Clinical practice of respiratory virus diagnostics in critically ill patients with a suspected pneumonia: A prospective observational study

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.

Epidemiologic Characteristics and Clinical Significance of Respiratory Viral Infections Among Adult Patients Admitted to the Intensive Care Unit

Background

The diagnosis of respiratory viral infections (RVIs) in critically ill patients is important for determining treatment options and adhering to infection-control protocols. However, data on the incidence and occurrence patterns of RVIs are scarce. We investigated the epidemiology and clinical impact of RVIs in critically ill patients.

Methods

This retrospective observational study was conducted in a tertiary hospital in South Korea between November 2014 and September 2020. Adult patients (≥ 18 years of age) who tested positive for an RVI by multiplex polymerase chain reaction (mPCR) and were admitted to the intensive care unit (ICU) were included in the study. Clinical characteristics and outcomes were obtained by reviewing electronic medical records. Pearson's χ2 test and Fisher's exact test, Mann-Whitney U test was used to compare between groups of patients. Trend analysis and the χ2-based Q test was used to analyze test behavior of physicians performing mPCR test.

Results

Among 22,517 patients admitted to the ICU during the study period, 2,222 (9.9%) underwent mPCR testing for an RVI. The median timing of mPCR testing after ICU admission was 1 day (IQR, 0-2). A total of 335 (15.1%) non-duplicative RVI-positive cases were included in the analysis. The incidence rate of RVIs in ICU patients was 30.45 per 10,000 patient-days. The most frequently detected RVI was influenza A (27.8%), followed by rhinovirus (25.4%). Thirty-two (9.6%) RVI-positive patients were diagnosed with upper respiratory infections, 193 (64.1%) with community-acquired, and 108 (35.9%) with hospital-acquired pneumonia. All-cause mortality and mortality related to respiratory tract infection (RTI) were 30.7% and 22.1%, respectively. The initial presentation of septic shock, requirement for mechanical ventilation, and lymphocytopenia were significant predictors of RTI-related mortality. Of the RVI-positive patients, 151 (45.1%) had nonviral coinfections and presented with higher clinical severity and longer hospital stays than patients infected solely with viral pathogens.

Conclusion

The incidence of RVIs in ICU patients is common. ICU patients with RVIs had high mortality and frequently presented with coinfections with nonviral pathogens, which were associated with a higher clinical severity than sole RVI. Increased testing for RVIs will enhance infection-control efforts and improve patient care.

Blood leukocyte transcriptomes in gram-positive and gram-negative community-acquired pneumonia

BACKGROUND

Gram-positive and Gram-negative bacteria are the most common causative pathogens in community-acquired pneumonia (CAP) on the intensive care unit (ICU). The aim of this study was to determine whether the host immune response differs between Gram-positive and Gram-negative CAP upon ICU admission.

METHODS

Sixteen host response biomarkers providing insight in pathophysiological mechanisms implicated in sepsis and blood leukocyte transcriptomes were analysed in patients with CAP upon ICU admission in two tertiary hospitals in the Netherlands.

RESULTS

309 patients with CAP with a definite or probable likelihood (determined by predefined criteria) were included. A causative pathogen was determined in 74.4% of admissions. Patients admitted with Gram-positive CAP (n=90) were not different from those admitted with Gram-negative CAP (n=75) regarding demographics, chronic comorbidities, severity of disease and mortality. Host response biomarkers reflective of systemic inflammation, coagulation activation and endothelial cell function, as well as blood leukocytes transcriptomes, were largely similar between Gram-positive and Gram-negative CAP. Blood leukocyte transcriptomes were also similar in Gram-positive and Gram-negative CAP in two independent validation cohorts. On a pathogen-specific level, Streptococcus pneumoniae and Escherichia coli induced the most distinct host immune response.

CONCLUSION

Outcome and host response are similar in critically ill patients with CAP due to Gram-positive bacteria compared to Gram-negative bacteria.

