Clinical characterization of influenza A and human respiratory syncytial virus among patients with influenza like illness

Novel Approach for Detecting Respiratory Syncytial Virus in Pediatric Patients Using Machine Learning Models Based on Patient-Reported Symptoms: Model Development and Validation Study

BACKGROUND

Respiratory syncytial virus (RSV) affects children, causing serious infections, particularly in high-risk groups. Given the seasonality of RSV and the importance of rapid isolation of infected individuals, there is an urgent need for more efficient diagnostic methods to expedite this process.

OBJECTIVE

This study aimed to investigate the performance of a machine learning model that leverages the temporal diversity of symptom onset for detecting RSV infections and elucidate its discriminatory ability.

METHODS

The study was conducted in pediatric and emergency outpatient settings in Japan. We developed a detection model that remotely confirms RSV infection based on patient-reported symptom information obtained using a structured electronic template incorporating the differential points of skilled pediatricians. An extreme gradient boosting-based machine learning model was developed using the data of 4174 patients aged ≤24 months who underwent RSV rapid antigen testing. These patients visited either the pediatric or emergency department of Yokohama City Municipal Hospital between January 1, 2009, and December 31, 2015. The primary outcome was the diagnostic accuracy of the machine learning model for RSV infection, as determined by rapid antigen testing, measured using the area under the receiver operating characteristic curve. The clinical efficacy was evaluated by calculating the discriminative performance based on the number of days elapsed since the onset of the first symptom and exclusion rates based on thresholds of reasonable sensitivity and specificity.

RESULTS

Our model demonstrated an area under the receiver operating characteristic curve of 0.811 (95% CI 0.784-0.833) with good calibration and 0.746 (95% CI 0.694-0.794) for patients within 3 days of onset. It accurately captured the temporal evolution of symptoms; based on adjusted thresholds equivalent to those of a rapid antigen test, our model predicted that 6.9% (95% CI 5.4%-8.5%) of patients in the entire cohort would be positive and 68.7% (95% CI 65.4%-71.9%) would be negative. Our model could eliminate the need for additional testing in approximately three-quarters of all patients.

CONCLUSIONS

Our model may facilitate the immediate detection of RSV infection in outpatient settings and, potentially, in home environments. This approach could streamline the diagnostic process, reduce discomfort caused by invasive tests in children, and allow rapid implementation of appropriate treatments and isolation at home. The findings underscore the potential of machine learning in augmenting clinical decision-making in the early detection of RSV infection.

Reclassification of respiratory syncytial virus genotypes in India

Respiratory syncytial virus (RSV) is known to be the major cause of lower respiratory tract infections in infants and in the elderly. RSV was recently reclassified and simplified into three genotypes of the RSV-A subgroup (GA1-GA3) and into seven genotypes of the RSV-B subgroup (GB1-GB7). This classification strategy was not implemented globally. This study intended to reclassify the sequences that were submitted in GenBank till September 2021 from India. The gene sequences of the ectodomain region, second hypervariable region (SHR), and the partial second hypervariable region (PSHR) of the G gene were selected for the analysis. 25 ectodomain, 36 s hypervariable, and 19 partial second hypervariable regions of the RSV-A subgroup and 42-ectodomain, 49-s hypervariable region and 11-partial second hypervariable region of RSV-B subgroup were used for phylogenetic analysis. P-distance was calculated to support the genotype determination done by phylogenetic analysis. Phylogenetic analysis revealed that GA2.3.1, GA2.3.3, GA2.3.4, GA2.3.5, and GA2.3.6b lineages of GA2 genotype for RSV-A; and GB5.0.1, GB5.0.2, GB5.0.3, GB5.0.4a, GB5.0.4c, GB5.0.5a, GB5.0.5c lineages of GB5 genotype and GB7 genotype for RSV-B were that circulated in India. This work has implication for RSV vaccine research, and also for strategies for the prevention and control of RSV infection in humans.

Supplementary Information

The online version contains supplementary material available at 10.1007/s13337-022-00802-x.

Assessing the patient experience of respiratory syncytial virus infection: development of a patient-reported outcome measure

BACKGROUND

Respiratory syncytial virus (RSV) causes significant morbidity and mortality in older adults. Despite a number of RSV vaccine candidates in clinical trials, there are no existing disease-specific, self-reported measures that assess the symptoms and severity of RSV infection from the perspective of adult patients with acute RSV. The objective of this study was to describe the initial conceptualization and development of the RSV Infection, Intensity and Impact Questionnaire (RSV-iiiQ), a new patient-reported outcome measure.

