification method for the diagnosis of bacterial and fungal infections, is presented as an innovative tool to investigate the protein profile of cell cultures infected by the most common viruses causing respiratory tract infections in humans. MALDI-TOF MS was applied to the identification of influenza A and B viruses, adenovirus C species, parainfluenza virus types 1, 2 and 3, respiratory syncytial virus, echovirus, cytomegalovirus and metapneumovirus. In this study MALDI-TOF MS was proposed as a model to be applied to the identification of cultivable respiratory viruses using cell culture as a viral proteins enrichment method to the proteome profiling of virus infected and uninfected cell cultures. The reference virus strains and 58 viruses identified from respiratory samples of subjects with respiratory diseases positive for one of the above mentioned viral agents by cell culture were used for the in vitro infection of suitable cell cultures. The isolated viral particles, concentrated by ultracentrifugation, were used for subsequent protein extraction and their spectra profiles were generated by MALDI-TOF MS analysis. The newly created library allowed us to discriminate between uninfected and respiratory virus infected cell cultures.

Etiology of Influenza-Like Illnesses from Sentinel Network Practitioners in Réunion Island, 2011-2012

In Réunion Island, despite an influenza surveillance established since 1996 by the sentinel general practitioner’s network, little is known about the etiology of Influenza like-illness (ILI) that differs from influenza viruses in a tropical area. We set up a retrospective study using nasal swabs collected by sentinel GPs from ILI patients in 2011 and 2012. A total of 250 swabs were randomly selected and analyzed by multiplex reverse transcriptase polymerase chain reaction (RT-PCR) including research of 18 viruses and 4 bacteria. We detected respiratory viruses in 169/222 (76.1%) samples, mostly rhinovirus (23.4%), influenza A virus (21.2%), influenza B virus (12.6%), coronavirus (4.9%) and Human metapneumovirus (3.6%). Nine swabs (5.3% of positive swabs) revealed co-infections with two viruses identified, among which six concerned co-infections with influenza viruses. We observed important seasonal differences, with circulation of Human Metapneumoviruses, RSV A and B and coronavirus only during summer; whereas parainfluenza viruses were identified only during winter. In conclusion, this study highlights a substantial circulation of multiple respiratory pathogens in Réunion Island throughout the year. It shows that ILI are not only attributable to influenza and underlines the need for biological surveillance. As the use of multiplex RT-PCR showed its efficacy, it is now used routinely in the surveillance of ILI.

Genomic Signatures of Emerging Viruses: A New Era of Systems Epidemiology

Compared to classical epidemiologic methods, genomics can be used to precisely monitor virus evolution and transmission in real time across large, diverse populations. Integration of pathogen genomics with data about host genetics and global transcriptional responses to infection allows for comprehensive studies of population-level responses to infection and provides novel methods for predicting clinical outcomes. As genomic technologies become more accessible, these methods will redefine how emerging viruses are studied and outbreaks are contained. Here we review the existing and emerging genomic technologies that are enabling systems epidemiology and systems virology and making it possible to respond rapidly to emerging viruses such as Zika.

Bacterial and viral co-infections complicating severe influenza: Incidence and impact among 507 U.S. patients, 2013-14

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22.5% of adult patients with H1N1 developed bacterial co-infection.

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Staphylococcus aureus was the most common cause of co-infection.

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Bacterial and viral co-infections were associated with death in bivariate.

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Patients with a bacterial co-infection had greater use of resources.

Background

Influenza acts synergistically with bacterial co-pathogens. Few studies have described co-infection in a large cohort with severe influenza infection.

Objectives

To describe the spectrum and clinical impact of co-infections.

Study design

Retrospective cohort study of patients with severe influenza infection from September 2013 through April 2014 in intensive care units at 33 U.S. hospitals comparing characteristics of cases with and without co-infection in bivariable and multivariable analysis.

