RAPID IDENTIFICATION OF ETIOLOGICAL AGENTS OF RESPIRATORY TRACT INFECTIONS DURING THE COVID-19 PANDEMIC USING THE MULTIPLEX-PCR METHOD.

Objective. Most respiratory infections have similar symptoms, so it is clinically difficult to determine their etiology. This study aimed to show the importance of molecular diagnostics in identifying the etiological agent of respiratory infections, especially during the coronavirus disease 2019 (COVID-19) pandemic. Methods. A total of 849 samples from patients hospitalized at the University Clinical Center Kragujevac (from January 1 to August 1, 2022) were examined using automated multiplex-polymerase chain reaction (PCR) tests. The BioFire-FilmArray-Respiratory Panel 2.1 test was used for 742 nasopharyngeal swabs [identification of 19 viruses (including SARS-CoV-2) and four bacteria], while the BioFire-FilmArray-Pneumonia Panel was used [identification of 18 bacteria and nine viruses] (BioMerieux, Marcy l'Etoile, France) for 107 tracheal aspirates. The tests were performed according to the manufacturer's instructions, and the results were available within an hour. Results. In 582 (78.4%) samples, the BioFire-FilmArray-Respiratory Panel 2.1 plus test identified at least one pathogen. The rhinovirus (20.6%), SARS-CoV-2 (17.7%), influenza A (17.5%), respiratory syncytial virus (12.4%), and parainfluenza 3 (10.1%) were the most common. Other viruses were found less frequently, and Bordetella parapertussis was detected in one sample. In 85 (79.4%) samples, the BioFire-FilmArray-Pneumonia Panel test identified at least one bacterium or virus. The most prevalent bacteria were Staphylococcus aureus (42.4%), Haemophilus influenzae (41.2%), Streptococcus pneumoniae (36.5%), Moraxella catarrhalis (22.3%), and Legionella pneumophila (2.4%). Among viruses, rhinovirus (36.5%), adenovirus (23.5%), influenza A (11.8%), and the genus Coronavirus (4.7%), were detected. Conclusion. Multiplex-PCR tests improved the implementation of therapeutic and epidemiological measures, preventing the spread of the COVID-19 infection and Legionnaires' disease.Copyright © 2022, Serbian Medical Society. All rights reserved.

Epidemiological investigation of an outbreak of human rhinovirus in a primary school in northern shaanxi

Objective To analyze the epidemiological characteristics of a Human rhinovirus outbreak in a primary school in northern Shaanxi, and to provide scientific evidence for the prevention and control. Methods On - site epidemiological investigation of an unexplained febrile aggregated outbreak reported in a primary school in northern Shaanxi on May 22, 2020. Nasopharyngeal swabs were collected from typical cases, and nucleic acid testing was performed to test for SARS COV 2, and 16 respiratory pathogens. Results A total of 37 cases were reported, including 1 adult teacher and 36 students, with the overall incidence rate of 1.75%, a male and female ratio of 3:1, and the incidence age mainly concentrated in 6 to 12 years old. The cases were mainly concentrated in 3 first-grade classes and 7 second-grade classes on the same floor, and the first grade cases accounted for 75.68% of the total number of cases. There was a statistically significant difference in the incidence rate of the cases in the classes (χ2 = 49.29, P<0.01). The clinical features of the cases were mainly fever (body temperature between 37.3 and 38.8°C), sore throat, runny nose, nasal congestion and cough, and some of which were accompanied by diarrhea and vomiting, and other gastrointestinal symptoms. Of the 33 nasopharyngeal swabs detected by laboratory, 14 were positive for Rhinovirus, and the positive rate was 42.42%. Conclusion This aggregated outbreak is caused by Rhinovirus infection. Primary and secondary schools in northern Shaanxi should be alert for aggregated unexplained fever due to Rhinovirus outbreaks during the epidemic season of respiratory infectious diseases. © 2023, Editorial Department of Medical Pest Control. All rights reserved.

