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Background Interactions of Streptococcus pneumoniae with viruses feature in the pathogenesis of numerous respiratory illnesses. Methods We undertook a case-control study among adults at Kaiser Permanente Southern California between 2015 and 2019. Case patients had diagnoses of lower respiratory tract infection (LRTI; including pneumonia or nonpneumonia LRTI diagnoses), with viral infections detected by multiplex polymerase chain reaction testing. Controls without LRTI diagnoses were matched to case patients by demographic and clinical attributes. We measured vaccine effectiveness (VE) for 13-valent (PCV13) against virus-associated LRTI by determining the adjusted odds ratio for PCV13 receipt, comparing case patients and controls. Results Primary analyses included 13 856 case patients with virus-associated LRTI and 227 887 matched controls. Receipt of PCV13 was associated with a VE of 24.9% (95% confidence interval, 18.4%–30.9%) against virus-associated pneumonia and 21.5% (10.9%–30.9%) against other (nonpneumonia) virus-associated LRTIs. We estimated VEs of 26.8% (95% confidence interval, 19.9%–33.1%) and 18.6% (9.3%–27.0%) against all virus-associated LRTI episodes diagnosed in inpatient and outpatient settings, respectively. We identified statistically significant protection against LRTI episodes associated with influenza A and B viruses, endemic human coronaviruses, parainfluenza viruses, human metapneumovirus, and enteroviruses but not respiratory syncytial virus or adenoviruses. Conclusions Among adults, PCV13 conferred moderate protection against virus-associated LRTI. The impacts of pneumococcal conjugate vaccines may be mediated, in part, by effects on polymicrobial interactions between pneumococci and respiratory viruses.

Multiple respiratory viruses can concurrently or sequentially infect the respiratory tract and lead to virus‒virus interactions. Infection by a first virus could enhance or reduce infection and replication of a second virus, resulting in positive (additive or synergistic) or negative (antagonistic) interaction. The concept of viral interference has been demonstrated at the cellular, host, and population levels. The mechanisms involved in viral interference have been evaluated in differentiated airway epithelial cells and in animal models susceptible to the respiratory viruses of interest. A likely mechanism is the interferon response that could confer a temporary nonspecific immunity to the host. During the coronavirus disease pandemic, nonpharmacologic interventions have prevented the circulation of most respiratory viruses. Once the sanitary restrictions are lifted, circulation of seasonal respiratory viruses is expected to resume and will offer the opportunity to study their interactions, notably with severe acute respiratory syndrome coronavirus 2.

Both human respiratory syncytial virus (RSV) and human metapneumovirus (hMPV) cause immune-mediated under-five acute respiratory infections (ARIs), but differences in their disease pathogenesis, if any, are not well-known. This study was undertaken to analyze the epidemiological and immunological features of RSV and hMPV infections. Nasopharyngeal aspirates from children (aged 2 months to 5 years) with ARI, presenting to our tertiary care center between December 2013 and March 2016, were subjected to real-time polymerase chain reaction for the detection of RSV and hMPV. Positive samples were analyzed for co-infection and cytokine levels. Of the 349 nasopharyngeal aspirates, RSV was detected in 40.68% (142/349), hMPV in 6.59% (23/349), and both in 1.4% (5/349). Co-infections were common, with rhinovirus being the most common co-offender. The demographic and clinical parameters of RSV- and hMPV-infected children were comparable. The MMP-9/TIMP-1 ratio was significantly higher in RSV-mediated ARI and IFN-γ in hMPV-mediated ARI. Both RSV and hMPV are common among North Indian children with ARI, and coinfections are common. Their clinical features are non-discriminatory, and molecular diagnosis should be utilized to ascertain their individual epidemiology. The differences in their immune-pathogenesis (MMP-9/TIMP-1 ratio in RSV and IFN-γ in hMPV) could serve as useful tools for developing newer drugs.

OBJECTIVE We evaluated the incidence of influenza and non-influenza respiratory viruses (NIRVs) pre-/post-implementation of public health (PH) measures aimed to decrease COVID-19 transmission using population-based surveillance data. We hypothesized that such measures could reduce the burden of respiratory viruses (RVs) transmitting via the same routes. PATIENTS AND METHODS An interrupted time-series analysis of RV surveillance data in Alberta, Canada from May 2017 – July 2020 was conducted. The burden of influenza and NIRVs before and after intervention initiation at week 11, 2020 was compared. The analysis was adjusted for seasonality, over-dispersion, and autocorrelation. RESULTS During the study period, an average of 708 and 4056 weekly respiratory multiplex molecular panels were conducted pre-/post-intervention respectively. We found significant reductions in test positivity rates in the post-intervention period for influenza (-94.3%; 95% CI -93.8 to 97.4%, p CONCLUSION The implementation of COVID-19 PH measures likely resulted in reduced transmission of common RVs. While drastic lockdowns are unlikely to be required given widespread COVID-19 vaccination, targeted implementation of such measures can lower RV disease burden. Studies to evaluate relative contributions of individual interventions are warranted.

BACKGROUND Human metapneumovirus (HMPVi) and parainfluenza virus (PIVi) infections are common community-acquired infections in lung transplant recipients (LTRs), but data are extremely limited. METHODS A retrospective study including all LTRs at the Johns Hopkins Hospital during July 2010-June 2019 with positive HMPV and PIV polymerase chain reaction respiratory specimens was performed. RESULTS Thirty-one HMPV- and 53 PIV-infected LTRs were identified. LTRs with HMPVi and PIVi had similar baseline characteristics, infection parameters, treatment allocation, and allograft function outcomes. Among entire cohort, 31.6% had chronic allograft dysfunction (CLAD) stage progression within 1 y postinfections (29.2% versus 35.5% for PIVi versus HMPVi, respectively, P = 0.56). In forced expiratory volume in 1 s percent (FEV1%) trajectory analysis showed steadily decline of FEV1 across time among CLAD stage progressors from both viruses. FEV1% decline ≥10% at 90 d had adjusted hazard ratio for CLAD stage progression of 18.4 (4.98-67.76) and 4.6 (1.36-15.34) for PIVi and HMPVi, respectively. PIVi caused higher donor-specific antigen development (11.8% versus 3.2%, P = 0.18) and 1-y mortality (9.4% versus 0%, P = 0.11), compared with HMPVi, even though the results were not statistically significant. Ribavirin did not show protective effect, and mycophenolate discontinuation during infection did not increase risk of CLAD stage progression. CONCLUSIONS One-third of HMPV- and PIV-infected LTRs developed CLAD stage progression within 1 y. The lack of early lung function recovery may predict long-term CLAD progression.

Background To combat the coronavirus disease 2019 (COVID-19) pandemic, nonpharmaceutical interventions (NPIs) were implemented worldwide, which impacted a broad spectrum of acute respiratory infections (ARIs). Methods Etiologically diagnostic data from 142 559 cases with ARIs, who were tested for 8 viral pathogens (influenza virus [IFV], respiratory syncytial virus [RSV], human parainfluenza virus [HPIV], human adenovirus [HAdV], human metapneumovirus [HMPV], human coronavirus [HCoV], human bocavirus [HBoV], and human rhinovirus [HRV]) between 2012 and 2021, were analyzed to assess the changes in respiratory infections in China during the first COVID-19 pandemic year compared with pre-pandemic years. Results Test-positive rates of all respiratory viruses decreased during 2020, compared to the average levels during 2012–2019, with changes ranging from −17.2% for RSV to −87.6% for IFV. Sharp decreases mostly occurred between February and August when massive NPIs remained active, although HRV rebounded to the historical level during the summer. While IFV and HMPV were consistently suppressed year-round, RSV, HPIV, HCoV, HRV, and HBoV resurged and went beyond historical levels during September 2020–January 2021, after NPIs were largely relaxed and schools reopened. Resurgence was more prominent among children Conclusions Activities of respiratory viral infections were reduced substantially in the early phases of the COVID-19 pandemic, and massive NPIs were likely the main driver. Lifting of NPIs can lead to resurgence of viral infections, particularly in children.