Results

Of 507 adult and pediatric patients, 114 (22.5%) developed bacterial co-infection and 23 (4.5%) developed viral co-infection. Staphylococcus aureus was the most common cause of co-infection, isolated in 47 (9.3%) patients. Characteristics independently associated with the development of bacterial co-infection of adult patients in a logistic regression model included the absence of cardiovascular disease (OR 0.41 [0.23–0.73], p = 0.003), leukocytosis (>11 K/μl, OR 3.7 [2.2–6.2], p < 0.001; reference: normal WBC 3.5–11 K/μl) at ICU admission and a higher ICU admission SOFA score (for each increase by 1 in SOFA score, OR 1.1 [1.0–1.2], p = 0.001). Bacterial co-infections (OR 2.2 [1.4–3.6], p = 0.001) and viral co-infections (OR 3.1 [1.3–7.4], p = 0.010) were both associated with death in bivariable analysis. Patients with a bacterial co-infection had a longer hospital stay, a longer ICU stay and were likely to have had a greater delay in the initiation of antiviral administration than patients without co-infection (p < 0.05) in bivariable analysis.

Conclusions

Bacterial co-infections were common, resulted in delay of antiviral therapy and were associated with increased resource allocation and higher mortality.

Southern Hemisphere Influenza and Vaccine Effectiveness Research and Surveillance

The 2009 influenza A(H1N1)pdm09 pandemic highlighted the need for improved scientific knowledge to support better pandemic preparedness and seasonal influenza control. The Southern Hemisphere Influenza and Vaccine Effectiveness Research and Surveillance (SHIVERS) project, a 5-year (2012–2016) multiagency and multidisciplinary collaboration, aimed to measure disease burden, epidemiology, aetiology, risk factors, immunology, effectiveness of vaccination and other prevention strategies for influenza and other respiratory infectious diseases of public health importance. Two active, prospective, population-based surveillance systems were established for monitoring influenza and other respiratory pathogens among those hospitalized patients with acute respiratory illness and those enrolled patients seeking consultations at sentinel general practices. In 2015, a sero-epidemiological study will use a sample of patients from the same practices. These data will provide a full picture of the disease burden and risk factors from asymptomatic infections to severe hospitalized disease and deaths and related economic burden. The results during the first 2 years (2012–2013) provided scientific evidence to (a) support a change to NZ's vaccination policy for young children due to high influenza hospitalizations in these children; (b) contribute to the revision of the World Health Organization's case definition for severe acute respiratory illness for global influenza surveillance; and (c) contribute in part to vaccine strain selection using vaccine effectiveness assessment in the prevention of influenza-related consultations and hospitalizations. In summary, SHIVERS provides valuable international platforms for supporting seasonal influenza control and pandemic preparedness, and responding to other emerging/endemic respiratory-related infections.

Benefits and drawbacks of molecular techniques for diagnosis of viral respiratory infections. Experience with two multiplex PCR assays

Molecular techniques have represented a major step forward in the diagnosis of viral respiratory infections. They are considered highly sensitive and specific compared to conventional techniques. In this study two nucleic acid amplification tests (NAATs) were compared to conventional methods (immunofluorescence and viral culture). The aim of this work was to discuss the clinical interpretation of the results obtained by NAATs on the basis of the two-decade experience of our group and the literature. Eighty nasopharyngeal aspirates were collected from children under six years attended for acute respiratory illness at the pediatric emergency room of a third level Hospital. Both NAATs tested (Seeplex(®) and Clart(®)) showed an overall higher performance regarding sensitivity (76% and 90%, respectively). Compared to Seeplex(®), the Clart(®) system tripled the number of multiple detections (8 by Seeplex(®) vs. 25 by Clart(®)). In some specimens both NAATs detected different viruses. Given these discrepancies and the fact that detection of viral nucleic acids is not necessarily related to the current clinical syndrome, the interpretation of molecular results may not always be so straightforward. The pros and cons of NAATs should always be taken into account when giving a result.