Phytocompounds as a source for the development of new drugs to treat respiratory viral infections

Respiratory viruses have an important history as a threat to global health. However, this problem has been aggravated due to the appearance of new outbreaks caused by a newly discovered virus or variant. Recently, the new coronavirus (SARS-CoV-2) has been a major concern for health authorities, and it was classified as a pandemic by the World Health Organization. Secondary metabolites obtained from plants represent an alternative to the discovery of new active molecules and have already shown potential to combat different viruses. In an effort to demonstrate the broad spectrum of antiviral action from these metabolites, this work describes the compounds that were effective against the major viruses that cause respiratory infections in humans. In addition, their mechanisms of action were highlighted as an approach to better understanding the virus-bioactive substance relationship. Finally, this study warns that, although phytocompounds have a broad antiviral action spectrum, the development of products and clinical trials based on these secondary metabolites is still scarce and therefore deserves greater attention from the scientific community. © 2023 Elsevier B.V.

Primary immunodeficiency associated with a SAMD9L mutation

Background: SAMD9L is a tumor suppressor involved in regulating the proliferation and maturation of cells, particularly those derived from the bone marrow, and appears to play an important role in cerebellar function. It can be activated in hematopoietic stem cells by type I and type II interferons. It has been hypothesized to act as a critical antiviral gatekeeper regulating interferon dependent demand driven hematopoiesis. Gain of function mutations can present with an immunodeficiency due to transient severe cytopenias during viral infection. Case presentation: We report a 3-year-old boy born full term with a history of severe thrombocytopenia requiring transfusions, developmental delay, ataxia, seizure disorder, and recurrent severe respiratory viral infections. His infectious history was significant for respiratory syncytial virus with shock requiring extracorporeal membrane oxygenation complicated by cerebral infarction and a group A streptococcus empyema, osteomyelitis requiring a left below the knee amputation, and infections with rhinovirus, COVID-19, and parainfluenza requiring hospitalizations for respiratory support. Initial immunologic evaluation was done during his hospitalization for parainfluenza. His full T cell subsets was significant for lymphopenia across all cell lines with CD3 934/microL, CD4 653/microL, CD8 227/microL, CD19 76/microL, and CD1656 61/microL. His mitogen stimulation assay to phytohemagglutinin and pokeweed was normal. Immunoglobulin panel showed a mildly decreased IgM of 25 mg/dL, but normal IgA and IgG. Vaccine titers demonstrated protective titers to 12/22 pneumococcus serotypes, varicella, diphtheria, mumps, rubella, and rubeola. Repeat full T cell subsets 6 weeks later revealed marked improvement in lymphocyte counts with CD3 3083/microL, CD4 2101/microL, CD8 839/microL, CD19 225/microL, and CD1656/microL. A primary immunodeficiency genetic panel was ordered and positive for a heterozygous SAMD9L c.1549T>C (p.Trp517Arg) mutation classified as a variant of unknown significance. Discussion(s): This patient's history of severe viral infections, ataxia, thrombocytopenia, and severe transient lymphopenia during infection is suggestive of a SAM9DL gain of function mutation. Protein modeling done by the laboratory suggests this missense mutation would affect protein structure. The mutation found has been observed in individuals with thrombocytopenia. This case highlights the importance of immunophenotyping both during acute illness and once recovered.Copyright © 2023 Elsevier Inc.

A baby girl with TBX1 haploinsufficiency who died after elective cardiac repair surgery due to suspected enteroviral meningitis