Publisher Copyright: © 2021 The Authors. Influenza and Other Respiratory Viruses published by John Wiley & Sons Ltd. Background: The clinical significance of respiratory syncytial virus (RSV) among adults remains underinvestigated. We compared the characteristics and population-based attack rates of RSV and influenza hospitalizations. Methods: During 2018–2020, we recruited hospitalized adults with respiratory infection to our prospective substudy at a tertiary care hospital in Finland and compared the characteristics of RSV and influenza patients. In our retrospective substudy, we calculated the attack rates of all RSV and influenza hospitalizations among adults in the same geographic area during 2016–2020. Results: Of the 537 prospective substudy patients, 31 (6%) had RSV, and 106 (20%) had influenza. Duration of hospitalization, need for intensive care or outcome did not differ significantly between RSV and influenza patients. RSV was more often missed or its diagnosis omitted from medical record (13% vs. 1%, p = 0.016 and 52% vs. 85%, p < 0.001). In the retrospective substudy, the mean attack rates of RSV, influenza A, and influenza B hospitalizations rose with age from 4.1 (range by season 1.9–5.9), 15.4 (12.3–23.3), and 4.7 (0.5–16.2) per 100,000 persons among 18- to 64-year-olds to 58.3 (19.3–117.6), 204.1 (31.0–345.0), and 60.4 (0.0–231.0) per 100,000 persons among 65+-year-olds and varied considerably between seasons. Discussion: While the attack rates of influenza hospitalizations were higher compared with RSV, RSV and influenza hospitalizations were similar in severity. Missing or underreporting of RSV infections may lead to underestimating its disease burden. Both RSV and influenza caused a substantial amount of hospitalizations among the elderly, stressing the need for more effective interventions.

Background Childhood pneumonia in developing countries is the foremost cause of morbidity and death. Fresh information on etiology is needed, considering the changing epidemiology of pneumonia in the setting of greater availability of effective vaccines, changing antibiotic use and improved access to care. We report here the Zambia site results of the Pneumonia Etiology Research for Child Health study on the etiology of pneumonia among HIV-uninfected children in Lusaka, Zambia. Methods We conducted a case-control study of HIV-uninfected children age 1-59 months admitted with World Health Organization-defined severe or very severe pneumonia to a large tertiary care hospital in Lusaka. History, physical examination, chest radiographs (CXRs), blood cultures and nasopharyngeal/oropharyngeal swabs were obtained and tested by polymerase chain reaction and routine microbiology for the presence of 30 bacteria and viruses. From age and seasonally matched controls, we tested blood and nasopharyngeal/oropharyngeal samples. We used the Pneumonia Etiology Research for Child Health integrated analysis to determine the individual and population etiologic fraction for individual pathogens as the cause of pneumonia. Results Among the 514 HIV-uninfected case children, 208 (40.5%) had abnormal CXRs (61 of 514 children were missing CXR), 8 (3.8%) of which had positive blood cultures. The overall mortality was 16.0% (82 deaths). The etiologic fraction was highest for respiratory syncytial virus [26.1%, 95% credible interval (CrI): 17.0-37.7], Mycobacterium tuberculosis (12.8%, 95% CrI: 4.3-25.3) and human metapneumovirus (12.8%, CrI: 6.1-21.8). Conclusions Childhood pneumonia in Zambia among HIV-uninfected children is most frequently caused by respiratory syncytial virus, M. tuberculosis and human metapneumovirus, and the mortality remains high.

Background Respiratory tract infections are common, often seasonal, and caused by multiple pathogens. We assessed whether seasonal respiratory illness patterns changed during the COVID-19 pandemic. Methods We categorized emergency department (ED) visits reported to the National Syndromic Surveillance Program according to chief complaints and diagnosis codes, excluding visits with diagnosed SARS-CoV-2 infections. For each week during 1 March 2020 through 26 December 2020 (“pandemic period”), we compared the proportion of ED visits in each respiratory category with the proportion of visits in that category during the corresponding weeks of 2017–2019 (“pre–pandemic period”). We analyzed positivity of respiratory viral tests from 2 independent clinical laboratories. Results During March 2020, cough, shortness of breath, and influenza-like illness accounted for twice as many ED visits compared with the pre–pandemic period. During the last 4 months of 2020, all respiratory conditions, except shortness of breath, accounted for a smaller proportion of ED visits than during the pre–pandemic period. Percent positivity for influenza virus, respiratory syncytial virus, human parainfluenza virus, adenoviruses, and human metapneumovirus was lower in 2020 than 2019. Although test volume decreased, percent positivity was higher for rhinovirus/enterovirus during the final weeks of 2020 compared with 2019, with ED visits similar to the pre–pandemic period. Conclusions Broad reductions in respiratory test positivity and respiratory ED visits (excluding COVID-19) occurred during 2020. Interventions for mitigating spread of SARS-CoV-2 likely also reduced transmission of other pathogens. Timely surveillance is needed to understand community health threats, particularly when current trends deviate from seasonal norms.

Objective To determine the presence of genetic material from potentially infectious airborne respiratory virus pathogens in a pediatric emergency department (PED) waiting room. Methods A cross-sectional study in the waiting room area of PED at Santo Antonio Children's Hospital, Porto Alegre, in southern Brazil. The room air samples were collected with a portable cyclone sampler (Coriolis®), twice a day (8 a.m. and 8 p.m.), during 5 consecutive weekdays, during two seasons, fall and spring (20 samples), in 2016. Reverse transcription polymerase chain reaction was used to detect influenza A, influenza B, parainfluenza 2, parainfluenza 3, human metapneumovirus, respiratory syncytial virus, human adenovirus, human bocavirus, and Bordetella pertussis. The PED provides care to an average of 6000 patients per month and the age of patients ranges from 1 month to 17 years old. It is waiting area has 645 ft square. Results Genetic material from pathogens was detected in 12 out of 20 samples (60%). In 5 samples, more than one pathogen of respiratory virus was identified. Human adenovirus was the most frequent pathogen (n = 9/52%), followed by Bordetella pertussis (n = 4/24%), respiratory syncytial virus (n = 2/12%) and human bocavirus (n = 2/12%). Season and number of people in the waiting room were not associated with the presence of genetic material from pathogens. Conclusions Genetic material from pathogens potentially associated with severe respiratory diseases was found in the room air of a pediatric ED waiting room.

Background: Outbreaks cause significant morbidity and mortality in healthcare settings. Current testing methods can identify specific viral respiratory pathogens, yet the approach to outbreak management remains general. Objectives: Our aim was to examine pathogen-specific trends in respiratory outbreaks, including how attack rates, case fatality rates and outbreak duration differ by pathogen between hospitals and long-term care (LTC) and retirement homes (RH) in Ontario. Methods: Confirmed respiratory outbreaks in Ontario hospitals and LTC/RH reported between September 1, 2007, and August 31, 2017, were extracted from the integrated Public Health Information System (iPHIS). Median attack rates and outbreak duration and overall case fatality rates of pathogen-specific outbreaks were compared in both settings. Results: Over the 10-year surveillance period, 9,870 confirmed respiratory outbreaks were reported in Ontario hospitals and LTC/RH. Influenza was responsible for most outbreaks (32% in LTC/RH, 51% in hospitals), but these outbreaks were shorter and had lower attack rates than most non-influenza outbreaks in either setting. Human metapneumovirus, while uncommon (

Background: Human metapneumovirus (hMPV) is a major novel cause of acute respiratory infections ranging from wheezing to bronchiolitis and pneumonia in children worldwide. The aim of this study was to detect hMPV in hospitalized children with acute respiratory tract infections (ARTIs) by using reverse transcription-loop mediated isothermal amplification (RT-LAMP) assay. Methods and Results: A total of 68 children with ARTIs who were clinically suspected of acquiring hMPV were included in the study in the period between January 2019 and February 2020. Posterior-pharyngeal (throat) swabs were obtained from each patient. hMPV RNA was revealed in 18(26.5%) cases. The age range was from

Objective: This study aimed to report viral respiratory pathogens during the coronavirus disease 2019 (COVID-19) pandemic. Materials and Methods: Other viral pathogens were identified. COVID-19 immunoglobulin M and immunoglobulin G were detected. Results: Of the 56 samples collected from women, 2 (3.5%) were positive for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), whereas 8 (10%) of the 80 samples from men were positive for SARS-CoV-2. The number of respiratory syncytial virus-A--positive cases was 6 (10.7%) in women and 14 (17.5%) in men. Two (3.5%) of the women were positive for parainfluenza-3, and 6 of the men were positive for influenza-B. The number of human metapneumovirus (HMPV)--positive women and men was 6 (10.7%) and 6 (7.5%), respectively. Rhinovirus caused 14.2% and 10% of the cases in men and women, respectively. With a ratio of 10.7% in women and 7.5% in men;SARS-CoV-2, with a ratio of 10% in men and 3.5% in women;influenza-B, with a ratio of 7.5% in men;and parainfluenza-3 and 4, with a ratio of 3.5% in women. SARS-CoV-2 had a mean incidence rate of 7% in men and women. The antibody screening results reveal that antibody formation did not occur in 3 women among the 10 patients who were diagnosed with COVID-19, and antibody formation occurred in 2 of 7 men. Antibody formation occurred in 5 women (16.6%) and 7 men (20.5%) among the 58 patients who were positive for other respiratory tract pathogens. However, 23 (29.5%) of the blood samples collected from 78 individuals who were negative for the COVID-19 agent and other respiratory tract viral pathogens were positive for the COVID-19 antibody. Conclusion: Because the climate is colder than normal in areas settled at higher altitudes, more than one pathogens act together. In addition, respiratory infections are seen in all seasons. This causes the diseases to be fewer and milder than in other regions. [ABSTRACT FROM AUTHOR] Copyright of Eurasian Journal of Medicine is the property of Ataturk University, School of Medicine and its content may not be copied or emailed to multiple sites or posted to a listserv without the copyright holder's express written permission. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)