Enhanced growth of influenza A virus by coinfection with human parainfluenza virus type 2

It has been reported that dual or multiple viruses can coinfect epithelial cells of the respiratory tract. However, little has been reported on in vitro interactions of coinfected viruses. To explore how coinfection of different viruses affects their biological property, we examined growth of influenza A virus (IAV) and human parainfluenza virus type 2 (hPIV2) during coinfection of Vero cells. We found that IAV growth was enhanced by coinfection with hPIV2. The enhanced growth of IAV was not reproduced by coinfection with an hPIV2 mutant with reduced cell fusion activity, or by ectopic expression of the V protein of hPIV2. In contrast, induction of cell fusion by ectopic expression of the hPIV2 HN and F proteins augments IAV growth. hPIV2 coinfection supported IAV growth in cells originated from the respiratory epithelium. The enhancement correlated closely with cell fusion ability of hPIV2 in those cells. These results indicate that cell fusion induced by hPIV2 infection is beneficial to IAV replication and that enhanced viral replication by coinfection with different viruses can modify their pathological consequences.

Application of Multiplex PCR Coupled with Matrix-Assisted Laser Desorption Ionization-Time of Flight Analysis for Simultaneous Detection of 21 Common Respiratory Viruses

Respiratory infections continue to pose a significant threat to human health. It is important to accurately and rapidly detect respiratory viruses. To compensate for the limits of current respiratory virus detection methods, we developed a 24-plex analysis (common respiratory virus-mass spectrometry [CRV-MS]) that can simultaneously detect and identify 21 common respiratory viruses based on a matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry system. To evaluate the efficacy of the CRV-MS method, we used 102 samples that were confirmed positive for these common respiratory viruses. All tests using the CRV-MS method were effective, with no cross-reactivity observed with other common respiratory viruses. To confirm the usefulness of the CRV-MS method, we screened 336 nasal and throat swabs that were collected from adults or children with suspected viral acute respiratory tract infections using the CRV-MS method and consensus PCR/reverse transcription-PCR (RT-PCR) methods. Excluding four RNase P-negative samples, the CRV-MS and consensus PCR/RT-PCR methods detected respiratory viruses in 92.5% (307/332) and 89.5% (297/332) of the samples, respectively. The two methods yielded identical results for 306 (92.2%) samples, including negative results for 25 samples (7.5%) and positive results for 281 samples (84.6%). Differences between the two methods may reflect their different sensitivities. The CRV-MS method proved to be sensitive and robust, and it can be used in large-scale epidemiological studies of common respiratory virus infections.

Emerging viral diseases: confronting threats with new technologies

Emerging viral diseases pose ongoing health threats, particularly in an era of globalization; however, new biomedical research technologies such as genome sequencing and structure-based vaccine and drug design have improved our ability to respond to viral threats.

Comparison of the performance of 2 commercial multiplex PCR platforms for detection of respiratory viruses in upper and lower tract respiratory specimens

The performance of the CLART® PneumoVir system with that of the Luminex xTAG RVP Fast v1 assay for detection of most common respiratory viruses in upper and lower tract respiratory specimens (n=183) from unique patients with influenza-like syndrome or lower tract respiratory infection. Nested PCR coupled to automated sequencing was used for resolution of discrepancies. Fully concordant results were obtained for a total of 122 specimens, whereas 56 specimens gave partially (n=21) or fully discordant (n=35) results (Kappa coefficient, 0.62). The overall specificity of the Luminex xTAG RVP Fast v1 assay was slightly higher than that of the CLART® PneumoVir assay for human bocavirus, influenza A virus/H3N2, influenza B virus, human metapneumovirus, and parainfluenza virus, whereas the sensitivity of the latter was higher for most targeted viruses except, notably, for picornaviruses. This was irrespective of either the origin of the respiratory specimen or the age group to which the patients belonged.

Clinical relevance of multiple respiratory virus detection in adult patients with acute respiratory illness

