Monitoring epidemic viral respiratory infections using one-step real-time triplex RT-PCR targeting influenza A and B viruses and respiratory syncytial virus

Interest of Absolute Eosinopenia as a Marker of Influenza in Outpatients during the Fall-Winter Seasons 2016-2018 in the Greater Paris Area: The SUPERFLUOUS Study

INTRODUCTION

Prior to the emergence of COVID-19, when influenza was the predominant cause of viral respiratory tract infections (VRTIs), this study aimed to analyze the distinct biological abnormalities associated with influenza in outpatient settings.

METHODS

A multicenter retrospective study was conducted among outpatients, with the majority seeking consultation at the emergency department, who tested positive for VRTIs using RT-PCR between 2016 and 2018. Patient characteristics were compared between influenza (A and B types) and non-influenza viruses, and predictors of influenza were identified using two different models focusing on absolute eosinopenia (0/mm³) and lymphocyte count <800/mm³.

RESULTS

Among 590 VRTIs, 116 (19.7%) were identified as outpatients, including 88 cases of influenza. Multivariable logistic regression analysis revealed the following predictors of influenza: in the first model, winter season (adjusted odds ratio [aOR] 7.1, 95% confidence interval [CI] 1.12-45.08) and absolute eosinopenia (aOR 6.16, 95% CI 1.14-33.24); in the second model, winter season (aOR 9.08, 95% CI 1.49-55.40) and lymphocyte count <800/mm³ (aOR 7.37, 95% CI 1.86-29.20). Absolute eosinopenia exhibited the highest specificity and positive predictive value (92% and 92.3%, respectively).

CONCLUSION

During the winter season, specific biological abnormalities can aid physicians in identifying influenza cases and guide the appropriate use of antiviral therapy when rapid molecular tests are not readily available.

Predictors of hospitalization and superinfection in viral respiratory tract infections between influenza and paramyxoviruses: the SUPERFLUOUS study

BACKGROUND

Viral respiratory tract infections (VRTIs) are one of the most common diseases, but the risk of superinfection has never been compared depending on virus species.

METHODS

Multicenter retrospective study conducted amongst adults tested positive to VRTIs by RT-PCR. We compared characteristics between influenza (A-B) and paramyxoviruses (RSV,PIV1,PIV3 and hMPV) and identified predictors of superinfection and hospitalization.

RESULTS

590 patients had a VRTI, including 347 (59%) influenza and 243 paramyxoviruses with comparable superinfections between groups (53% vs 60%). In multivariate analyses, predictors of superinfections were: age>75 years-old (aOR=2.37, 95%CI [1.65-3.40]), chronic respiratory disease (aOR=1.79, 95%CI [1.20-2.67]) and biological abnormalities (neutrophils>7000/mm 3, aOR=1.98, 95%CI [1.34-2.91]; eosinophils<50/mm 3, aOR=2.53, 95%CI [1.61-3.98]; PCT>0.25ng/mL, aOR=2.8, 95%CI [1.65-4.73]). Predictors of hospitalisation were: age>75 years-old (aOR=3.49, 95%CI [2.17-5.63]), paramyxovirus infection (aOR=2.28, 95%CI [1.39-3.75]), long-term use of inhaled corticosteroids (aOR=2.49, 95%CI [1.13-5.49]) and biological abnormalities (neutrophils>7000/mm 3, aOR=2.38, 95%CI [1.37-4.12]; PCT>0.25ng/mL, aOR=2.49, 95%CI [1.23-5.02]). Kaplan-Meier survival curves showed that influenza-infected patients experienced a higher mortality than paramyxoviruses (8.9% versus 4.5% respectively, p=0.017).

CONCLUSION

Our study revealed a high rate of superinfection (56%), not related to viral species. However influenza was associated with a poorer prognosis than paramyxoviruses, pleading for a broader and large-scale vaccination of individual at risk of VRTIs.