Experience of establishing severe acute respiratory surveillance in the Netherlands: Evaluation and challenges

The 2009 influenza A (H1N1) pandemic prompted the World Health Organization (WHO) to recommend countries to establish a national severe acute respiratory infections (SARI) surveillance system for preparedness and emergency response. However, setting up or maintaining a robust SARI surveillance system has been challenging. Similar to other countries, surveillance data on hospitalisations for SARI in the Netherlands are still limited, in contrast to the robust surveillance data in primary care. The objective of this narrative review is to provide an overview, evaluation, and challenges of already available surveillance systems or datasets in the Netherlands, which might be used for near real-time surveillance of severe respiratory infections. Seven available surveillance systems or datasets in the Netherlands were reviewed. The evaluation criteria, including data quality, timeliness, representativeness, simplicity, flexibility, acceptability and stability were based on United States Centers for Disease Control and Prevention (CDC) and European Centre for Disease Prevention and Control (ECDC) guidelines for public health surveillance. We added sustainability as additional evaluation criterion. The best evaluated surveillance system or dataset currently available for SARI surveillance is crude mortality monitoring, although it lacks specificity. In contrast to influenza-like illness (ILI) in primary care, there is currently no gold standard for SARI surveillance in the Netherlands. Based on our experience with sentinel SARI surveillance, a fully or semi-automated, passive surveillance system seems most suited for a sustainable SARI surveillance system. An important future challenge remains integrating SARI surveillance into existing hospital programs in order to make surveillance data valuable for public health, as well as hospital quality of care management and individual patient care.

Detection of respiratory viruses in adults with respiratory tract infection using a multiplex PCR assay at a tertiary center

Background

Respiratory viruses (RVs) are among the most common pathogens for both upper and lower respiratory tract infections (RTIs). However, the viral epidemiology of RV-associated RTIs in adults has long been under-recognized. Through a sensitive molecular assay, it would be possible to have a better understanding of the epidemiology of RV-associated RTIs.

Material and methods

Respiratory tract (RT) specimens from adults hospitalized due to RTIs were tested for RVs, using the multiplex PCR-based Luminex xTAG® Respiratory Viral Panel assay. A total of nineteen RVs, including influenza viruses and non-influenza respiratory viruses (NIRVs) were detected. Positive rates were compared using a chi-square test.

Results

A total of 2292 samples from adult patients hospitalized with RTIs were screened for RVs. The overall positive rate was 22%, with 17.8% samples positive for at least one NIRV. NIRVs had a higher positive rate in non-winter seasons. As many as 12.7% (46/363) of the samples collected through broncho-alveolar lavage and 20.5% (176/859) of the samples collected in ICUs were positive for RVs. Distribution of corona virus (CoV), human metapneumovirus (hMPV) and parainfluenza virus (PIV) demonstrated seasonal variation. Also, temperature was associated with the positive rates of specific viruses, including CoV, respiratory syncytial virus (RSV), hMPV and PIV.

Conclusion

Respiratory viruses, notably NIRVs, were frequently detected in adults hospitalized with RTIs. Several RVs were detected with distinctive seasonal variations. A substantial number of RVs were identified in lower RT specimens or from patients admitted to ICU, highlighting their important role in causing severe respiratory infection.

The association between influenza infections in primary care and intensive care admissions for severe acute respiratory infection (SARI): A modelling approach

Background

The burden of severe influenza virus infections is poorly known, for which surveillance of severe acute respiratory infection (SARI) is encouraged. Hospitalized SARI patients are however not always tested for influenza virus infection. Thus, to estimate the impact of influenza circulation we studied how influenza in primary care relates to intensive care unit (ICU) admissions using a modelling approach.

Methods

We used time‐series regression modelling to estimate a) the number of SARI admissions to ICU associated with medically attended influenza infections in primary care; b) how this varies by season; and c) the time lag between SARI and influenza time series. We analysed weekly adult ICU admissions (registry data) and adult influenza incidence (primary care surveillance data) from July 2007 through June 2016.

Results

Depending on the year, 0% to 12% of annual SARI admissions were associated with influenza (0‐554 in absolute numbers; population rate: 0/10 000‐0.39/10 000 inhabitants), up to 27% during influenza epidemics. The average optimal fitting lag was +1 week (SARI trend preceding influenza by 1 week), varying between seasons (−1 to +4) with most seasons showing positive lags.

Conclusion

Up to 12% of yearly SARI admissions to adult ICU are associated with influenza, but with large year‐to‐year variation and higher during influenza epidemics. In most years, SARI increases earlier than medically attended influenza infections in the general population. SARI surveillance could thus complement influenza‐like illness surveillance by providing an indication of the season‐specific burden of severe influenza infections and potential early warning of influenza activity and severity.