Because increasing numbers of nasopharyngeal swab specimens from adult patients with acute respiratory illness (ARI) are being tested by respiratory virus (RV) multiplex reverse transcriptase PCR (RVM-RT-PCR), multiple RV detection (MRVD) is being encountered more frequently. However, the clinical relevance of MRVD in adult patients has rarely been evaluated. The clinical characteristics of hospitalized adult patients with ARI and MRVD by RVM-RT-PCR tests were compared to those of patients with single RV detection (SRVD) during a single year at a tertiary care center. MRVD was observed in 26 of the 190 adult patients (13.7%). The patients with MRVD had a higher incidence of chronic lung disease than the patients with SRVD (34.6% versus 15.9%, crude odds ratio [OR]=2.81, 95% confidence interval [CI]=1.13 to 6.98, P=0.03). Although the former were more likely than the latter to receive mechanical ventilation (19.2% versus 6.7%, crude OR=3.31, 95% CI=1.05 to 10.47, P=0.049), the length of hospital stay (median, 7 versus 6.5 days; P=0.66), and the in-hospital mortality rate (7.7% versus 4.3%, crude OR=1.87, 95% CI=0.37 to 9.53, P=0.35) were not different between the two groups. In multivariate analysis, chronic lung disease was associated with MRVD (adjusted OR=3.08, 95% CI=1.12 to 8.46, P=0.03). In summary, it was not uncommon to encounter adult patients with ARI and MRVD by RVM-RT-PCR tests of nasopharyngeal swab specimens. MRVD was associated with chronic lung disease rather than the severity of the ARI.

Viral coinfection in childhood respiratory tract infections

INTRODUCTION

The introduction of molecular techniques has enabled better understanding of the etiology of respiratory tract infections in children. The objective of the study was to analyze viral coinfection and its relationship to clinical severity.

METHODS

Hospitalized pediatric patients with a clinical diagnosis of respiratory infection were studied during the period between 2009-2010. Clinical and epidemiological data, duration of hospitalization, need for oxygen therapy, bacterial coinfection and need for mechanical ventilation were collected. Etiology was studied by multiplex PCR and low-density microarrays for 19 viruses.

RESULTS

A total of 385 patients were positive, 44.94% under 12 months. The most frequently detected viruses were RSV-B: 139, rhinovirus: 114, RSV-A: 111, influenza A H1N1-2009: 93 and bocavirus: 77. Coinfection was detected in 61.81%, 36.36% with 2 viruses, 16.10% and 9.35% with 3 to 4 or more. Coinfection was higher in 2009 with 69.79 vs. 53.88% in 2010. Rhinovirus/RSV-B on 10 times and RSV-A/RSV-B on 5 times were the most detected coinfections. Hospitalization decreased with greater number of viruses (P<0,001). Oxygen therapy was required by 26.75% (one virus was detected in 55.34% of cases). A larger number of viruses resulted in less need for oxygen (P<0,001). Ten cases required mechanical ventilation, 4 patients with bacterial coinfection and 5 with viral coinfection (P=0,69).

CONCLUSIONS

An inverse relationship was found between the number of viruses detected in nasopharyngeal aspirate, the need for oxygen therapy and hospitalization days. More epidemiological studies and improved quantitative detection techniques are needed to define the role of viral coinfections in respiratory disease and its correlation with the clinical severity.

Epidemiology of pathogen-specific respiratory infections among three US populations

BACKGROUND

Diagnostic tests for respiratory infections can be costly and time-consuming. Improved characterization of specific respiratory pathogens by identifying frequent signs, symptoms and demographic characteristics, along with improving our understanding of coinfection rates and seasonality, may improve treatment and prevention measures.

METHODS

Febrile respiratory illness (FRI) and severe acute respiratory infection (SARI) surveillance was conducted from October 2011 through March 2013 among three US populations: civilians near the US-Mexico border, Department of Defense (DoD) beneficiaries, and military recruits. Clinical and demographic questionnaire data and respiratory swabs were collected from participants, tested by PCR for nine different respiratory pathogens and summarized. Age stratified characteristics of civilians positive for influenza and recruits positive for rhinovirus were compared to other and no/unknown pathogen. Seasonality and coinfection rates were also described.

RESULTS

A total of 1444 patients met the FRI or SARI case definition and were enrolled in this study. Influenza signs and symptoms varied across age groups of civilians. Recruits with rhinovirus had higher percentages of pneumonia, cough, shortness of breath, congestion, cough, less fever and longer time to seeking care and were more likely to be male compared to those in the no/unknown pathogen group. Coinfections were found in 6% of all FRI/SARI cases tested and were most frequently seen among children and with rhinovirus infections. Clear seasonal trends were identified for influenza, rhinovirus, and respiratory syncytial virus.