Influenza in the Emergency Department: Vaccination, Diagnosis, and Treatment: Clinical Practice Paper Approved by American Academy of Emergency Medicine Clinical Guidelines Committee

BACKGROUND

Influenza is an acute respiratory virus that results in significant worldwide morbidity and mortality each year. As emergency physicians, we are often the first to encounter patients with seasonal influenza. It is therefore critical that we draw on the most recent and relevant research when we make clinical decisions regarding the diagnosis, treatment, and prophylaxis of this disease.

METHODS

A MEDLINE literature search from August 2009 to August 2015 was performed using the keywords influenza vaccination efficacy AND systematic, influenza AND rapid antigen testing, and Oseltamivir AND systematic, while limiting the search to human studies written in the English language. General review articles and case reports were omitted. Each of the selected articles then underwent a structured review.

RESULTS

We identified 163 articles through our literature search, of which 68 were found to be relevant to our clinical questions. These studies then underwent a rigorous review from which recommendations were given.

CONCLUSIONS

Influenza vaccine efficacy continues to range between 40% and 80%. Vaccination has the potential to decrease disease severity and is recommended for individuals older than 6 months of age. If resources permit, vaccination can be offered to patients presenting to the emergency department. Rapid antigen detection for influenza is a simple bedside test with high specificity, but generally low sensitivity. If a patient presents with a syndrome consistent with influenza and has negative rapid antigen detection, they should either receive a confirmatory reverse transcriptase polymerase chain reaction or be treated as if they have influenza. Treatment with neuraminidase inhibitors can decrease the duration of influenza and is recommended in hospitalized patients, or in those with high risk of complications.

Fabricating Upconversion Fluorescent Probes for Rapidly Sensing Foodborne Pathogens

Rare earth-doped upconversion nanoparticles (UCNPs) have promising potential in the field of food safety because of their unique frequency upconverting capability and high detection sensitivity. Here, we report a rapid and sensitive UCNP-based bacterium-sensing strategy using Escherichia coli. Highly fluorescent and water-soluble UCNPs were fabricated and conjugated with antibodies against E. coli for use as fluorescent probes. The E. coli were successively captured by the fluorescent probes. After the captured cell samples were pelleted, the differences in the fluorescence intensities between sample supernatants and the control were observed to increase linearly with E. coli concentration from 42 to 42 × 10(6) colony-forming units (cfu)/mL (R(2) = 0.9802), resulting in a relatively low limit of detection of 10 cfu/mL. Furthermore, the ability of the bioassay to detect E. coli was also confirmed in adulterated meat and milk samples.

Fatal human metapneumovirus infection following allogeneic hematopoietic stem cell transplantation

Respiratory viruses are an important yet underestimated cause of infectious morbidity and mortality in immunocompromised children and adolescents. Here, we report the occurrence of fatal lower respiratory tract disease associated with human metapneumovirus (HMPV) infection in a 10-year-old girl with chronic graft-versus-host disease following allogeneic hematopoietic stem cell transplantation (HSCT) for secondary chronic myeloid leukemia. Symptoms occurred 8 months after HSCT while on immunosuppression with 0.2 mg/kg/day of prednisone, and presented as dry cough, bilateral pneumonitis, and progressive respiratory distress. Non-invasive and invasive microbiological investigations revealed HMPV type B as the sole pathogen. Histopathological findings showed interstitial and intra-alveolar pneumonitis with profound alveolar cell damage. The patient was treated with intravenous and oral ribavirin and polyvalent immunoglobulins, but ultimately died from respiratory failure. The case reflects the potentially fatal impact of infections by respiratory viruses in immunocompromised patients and the need for effective approaches to their prevention and treatment.

Severe acute respiratory infections in the postpandemic era of H1N1

PURPOSE OF REVIEW

Shortly after the advent of severe acute respiratory syndrome and the avian influenza, the emergence of the influenza A(H1N1)2009 pandemic caused significant vibrations to the public health authorities and stressed the health systems worldwide. We sought to investigate whether this experience has altered our knowledge and our current and future practice on the management of severe acute respiratory infections (SARI) and community-acquired pneumonia.