Introduction: TBX1 haploinsufficiency is an inborn error of immunity with the phenotype of DiGeorge Syndrome. DiGeorge Syndrome has variable immunodeficiency associated with grade of thymic hypoplasia ranging from mild with no infections to severe requiring thymus implant. Enterovirus is an example of an opportunistic infection that can be fatal in these patients. Case Presentation: A 1 year old girl with TBX1 haploinsufficiency complicated by Tetralogy of Fallot, pulmonary atresia, high arched palate, and vesicovaginal fistula presented for elective cardiac repair surgery from another country due to failure to thrive and cyanosis. She had no prior infectious history but was on sulfamethoxazole-trimethoprim for prophylaxis. She was asymptomatic with a negative COVID test but no other infectious studies performed. Immediately postoperatively, she was febrile and nasal respiratory viral panel was positive for rhinovirus/enterovirus with increased procalcitonin and leukocytosis with left shift. She decompensated with multi-organ failure and cardiac arrest on postoperative day two. She was cannulated to veno-arterial extracorporeal membrane oxygenation (ECMO). Pre-operatively, she had a normal absolute lymphocyte count. No thymus tissue was observed in surgery. She had profound CD3 lymphopenia to 130 cells/cmm when critically ill. Enteroviral meningitis was suspected as no infectious, cardiac, or other pathology could be identified causing decompensation. Enteroviral serum polymerase chain reaction (PCR) test was negative while lumbar puncture deferred due to clinical status. She was treated with immunoglobulin. Offlabel investigational drug pocapavir was considered but deferred to patient's irreversible neurological status. The patient was disconnected from ECMO and expired. Discussion(s): Though we cannot confirm that this patient had enteroviral meningitis, invasive enteroviral infections are associated with elevated transaminases, coagulopathy, and seizures all present in our patient. There has also been reported negative serum enteroviral PCR but positive CSF enteroviral PCR in an immunodeficient patient. Additionally, this case highlights the importance of immunologic evaluation in patients with DiGeorge Syndrome and questions if asymptomatic viral screening for viruses like enterovirus should be considered pre-operatively in patients with inborn errors of immunity. This case highlights potential treatment options for invasive enteroviral infections in patients with inborn errors of immunity: high dose immunoglobulin, fluoxetine, and pocapavir.Copyright © 2023 Elsevier Inc.

Genotypic Diversity of Childhood Rhinovirus Infections.

Our objective was to describe the distribution of rhinovirus (RV) by species and type in both symptomatic and asymptomatic children in a prospective study over multiple years. A large and diverse distribution of RV types was seen among children with and without symptoms. RV-A and RV-C were predominant at all visits.

Nausea, Vomiting, and Diarrhea Are Common in Community-Acquired Acute Viral Respiratory Illness.

BACKGROUND: Gastrointestinal (GI) symptoms are recognized sequelae of acute respiratory illness (ARI), but their prevalence is not well documented. Our study aim was to assess the incidence of GI symptoms in community ARI cases for persons of all ages and their association with clinical outcomes. METHODS: We collected mid-nasal swabs, clinical, and symptom data from Seattle-area individuals during the 2018-2019 winter season as part of a large-scale prospective community surveillance study. Swabs were tested by polymerase chain reaction (PCR) for 26 respiratory pathogens. Likelihood of GI symptoms given demographic, clinical, and microbiological covariates were analyzed with Fisher's exact, Wilcoxon-rank-sum, and t-tests and multivariable logistic regression. RESULTS: In 3183 ARI episodes, 29.4% had GI symptoms (n = 937). GI symptoms were significantly associated with pathogen detection, illness interfering with daily life, seeking care for the illness, and greater symptom burden (all p < 0.05). Controlling for age, > 3 symptoms, and month, influenza (p < 0.001), human metapneumovirus (p = 0.004), and enterovirus D68 (p = 0.05) were significantly more likely to be associated with GI symptoms than episodes with no pathogen detected. Seasonal coronaviruses (p = 0.005) and rhinovirus (p = 0.04) were significantly less likely to be associated with GI symptoms. CONCLUSION: In this community-surveillance study of ARI, GI symptoms were common and associated with illness severity and respiratory pathogen detection. GI symptoms did not track with known GI tropism, suggesting GI symptoms may be nonspecific rather than pathogen-mediated. Patients presenting with GI and respiratory symptoms should have respiratory virus testing, even if the respiratory symptom is not the primary concern.

Etiological structure of acute respiratory viral infections in children hospitalized in 2015-2018