Respiratory infections are one of the most frequent reasons for medical consultations in children. In low resource settings such as in Lao People's Democratic Republic, knowledge gaps and the dearth of laboratory capacity to support differential diagnosis may contribute to antibiotic overuse. We studied the etiology, temporal trends, and genetic diversity of viral respiratory infections in children to provide evidence for prevention and treatment guidelines. From September 2014 to October 2015, throat swabs and nasopharyngeal aspirates from 445 children under 10 years old with symptoms of acute respiratory infection were collected at the Children Hospital in Vientiane. Rapid antigen tests were performed for influenza A and B and respiratory syncytial virus. Real‐time reverse‐transcription polymerase chain reactions (RT‐PCRs) were performed to detect 16 viruses. Influenza infections were detected with a higher sensitivity using PCR than with the rapid antigen test. By RT‐PCR screening, at least one pathogen could be identified for 71.7% of cases. Human rhinoviruses were most frequently detected (29.9%), followed by influenza A and B viruses combined (15.9%). We identify and discuss the seasonality of some of the infections. Altogether these data provide a detailed characterization of respiratory pathogens in Lao children and we provide recommendations for vaccination and further studies.

Background We hypothesized that nationwide social distancing and other preventive measures for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were associated with reduced detection of other respiratory viruses in South Korea. Methods We analyzed national surveillance data to compare incidence of respiratory viruses during 2016–2019 vs 2020. Results of multiplex reverse-transcription polymerase chain reaction assays for 8 respiratory viruses were included: adenovirus (ADV), parainfluenza virus (PIV), respiratory syncytial virus (RSV), influenza virus (IFV), human coronavirus (HCoV; non–SARS-CoV-2), human rhinovirus (HRV), human bocavirus (HBoV), and human metapneumovirus (HMPV). Results During 2016–2019, rates of detection of respiratory viruses were relatively stable: ADV, 3.7%–9.2%; PIV, 1.4%–17.0%; RSV, 0.3%–15.3%; IFV, 0.4%–35.6%; HCoV, 1.5%–8.4%; HRV, 7.0%–25.1%; HBoV, 0.6%–6.3%; and HMPV, 0.7%–14.5%. Following implementation of social distancing in February 2020, rates of detection of enveloped viruses (HCoV, HMPV, IFV, PIV, and RSV) were significantly reduced by up to 100%. However, nonenveloped viruses (ADV, HRV, and HBoV) persisted throughout 2020, and HRV rates in hospitalized patients significantly increased. Conclusions After implementation of social distancing for SARS-CoV-2 in South Korea, rates of detection of enveloped respiratory viruses decreased significantly, whereas nonenveloped viruses persisted, suggesting that enhanced infection prevention strategies are required to mitigate spread of these viruses.

Background: Like endemic coronaviruses, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is believed to have emerged in humans from a zoonotic source and may ultimately develop a seasonal pattern. A seasonal pattern, particularly if combined with other seasonal outbreaks of respiratory virus infections, may have significant impacts on the healthcare system. We evaluated the seasonal pattern of existing endemic coronaviruses and several other common respiratory viruses to determine the potential impacts of added burden of respiratory disease should SARS-CoV-2 establish seasonality. Methods: National surveillance data for laboratory confirmations of endemic coronaviruses, influenza A and B viruses, rhinovirus/enterovirus, human metapneumovirus, respiratory syncytial virus and parainfluenza virus for the past 10 years were obtained from the Government of Canada Open Data and FluWatch. Epidemic curves were generated from total case numbers and percent of samples testing positive for each respiratory virus by epidemiological week. Results: In Canada, endemic coronaviruses and other common respiratory viruses cause annual seasonal outbreaks in the winter months. Should SARS-CoV-2 develop a seasonal pattern similar to endemic coronaviruses and respiratory viruses, co-circulation would be expected to peak between January and March. Peak endemic coronavirus activity occurs during the nadir of rhinovirus/enterovirus and parainfluenza activity. Conclusion: Healthcare settings, assisted-living and long-term care homes, schools and essential services employers should anticipate and have contingencies for seasonal outbreaks of SARS-CoV-2 and co-circulating respiratory viruses during peak seasons. Given the likelihood of co-circulation, diagnostic multiplex testing targeting co-circulating pathogens may be more efficient than single target assays for symptomatic individuals if a seasonal pattern to coronavirus disease 2019 (COVID-19) is established.

Human metapneumovirus (hMPV) is an enveloped virus that causes serious respiratory tract infection among immunocompromised populations especially haematopoietic stem cell transplant (HSCT) recipients. Here, we describe 3 cases of hMPV infection which led to mortality among post HSCT adults. 66 post HSCT adults enrolled between January 2017 and March 2019 at Dr. B. R. Ambedkar Institute Rotary Cancer Hospital, AIIMS, New Delhi, were followed up for a period varying from 16 days to 18 months for any episode of respiratory illness until March 2019. Real time reverse transcriptase polymerase chain reaction (rRT-PCR) was used to detect the virus from appropriate specimens when symptoms of acute respiratory infection appeared. Samples from 88 out of a total of 172 episodes of suspected acute respiratory infection could be tested by rRT-PCR. Of these, 9 episodes were positive for hMPV. Three patients with hMPV associated lower respiratory tract infection (LRTI) expired within 30 days of HSCT. The possible risk factors associated with mortality included LRTI, infection during early post-transplant period (first week following HSCT), absolute lymphocyte count less than 200/µl, absolute neutrophil count less than 500/µl, use of steroid within 30 days prior to infection and need for mechanical ventilation.

Background: The first outbreak of coronavirus disease 2019 (COVID-19) occurred in March 2020 in Europe, which is normally the peak incidence period of human metapneumovirus (HMPV) infections, implying cocirculation and potentially causing competition between them. Methods: We investigated differences in clinical characteristics and outcomes of HMPV infections in hospitalized patients before (January 2016–28 February, 2020) and HMPV and COVID-19 during part of the COVID-19 pandemic (28 February, 2020–1 April, 2020). Results: A total of 239 HMPV patients and 303 COVID-19 patients were included. Incidence of HMPV peaked in March. Despite a 324% increase in HMPV testing during the COVID-19 outbreak, incidence of HMPV remained stable. Clinical characteristics showed 25 (11%) ICU admissions and 14 (6%) deaths. History of myocardial infarction, higher age and lower BMI were independently associated with increased 30-day mortality. Clinical characteristics of HMPV-infected patients did not differ between the non-COVID-19 period and the examined COVID-19 period except for length of hospital stay (7 vs. 5 days). HMPV infection and COVID-19 shared many clinical features but HMPV was associated with female gender, elderly patients and chronic conditions (COPD and chronic heart failure). Clinical outcomes did not differ between the viruses during the COVID-19 period. Conclusions: The clinical impact of HMPV infection did not change during the COVID-19 outbreak in terms of incidence and/or disease severity; hence, HMPV and SARS-CoV-2 are probably co-circulating independently. Despite the current clinical focus on the COVID-19 pandemic, clinicians should keep in mind that HMPV-infection may mimic COVID-19 and is also associated with serious adverse outcomes.