RECENT FINDINGS

A changing epidemiology was demonstrated, with obesity and pregnancy beyond established risk groups for influenza A, other clinical syndromes beyond primary viral pneumonia, possible coinfections by other viral beyond bacterial pathogens and a disappointing performance of all available severity assessment tools. On the treatment topic, accumulating evidence suggesting worse outcomes argues against the use of corticosteroids, but some noninvasive ventilating modalities require further assessment.

SUMMARY

The recent influenza A(H1N1)2009 pandemic has highlighted our weaknesses relating to the diagnosis and assessment of severity of SARI, compromising early treatment and ultimate outcomes; further research based on this experience will help to improve prognosis and boost our future preparedness. An important message is the necessity of international collaboration for the rapid dissemination of locally acquired knowledge.

A universal influenza A and B duplex real-time RT-PCR assay

A high throughput universal influenza A and B duplex real-time RT-PCR was developed to meet effectively the heightened surveillance and diagnostic needs essential in managing influenza infections and outbreaks. Primers and probes, designed to target highly conserved regions of the matrix protein of influenza A and the nucleoprotein of influenza B, were optimized using the high-throughput LightCycler 480 II system. Analytical sensitivity and specificity were characterized using RNA transcripts diluted serially, archived non-influenza respiratory viruses, and proficiency test samples. Eighty-nine clinical samples were tested in parallel against existing influenza A and B monoplex assays. Once validated, the duplex assay was applied prospectively on 2,458 clinical specimens that were later subtyped. In April 2011, the emergence of an influenza B variant necessitated the inclusion of an additional modified probe for influenza B and revalidation of the revised protocol. The lower detection limits of the assay were 50 copies/PCR. There was no cross-reactivity against any non-influenza respiratory virus and all proficiency testing materials were identified correctly. The parallel testing revealed a 98.9% overall agreement. Routine application of the assay revealed high sensitivity and specificity for the detection of influenza A/H1N1/2009, A/H3N2 and influenza B. Assay C(q) values correlated well between the pre- and post-revision protocols for influenza A (r(2) = 0.998) and B (r(2) = 0.999). The revised protocol detected three additional novel influenza B variant cases in 200 specimens reported previously as influenza B negative. This in-house assay offers a highly sensitive and specific option for laboratories seeking to expand their influenza testing capacity.

First influenza season after the 2009 pandemic influenza: characteristics of intensive care unit admissions in adults and children in Vall d'Hebron Hospital

To assess potential differences in epidemiology and management of patients admitted with influenza infection in the intensive care unit (ICU) during the first post-pandemic influenza period. Observational prospective study comparing September 2009-January 2010 with September 2010-January 2011. Variables captured: demographics, co-morbidities, physiological parameters, outcomes and management. Analysis was performed using SPSS v. 13.0; significance was set at p 0.5. Data from 53 patients, 38 adults (age, median 41.5 years; interquartile range (IQR) 32.8-51.3) and 15 children (age, median 2 years, IQR 0.5-9) are presented. Vaccination rates were 0% and 4.3% during the first and second periods, respectively. Differences postpandemic were: 100% of episodes developed after December compared with 16.7% in the 2009 season. Younger children were affected (median age 0.8 years (IQR 0.3-4.8) vs 7 years (IQR 1.25-11.5), p 0.05) and influenza B caused 8.7% of ICU admissions. Influenza A (H1N1) 2009 and respiratory syncytial virus epidemics occurred simultaneously (42.8% of children) and bacterial co-infections doubled (from 10% to 21.7%); the prevalence of co-infections (viral or bacterial) increased from 10% to 39.1% (OR 5.8, 95% CI 1.3-24.8). Respiratory syndromes without chest X-ray opacities reflecting exacerbation of asthma or chronic obstructive pulmonary disease, bronchitis or bronchiolitis increased (from 6.9% to 39.1%, p<0.05) and pneumonia decreased (from 83.3% to 56.5%, p <0.05). Primary viral pneumonia predominated among ICU admissions. Postpandemic ICU influenza developed later, with some cases of influenza B, more frequent bacterial and viral co-infections and more patients with severe acute respiratory infection with normal chest X-ray. Increasing vaccination rates among risk-group individuals is warranted to prevent ICU admission and death.