METHODS

A targeted review of the literature identified relevant existing measures, symptoms, and impacts of RSV. A draft version of the RSV-iiiQ was developed based on the Influenza Intensity and Impact Questionnaire (Flu-iiQ) with expert input. Qualitative interviews (N = 20) were conducted with participants to optimize the RSV-iiiQ conceptual model and confirm the content validity of the RSV-iiiQ. Interviews included concept elicitation and a cognitive debriefing assessment. A draft conceptual framework was developed, and the electronic clinical outcome assessment was piloted. All steps of instrument development followed Food and Drug Administration guidance for patient-reported outcomes.

RESULTS

In-depth concept elicitation interviews followed by cognitive debriefings demonstrated that the content of the items was comprehensive, covered the breadth of RSV symptoms and impacts, and was relevant to the experiences of individuals with RSV. Both the paper and electronic versions of the RSV-iiiQ were easily completed. Minor refinements were made to some items based on participant feedback, and the draft conceptual framework was refined.

CONCLUSIONS

The RSV-iiiQ was developed for use in clinical trials to measure the symptom intensity and impact of acute RSV infection from the perspective of adult patients. The tool was developed in accordance with current regulatory guidance and is useful to support patient-focused drug development.

Respiratory syncytial virus among children hospitalized with severe acute respiratory infection in Kashmir, a temperate region in northern India

Background

Severe acute respiratory infections (SARI) are a leading cause of hospitalizations in children, especially due to viral pathogens. We studied the prevalence of respiratory viruses among children aged <5 years hospitalized with severe acute respiratory infections (SARI) in Kashmir, India.

Methods

We conducted a prospective observational study in two tertiary care hospitals from October 2013 to September 2014, systematically enrolling two children aged <5 years with SARI per day. We defined SARI as history of fever or measured fever (≥38°C) and cough with onset in the last 7 days requiring hospitalization for children aged 3-59 months and as physician-diagnosed acute lower respiratory infection for children aged <3 months. Trained study staff screened children within 24 hours of hospitalization for SARI and collected clinical data and nasopharyngeal swabs from enrolled participants. We tested for respiratory syncytial virus (RSV) A and B, influenza viruses, rhinoviruses (HRV)/enteroviruses, adenovirus (AdV), bocavirus (BoV), human metapneumovirus (hMPV) A and B, coronaviruses (OC43, NL65, C229E), and parainfluenza viruses (PIV) 1, 2, 3 and 4 using standardized duplex real-time polymerase chain reaction.

Results

Among 4548 respiratory illness admissions screened from October 2013 to September 2014, 1026 met the SARI case definition, and 412 were enrolled (ages = 5 days to 58 months; median = 12 months). Among enrolees, 256 (62%) were positive for any virus; RSV was the most commonly detected (n = 118, 29%) followed by HRV/enteroviruses (n = 88, 21%), PIVs (n = 31, 8%), influenza viruses (n = 18, 4%), BoV (n = 15, 4%), coronaviruses (n = 16, 4%), AdV (n = 14, 3%), and hMPV (n = 9, 2%). Fifty-four children had evidence of virus co-detection. Influenza-associated SARI was more common among children aged 1-5 years (14/18, 78%) while most RSV detections occurred in children <12 months (83/118, 70%). Of the RSV viruses typed (n = 116), the majority were type B (94, 80%). Phylogenetic analysis of G gene of RSV showed circulation of the BA9 genotype with 60bp nucleotide duplication.

Conclusions

Respiratory viruses, especially RSV, contributed to a substantial proportion of SARI hospitalizations among children <5 years in north India. These data can help guide clinicians on appropriate treatment and prevention strategies.