Acute respiratory viral infections (ARVI) play an important role in morbidity formation among children. At the same time, studies about the ARVI etiological structure are not enough. The article presents the results of structure analyses of ARVI in children with severe and moderate degrees of disease hospitalized in the children's clinical hospital of Novosibirsk for the period 2015-2018. This research aimed to analyze the morbidity of acute respiratory viral infections with the estimation of a causal virus in children admitted to the hospital for the period 2015-2018. Material and methods. In this study, 1137 children aged between 0 and 15 years were examined. In order to determine the etiological factor in children with damage of the upper or lower respiratory tract, by using the method of RT-PCR (AmpliSensARVI-screen-FL test systems (InterLabService, Russia), mucus from the nose and throat was examined for the presence of genetic material of viruses that cause ARVI (influenza A and B viruses, parainfluenza viruses of types 1-4, respiratory syncytial virus, metapneumovirus, four types of human coronavirus, rhinovirus, adenovirus, and bocavirus). Results. The research found that the most frequently detected pathogens are respiratory syncytial virus (23.52%), influenza A and B viruses (19.73%) and rhinovirus (19.21%). Observe the dynamics some fluctuations in the detection of mentioned viral agents and increasing of mixed infections were detected. In addition, the importance of respiratory and gastrointestinal tract combined lesions, particularly for infants and preschool - age children has been noted. Conclusion. The distribution of respiratory viruses in children with severe ARVI who required hospitalization was assessed. It was shown the significance of the respiratory syncytial infection virus, influenza virus and rhinovirus in the etiological structure of hospitalized children of different ages that damage not only the respiratory tract, but also to the gastrointestinal tract. This is an important factor in optimizing the diagnosis, treatment and prevention of viral infections in children.Copyright © Infectious Diseases: News, Opinions, Training 2021.

RAPID IDENTIFICATION OF ETIOLOGICAL AGENTS OF RESPIRATORY TRACT INFECTIONS DURING THE COVID-19 PANDEMIC USING THE MULTIPLEX-PCR METHOD.

Objective. Most respiratory infections have similar symptoms, so it is clinically difficult to determine their etiology. This study aimed to show the importance of molecular diagnostics in identifying the etiological agent of respiratory infections, especially during the coronavirus disease 2019 (COVID-19) pandemic. Methods. A total of 849 samples from patients hospitalized at the University Clinical Center Kragujevac (from January 1 to August 1, 2022) were examined using automated multiplex-polymerase chain reaction (PCR) tests. The BioFire-FilmArray-Respiratory Panel 2.1 test was used for 742 nasopharyngeal swabs [identification of 19 viruses (including SARS-CoV-2) and four bacteria], while the BioFire-FilmArray-Pneumonia Panel was used [identification of 18 bacteria and nine viruses] (BioMerieux, Marcy l'Etoile, France) for 107 tracheal aspirates. The tests were performed according to the manufacturer's instructions, and the results were available within an hour. Results. In 582 (78.4%) samples, the BioFire-FilmArray-Respiratory Panel 2.1 plus test identified at least one pathogen. The rhinovirus (20.6%), SARS-CoV-2 (17.7%), influenza A (17.5%), respiratory syncytial virus (12.4%), and parainfluenza 3 (10.1%) were the most common. Other viruses were found less frequently, and Bordetella parapertussis was detected in one sample. In 85 (79.4%) samples, the BioFire-FilmArray-Pneumonia Panel test identified at least one bacterium or virus. The most prevalent bacteria were Staphylococcus aureus (42.4%), Haemophilus influenzae (41.2%), Streptococcus pneumoniae (36.5%), Moraxella catarrhalis (22.3%), and Legionella pneumophila (2.4%). Among viruses, rhinovirus (36.5%), adenovirus (23.5%), influenza A (11.8%), and the genus Coronavirus (4.7%), were detected. Conclusion. Multiplex-PCR tests improved the implementation of therapeutic and epidemiological measures, preventing the spread of the COVID-19 infection and Legionnaires' disease.Copyright © 2022, Serbian Medical Society. All rights reserved.

Pathogen spectrum analysis of acute respiratory infection among inpatients before and after the outbreak of COVID-19 pandemic in Huairou district of Beijing