The clinical significance of molecular detection of respiratory viruses in bronchoalveolar lavage (BAL) samples is poorly defined. We performed an observational retrospective study including all patients who underwent a BAL procedure in our institution, regardless of the reason for bronchoscopy, from January 2015-December 2018. Respiratory viruses were detected by real-time polymerase chain reaction with a commercial multiplex panel, and a cell culture was performed to detect cytomegalovirus and herpes simplex virus. Positive results were correlated with clinical symptoms and patients' characteristics. Of 540 BAL samples analysed, 113 (20.9%) were positive for any respiratory virus. Viral detection was significantly associated with respiratory symptoms (83.2% vs 68.9%, P=.004) and radiological infiltrates (67.3% vs 52.2%, P=.006). The most frequent viruses detected were rhinovirus (42/113, 37.2%), influenza virus (20/113, 17.7%) and parainfluenza virus (PIV) (16/113, 14.2%). Respiratory pathogens codetections were found in 51/113 (45.1%) BAL samples, including more than one virus (16/51, 31.4%), fungi (8/51, 15.7%, and bacteria (9/51, 17.6%). Viral detection was significantly higher in immunocompromised patients (26.5% vs 16.9%; P=.022). PIV and human metapneumovirus were mostly observed in lung (50.0%, 8/16) and haemopoietic transplant recipients (25%, 2/8), respectively, with clinical repercussions. Our data underline that molecular diagnosis allows identification of viral agents as the aetiology of respiratory infections; however, the high frequency of co-detections hinders identification of the agent responsible for the current respiratory symptomatology. Immunocompromised patients are the target population in whom to investigate the presence of respiratory viruses in their BAL samples. This article is protected by copyright. All rights reserved.

Objective Respiratory viruses are the most important cause of lower respiratory tract infections (LRTI) in children. Meteorological factors can influence viral outbreaks. The objective of this study was to determine the association between climate variables and respiratory virus detection.Methods Multicenter prospective 1-year surveillance was conducted among children hospitalized for LRTI in Tunisia. Nasopharyngeal aspirates were tested by direct immunofluorescence assay (DIFA) for the detection of respiratory syncytial virus (RSV); adenovirus (AdV); influenza virus (IFV) A and B; and parainfluenza virus 1, 2, and 3 (PIV1/2/3). Samples were further analyzed by reverse-transcription polymerase chain reaction for the detection of human metapneumovirus (hMPV). Monthly meteorological data were determined by consulting the National Institute of Meteorology and the World Weather Online Meteorological Company websites. Pearson's correlation tests were used to determine the statistical association between the detection of respiratory viruses and climatic characteristics.Results Among 572 patients, 243 (42.5%) were positive for at least one virus. The most frequently detected viruses by DIFA were RSV (30.0%), followed by IFVA (3.8%), IFVB (3.5%), PIV (0.9%), and AdV (0.9%). HMPV was detected in 13 RSV-negative samples (3.3%). Dual infections were detected in seven cases (1.2%). Monthly global respiratory viruses and RSV detections correlated significantly with temperature, rainfall, cloud cover, wind speed, wind temperature, and duration of sunshine. Monthly IFV detection significantly correlated with rainfall, wind speed, wind temperature, and duration of sunshine. HMPV detection significantly correlated with temperature and wind temperature.Conclusion Respiratory viral outbreaks are clearly related to meteorological factors in Tunisia.

Respiratory tract infections (RTIs) are the most common diseases globally among children. This study aimed to assess the epidemiology of admission-requiring pediatric RTI cases and evaluate the effect of the pathogen type on the length of hospital stay (LOS) using the FilmArray® respiratory panel, a multiplex PCR test. The age-specific distribution and seasonality of viruses were investigated between March 26, 2018 and April 12, 2019. Multivariable linear regression analyses were performed to evaluate the effect of pathogen type and coinfection on LOS. Among 153 hospitalized RTI patients, respiratory syncytial virus was the leading cause of hospitalization in infants < 12 months of age (27.7%). Human metapneumovirus and parainfluenza virus were also major causes of hospitalization in patients aged 2-3 years (22.6% and 22.6%, respectively). In the multivariable linear regression model excluding rhinovirus/enterovirus, there was a significant association between viral coinfection and longer LOS (p = 0.012), while single viral infection of any type was not positively correlated with LOS. This study revealed the epidemiology of admission-requiring pediatric RTIs.

Background We assessed performance of participant-collected midturbinate nasal swabs compared to study staff-collected midturbinate nasal swabs for the detection of respiratory viruses among pregnant women in Bangkok, Thailand. Methods We enrolled pregnant women aged ≥18 years and followed them throughout the 2018 influenza season. Women with acute respiratory illness self-collected midturbinate nasal swabs at home for influenza viruses, respiratory syncytial viruses (RSV), and human metapneumoviruses (hMPV) real-time RT-PCR testing and the study nurse collected a second midturbinate nasal swab during home visits. Paired specimens were processed and tested on the same day. Results The majority (109, 60%) of 182 participants were 20–30 years old. All 200 paired swabs had optimal specimen quality. The median time from symptom onsets to participant-collected swabs was 2 days and to staff-collected swabs was also 2 days. The median time interval between the 2 swabs was 2 hours. Compared to staff-collected swabs, the participant-collected swabs were 93% sensitive and 99% specific for influenza virus detection, 94% sensitive and 99% specific for RSV detection, and 100% sensitive and 100% specific for hMPV detection. Conclusions Participant-collected midturbinate nasal swabs were a valid alternative approach for laboratory confirmation of influenza-, RSV-, and hMPV-associated illnesses among pregnant women in a community setting.

Objectives: This study determined associations between respiratory viruses and subsequent illness course in primary care adult patients presenting with acute cough and/or suspected lower respiratory tract infection. Methods: A prospective European primary care study recruited adults with symptoms of lower respiratory tract infection between November 2007 and April 2010. Real-time in-house polymerase chain reaction (PCR) was performed to test for six common respiratory viruses. In this secondary analysis, symptom severity (scored 1 = no problem, 2 = mild, 3 = moderate, 4 = severe) and symptom duration were compared between groups with different viral aetiologies using regression and Cox proportional hazard models, respectively. Additionally, associations between baseline viral load (cycle threshold (Ct) value) and illness course were assessed. Results: The PCR tested positive for a common respiratory virus in 1354 of the 2957 (45.8%) included patients. The overall mean symptom score at presentation was 2.09 (95% confidence interval (CI) 2.07-2.11) and the median duration until resolution of moderately bad or severe symptoms was 8.70 days (interquartile range 4.50-11.00). Patients with influenza virus, human metapneumovirus (hMPV), respiratory syncytial virus (RSV), coronavirus (CoV) or rhinovirus had a significantly higher symptom score than patients with no virus isolated (0.07-0.25 points or 2.3-8.3% higher symptom score). Time to symptom resolution was longer in RSV infections (adjusted hazard ratio (AHR) 0.80, 95% CI 0.65-0.96) and hMPV infections (AHR 0.77, 95% CI 0.62-0.94) than in infections with no virus isolated. Overall, baseline viral load was associated with symptom severity (difference 0.11, 95% CI 0.06-0.16 per 10 cycles decrease in Ct value), but not with symptom duration. Conclusions: In healthy, working adults from the general community presenting at the general practitioner with acute cough and/or suspected lower respiratory tract infection other than influenza impose an illness burden comparable to influenza. Hence, the public health focus for viral respiratory tract infections should be broadened. (C) 2020 Published by Elsevier Ltd on behalf of European Society of Clinical Microbiology and Infectious Diseases.

Objective The aim: Is to provide data on the presence of potential pathogens of ARTIs in children in Ukraine. Patients and methods Materials and methods: The etiology of ARTIs was investigated in 487 children in MC 'Eurolab', Kyiv, Ukraine during 2018-2020 years. Seven respiratory viruses - Respiratory Syncytial virus (RSV), Parainfluenza virus (PIV), Adenovirus (AdV), human Metapneumovirus (MPV), Rhinovirus (RV), human Bocavirus (BoV), Coronavirus (CoV), were identified by PCR. Qualitative detection of Influenza type A, type B, Group A Streptococcal was performed by chromatographic immunoassay. Pathogens profiles, clinical characteristics and seasonality were analyzed. Results Results: 487 nasal and throat swabs from children with ARVI were collected. 400 (82,1%) samples were found to be positive: 319 swabs were positive at least for one respiratory virus, 43 children had positive rapid influenza test, 38 - positive strep test. A total of 403 viruses were identified. RV (27,1%), ADV (13,4%), RSV (13,2 %), IVA (10,7 %) were the most commonly identified viruses. Conclusion Conclusions: Detection of viral seasonality in Ukraine and estimating of clinical features in case of infection allows predicting probable clinical course of disease, to provide, optimize the therapy and to develop preventive measures, vaccination, in particular.