Respiratory Syncytial Virus: New Challenges for Molecular Epidemiology Surveillance and Vaccination Strategy in Patients with ILI/SARI

Several respiratory pathogens are responsible for influenza-like illness (ILI) and severe respiratory infections (SARI), among which human respiratory syncytial virus (hRSV) represents one of the most common aetiologies. We analysed the hRSV prevalence among subjects with ILI or SARI during the five influenza seasons before the emergence of SARS-CoV-2 epidemic in Sicily (Italy). Respiratory specimens from ILI outpatients and SARI inpatients were collected in the framework of the Italian Network for the Influenza Surveillance and molecularly tested for hRSV-A and hRSV-B. Overall, 8.1% of patients resulted positive for hRSV. Prevalence peaked in the age-groups <5 years old (range: 17.6–19.1%) and ≥50 years old (range: 4.8–5.1%). While the two subgroups co-circulated throughout the study period, hRSV-B was slightly predominant over hRSV-A, except for the season 2019–2020 when hRSV-A strongly prevailed (82.9%). In the community setting, the distribution of hRSV subgroups was balanced (47.8% vs. 49.7% for hRSV-A and hRSV-B, respectively), while most infections identified in the hospital setting were caused by hRSV-B (69.5%); also, this latter one was more represented among hRSV cases with underlying diseases, as well as among those who developed a respiratory complication. The molecular surveillance of hRSV infections may provide a valuable insight into the epidemiological features of ILI/SARI. Our findings add new evidence to the existing knowledge on viral aetiology of ILI and SARI in support of public health strategies and may help to define high-risk categories that could benefit from currently available and future vaccines.

Burden of influenza disease in children under 2 years of age hospitalized between 2011 and 2020 in France

BACKGROUND

Although influenza viruses cause significant morbidity and mortality worldwide, the impact of these infections on children in France and in other European countries has not been extensively characterized. The primary objective of the present study was to describe the burden of influenza disease on hospitalized children under 2 years of age in France, using data from the national hospital discharge summary database (Programme de Médicalisation des Systèmes d'Information, PMSI).

METHODS

In a retrospective study of hospital admissions for influenza among children under the age of 2 in France, we extracted and analyzed hospital administrative data from the PMSI database (from January 1, 2011, to December 31, 2020).

RESULTS

From 2011 to 2020, 28,507 children under the age of 2 were admitted to hospital with a primary or secondary diagnosis of influenza infection. The hospital admission rate was 205 per 100,000 for children under the age of 2, 276 per 100,000 for children under the age of 12 months, and 135 per 100,000 for children aged between 12 and 23 months. Children under 6 months of age were the most affected (45.4%). An underlying condition was identified for 9.4% of the children, and 2.2% of the children were admitted to the intensive care unit. The death rate was 0.12 per 100,000 for children under 2, 0.11 per 100,000 for children under 12 months, and 0.16 per 100,000 for children aged between 12 and 23 months.

CONCLUSIONS

In France, the burden of influenza disease is significant in children under the age of 2.

Disease Burden Due to Respiratory Syncytial Virus in Indian Pediatric Population: A Literature Review

Respiratory syncytial virus (RSV) is one of the leading causes of lower respiratory tract infections in young children. Globally, there is huge disease burden, high treatment cost, and health impact beyond acute episodes due to RSV which necessitate development and implementation of preventive strategies for the control of RSV infection. The disease burden due to RSV in pediatric population across India is still not clearly understood so this literature review was therefore conducted to gather data on disease burden due to RSV in Indian pediatric population. Systematic literature search was performed using PubMed and Google search with different medical subject headings from 2007 to 2020. Studies performed in Indian pediatric population were selected for review. Literature review revealed that in India, epidemiology of RSV infection is well documented in young children (0-5 years) as compared to children from other age groups. The rates of RSV detection in various studies conducted in younger children (0-5 years) vary from 2.1% to 62.4% in India which is higher as compared to children from other age groups. In India, RSV mainly peaks around rainy to early winter season, that is, during months of June through October while smaller peak was noted during December, January, and February. In 2020, higher RSV-associated disease burden was reported among children (<5 years) in low-income and lower-middle-income countries. Considering significant disease burden due to RSV in young Indian children, availability of RSV vaccine would be crucial to prevent RSV infections in children and its spread in the community.

Delayed Diagnosis of Respiratory Syncytial Virus Infections in Hospitalized Adults: Individual Patient Data, Record Review Analysis and Physician Survey in the United States

BACKGROUND

Despite the prevalence of respiratory syncytial virus (RSV) in adults hospitalized with acute respiratory infections, guidelines for the diagnosis and management of RSV have not been established. This analysis evaluated the role and timeliness of RSV diagnostic testing and its potential impact on clinical outcomes.