CONCLUSIONS

The age-stratified clinical characteristics associated with influenza suggest that age-specific case definitions may improve influenza surveillance and identification. Improving identification of rhinoviruses, the most frequent respiratory infection among recruits, may be useful for separating out contagious individuals, especially when larger outbreaks occur. Overall, describing the epidemiology of pathogen specific respiratory diseases can help improve clinical diagnoses, establish baselines of infection, identify outbreaks, and help prioritize the development of new vaccines and treatments.

Detection of human bocavirus in children with acute respiratory tract infections in Lanzhou and Nanjing, China

OBJECTIVE

The aim of this study was to explore the prevalent characteristics of HBoV1 and its co-infection.

METHODS

PCR was used to detect HBoV1-DNA (HBoV1) and other viruses. A multivariate logistic regression model was used to explore possibility of co-detected for related viruses.

RESULTS

The positivity rates in Nanjing and Lanzhou were 9.38% (74/789) and 11.62% (161/1386), respectively (P>0.05). The HBoV1 positive group was younger than negative group (P<0.05). Seasonal differences were noted, with a higher frequency of infection in December and July. HBoV1-positive children [72.34% (169/235)] were co-infected with other respiratory viruses. Multifactorial analysis showed no correlations between HBoV1 and the clinical classification, region, gender, age, or treatment as an outpatient or in a hospital. Correlations were identified between HBoV1 infections with ADV (OR=1.53, 95% CI 1.03-2.28), RSV (OR=0.71, 95% CI 0.52-0.98), and IFVA (OR=1.77, 95% CI 1.00-3.13).

CONCLUSION

Presence of HBoV1 in nasopharyngeal aspirates did not correlate with region or gender, although the prevalence of HBoV1 was higher in younger children. There were no correlations between HBoV1 and other variables, except for the season and ADV, RSV, or IFVA infections.

Influenza and other respiratory virus infections in outpatients with medically attended acute respiratory infection during the 2011-12 influenza season

BACKGROUND

Respiratory tract infections are a major cause of outpatient visits, yet only a portion is tested to determine the etiologic organism. Multiplex reverse transcriptase polymerase chain reaction (MRT-PCR) assays for detection of multiple viruses are being used increasingly in clinical settings.

METHODS

During January-April 2012, outpatients with acute respiratory illness (≤ 7 days) were tested for influenza using singleplex RT-PCR (SRT-PCR). A subset was assayed for 18 viruses using MRT-PCR to compare detection of influenza and examine the distribution of viruses and characteristics of patients using multinomial logistic regression.

RESULTS

Among 662 participants (6 months-82 years), detection of influenza was similar between the MRT-PCR and SRT-PCR (κ = 0.83). No virus was identified in 267 (40.3%) samples. Commonly detected viruses were human rhinovirus (HRV, 15.4%), coronavirus (CoV, 10.4%), respiratory syncytial virus (RSV, 8.4%), human metapneumovirus (hMPV, 8.3%), and influenza (6%). Co-detections were infrequent (6.9%) and most commonly occurred among those <18 years old. In regression analyses, compared with non-viral illnesses, RSV and hMPV were significantly more frequent in children and less frequent in 18- to 49-year-olds than in those ≥ 50 years (P = 0.01), fever was more common in hMPV and influenza infections (P = 0.008), nasal congestion was more frequent in CoV, HRV, hMPV, influenza and RSV infections (P = 0.001), and body mass index was higher among those with influenza (P = 0.036).

CONCLUSIONS

Using MRT-PCR, a viral etiology was found in three-fifths of patients with medically attended outpatient visits for acute respiratory illness during the influenza season; co-detected viruses were infrequent. Symptoms varied by viral etiology.