Media Reports as a Source for Monitoring Impact of Influenza on Hospital Care: Qualitative Content Analysis

Background

The Netherlands, like most European countries, has a robust influenza surveillance system in primary care. However, there is a lack of real-time nationally representative data on hospital admissions for complications of influenza. Anecdotal information about hospital capacity problems during influenza epidemics can, therefore, not be substantiated.

Objective

The aim of this study was to assess whether media reports could provide relevant information for estimating the impact of influenza on hospital capacity, in the absence of hospital surveillance data.

Methods

Dutch news articles on influenza in hospitals during the influenza season (week 40 of 2017 until week 20 of 2018) were searched in a Web-based media monitoring program (Coosto). Trends in the number of weekly articles were compared with trends in 5 different influenza surveillance systems. A content analysis was performed on a selection of news articles, and information on the hospital, department, problem, and preventive or response measures was collected.

Results

The trend in weekly news articles correlated significantly with the trends in all 5 surveillance systems, including severe acute respiratory infections (SARI) surveillance. However, the peak in all 5 surveillance systems preceded the peak in news articles. Content analysis showed hospitals (N=69) had major capacity problems (46/69, 67%), resulting in admission stops (9/46, 20%), postponement of nonurgent surgical procedures (29/46, 63%), or both (8/46, 17%). Only few hospitals reported the use of point-of-care testing (5/69, 7%) or a separate influenza ward (3/69, 4%) to accelerate clinical management, but most resorted to ad hoc crisis management (34/69, 49%).

Conclusions

Media reports showed that the 2017/2018 influenza epidemic caused serious problems in hospitals throughout the country. However, because of the time lag in media reporting, it is not a suitable alternative for near real-time SARI surveillance. A robust SARI surveillance program is important to inform decision making.

Characteristics of community-acquired respiratory viruses infections except seasonal influenza in transplant recipients and non-transplant critically ill patients

Background/Purpose

Transplant recipients are vulnerable to life-threatening community-acquired respiratory viruses (CA-RVs) infection (CA-RVI). Even if non-transplant critically ill patients in intensive care unit (ICU) have serious CA-RVI, comparison between these groups remains unclear. We aimed to evaluate clinical characteristics and mortality of CA-RVI except seasonal influenza A/B in transplant recipients and non-transplant critically ill patients in ICU.

Methods

We collected 37,777 CA-RVs multiplex real-time reverse transcription-polymerase chain reaction test results of individuals aged ≥18 years from November 2012 to November 2017. The CA-RVs tests included adenovirus, coronavirus 229E/NL63/OC43, human bocavirus, human metapneumovirus, parainfluenza virus 1/2/3, rhinovirus, and respiratory syncytial virus A/B.

Results

We found 286 CA-RVI cases, including 85 solid organ transplantation recipients (G1), 61 hematopoietic stem cell transplantation recipients (G2), and 140 non-transplant critically ill patients in ICU (G3), excluding those with repeated isolation within 30 days. Adenovirus positive rate and infection cases were most prominent in G2 (p < 0.001). The median time interval between transplantation and CA-RVI was 30 and 20 months in G1 and G2, respectively. All-cause in-hospital mortality was significantly higher in G3 than in G1 or G2 (51.4% vs. 28.2% or 39.3%, p = 0.002, respectively). The mechanical ventilation (MV) was the independent risk factor associated with all-cause in-hospital mortality in all three groups (hazard ratio, 3.37, 95% confidence interval, 2.04–5.56, p < 0.001).

Conclusions

This study highlights the importance of CA-RVs diagnosis in transplant recipients even in long-term posttransplant period, and in non-transplant critically ill patients in ICU with MV.

Estimating severity of influenza epidemics from severe acute respiratory infections (SARI) in intensive care units

BACKGROUND

While influenza-like-illness (ILI) surveillance is well-organized at primary care level in Europe, few data are available on more severe cases. With retrospective data from intensive care units (ICU) we aim to fill this current knowledge gap. Using multiple parameters proposed by the World Health Organization we estimate the burden of severe acute respiratory infections (SARI) in the ICU and how this varies between influenza epidemics.

METHODS

We analyzed weekly ICU admissions in the Netherlands (2007-2016) from the National Intensive Care Evaluation (NICE) quality registry (100% coverage of adult ICUs in 2016; population size 14 million) to calculate SARI incidence, SARI peak levels, ICU SARI mortality, SARI mean Acute Physiology and Chronic Health Evaluation (APACHE) IV score, and the ICU SARI/ILI ratio. These parameters were calculated both yearly and per separate influenza epidemic (defined epidemic weeks). A SARI syndrome was defined as admission diagnosis being any of six pneumonia or pulmonary sepsis codes in the APACHE IV prognostic model. Influenza epidemic periods were retrieved from primary care sentinel influenza surveillance data.