METHODS

We analyzed individual patient data from hospitalized adults with confirmed RSV infections during 2 North American RSV seasons. Participating physicians reported clinical, virologic diagnosis, and outcome variables using a standardized online case form.

RESULTS

Across 32 US states, 132 physicians reported 379 RSV cases. Polymerase chain reaction-based diagnostics were the most common type of test ordered (94.2%) with <5% ordered specifically to diagnose RSV. Most tests (67.6%) were ordered in hospital wards or intensive care units. Overall, 47.4%, 30.9%, and 21.7% of patients had RSV diagnosed <12, 12‒24, and >24 hours after hospital admission, respectively. Later diagnosis was associated with longer hospital stays (n = 145; R = +0.191; P < .05) and greater antibiotic use.

CONCLUSION

Diagnosis of RSV infection in hospitalized adults is often delayed, which may affect clinical management and outcomes. Our findings indicate the need to improve the diagnostic strategies in this patient population.

Molecular epidemiology of influenza, RSV, and other respiratory infections among children in Qatar: A six years report (2012-2017)

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Throughout a five years period, HRV, RSV, and influenza viruses were responsible for two-thirds of acute respiratory infections among children in Qatar.

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RSV, influenza, and HMPV circulated in winter, whereas HRV was highly active during other seasons.

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RSV is more prevalent among infants, while influenza circulates more among children above five years of age.

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Influenza–RSV co-infections are significantly associated with age.

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Gender-dependent differences affect infection rates.

Background

Studies on the etiology of respiratory infections among children in Qatar and surrounding countries are limited.

Objectives

To describe the prevalence and seasonality of RSV, influenza, and other respiratory pathogens among children in Qatar.

Methods

We retrospectively collected and analyzed data of 33,404 children (<15 years) presented with influenza-like illness from 2012 to 2017.

Results

At least one respiratory pathogen was detected in 26,138 (78%) of patients. Together, human rhinoviruses (HRV), respiratory syncytial virus (RSV), and influenza viruses comprised nearly two-thirds of all cases, affecting 24%, 19.7%, and 18.5%, respectively. A prevalence of 5-10% was recorded for adenovirus, parainfluenza viruses (PIVs), human bocavirus (HboV), and human coronaviruses (HCoVs). Human metapneumovirus (HMPV), enteroviruses, M. pneumonia, and parechovirus had prevalences below 5%. While RSV, influenza, and HMPV exhibited strong seasonal activity in the winter, HRV was active during low RSV and influenza circulation. The burden of RSV exceeds that of influenza among young age groups, whereas influenza correlated positively with age. Further, HRV, adenovirus, influenza, and RSV infection rates varied significantly between male and females.

Conclusion

This comprehensive multi-year study provides insights into the etiology of ILI among children in Qatar, which represents the Gulf region. Our results reinforce the significance of active surveillance of respiratory pathogens to improve infection prevention and control strategies, particularly among children.

Safety and immunogenicity of novel modified vaccinia Ankara-vectored RSV vaccine: A randomized phase I clinical trial

Respiratory disease caused by RSV infection is recognized as a severe public health issue in infants, young children and elderly with no specific treatment option. Vaccination may be the most effective strategy to combat this highly infectious virus although no vaccine has been approved. The novel vaccine candidate MVA-BN-RSV encodes RSV surface proteins F and G (subtypes A, B) as well as internal proteins N and M2 in the MVA-BN viral vector backbone to provide broad protection against RSV. This was a first in human study to investigate safety, reactogenicity and immunogenicity of MVA-BN-RSV. Sixty-three participants were allocated to 3 groups: adult (18-49 years) low (1 × 10⁷ TCID₅₀) or high (1 × 10⁸ TCID₅₀) dose and older adult (50-65 years) high dose. Participants in each group were randomized in a 6:1 ratio to receive 2 doses of MVA-BN-RSV or placebo 4 weeks apart and were monitored for 30 weeks. All participants completed the study, receiving both doses. No serious AEs or AEs of special interest were reported. The most common AEs were injection site pain (56% in the combined high dose groups, 17% in the low dose group). MVA-BN-RSV induced robust T cell responses covering all 5 inserts with fold increases ranging from 1.8 to 3.8. Higher and broader responses were observed in the high dose groups (83% responders to at least 3 peptide pools in the combined high dose groups compared to 63% in the low dose group). Moderate but consistent humoral responses were observed against A and B RSV subtypes (up to approximately 2-fold increases in the high dose groups). No differences were observed between the adult and the older adult groups in safety, reactogenicity or immunogenicity. The study demonstrated that the well tolerated MVA-BN-RSV vaccine candidate induces broad cellular and humoral immune responses, warranting further development.