Background Acute respiratory tract infections are a serious clinical burden in infants; human metapneumovirus (HMPV) is an important etiological agent. We investigated genotypic variation and molecular epidemiological patterns among infants infected with HMPV in Sarlahi, Nepal, to better characterize infection in a rural, low-resource setting. Methods Between May 2011 and April 2014, mid-nasal swabs were collected from 3528 infants who developed respiratory symptoms during a longitudinal maternal influenza vaccine study. Sequencing glycoprotein genes permitted genotyping and analyses among subtypes. Results HMPV was detected by reverse-transcriptase polymerase chain reaction (RT-PCR) in 187 (5%) infants, with seasonality observed during fall and winter months. Phylogenetic investigation of complete and partial coding sequences for the F and G genes, respectively, revealed that 3 genotypes were circulating: A2, B1, and B2. HMPV-B was most frequently detected with a single type predominating each season. Both HMPV genotypes exhibited comparable median viral loads. Clinically significant differences between genotypes were limited to increased cough duration and general respiratory symptoms for type B. Conclusions In rural Nepal, multiple HMPV genotypes circulate simultaneously with an alternating predominance of a single genotype and definitive seasonality. No difference in viral load was detected by genotype and symptom severity was not correlated with RT-PCR cycle threshold or genotype.

Coronavirus disease 2019 (COVID-19) is a severe infectious disease of the respiratory tract caused by a novel coronavirus, severe acute respiratory syndrome coronavirus 2, and has a high mortality rate. The disease emerged from Wuhan, China, in late 2019, and spread to Japan, including Hokkaido, in January 2020. In February 2020, 3 children were diagnosed with COVID-19 in Furano, Hokkaido, Japan. During this period, influenza and human metapneumovirus infections were prevalent among children in the Furano region. Two of the 3 patients experienced co-infection with other respiratory viruses, including influenza virus A or human metapneumovirus. To the authors' knowledge, the cases described in the present report were the first pediatric patients with COVID-19 in Japan. In children with COVID-19, the possibility of co-infection with other respiratory pathogens should be considered.

In the last months of 2019, an outbreak of fatal respiratory disease started in Wuhan, China, and quickly spread to other parts of the world. It was named COVID-19, and to date, thousands of cases of infection and death are reported worldwide. This disease is associated with a wide range of symptoms, which makes accurate diagnosis of it difficult. During previous severe acute respiratory syndrome (SARS) pandemic in 2003, researchers found that the patients with fever, cough, or sore throat had a 5% influenza virus-positive rate. This finding made us think that the wide range of symptoms and also relatively high prevalence of death in our patients may be due to the coinfection with other viruses. Thus, we evaluated the coinfection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) with other respiratory viruses in dead patients in North Khorasan. We evaluated the presence of influenza A/B virus, human metapneumovirus, bocavirus, adenovirus, respiratory syncytial virus (RSV), and parainfluenza viruses in 105 SARS-CoV-2 positive dead patients, using polymerase chain reaction (PCR) and reverse transcription PCR tests. We found coinfection with influenza virus in 22.3%, RSV, and bocavirus in 9.7%, parainfluenza viruses in 3.9%, human metapneumovirus in 2.9%, and finally adenovirus in 1.9% of SARS-CoV-2 positive dead cases. Our findings highlight a high prevalence of coinfection with influenza A virus and the monopoly of coinfection with Human metapneumovirus in children.

Background For pediatric pneumonia, the meteorological and air pollution indicators have been frequently investigated for their association with viral circulation but not for their impact on disease severity. Methods We performed a 10-year prospective, observational study in 1 hospital in Chongqing, China, to recruit children with pneumonia. Eight commonly seen respiratory viruses were tested. Autoregressive distributed lag (ADL) and random forest (RF) models were used to fit monthly detection rates of each virus at the population level and to predict the possibility of severe pneumonia at the individual level, respectively. Results Between 2009 and 2018, 6611 pediatric pneumonia patients were included, and 4846 (73.3%) tested positive for at least 1 respiratory virus. The patient median age was 9 months (interquartile range, 4‒20). ADL models demonstrated a decent fitting of detection rates of R2 > 0.7 for respiratory syncytial virus, human rhinovirus, parainfluenza virus, and human metapneumovirus. Based on the RF models, the area under the curve for host-related factors alone was 0.88 (95% confidence interval [CI], .87‒.89) and 0.86 (95% CI, .85‒.88) for meteorological and air pollution indicators alone and 0.62 (95% CI, .60‒.63) for viral infections alone. The final model indicated that 9 weather and air pollution indicators were important determinants of severe pneumonia, with a relative contribution of 62.53%, which is significantly higher than respiratory viral infections (7.36%). Conclusions Meteorological and air pollution predictors contributed more to severe pneumonia in children than did respiratory viruses. These meteorological data could help predict times when children would be at increased risk for severe pneumonia and when interventions, such as reducing outdoor activities, may be warranted.

Community-acquired pneumonia (CAP) is a major cause of morbidity and mortality worldwide. There is growing appreciation of the burden of noninfluenza viral pathogens in CAP. Due to multiple factors including pneumococcal vaccination programs, declining rates of cigarette smoking, an aging population, and increasingly sensitive diagnostic tests, respiratory viruses are now the most common pathogens detected in CAP, outpacing Streptococcus pneumoniae. Noninfluenza respiratory pathogens are widely accepted as causal pathogens in CAP including in immunocompetent patients. This review provides an overview of five noninfluenza respiratory viral pathogens commonly implicated in CAP pathogenesis: rhinovirus, human metapneumovirus, respiratory syncytial virus, human parainfluenza virus, and human adenoviruses. Nucleic acid amplification testing platforms and their impact on antimicrobial stewardship efforts are also considered.

The novel coronavirus SARS‐CoV‐2 has rapidly spread around the world, causing serious illness and death and creating a heavy burden on the health care systems of many countries. Since the virus first emerged in late November 2019, its spread has coincided with peak circulation of several seasonal respiratory viruses, yet some studies have noted limited coinfections between SARS‐CoV‐2 and other viruses. We use a mathematical model of viral coinfection to study SARS‐CoV‐2 coinfections, finding that SARS‐CoV‐2 replication is easily suppressed by many common respiratory viruses. According to our model, this suppression is because SARS‐CoV‐2 has a lower growth rate (1.8 /d) than the other viruses examined in this study. The suppression of SARS‐CoV‐2 by other pathogens could have implications for the timing and severity of a second wave. This article is protected by copyright. All rights reserved.

Knowledge regarding the prevalence, clinical features and etiology of pediatric influenza-like illness (ILI) remains limited in African settings. Furthermore, it is likely that many children presenting with ILI receive antibiotics unnecessarily. More data are required to develop antimicrobial stewardship practice and guide effective vaccine strategies. We undertook a 1-year prospective study of ILI in the Gambia.Children5 years of age presenting with ILI from March 2018 to March 2019 were recruited. Clinical and antibiotic prescribing data were collected. Nasopharyngeal swabs were collected and analyzed for 12 respiratory viruses using a multiplex polymerase chain reaction.From a total of 735 ILI episodes, 530 (72.1%) nasopharyngeal swabs were positive for ≥1 virus. Of these, 36.7% were positive for rhinovirus, 14.7% for respiratory syncytial virus, 8.4% for influenza and 7.2% for human metapneumovirus. Compared with children6 months of age, influenza was more common in 6- to 23-month-old children [odd ratio (OR): 5.68; 95% confidence interval (CI): 1.72-18.76; P = 0.004]. Respiratory syncytial virus and human metapneumovirus were associated with low peripheral oxygen saturations (OR: 2.13; 95% CI: 1.23-3.69; P = 0.007; and OR: 2.44; 95% CI: 1.13-5.27; P = 0.023, respectively). Antibiotics were prescribed in 78.3% of all ILI cases.A broad range of viruses are responsible for pediatric ILI in the Gambia. Refined treatment guidelines, improved diagnostic capacity and vaccines to prevent respiratory viruses will all play a role in reducing antimicrobial use for these cases.

Background:Lower respiratory tract infections caused by respiratory syncytial virus can be severe during infancy, which requires admission to the hospital. These infections may be more severe especially in patients with congenital heart disease. Passive immunisation with palivizumab, a monoclonal antibody, is recommended in high-risk infants. We tried to determine the compliance rates, factors affecting compliance, and also other microorganisms responsible for lower respiratory tract infections after palivizumab prophylaxis in these patients.Methods:We evaluated patients’ compliance to prophylaxis with palivizumab in two consecutive respiratory syncytial virus seasons from pharmacy records. We also investigated factors affecting compliance and the frequency of hospitalisations for lower respiratory tract infections. We investigated the causative microorganisms detected in hospitalised patients.Results:In this study, 86.7% of the desired number of injections was achieved in 176 patients in two seasons. Out of these, 117 patients (66.4%) received all the doses they were prescribed. Although not statistically significant, compliance to prophylaxis was higher in male patients, cyanotic patients, those who started under 1 year old, and who lived in the city centre. Human metapneumovirus, parainfluenza type 3, and bocavirus were detected in the hospitalised patients.Conclusion:Patients with congenital heart disease can survive the period of infancy with less problem by making palivizumab prophylaxis more effective, and awareness about non- respiratory syncytial virus factors may be a guide for the development of new treatments.