RESULTS

Annually, an average of 13% of medical admissions to adult ICUs were for a SARI but varied widely between weeks (minimum 5% to maximum 25% per week). Admissions for bacterial pneumonia (59%) and pulmonary sepsis (25%) contributed most to ICU SARI. Between the eight different influenza epidemics under study, the value of each of the severity parameters varied. Per parameter the minimum and maximum of those eight values were as follows: ICU SARI incidence 558-2400 cumulated admissions nationwide, rate 0.40-1.71/10,000 inhabitants; average APACHE score 71-78; ICU SARI mortality 13-20%; ICU SARI/ILI ratio 8-17 cases per 1000 expected medically attended ILI in primary care); peak-incidence 101-188 ICU SARI admissions in highest-incidence week, rate 0.07-0.13/10,000 population).

CONCLUSIONS

In the ICU there is great variation between the yearly influenza epidemic periods in terms of different influenza severity parameters. The parameters also complement each other by reflecting different aspects of severity. Prospective syndromic ICU SARI surveillance, as proposed by the World Health Organization, thereby would provide insight into the severity of ongoing influenza epidemics, which differ from season to season.

Practical Guidance for Clinical Microbiology Laboratories: Viruses Causing Acute Respiratory Tract Infections

Respiratory viral infections are associated with a wide range of acute syndromes and infectious disease processes in children and adults worldwide. Many viruses are implicated in these infections, and these viruses are spread largely via respiratory means between humans but also occasionally from animals to humans. This article is an American Society for Microbiology (ASM)-sponsored Practical Guidance for Clinical Microbiology (PGCM) document identifying best practices for diagnosis and characterization of viruses that cause acute respiratory infections and replaces the most recent prior version of the ASM-sponsored Cumitech 21 document, Laboratory Diagnosis of Viral Respiratory Disease, published in 1986. The scope of the original document was quite broad, with an emphasis on clinical diagnosis of a wide variety of infectious agents and laboratory focus on antigen detection and viral culture. The new PGCM document is designed to be used by laboratorians in a wide variety of diagnostic and public health microbiology/virology laboratory settings worldwide. The article provides guidance to a rapidly changing field of diagnostics and outlines the epidemiology and clinical impact of acute respiratory viral infections, including preferred methods of specimen collection and current methods for diagnosis and characterization of viral pathogens causing acute respiratory tract infections. Compared to the case in 1986, molecular techniques are now the preferred diagnostic approaches for the detection of acute respiratory viruses, and they allow for automation, high-throughput workflows, and near-patient testing. These changes require quality assurance programs to prevent laboratory contamination as well as strong preanalytical screening approaches to utilize laboratory resources appropriately. Appropriate guidance from laboratorians to stakeholders will allow for appropriate specimen collection, as well as correct test ordering that will quickly identify highly transmissible emerging pathogens.

Impact of microbial Aetiology on mortality in severe community-acquired pneumonia

BACKGROUND

The impact of different classes of microbial pathogens on mortality in severe community-acquired pneumonia is not well elucidated. Previous studies have shown significant variation in the incidence of viral, bacterial and mixed infections, with conflicting risk associations for mortality. We aimed to determine the risk association of microbial aetiologies with hospital mortality in severe CAP, utilising a diagnostic strategy incorporating molecular testing. Our primary hypothesis was that respiratory viruses were important causative pathogens in severe CAP and was associated with increased mortality when present with bacterial pathogens in mixed viral-bacterial co-infections.

METHODS

A retrospective cohort study from January 2014 to July 2015 was conducted in a tertiary hospital medical intensive care unit in eastern Singapore, which has a tropical climate. All patients diagnosed with severe community-acquired pneumonia were included.