Objective To analyze the composition and epidemiological characteristics of respiratory pathogens in hospitalized patients with respiratory tract infections in Huairou district before and after the outbreak of corona virus disease 2019（COVID-19）. Methods Respiratory specimens were collected from hospitalized patients who met the case definition in Huairou district during the period of January 2018 and December 2021. The samples were tested for influenza virus, respiratory syncytial virus, adenovirus, parainfluenza virus, metapneumovirus, coronavirus, rhinovirus, bocavirus, enterovirus, mycoplasma pneumoniae, chlamydophila pneumoniae and other respiratory pathogens by using ABI 7500 real-time fluorescent quantitative PCR assay. Results From January 2018 to December 2021, a total of 1 148 samples were tested and the overall positive rate was 24. 65%（283cases）. The positive detection rate after the outbreak of COVID-19 in 2020-2021（79/522） was significantly lower than that before the outbreak of COVID-19 in 2018-2019（204/626）（15. 13% vs 32. 59%, χ~2=46. 683, P＜0. 01）. The positive rates in children aged 0-＜2 years and 2-＜5 years after the outbreak of COVID-19were 46. 15% and 45. 45% respectively, were significantly higher than those in other age groups （χ~2=73. 053,P＜0. 01）. Mycoplasma pneumoniae（12. 75%）, enterovirus（10. 29%） and adenovirus（10. 29%） were the top three pathogens before the outbreak, while, after the outbreak, the top three pathogens were syncytial virus（21. 52%）, parainfluenza（17. 72%） and rhinovirus（17. 72%）. In Huairou district, the detection rate of respiratory pathogens peaked in winter, there was also a small peak in summer. Conclusion After the outbreak of COVID-19, children under 5 years old are still the main population for respiratory infection control. The change of pathogen spectrum before and after the outbreak of covid-19 is helpful for clinician to recognize and diagnose the disease.

Circulation of genetically diverse non-polio enteroviruses in respiratory samples during COVID-19 pandemic period (2021-22)

Enteroviruses, beyond poliovirus, are important pathogens. Several non-polio enteroviruses (NPEVs) are causing epidemics all around the world. Limited data is available on the prevalence and diversity of these viruses from India. Objective(s): Detection and characterization of NPEVs in respiratory samples during the COVID-19 pandemic period. Material(s) and Method(s): COVID-19 negative samples from acute respiratory infections (ARI) [n = 105] and severe-acute respiratory infections (SARI) [n = 148] during the period 2021-22 were screened for NPEVs. Detection was carried out using the one step RT-PCR method targeting the 5'UTR region followed by molecular analysis. Results and Conclusion(s): Total positivity of NPEVs was noted in 35.23% and 31.08% of the ARI and SARI cases, respectively. Comparison within the two groups studied, showed significant difference in the age-wise distribution for cases>18 years of age. Year round seasonality for ARI cases while autumn seasonality for SARI cases was observed. Sequencing of representative samples of ARI cases showed prevalence of Rhinovirus A (RVA), Rhinovirus B (RVB), Rhinovirus C (RVC) and Echovirus, while predominance of RVC followed by RVA was observed for the SARI cases. Phylogenetic analysis of all the strains showed clustering of RVC strains in different clusters. Divergence was also noted in RVA and RVB strains studied. Circulation of a rare Echovirus-29 strain was noted in the ARI cases. The study highlighted significant divergence in the Rhinovirus strains studied. It warrants the need for surveillance of NPEVs, whole-genome sequencing of the circulating strains for better understanding of biodiversity among the NPEVs and the potential health burden.

SARS COV-2 and other viral etiology as a possible clue for the olfactory dilemma

Background: Post-viral anosmia is responsible for more than 40% of cases of anosmia. Anosmia has been a neglected symptom in the primary healthcare setting until the emergence of the SARS-CoV-2 pandemic. The spread of SARS-CoV-2 infection highlighted new atypical symptoms of the disease, including anosmia, which has become one of the diagnostic symptoms of the disease, and epidemiological concern. We aimed to detect the incidence of SARS-CoV-2 infection within patients presented with anosmia and to test for other respiratory viruses in the negative COVID-19 patients. We also detected the recovery of anosmia and IgM/IgG against COVID-19. We prospectively included 60 outpatients with the major complaint of anosmia. Nasopharyngeal swabs were done for SARS-CoV-2 real-time PCR, and if negative, PCR to other respiratory pathogens was tested. After one month, we inquired about the recovery of smell loss together with testing for antibodies against SARS-CoV-2. Result(s): Sixty patients were enrolled in the study. Forty-six patients (76.7%) were SARS-CoV-2 PCR positive and 14 (23.3%) were negative. Rhinovirus was the commonest isolated pathogen in the negative cases (5/14). Complete recovery of anosmia occurred in 34 patients (56.7%), while partial recovery in 24 (40.0%), and no recovery in 2 patients (3.3%). The median time to complete recovery was 10 days. 28.3% (13/46) of the patients showed negative antibody response for both IgG and IgM. Conclusion(s): Sudden-onset anosmia is a symptom that is highly predictive of being COVID-19-infected. While recovery is expected within 2 weeks, some patients have no antibodies against SARS-CoV-2.Copyright © 2022, The Author(s).