Detection of Herpesviridae in whole blood by multiplex PCR DNA-based microarray analysis after hematopoietic stem cell transplantation

Viral infections are important causes of morbidity and mortality in patients after hematopoietic stem cell transplantation. The monitoring by PCR of Herpesviridae loads in blood samples has become a critical part of posttransplant follow-up, representing mounting costs for the laboratory. In this study, we assessed the clinical performance of the multiplex PCR DNA microarray Clart Entherpex kit for detection of cytomegalovirus (CMV), Epstein-Barr virus (EBV), and human herpesvirus 6 (HHV-6) as a screening test for virological follow-up. Two hundred fifty-five blood samples from 16 transplanted patients, prospectively tested by routine PCR assays, were analyzed by microarray. Routine PCR detected single or multiple viruses in 42% and 10% of the samples, respectively. Microarray detected single or multiple viruses in 34% and 18% of the samples, respectively. Microarray results correlated well with CMV and EBV detections by routine PCR (kappa tests = 0.79 and 0.78, respectively), whereas a weak correlation was observed with HHV-6 (0.43). HHV-7 was also detected in 48 samples by microarray. In conclusion, the microarray is a reliable screening assay for a posttransplant virological follow-up to detect CMV and EBV infections in blood. However, positive samples must be subsequently confirmed and viral loads must be quantified by PCR assays. Limitations were identified regarding HHV-6 detection. Although it is promising, is easy to use as a first-line test, and allows a reduction in the cost of analysis without undue delay in the reporting of the final quantitative result to the clinician, some characteristics of this microarray should be improved, particularly regarding quality control and the targeted virus panel, such that it could then be used as a routine test.

A DNA microarray-based assay to detect dual infection with two dengue virus serotypes

Here; we have described and tested a microarray based-method for the screening of dengue virus (DENV) serotypes. This DNA microarray assay is specific and sensitive and can detect dual infections with two dengue virus serotypes and single-serotype infections. Other methodologies may underestimate samples containing more than one serotype. This technology can be used to discriminate between the four DENV serotypes. Single-stranded DNA targets were covalently attached to glass slides and hybridised with specific labelled probes. DENV isolates and dengue samples were used to evaluate microarray performance. Our results demonstrate that the probes hybridized specifically to DENV serotypes; with no detection of unspecific signals. This finding provides evidence that specific probes can effectively identify single and double infections in DENV samples.

Viral coinfection in childhood respiratory tract infections

Introduction

The introduction of molecular techniques has enabled better understanding of the etiology of respiratory tract infections in children. The objective of the study was to analyze viral coinfection and its relationship to clinical severity.

Methods

Hospitalized pediatric patients with a clinical diagnosis of respiratory infection were studied during the period between 2009 and 2010. Clinical and epidemiological data, duration of hospitalization, need for oxygen therapy, bacterial coinfection and need for mechanical ventilation were collected. Etiology was studied by multiplex PCR and low-density microarrays for 19 viruses.

Results

A total of 385 patients were positive, 44.94% under 12 months. The most frequently detected viruses were RSV-B: 139, rhinovirus: 114, RSV-A: 111, influenza A H1N1-2009: 93 and bocavirus: 77. Coinfection was detected in 61.81%, 36.36% with two viruses, 16.10% and 9.35% with three to four or more. Coinfection was higher in 2009 with 69.79 vs 53.88% in 2010. Rhinovirus/RSV-B on 10 times and RSV-A/RSV-B on five times were the most detected coinfections. Hospitalization decreased with greater number of viruses (P<.001). Oxygen therapy was required by 26.75% (one virus was detected in 55.34% of cases). A larger number of viruses resulted in less need for oxygen (P<.001). Ten cases required mechanical ventilation, four patients with bacterial coinfection and five with viral coinfection (P=.69).

Conclusions

An inverse relationship was found between the number of viruses detected in nasopharyngeal aspirate, the need for oxygen therapy and hospitalization days. More epidemiological studies and improved quantitative detection techniques are needed to define the role of viral coinfections in respiratory disease and its correlation with the clinical severity.

Type I IFN exhaustion is a host defence protecting against secondary bacterial infections

Type I interferons (IFN‐I) have been known for decades for their indispensable role in curtailing viral infections. It is, however, now also increasingly recognized that IFN‐I is detrimental to the host in combating a number of bacterial infections. We have previously reported that viral infections induce partial lymphocyte activation, characterized by significant increases in the cell surface expression of CD69 and CD86, but not CD25. This systemic partial activation of lymphocytes, mediated by IFN‐I, is rapid and is followed by a period of IFN‐I unresponsiveness. Here we propose that IFN‐I exhaustion that occurs soon after a primary viral infection may be a host response protecting it from secondary bacterial infections.