RESULTS

A total of 117 patients were in the study. Microbial pathogens were identified in 84 (71.8%) patients. Mixed viral-bacterial co-infections occurred in 18 (15.4%) of patients. Isolated viral infections were present in 32 patients (27.4%); isolated bacterial infections were detected in 34 patients (29.1%). Hospital mortality occurred in 16 (13.7%) patients. The most common bacteria isolated was Streptococcus pneumoniae and the most common virus isolated was Influenza A. Univariate and multivariate logistic regression showed that serum procalcitonin, APACHE II severity score and mixed viral-bacterial infection were associated with increased risk of hospital mortality. Mixed viral-bacterial co-infections were associated with an adjusted odds ratio of 13.99 (95% CI 1.30-151.05, p = 0.03) for hospital mortality.

CONCLUSIONS

Respiratory viruses are common organisms isolated in severe community-acquired pneumonia. Mixed viral-bacterial infections may be associated with an increased risk of mortality.

Duration of Stay of Patients with Community-Acquired Pneumonia in Influenza Season

OBJECTIVES

There is a seasonal variation in the incidence of some infectious diseases. We analyzed the impact of influenza season (IS) on duration of stay (DOS) and some other characteristics of patients with community-acquired pneumonia (CAP).

MATERIALS AND METHODS

In our retrospective cohort study, we analyzed data of 369 patients with CAP.

RESULTS

The mean patient age was 65.5±16.69 years, and 267 (72.4%) patients were male. There was no difference between patients with CAP admitted to hospital and intensive care unit during IS and non-influenza season (NIS) with respect to age, mortality, and DOS. There was no difference in leukocyte and neutrophil counts, C-reactive protein level, and erythrocyte sedimentation rate in different seasons. Although most comorbid disease rates were similar, only cancer, especially lung cancer, was more prevalent in NIS. Bilateral CAP confirmed using thorax computed tomography was more frequent in IS.

CONCLUSION

Although more patients with bilateral pneumonias were hospitalized in IS, DOS was not different between IS and NIS.

Are we missing respiratory viral infections in infants and children? Comparison of a hospital-based quality management system with standard of care

OBJECTIVES

Hospital-based surveillance of influenza and acute respiratory infections relies on International Classification of Diseases (ICD) codes and hospital laboratory reports (Standard-of-Care). It is unclear how many cases are missed with either method, i.e. remain undiagnosed/coded as influenza and other respiratory virus infections. Various influenza-like illness (ILI) definitions co-exist with little guidance on how to use them. We compared the diagnostic accuracy of standard surveillance methods with a prospective quality management (QM) programme at a Berlin children's hospital with the Robert Koch Institute.

METHODS

Independent from routine care, all patients fulfilling pre-defined ILI-criteria (QM-ILI) participated in the QM programme. A separate QM team conducted standardized clinical assessments and collected nasopharyngeal specimens for blinded real-time quantitative PCR for influenza A/B viruses, respiratory syncytial virus, adenovirus, rhinovirus and human metapneumovirus.

RESULTS

Among 6073 individuals with ILI qualifying for the QM programme, only 8.7% (528/6073) would have undergone virus diagnostics during Standard-of-Care. Surveillance based on ICD codes would have missed 61% (359/587) of influenza diagnoses. Of baseline ICD codes, 53.2% (2811/5282) were non-specific, most commonly J06 ('acute upper respiratory infection'). Comparison of stakeholder case definitions revealed that QM-ILI and the WHO ILI case definition showed the highest overall sensitivities (84%-97% and 45%-68%, respectively) and the CDC ILI definition had the highest sensitivity for influenza infections (36%, 95% CI 31.4-40.8 for influenza A and 48%, 95% CI 40.5-54.7 for influenza B).

CONCLUSIONS

Disease-burden estimates and surveillance should account for the underreporting of cases in routine care. Future studies should explore the effect of ILI screening and surveillance in various age groups and settings. Diagnostic algorithms should be based on the WHO ILI case definition combined with targeted testing.

The impact of 13-valent pneumococcal conjugate vaccination on virus-associated community-acquired pneumonia in elderly: Exploratory analysis of the CAPiTA trial

Objectives

Our objective was to evaluate whether vaccination with the 13-valent pneumococcal conjugate vaccine (PCV13) prevents the incidence of community-acquired pneumonia (CAP) caused by influenza (influenza-associated CAP, IA-CAP) or other respiratory viruses in the elderly.

Methods

This analysis was part of the Community-Acquired Pneumonia immunization Trial in Adults (CAPiTA); a double blind, randomized, placebo-controlled trial in 84 496 immunocompetent individuals aged ≥65 years. CAP was defined by clinical and radiological criteria, and oropharyngeal swabs were collected from all individuals referred to a sentinel centre with a clinical suspicion of pneumonia. Presence of influenza A and B, parainfluenza 1, 2, 3 and 4, human adeno-, boca-, corona-, metapneumo-, rhino- and respiratory syncytial viruses was determined by real-time PCR.