Human coronaviruses, along with influenza virus, human metapneumovirus, respiratory syncytial virus, and rhinovirus, are endemic and cause approximately 15% to 30% of annual respiratory tract infections. Coronavirus infections are generally mild in healthy adults, obviating any urgent need to

Background Human metapneumovirus (HMPV) infection causes a spectrum of respiratory tract disease, and may be a significant pathogen in the context of immunocompromise. Here, we report direct-from-sample metagenomic sequencing of HMPV using Oxford Nanopore Technology. Methods We applied this sequencing approach to 25 respiratory samples that had been submitted to a clinical diagnostic laboratory in a UK teaching hospital. These samples represented 13 patients under the care of a haematology unit over a 20-day period in Spring 2019 (two sampled twice), and ten other patients elsewhere in the hospital between 2017–2019. Results We generated HMPV reads from 20/25 samples (sensitivity 80% compared to routine diagnostic testing) and retrieved complete HMPV genomes from 15/20 of these. Consensus sequences from Nanopore data were identical to those generated by Illumina, and represented HMPV genomes from two distinct sublineages, A2b and B2. Sequences from ten haematology patients formed a unique genetic group in the A2b sublineage, not previously reported in the UK. Among these, eight HMPV genomes formed a cluster (differing by ≤3 SNPs), likely to reflect nosocomial transmission, while two others were more distantly related and may represent independent introductions to the haematology unit. Conclusion Nanopore metagenomic sequencing can be used to diagnose HMPV infection, although more work is required to optimise sensitivity. Improvements in the use of metagenomic sequencing, particularly for respiratory viruses, could contribute to antimicrobial stewardship. Generation of full genome sequences can be used to support or rule out nosocomial transmission, and contribute to improving infection prevention and control practices.

Alt solunum yolu enfeksiyonları (ASYE) çoğunlukla respiratuvar sinsisyal virüs (RSV), influenza, parainfluenza, rhinovirüs ve adenovirüs kaynaklıdır. Ancak, son yıllarda bu virüslere ek olarak insan metapnömovirüs (iMPV), parainfluenza 4 ve bocavirüs gibi virüslerinde ASYE’ye sebep olduğu gösterilmiştir. Çocukluk çağında birden fazla virüsün ko-enfeksiyonu ile bronşiolit geliştiği unutulmamalıdır. Bu çalışmamızda, ateş ve öksürük şikâyeti ile hastanemize başvuran 4.5 aylık erkek bir bebekte iki farklı virüsün (iMPV ve influenza A) ko-enfeksiyonu sonucu gelişen bronşiolit olgu sunumu anlatılmıştır.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the agent of coronavirus disease 2019 (COVID-19), is similar to 2 other coronaviruses, SARS-CoV and Middle East respiratory syndrome coronavirus (MERS-CoV), in causing life-threatening maternal respiratory infections and systemic complications. Because of global concern for potential intrauterine transmission of SARS-CoV-2 from pregnant women to their infants, this report analyzes the effects on pregnancy of infections caused by SARS-CoV-2 and other respiratory RNA viruses, and examines the frequency of maternal-fetal transmission with SARS-CoV-2, severe acute respiratory syndrome (SARS), Middle East respiratory syndrome (MERS), influenza, respiratory syncytial virus (RSV), parainfluenza (HPIV), and metapneumovirus (hMPV). There have been no confirmed cases of intrauterine transmission reported with SARS-CoV-2 or any other coronaviruses—SARS and MERS. Influenza virus, despite causing approximately 1 billion annual infections globally, has only a few cases of confirmed or suspected intrauterine fetal infections reported. Respiratory syncytial virus is an unusual cause of illness among pregnant women, and with the exception of 1 premature infant with congenital pneumonia, no other cases of maternal-fetal infection are described. Parainfluenza virus and hMPV can produce symptomatic maternal infections but do not cause intrauterine fetal infection. In summary, it appears that the absence thus far of maternal-fetal transmission of the SARS-CoV-2 virus during the COVID-19 pandemic is similar to other coronaviruses, and is also consistent with the extreme rarity of suggested or confirmed cases of intrauterine transmission of other respiratory RNA viruses. This observation has important consequences for pregnant women because it appears that if intrauterine transmission of SARS-CoV-2 does eventually occur, it will be a rare event. Potential mechanisms of fetal protection from maternal viral infections are also discussed.

Background Inappropriate antibiotic prescribing, such as for viral illness, remains common in primary care. The objective of this study was to estimate the proportion of community-prescribed antibiotics to children aged less than 5 years attributable to common respiratory viruses. Methods We fitted time-series negative binomial models to predict weekly antibiotic prescribing rates from positive viral pathogen tests for the period 1 April 2009 through 27 December 2017 using comprehensive, population-based administrative data for all children ( Results We included data on 6 066 492 antibiotic prescriptions among 452 877 children. The antibiotic-prescribing rate among all Scottish children ( Conclusions Nearly 14% of antibiotics prescribed to children in this study were estimated to be attributable to common viruses for which antibiotics are not recommended. A future RSV vaccine could substantially reduce unnecessary antibiotic prescribing among children.

To assess the effectiveness of the use of the antiviral drug enisamium iodide in the complex treatment of acute respiratory viral infections (ARVI) caused by various pathogens in routine clinical practice.А prospective randomized study included 134 patients who were treated in the epidemic season of influenza and ARVI in 20182019. All patients were examined for the presence of influenza A and B viruses, respiratory syncytial virus, human metapneumovirus, parainfluenza virus, coronaviruses, rhinoviruses, adenoviruses in nasopharyngeal swabs by PCR. Patients of the main group received enisamium iodide along with symptomatic therapy, the control group received only symptomatic therapy. The primary parameter of the effectiveness of therapy was evaluated on the scale of the general severity of the manifestations of ARVI (Total Symptom Score TSS) from the 2nd to the 4th day and by the secondary criteria of effectiveness: assessment of the duration of ARVI, the severity of fever, the proportion of patients with normal body temperature, the duration of the main clinical symptoms of acute respiratory viral infections, the proportion of patients in whom complications requiring antibiotics were noted, the dynamics of interferon status on the 6th day. To conduct a statistical analysis, depending on the efficiency parameter, the ANCOVA method with a fixed group factor and an initial score on the TSS severity scale was used as covariates, a criterion for comparing quantitative indicators in two independent groups.According to the results of the analysis of the primary efficacy parameter, the median (interquartile range) of the average score on the scale of the general severity of ARVI manifestations in the main group was 4.33 (3.675.83), in the comparison group 6.00 (4.677.25; p0.001). The duration of systemic and local manifestations of acute respiratory viral infections was statistically significantly less in the main group (p=0.002 and p=0.019, respectively). Prescription of additional therapy was required in 2 (2.9%) patients of the main group (patients taking enisamium iodide), compared with 8 (11.9%) patients in the control group. Serum levels of interferon  and interferon  on the last day of treatment were statistically significantly higher in patients of the main group compared with the control group (p0.001). Treatment (excellent) was evaluated by 42 (62.7%) patients, while in the control group only 17 (25.8%) patients gave similar ratings. Both patients (p0.001) and doctors (p0.002) rated therapy tolerance better in the study group.The results confirmed the safety and effectiveness of enisamium iodide as a treatment for ARVI and influenza. The antiviral, interferonogenic and anti-inflammatory properties of the drug are involved in the formation of an antiviral response and reduce the risk of complications, which makes it possible to reduce the number of symptomatic agents used.Цель. Оценка эффективности применения в рутинной клинической практике противовирусного препарата энисамия йодида в комплексной терапии острых респираторных вирусных инфекций (ОРВИ), вызванных различными возбудителями. Материалы и методы. В проспективное рандомизированное исследование включены 134 пациента, проходивших лечение в эпидемический сезон гриппа и ОРВИ в 20182019 гг. Все пациенты обследованы на наличие вирусов гриппа А и B, респираторно-синцитиального вируса, метапневмовируса человека, вируса парагриппа, коронавирусов, риновирусов, аденовирусов в мазках из носоглотки методом полимеразной цепной реакции. Пациенты основной группы получали энисамия йодид наряду с симптоматической терапией, контрольная группа получала только симптоматическую терапию. Первичный параметр эффективности лечения оценивали по шкале общей выраженности проявлений ОРВИ (Total Symptom Score TSS) со 2 по 4-й день и вторичным критериям эффективности: оценка продолжительности ОРВИ, выраженность лихорадки, доля пациентов с нормальной температурой тела, продолжительность основных клинических симптомов ОРВИ, доля больных, у которых отмечено развитие осложнений, требующих назначения антибиотиков, динамика интерферонового статуса на 6-й день. Для проведения статистического анализа в зависимости от параметра эффективности применялся метод ANCOVA с фиксированным фактором группы и исходным баллом по шкале выраженности TSS в качестве ковариаты, критерий сравнения количественных показателей в двух независимых группах. Результаты. По результатам анализа первичного параметра эффективности медиана (межквартильный диапазон) средней оценки по шкале общей выраженности проявлений ОРВИ в основной группе составила 4,33 (3,675,83), в группе сравнения 6,00 (4,677,25; p0,001. Продолжительность системных и локальных проявлений ОРВИ была статистически значимо меньше в основной группе (р=0,002 и р=0,019 соответственно). Назначение дополнительной терапии потребовалось 2 (2,9%) пациентам основной группы (принимающие энисамия йодид) по сравнению с 8 (11,9%) пациентами из контрольной группы. Сывороточные уровни интерферона  и интерферона  на последний день лечения были статистически значимо выше у пациентов основной группы по сравнению с контрольной (p0,001). Оценку лечению отлично дали 42 (62,7%) пациента, в то время как в контрольной группе аналогичные оценки поставили только 17 (25,8%) больных. И пациенты (p0,001), и врачи (p0,002) оценивали переносимость терапии лучше в основной группе. Заключение. Полученные результаты подтвердили безопасность и эффективность энисамия йодида как средства терапии ОРВИ и гриппа. Противовирусные, интерфероногенные и противовоспалительные свойства препарата участвуют в формировании противовирусного ответа и снижают риск осложнений, что дает возможность уменьшить количество применяемых симптоматических средств.