Circulation of respiratory viruses during the COVID-19 pandemic in The Gambia

Background: In many countries, non-pharmaceutical interventions to limit severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) transmission resulted in significant reductions in other respiratory viruses. However, similar data from Africa are limited. We explored the extent to which viruses such as influenza and rhinovirus co-circulated with SARS-CoV-2 in The Gambia during the COVID-19 pandemic. Methods: Between April 2020 and March 2022, respiratory viruses were detected using RT-PCR in nasopharyngeal swabs from 1397 participants with influenza-like illness. An assay to detect SARS-CoV-2 and a viral multiplex RT-PCR assay was used as previously described to detect influenza A and B, respiratory syncytial virus (RSV) A and B, parainfluenza viruses 1-4, human metapneumovirus (HMPV), adenovirus, seasonal coronaviruses (229E, OC43, NL63) and human rhinovirus. Result(s): Overall virus positivity was 44.2%, with prevalence higher in children <5 years (80%) compared to children aged 5-17 years (53.1%), adults aged 18-50 (39.5%) and >50 years (39.9%), p<0.0001. After SARS-CoV-2 (18.3%), rhinoviruses (10.5%) and influenza viruses (5.5%) were the most prevalent. SARS-CoV-2 positivity was lower in children <5 (4.3%) and 5-17 years (12.7%) than in adults aged 18-50 (19.3%) and >50 years (24.3%), p<0.0001. In contrast, rhinoviruses were most prevalent in children <5 years (28.7%), followed by children aged 5-17 (15.8%), adults aged 18-50 (8.3%) and >50 years (6.3%), p<0.0001. Four SARS-CoV-2 waves occurred, with 36.1%-52.4% SARS-CoV-2 positivity during peak months. Influenza infections were observed in both 2020 and 2021 during the rainy season as expected (peak positivity 16.4%-23.5%). Peaks of rhinovirus were asynchronous to the months when SARS-CoV-2 and influenza peaked. Conclusion(s): Our data show that many respiratory viruses continued to circulate during the COVID-19 pandemic in The Gambia, including human rhinoviruses, despite the presence of NPIs during the early stages of the pandemic, and influenza peaks during expected months.Copyright: © 2023 Jarju S et al.

Epidemiological characteristics of respiratory syncytial virus in hospitalized patients in Guangzhou from 2018 to 2022

Objective To analyze the epidemiological characteristics of respiratory syncytial virus（RSV） before and after the COVID-19 epidemic in Guangzhou in recent years. Methods Nasopharynx swabs from hospitalized patients with acute respiratory infection were collected from two sentinel hospitals in Guangzhou（Guangdong Maternal and Child Health Hospital and Sun Yat-Sen Memorial Hospital, Sun Yat-Sen University） from 2018 to 2022. Luminex respiratory multi-pathogen detection technology was used to detect and type RSV in samples. Results A total of 1 243 nasopharyngeal swab samples were collected. The overall positive rate of RSV was 6. 11%（76/1 243）, including 39 RSV-A（51. 32%, 39/76） and 37 RSV-B（48. 68%, 37/76）. The highest detection rate of RSV in children under 3 years old was 8. 79%（66 cases）. Compared with 2018（8. 30%, 22/265） and 2020（14. 78%, 30/203）, the positive rate of RSV decreased significantly in 2019（3. 13%, 10/319）, 2021（4. 08%, 10/245） and 2022（1. 90%, 4/211）. Compared with 2018（8. 30%,22/265） and 2020（14. 78%,30/203）,the positive rate of RSV decreased significantly in 2019（3. 13%,10/319）, 2021（4. 08%,10/245） and 2022（1. 90%,4/211）. Type A prevailed in 2018（19/22） and 2022（4/4）, type B（25/30） prevailed in 2020, type A and type B coexisted in 2019 and 2021. The detection rate showed had no statistically significant seasonal difference except for 2020 [7. 14%（3/42）, 16. 39%（10/61）, 27. 12%（16/59）, 0（0/42）,χ~2= 16. 975,P＜0. 001]. Among all the 76 RSV positive samples, 17（22. 37%） showed multiple infections. Among them, human rhinovirus was the most common virus causing mixed infection, accounting for 58. 83%（10/17） of the mixed infection. Conclusion RSV is a common respiratory virus prevalent in Guangzhou, and children under 3 years old are the main population infected with RSV. RSV infection is prevalent every other year, with the characteristics of alternating epidemic of type A and type B, and the anti-seasonal epidemic appeared after the COVID-19. After the outbreak of COVID-19, the detection rate of RSV increased significantly in 2020. With the change of the national COVID-19 epidemic prevention and control policy, the detection rate of RSV declined significantly during 2021-2022.