Results

Of 3209 episodes of suspected pneumonia, viral aetiology was tested in 2917 and proportions with influenza virus, human metapneumovirus and respiratory syncytial virus were 4.6%, 2.5% and 3.1%, respectively. There were 1653 oropharyngeal swabs for PCR testing available from 1814 episodes that fulfilled criteria for CAP, yielding 23 first episodes of IA-CAP in the PCV13 and 35 in the in placebo group—vaccine efficacy for IA-CAP of 34.4% (95% CI –11.1% to 61.2%; p 0.117). Annual influenza vaccination was received by 672 (87.2%) in the PCV13 group and 719 (87.7%) in the placebo group of the confirmed CAP cases.

Conclusion

In a randomized study of 84 496 elderly individuals with a high uptake of influenza vaccination, PCV13 was not associated with a statistically significant reduction of influenza or virus-associated CAP. Overall incidence of non-influenza viral pneumonia was low.

Prevalence of respiratory viruses among adults, by season, age, respiratory tract region and type of medical unit in Paris, France, from 2011 to 2016

BACKGROUND

Multiplex PCR tests have improved our understanding of respiratory viruses' epidemiology by allowing their wide range detection. We describe here the burden of these viruses in hospital settings over a five-year period.

METHODS

All respiratory samples from adult patients (>20 years old) tested by multiplex-PCR at the request of physicians, from May 1 2011 to April 30 2016, were included retrospectively. Viral findings are reported by season, patient age group, respiratory tract region (upper or lower) and type of clinical unit (intensive care unit, pneumology unit, lung transplantation unit and other medical units).

RESULTS

In total, 7196 samples (4958 patients) were included; 29.2% tested positive, with viral co-infections detected in 1.6% of samples. Overall, two viral groups accounted for 60.2% of all viruses identified: picornaviruses (rhinovirus or enterovirus, 34.3%) and influenza (26.6%). Influenza viruses constituted the group most frequently identified in winter (34.4%), in the upper respiratory tract (32%) and in patients over the age of 70 years (36.4%). Picornavirus was the second most frequently identified viral group in these populations and in all other groups, including lower respiratory tract infections (41.3%) or patients in intensive care units (37.6%).

CONCLUSION

This study, the largest to date in Europe, provides a broad picture of the distribution of viruses over seasons, age groups, types of clinical unit and respiratory tract regions in the hospital setting. It highlights the burden associated with the neglected picornavirus group. These data have important implications for the future development of vaccines and antiviral drugs.

Frequency of respiratory virus infections and next-generation analysis of influenza A/H1N1pdm09 dynamics in the lower respiratory tract of patients admitted to the ICU

Recent molecular diagnostic methods have significantly improved the diagnosis of viral pneumonia in intensive care units (ICUs). It has been observed that 222G/N changes in the HA gene of H1N1pdm09 are associated with increased lower respiratory tract (LRT) replication and worse clinical outcome. In the present study, the frequency of respiratory viruses was assessed in respiratory samples from 88 patients admitted to 16 ICUs during the 2014–2015 winter-spring season in Lombardy. Sixty-nine out of 88 (78.4%) patients were positive for a respiratory viral infection at admission. Of these, 57/69 (82.6%) were positive for influenza A (41 A/H1N1pdm09 and 15 A/H3N2), 8/69 (11.6%) for HRV, 2/69 (2.9%) for RSV and 2/69 (2.9%) for influenza B. Phylogenetic analysis of influenza A/H1N1pdm09 strains from 28/41 ICU-patients and 21 patients with mild respiratory syndrome not requiring hospitalization, showed the clear predominance of subgroup 6B strains. The median influenza A load in LRT samples of ICU patients was higher than that observed in the upper respiratory tract (URT) (p<0.05). Overall, a greater number of H1N1pdm09 virus variants were observed using next generation sequencing on partial HA sequences (codons 180–286) in clinical samples from the LRT as compared to URT. In addition, 222G/N/A mutations were observed in 30% of LRT samples from ICU patients. Finally, intra-host evolution analysis showed the presence of different dynamics of viral population in LRT of patients hospitalized in ICU with a severe influenza infection.