Viral etiology of respiratory infections in children in southwestern Saudi Arabia using multiplex reverse-transcriptase polymerase chain reaction

OBJECTIVES

To investigate 15 respiratory viruses in children with acute respiratory tract infections (ARTIs) using multiplex reverse-transcriptase polymerase chain reaction (RT-PCR), and to analyze the clinical and epidemiological features of these viruses.

METHODS

In a cross-sectional study, 135 children, ≤5 years of age who presented with ARTIs in Najran Maternity and Children Hospital, Najran, Saudi Arabia between October 2012 and July 2013 were included. The clinical and sociodemographic data, and the laboratory results were recorded using a standardized questionnaire. Two nasopharyngeal swabs were collected from each child: one for bacteriological examination, and the second for viral detection using multiplex RT-PCR.

RESULTS

A single viral pathogen was detected in 76 patients, viral coinfections in 9, and mixed viral and bacterial pathogens in 15. Respiratory syncytial virus was isolated in 33 patients, human rhinovirus (hRV) in 22, adenovirus (AdV) in 19, human metapneumovirus in 13, influenza virus in 10, parainfluenza virus in 7, human corona virus (hCoV) in 4, and human bocavirus in one.

CONCLUSION

Respiratory syncytial virus, hRV, and AdV were the most frequent viruses, accounting for more than two-thirds of the cases. Other viruses, such as MPV, hCoV NL63, and hCoV OC43, may play a role in pediatric ARTIs. Of significance is the potential use of multiplex RT-PCR to provide epidemiological and virological data for early detection of the emergence of novel respiratory viruses in the era of the Middle East respiratory syndrome coronavirus. 

Circulation of other respiratory viruses and viral co-infection during the 2009 pandemic influenza

Coinciding with the pandemic wave of the influenza A(H1N1)pdm09 virus, other respiratory viruses have co-circulated in our area and were responsible for many acute respiratory infections and influenza-like illness (ILI). Apart from the pandemic virus that was responsible for most ILI cases, incidence rates of other viruses have varied among geographical areas. In general, human rhinovirus was the most frequent among individuals from the community, and respiratory syncytial virus among hospitalized patients. Detection rates of other respiratory viruses such as human metapneumovirus, adenovirus or parainfluenza viruses have been much lower. On the basis of an interference mechanism, human rhinovirus may contribute to modulate the pandemic wave, although available data are not conclusive to support this hypothesis. In contrast, the epidemic wave of respiratory syncytial virus during 2009–2010 was similar to previous seasons. Overall, incidence rates of respiratory viruses other than influenza did not change significantly during the pandemic season compared to other seasons. No association has been found between coinfection of pandemic influenza and other respiratory viruses with the prognosis of patients with influenza. The involvement of clinical virology laboratories in the etiological diagnosis of ILI cases has improved and has optimized diagnostic procedures.

Microarray multiplex assay for the simultaneous detection and discrimination of influenza a and influenza B viruses

In this study, we present a microarray approach for the typing of influenza A and B viruses, and the subtyping of H1 and H3 subtypes. We designed four pairs of specific multiplex RT-PCR primers and eight specific oligonucleotide probes and prepared microarrays to identify the specific subtype of influenza virus. Through amplification and fluorescent marking of the multiplex RT-PCR products on the M gene of influenza A and B viruses and the HA gene of subtypes H1 and H3, the PCR products were hybridized with the microarray, and the results were analyzed using a microarray scanner. The results demonstrate that the chip developed by our research institute can detect influenza A and B viruses specifically and identify the subtypes H1 and H3 at a minimum concentration of 1 × 10(2) copies/μL of viral RNA. We tested 35 clinical samples and our results were identical to other fluorescent methods. The microarray approach developed in this study provides a reliable method for the monitoring and testing of seasonal influenza.