BACKGROUND: Most children are exposed to human metapneumovirus (HMPV) by the age of 5 y. This study aimed to describe the morbidity associated with HMPV infections in a cohort of children in the Midwest of the United States. METHODS: This was a retrospective 2-center cohort study including children (0–17 y old) hospitalized with HMPV infections at 2 tertiary care pediatric hospitals from 2009 to 2013. Demographics, chronic medical conditions, viral coinfections, and hospitalization characteristics, including the need for respiratory support, high-flow nasal cannula, CPAP, bi-level positive airway pressure, invasive mechanical ventilation, pediatric ICU admission, acute kidney injury (AKI), use of extracorporeal membrane oxygenation, and length of stay, were collected. RESULTS: In total, 131 subjects were included. Those with one or more comorbidities were older than their otherwise healthy counterparts, with a median age of 2.8 y (interquartile range [IQR] 1.1–7.0) compared to 1.3 y (IQR 0.6–2.0, P CONCLUSIONS: Children hospitalized with HMPV may be at risk for AKI. Risk of HMPV-associated AKI appears to increase with age regardless of severity of respiratory illness or presence of comorbidities.

Internal N6-methyladenosine (m6A) modification is one of the most common and abundant modifications of RNA. However, the biological roles of viral RNA m6A remain elusive. Here, using human metapneumovirus (HMPV) as a model, we demonstrate that m6A serves as a molecular marker for innate immune discrimination of self from non-self RNAs. We show that HMPV RNAs are m6A methylated and that viral m6A methylation promotes HMPV replication and gene expression. Inactivating m6A addition sites with synonymous mutations or demethylase resulted in m6A-deficient recombinant HMPVs and virion RNAs that induced increased expression of type I interferon, which was dependent on the cytoplasmic RNA sensor RIG-I, and not on melanoma differentiation-associated protein 5 (MDA5). Mechanistically, m6A-deficient virion RNA induces higher expression of RIG-I, binds more efficiently to RIG-I and facilitates the conformational change of RIG-I, leading to enhanced interferon expression. Furthermore, m6A-deficient recombinant HMPVs triggered increased interferon in vivo and were attenuated in cotton rats but retained high immunogenicity. Collectively, our results highlight that (1) viruses acquire m6A in their RNA as a means of mimicking cellular RNA to avoid detection by innate immunity and (2) viral RNA m6A can serve as a target to attenuate HMPV for vaccine purposes. This study reports a novel function for the N6-methyladenosine RNA modification in allowing RIG-I to discriminate self from non-self RNA and shows that human metapneumovirus induces this modification of its RNA to evade recognition in vivo.

Human metapneumovirus (hMPV) is an important respiratory pathogen especially in young children and elderly subjects. Our objective was to assess the immunogenicity and protection conferred by predominant pre- and post-fusion (F) hMPV-F constructs in Balb/C mice. Immunizations without adjuvant were not immunogenic whereas alum-adjuvanted hMPV-F proteins, regardless of their conformations, generated comparable neutralizing antibody titers with undetectable pulmonary viral titers following viral challenge. In conclusion, we found no apparent advantage for mixtures of predominant pre-fusion F proteins over post-fusion conformations for hMPV vaccination in opposite to recent data obtained with the human respiratory syncytial virus.

Human metapneumovirus (HMPV) is an important respiratory pathogen and is divided in two main groups (A and B). HMPV strains with partial duplications (111-nt and 180-nt duplication) of the G gene have been reported in recent years. Since the initial reports, viruses with these characteristics have been reported in several countries. We analyzed all complete HMPV G gene ectodomain sequences available at GenBank to determine if viruses with 111-nt or 180-nt duplication have become the leading HMPV strains worldwide, and to describe their temporal and geographic distribution. We identified 1462 sequences that fulfilled study criteria (764 HMPV A and 698 HMPV B) reported from 37 countries. The most frequent HMPV A genotype was A2b2 (n = 366), and the most frequent B genotype was B2 (n = 374). A total of 84 sequences contained the 111-nt duplication, and 90 sequences contained the 180-nt duplication. Since 2016, viruses with a partial duplication comprise the most frequent HMPV A sequences globally and have displaced other HMPV A viruses in Asia, Europe, and South America; no sequences of viruses with partial duplication have been reported in North America or Africa so far. Continued surveillance of HMPV is required to identify the emergence and spread of epidemiologically relevant variants.

BackgroundNon-pharmaceutical interventions (NPIs) and voluntary behavioral changes during the COVID-19 pandemic have influenced the circulation of non-SARS-CoV-2 respiratory infections. We aimed to examine interactions among common non-SARS-CoV-2 respiratory virus and further estimate the impact of the COVID-19 pandemic on these viruses.MethodsWe analyzed incidence data for seven groups of respiratory viruses in New York City (NYC) during Oct 2015 - May 2021 (i.e., before and during the COVID-19 pandemic). We first used elastic net regression to identify potential virus interactions and further examined the robustness of the found interactions by comparing the performance of Auto Regressive Integrated Moving Average (ARIMA) models with and without the interactions. We then used the models to compute counterfactual estimates of cumulative incidence and estimate the reduction during the COVID-19 pandemic period from March 2020 to May 2021, for each virus.ResultsWe identified potential interactions for three endemic human coronaviruses (CoV-NL63, CoV-HKU, and CoV-OC43), parainfluenza (PIV)-1, rhinovirus, and respiratory syncytial virus (RSV). We found significant reductions (by ~70-90%) in cumulative incidence of CoV-OC43, CoV-229E, human metapneumovirus, PIV-2, PIV-4, RSV, and influenza virus during the COVID-19 pandemic. In contrast, the circulation of adenovirus and rhinovirus was less affected.ConclusionsCirculation of several respiratory viruses has been low during the COVID-19 pandemic, which may lead to increased population susceptibility. It is thus important to enhance monitoring of these viruses and promptly enact measures to mitigate their health impacts (e.g., influenza vaccination campaign and hospital infection prevention) in the coming months.