The effects of age on clinical characteristics, hospitalization and mortality of patients with influenza-related illness at a tertiary care centre in Malaysia

Background

Age is an established risk factor for poor outcomes in individuals with influenza‐related illness, and data on its influence on clinical presentations and outcomes in the South‐East Asian settings are scarce. The aim of this study was to determine the above among adults with influenza‐related upper respiratory tract infection at a teaching hospital in Malaysia.

Methods

A retrospective case‐note analysis was conducted on a cohort of 3935 patients attending primary care at the University Malaya Medical Centre, Malaysia from February 2012 till May 2014 with URTI symptoms. Demographics, clinical characteristics, medical and vaccination history were obtained from electronic medical records, and mortality data from the National Registration Department. Comparisons were made between those aged <25, ≥25 to <65 and ≥65 years.

Results

470 (11.9%) had PCR‐confirmed influenza virus infection. Six (1.3%) received prior influenza vaccination. Those aged ≥65 years were more likely to have ≥2 comorbidities (P < .001) and were less likely to present with fever (P = .004). One‐third of those aged ≥65 years experienced hospitalization, intensive care admission or death within a year compared to 10% in the ≥25 to <65 years. Age ≥65 years was an independent predictor of hospitalization and death (OR = 9.97; 95% CI = 3.11‐31.93) compared to those aged <25 years.

Conclusion

Older patients in our cohort were more likely to have comorbidities and present with atypical features, with older age being an independent predictor of poor health outcomes. Our findings will now inform future health policies on older persons and economic modelling of adult vaccination programmes.

Respiratory syncytial virus infections in India: Epidemiology and need for vaccine

Respiratory syncytial virus (RSV) has been identified as a leading cause of lower respiratory tract infections in young children and elderly. It is an enveloped negative-sense RNA virus belonging to Genus Orthopneumovirus. The clinical features of RSV infection range from mild upper-respiratory-tract illnesses or otitis media to severe lower-respiratory-tract illnesses. Current estimates show that about 33.1 million episodes of RSV-acute lower respiratory infection (ALRI) occurred in young children in 2015, of these majority that is, about 30 million RSV-ALRI episodes occurred in low-middle-income countries. In India, the rates of RSV detection in various hospital- and community-based studies mostly done in children vary from 5% to 54% and from 8% to 15%, respectively. Globally, RSV epidemics start in the South moving to the North. In India, RSV mainly peaks in winter in North India and some correlation with low temperature has been observed. Different genotypes of Group A (GA2, GA5, NA1 and ON1) and Group B (GB2, SAB4 and BA) have been described from India. The burden of RSV globally has kept it a high priority for vaccine development. After nearly 50 years of attempts, there is still no licensed vaccine and challenges to obtain a safe and effective vaccine is still facing the scientific community. The data in this review have been extracted from PubMed using the keywords RSV and Epidemiology and India. The data have been synthesised by the authors.

Prevalence of respiratory syncytial virus infection among children hospitalized with acute lower respiratory tract infections in Southern India

BACKGROUND

Respiratory syncytial virus (RSV) is a leading cause of lower respiratory infections among children.

AIM

To investigate the proportion of RSV and non-RSV respiratory viral infections among hospitalized children ≤ 5 years.

METHODS

Hospitalized children aged < 5 years, with a diagnosis of acute lower respiratory infections (ALRI), admitted between August 2011-August 2013, were included. Cases were defined as laboratory-confirmed RSV and non-RSV respiratory viruses by direct fluorescence assay from the nasopharyngeal wash.