Comparative evaluation of six commercialized multiplex PCR kits for the diagnosis of respiratory infections

The molecular diagnosis of respiratory infection can be performed using different commercial multiplex-based PCR kits whose performances have been previously compared individually to those of conventional techniques. This study compared the practicability and the diagnostic performances of six CE-marked kits available in 2011 on the French market, including 2 detecting viruses and atypical bacteria (from Pathofinder and Seegene companies) and 4 detecting only viruses (from Abbott, Genomica, Qiagen and Seegene companies). The respective sensitivity, specificity, accuracy and agreement of each multiplex technique were calculated by comparison to commercial duplex PCR tests (Argene/bioMérieux) used as gold standard. Eighty-eight respiratory specimens with no pathogen (n = 11), single infections (n = 33) or co-infections (n = 44) were selected to cover 9 viruses or groups of viruses and 3 atypical bacteria. All samples were extracted using the NUCLISENS® easyMAG™ instrument (bioMérieux). The overall sensitivity ranged from 56.25% to 91.67% for viruses and was below 50% with both tests for bacteria. The overall specificity was excellent (>94% for all pathogens). For each tested kit, the overall agreement with the reference test was strong for viruses (kappa test >0.60) and moderate for bacteria. After the extraction step, the hands-on time varied from 50 min to 2h30 and the complete results were available in 2h30 to 9 h. The spectrum of tested agents and the technology used to reveal the PCR products as well as the laboratory organization are determinant for the selection of a kit.

Virus detection and semiquantitation in explanted heart tissues of idiopathic dilated cardiomyopathy adult patients by use of PCR coupled with mass spectrometry analysis

Viral detection in heart tissues has become a central issue for the diagnosis and exploration of the pathogenesis of idiopathic dilated cardiomyopathy (IDCM). In the present study, common cardiotropic viruses in 67 explanted heart samples of 31 IDCM adult patients were detected and semiquantified by using for the first time a new technology based on PCR assay coupled to electrospray ionization-time of flight mass spectrometry analysis (PCR-MS), with comparison to reference quantitative real-time PCR (RT-qPCR) assay. PCR-MS identified single or mixed enterovirus (EV) and parvovirus B19 (PVB19) infections in 27 (40.2%) of 67 samples, corresponding to 15 (48.3%) of the 31 patients, whereas RT-qPCR identified viral infections in 26 (38.8%) samples, corresponding to 16 (51.6%) of the patients. The PCR-MS results correlated well with EV and PVB19 detection by RT-qPCR (kappa = 0.85 [95% confidence interval {CI}, 0.72 to 1.00] and kappa = 0.82 [95% CI, 0.66 to 0.99], respectively). The levels of EV RNA (median, 550 [range, 178 to 3,200] copies/μg of total extracted nucleic acids) and of PVB19 DNA (median, 486 [range, 80 to 1,157] copies/μg of total extracted nucleic acids) were measured using PCR-MS and correlated with those obtained by RT-qPCR (r(2) = 0.57, P = 0.002 and r(2) = 0.64, P < 0.001 for EV and PVB19, respectively). No viruses other than EV and PVB19 strains were detected using the new PCR-MS technology, which is capable of simultaneously identifying 84 known human viruses in one assay. In conclusion, we identified single or mixed EV and PVB19 cardiac infections as potential causes of IDCM. The PCR-MS analysis appeared to be a valuable tool to rapidly detect and semiquantify common viruses in cardiac tissues and may be of major interest to better understand the role of viruses in unexplained cardiomyopathies.

Clinical and economical impact of multiplex respiratory virus assays

During the last decade, a variety of molecular assays targeting respiratory viruses have been developed and commercialized. Therefore, multiplex PCR are increasingly used in everyday clinical practice. This improves our understanding of respiratory virus epidemiology and enhances our concerns about their clinical impact in specific patient populations. However, questions remain regarding cost-effectiveness of performing these diagnostic tests in routine and their real impact on patient care. This article will review available data and highlight unresolved questions about cost-effectiveness, infection control, clinical utility and public health impact of multiplex respiratory virus assays.