Background Coronavirus disease 2019 (COVID‐19) has drastically changed the recommended activities and environment of patients worldwide. Our aim was to assess the impact of COVID‐19 on pediatric hospitalizations in Kitami, Japan. Methods A retrospective, single‐center study was conducted on hospitalized patients aged 0–14 years at the Japanese Red Cross Kitami Hospital. We compared the incidence of pediatric patients hospitalized in 2020 with those in 2017–2019. Results The number of pediatric hospitalized patients dropped significantly in 2020 compared to that in 2017–2019 (median 43.0 vs. 78.5 per month, p < 0.001). The age was significantly older in 2020 (4.3 vs. 3.4 years, p < 0.001). Hospitalization from respiratory (8.5 vs. 30.5, p < 0.001) and gastrointestinal infections (3.0 vs. 6.0, p = 0.004) significantly decreased. Admission due to respiratory syncytial virus (0.0 vs. 4.0, p < 0.001), human metapneumovirus (0.0 vs. 1.0, p = 0.005), influenza (0.0 vs. 0.0, p = 0.009), adenovirus (0.0 vs. 1.0, p = 0.003), and rotavirus infection (0.0 vs. 0.0, p = 0.025) also decreased significantly. The

Respiratory viruses cause a substantial proportion of respiratory tract infections in children but are underrecognized as a cause of severe pneumonia hospitalization in low-income settings. We employed 22 real-time PCR assays and retrospectively reanalyzed 610 nasopharyngeal aspirate specimens from children aged 2 to 35 months with severe pneumonia (WHO definition) admitted to Kanti Childrens’ Hospital in Kathmandu, Nepal, from January 2006 through June 2008. Previously, ≥1 of 7 viruses had been detected by multiplex reverse transcription-PCR in 30% (188/627) of cases. Reanalyzing the stored specimens, we detected ≥1 pathogens, including 18 respiratory viruses and 3 atypical bacteria, in 98.7% (602/610) of cases. Rhinovirus (RV) and respiratory syncytial virus (RSV) were the most common, detected in 318 (52.1%) and 299 (49%) cases, respectively, followed by adenovirus (AdV) (10.6%), human metapneumovirus (hMPV) (9.7%), parainfluenza virus type 3 (8.4%), and enterovirus (7.7%). The remaining pathogens were each detected in less than 5%. Mycoplasma pneumoniae was most common among the atypical bacteria (3.7%). Codetections were observed in 53.3% of cases. Single-virus detection was more common for hMPV (46%) and RSV (41%) than for RV (22%) and AdV (6%). The mean cycle threshold value for detection of each pathogen tended to be lower in single-pathogen detections than in codetections. This finding was significant for RSV, RV, and AdV. RSV outbreaks occurred at the end of the monsoon or during winter. An expanded diagnostic PCR panel substantially increased the detection of respiratory viruses in young Nepalese children hospitalized with severe pneumonia. IMPORTANCE Respiratory viruses are an important cause of respiratory tract infections in children but are underrecognized as a cause of pneumonia hospitalization in low-income settings. Previously, we detected at least one of seven respiratory viruses by PCR in 30% of young Nepalese children hospitalized with severe pneumonia over a period of 36 months. Using updated PCR assays detecting 21 different viruses and atypical bacteria, we reanalyzed 610 stored upper-respiratory specimens from these children. Respiratory viruses were detected in nearly all children hospitalized for pneumonia. RSV and rhinovirus were the predominant pathogens detected. Detection of two or more pathogens was observed in more than 50% of the pneumonia cases. Single-virus detection was more common for human metapneumovirus and RSV than for rhinovirus and adenovirus. The concentration of virus was higher (low cycle threshold [CT] value) for single detected pathogens, hinting at a high viral load as a marker of clinical significance.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), the etiological agent of coronavirus disease 2019 (COVID-19), has infected all age groups and disproportionately impacted vulnerable populations globally. Polymicrobial infections may play an important role in the development of SARS-CoV-2 infection in susceptible hosts. These coinfections may increase the risk of disease severity and pose challenges to the diagnosis, treatment, and prognosis of COVID-19. There have been limited SARS-CoV-2 coinfection studies. In this retrospective study, residual nucleic acid extracts from 796 laboratory-confirmed COVID-19-positive specimens, collected between March 2020 and February 2021, were analyzed using a Luminex NxTAG respiratory pathogen panel (RPP). Of these, 745 returned valid results and were used for analysis; 53 (7.1%) were positive for one or more additional pathogens. Six different respiratory viruses were detected among the 53 SARS-CoV-2-positive patient specimens, and 7 of those specimens tested positive for more than one additional respiratory virus. The most common pathogens include rhinovirus/enterovirus (RV/EV) (n = 22, 41.51%), human metapneumovirus (hMPV) (n = 18, 33.9%), and adenovirus (n = 12, 22.6%). Interestingly, there were no SARS-CoV-2 coinfections involving influenza A or influenza B in the study specimens. The median age of the SARS-CoV-2-positive patients with coinfections was 38 years; 53% identified as female, and 47% identified as male. Based on our retrospective analysis, respiratory coinfections associated with SARS-CoV-2-positive patients were more common in young children (≤9 years old), with white being the most common race. Our findings will likely prompt additional investigation of polymicrobial infection associated with SARS-CoV-2 during seasonal respiratory pathogen surveillance by public health laboratories. IMPORTANCE This examination of respiratory pathogen coinfections in SARS-CoV-2 patients will likely shed light on our understanding of polymicrobial infection associated with COVID-19. Our results should prompt public health authorities to improve seasonal respiratory pathogen surveillance practices and address the risk of disease severity.

Background The aim of this study was to determine the sensitivity and specificity of a novel immunochromatographic (IC) assay (APD1806) using monoclonal antibodies against the matrix (M) protein of human metapneumovirus (hMPV) for detection of hMPV from nasopharyngeal swab samples based on the results of real-time RT-PCR. Methods Nasopharyngeal swab samples taken from 189 patients aged 0 - 5 years who were suspected of having respiratory tract infections associated with hMPV were used in this study. The samples were tested both by the IC assay and by real-time RT-PCR for detection of hMPV. Results The sensitivity and specificity of the IC assay for detection of hMPV were 88.8% (95/107) and 92.7% (76/82), respectively. Conclusions The IC assay using monoclonal antibodies against the M protein of hMPV is an accurate and fast assay that is suitable as a diagnostic tool for hMPV infection. The optimal timing of the IC assay is 12 hours or more after the onset of fever due to hMPV infection.

Background The effect of SARS-CoV-2 on existing respiratory pathogens in circulation remains uncertain. This study aimed to assess the impact of SARS-CoV-2 on the prevalence of respiratory pathogens among hospitalized children. Methods This study enrolled hospitalized children with acute respiratory infections in Shenzhen Children’s Hospital from September to December 2019 (before the COVID-19 epidemic) and those from September to December 2020 (during the COVID-19 epidemic). Nasopharyngeal swabs were collected, and respiratory pathogens were detected using multiplex PCR. The absolute case number and detection rates of 11 pathogens were collected and analyzed. Results A total of 5696 children with respiratory tract infection received multiplex PCR examination for respiratory pathogens: 2298 from September to December 2019 and 3398 from September to December 2020. At least one pathogen was detected in 1850 (80.5%) patients in 2019, and in 2380 (70.0%) patients in 2020; the detection rate in 2020 was significantly lower than that in 2019.The Influenza A (InfA) detection rate was 5.6% in 2019, but 0% in 2020. The detection rates of Mycoplasma pneumoniae, Human adenovirus, and Human rhinovirus also decreased from 20% (460), 8.9% (206), and 41.8% (961) in 2019 to 1.0% (37), 2.1% (77), and 25.6% (873) in 2020, respectively. In contrast, the detection rates of Human respiratory syncytial virus, Human parainfluenza virus, and Human metapneumovirus increased from 6.6% (153), 9.9% (229), and 0.5% (12) in 2019 to 25.6% (873), 15.5% (530), and 7.2% (247) in 2020, respectively (p Conclusions Successful containment of seasonal influenza as a result of COVID-19 control measures will ensure we are better equipped to deal with future outbreaks of both influenza and COVID-19.Caused by virus competition, the detection rates of Human respiratory syncytial virus, Human parainfluenza virus, and Human metapneumovirus increased in Shenzhen,that reminds us we need to take further monitoring and preventive measures in the next epidemic season.

Respiratory viruses can be detected in 18.3 to 48.9% of critically ill adults with severe respiratory tract infections (RTIs). The present study aims to assess the clinical significance of respiratory viruses in pragmatically selected adults in medical intensive care unit patients and to identify factors associated with viral respiratory viral tract infections (VRTIs). We conducted a prospective study on critically ill adults with suspected RTIs without recognized respiratory pathogens. Viral cultures with monoclonal antibody identification, in-house real-time polymerase chain reaction (PCR) for influenza virus, and FilmArray respiratory panel were used to detect viral pathogens. Multivariable logistic regression was applied to identify factors associated with VRTIs. Sixty-four (40.5%) of the included 158 critically ill adults had respiratory viruses detected in their respiratory specimens. The commonly detected viruses included influenza virus (20), followed by human rhinovirus/enterovirus (11), respiratory syncitial virus (9), human metapneumovirus (9), human parainfluenza viruses (8), human adenovirus (7), and human coronaviruses (2). The FilmArray respiratory panel detected respiratory viruses in 54 (34.6%) patients, but showed negative results for seven of 13 patients with influenza A/H3 infection. In the multivariable logistic regression model, patient characters associated with VRTIs included those aged