RESULTS

Of 383 1-59 mo old children hospitalized with an acute lower respiratory infection, 33.9% (130/383) had evidence of viral infection, and RSV was detected in 24.5% (94/383). Co-infections with RSV and other respiratory viruses (influenza A or B, adenovirus, para influenza 1, 2 or 3) were seen in children 5.5% (21/383). Over 90% of the RSV-positive children were under 2 years of age. RSV was detected throughout the year with peaks seen after the monsoon season. Children hospitalized with RSV infection were more likely to have been exposed to a shorter duration of breastfeeding of less than 3 mo. RSV positive children had a shorter hospital stay, although there were significant complications requiring intensive care. Use of antibiotics was high among those with RSV and non-RSV viral infections.

CONCLUSION

Our study provides evidence of a high proportion of RSV and other virus-associated ALRI among hospitalized children in India. RSV infection was associated with fewer days of hospital stay compared to other causes of lower respiratory infections. A high level of antibiotic use was seen among all respiratory virus-associated hospitalizations. These results suggest the need for implementing routine diagnostics for respiratory pathogens in order to minimize the use of unnecessary antibiotics and plan prevention strategies among pediatric populations.

Analysis of acute respiratory infections due to influenza virus A, B and RSV during an influenza epidemic 2018

PURPOSE

We studied the incidence, morbidity and mortality of all patients presenting in our teaching hospital with proven influenza virus and/or respiratory syncytial virus (RSV) infection during the influenza epidemic season 2018 which was characterized by a predominant incidence of influenza virus B type B of the Yamagata line.

METHODS

In the fall of 2017, specific precaution measures in addition to standard measures were implemented, including standardized testing for influenza virus A,B and RSV by multiplex PCR of pharyngeal swabsData from all consecutive patients were analyzed retrospectively.

RESULTS

Overall 651 patients were examined for the presence of influenza virus and RSV; 214 patients had influenza virus A (n = 36), B (n = 152), and/or RSV (n = 30), including four patients with dual infection. 86% of cases had influenza virus (80% B), and 14% RSV infection. N = 23 cases were treated as outpatients. The rate of acute viral respiratory infections (influenza virus and RSV) was 191 of 2776 (6.9%) admissions to medical wards. Of n = 191 hospitalized cases, n = 44 cases (20.6%) had nosocomial infection. Viral infections were associated with a high morbidity (pneumonia 28.5%, mortality 4.7%). Independent predictors of prolonged hospitalization were the presence of pneumonia, NIV and renal complications, and independent predictors of pneumonia were age ≥ 65 years, bedridden status and CRP ≥ 2.9 mg/dL.

CONCLUSIONS

The rate of nosocomial cases was high despite established precaution measures. RSV was associated with morbidity and mortality comparable to influenza. Pneumonia remains the main complication of acute viral respiratory infections, and antimicrobial treatment should include both antiviral as well as antibacterial agents.

Sequence Analysis of the Fusion Protein Gene of Human Respiratory Syncytial Virus Circulating in China from 2003 to 2014

The human respiratory syncytial virus (HRSV) fusion (F) protein is important for HRSV infection, but few studies have examined the genetic diversity of the F gene from Chinese samples. In this study, a total of 330 HRSV F sequences collected from different regions of China between 2003 and 2014 were analyzed to understand their genetic characteristics. In addition, these sequences were compared with 1150 HRSV F sequences in Genbank from 18 other countries. In phylogenetic analysis, Chinese HRSV F sequences sorted into a number of clusters containing sequences from China as well as other countries. F sequences from different genotypes (as determined based on the G gene sequences) within a HRSV subgroup could be found in the same clusters in phylogenetic trees generated based on F gene sequences. Amino acid analysis showed that HRSV F sequences from China and other countries were highly conserved. Of interest, F protein sequences from all Chinese samples were completely conserved at the palivizumab binding site, thus predicting the susceptibility of these strains to this neutralizing antibody. In conclusion, HRSV F sequences from China between 2003 and 2014, similar to those from other countries, were highly conserved.

Evaluation of Seegene Allplex Respiratory Panel 1 kit for the detection of influenza virus and human respiratory syncytial virus

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Allplex RP1 assay is a highly sensitive, specific, and suitable for detection of FLUV and HRSV, including FLUAV subtyping.

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Allplex RP1 is a hands-on-time saving assay due to the automated nucleic acid extraction and PCR setup on the NIMBUS platform suitable for the hospital routine diagnostic.

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Beyond the respiratory virus detection, Allplex RP1 assay provides a valuable data for epidemiological purposes.

Background

Influenza (FLUV) and human respiratory syncytial (HRSV) viruses are etiological agents of respiratory infections that cause a significant morbidity and mortality worldwide. A rapid and accurate diagnosis of these respiratory viruses is essential for an appropriate patient management. Molecular tests are the best detection option due to their high sensitivity and specificity. Seegene’s Allplex™ Respiratory Panel 1 (Allplex RP1) is a real-time one-step RT-PCR assay for the simultaneous detection of FLUAV, FLUBV, HRSV-A and HRSV-B. In addition, it allows the determination of FLUAV subtype (H1, H3 and H1pdm09).

Objectives

This study aims to evaluate Allplex RP1 as a rapid molecular test for the detection of FLUAV, FLUBV, HRSV-A and HRSV-B viruses.

Study design

The Allplex RP1 assay will be compared with other two commercial molecular assays, Prodesse ProFlu+ and ProFAST+ (Hologic, Madison, WI, USA), and GeneXpert Flu/RSV XC (Cepheid, USA).

Results

Allplex RP1, ProFlu+ and GeneXpert tests showed 95%, 91% and 96% of accuracy; and 94%, 88% and 95% of sensitivity, respectively. Moreover, Allplex RP1 showed a FLUAV subtype sensitivity of 91% and 88% for FLUAV-H1pdm09 and FLUAV-H3 respectively, and ProFAST+ assay showed sensitivities of 100% for both targets. The three assays showed a 100% of specificity and PPV, while the NPV were 84%, 73% and 86% for Allplex RP1, Prodesse and GeneXpert, respectively.

Conclusions

In this study, Seegene’s Allplex RP1 assay showed to be highly sensitive, specific, and suitable for detection of FLUV and HRSV, including FLUAV subtyping. In addition, it is also a hands-on-time saving assay due to the automated nucleic acid extraction and PCR setup.

Influenza A Virus as a Predisposing Factor for Cryptococcosis

Influenza A virus (IAV) infects millions of people annually and predisposes to secondary bacterial infections. Inhalation of fungi within the Cryptococcus complex causes pulmonary disease with secondary meningo-encephalitis. Underlying pulmonary disease is a strong risk factor for development of C. gattii cryptococcosis though the effect of concurrent infection with IAV has not been studied. We developed an in vivo model of Influenza A H1N1 and C. gattii co-infection. Co-infection resulted in a major increase in morbidity and mortality, with severe lung damage and a high brain fungal burden when mice were infected in the acute phase of influenza multiplication. Furthermore, IAV alters the host response to C. gattii, leading to recruitment of significantly more neutrophils and macrophages into the lungs. Moreover, IAV induced the production of type 1 interferons (IFN-α4/β) and the levels of IFN-γ were significantly reduced, which can be associated with impairment of the immune response to Cryptococcus during co-infection. Phagocytosis, killing of cryptococci and production of reactive oxygen species (ROS) by IAV-infected macrophages were reduced, independent of previous IFN-γ stimulation, leading to increased proliferation of the fungus within macrophages. In conclusion, IAV infection is a predisposing factor for severe disease and adverse outcomes in mice co-infected with C. gattii.

Reduced activation and proliferation of human lymphocytes exposed to respiratory syncytial virus compared to cells exposed to influenza virus

Both respiratory syncytial virus (RSV) and influenza A virus (IAV) may infect human peripheral blood mononuclear leukocytes (PBMC) during the immune response to viral challenge as the cells are recruited to the respiratory tract. The current studies demonstrated differences in PBMC responses to the two viruses very early after exposure, including reduced fos protein and CD69 expression and IL-2 production by RSV-exposed T lymphocytes. Exposure to RSV resulted in reduced lymphocyte proliferation despite evidence of a virus-specific T lymphocyte frequency equivalent to that for influenza virus. Reduced RSV-induced proliferation was not due to apoptosis, which was itself reduced relative to that of influenza virus-exposed T lymphocytes. The data indicate that differential immune responses to RSV and influenza virus are determined early after exposure of human PBMC and support the concept that the anamnestic immune response that might prevent clinically evident reinfection is attenuated very soon after exposure to RSV. Thus, candidate RSV vaccines should be expected to reduce but not prevent clinical illness upon subsequent infection by RSV. Furthermore, effective therapeutic agents for RSV are likely to be needed, especially for high-risk populations, even after vaccine development.