Bacterial and viral upper and lower airways infection in people with cystic fibrosis in stable condition

Background: Bacterial and viral airway infections are adverse factors for prognosis in people with cystic fibrosis (CF). The role of viral infections is unclear. Proper microbiological follow-up is essential, and the correlation between upper (UAW) and lower airway (LAW) microbiology may be important for lung disease management. We aim to evaluate airway microbiology in patients in stable clinical condition. Method(s): Between September 2021 and March 2022 in the Florence CF center, 144 nasal lavage-throat swab paired samples were collected from 72 clinically stable people with CF not chronically colonized by Pseudomonas aeruginosa. The study enrolled 59 children (median age 9, range 2-16) and 13 adults (median age 28, range 18-59). LAW specimens (72)were sampled as throat swab and UAWspecimens (72)were randomly collected by nasal lavage with two methods-Mainz (44) or Ryno-set (28). We performed conventional microbiological analyses on all samples. To screen for respiratory viruses, multiplex polymerase chain reaction (BioFire FilmArray RP 2.1 Plus) was performed. Respiratory symptoms and forced expiratory volume in 1 second (FEV1) valueswere evaluated for all patients. Result(s): Twenty-one (29%) patients tested positive for at least one virus in UAW and LAW specimens. The most frequently identified viruses were human rhinovirus or enterovirus (22%) and respiratory syncytial virus (6%). Two (3%) patients tested positive for SARS-CoV-2. Concordance between sampling methods for viral detection in UAW and LAW specimens was observed in 59 paired samples (82%), including 40 patients with no viral infections and 19 virus positive for both samples. Discordance was described in 13 subjects;10 of 13 did not show viral infection in nasal lavage. Twenty-one percent of positive nasal lavage was performed using Ryno-set and 36% using the Mainz approach. The prevalent bacteriumwas Staphylococcu aureus in UAW (53%) and LAW (69%) cultures, followed by Enterobacteriaceae (UAW 8%, LAW 6%), methicillin-resistant S. aureus (UAW 7%, LAW 6%), P. aeruginosa (UAW 4%, LAW 6%), and other clinically relevant gram-negative bacteria such as Achromobacter xylosoxidans, Stenotrophomonas maltophilia, and Ochrobactrum anthropi (UAW 7%, LAW 13%). Nasal lavage performed with Ryno-set tested positive in 72% of patients, and 64% of Mainz lavage were positive. Mainz nasal lavage showed different S. aureus and P. aeruginosa isolations (48% and 5%, respectively) than the samples collected with Ryno-set technique (61% and 4%, respectively). Concordance between sampling methods for bacterial detection in UAW and LAW was the same with the two methods (53%). Bacterial and viral infections were found in UAWand LAWof stable people with CF, but no clinical correlation was observed. Conclusion(s): The two methods of UAW lavage had slight differences in performance. Virus infection appeared to be less prevalent than bacterial infection in UAWand LAW.We did not find correlations between presence of viruses and respiratory symptoms, but further investigation is needed for a better understanding of the clinical role of viral infection in people with CF.Copyright © 2022, European Cystic Fibrosis Society. All rights reserved

PRIOR SARS-CoV-2 INFECTION PROTECTS AGAINST SYMPTOMATIC COMMON COLD CORONAVIRUSES

Background: Current COVID-19 vaccines provide substantial protection against severe COVID-19, but they do not completely eliminate subsequent SARS-CoV-2 infections. We examined incidence of and immune differences against related but different common cold coronaviruses (ccCoV) as a proxy for response against a future emerging CoV among those with SARS-CoV-2 infection, COVID-19 vaccination, or neither exposure. Method(s): We assessed incidence of ccCoV (229E, HKU1, NL63, OC43) and rhinovirus/enterovirus infections among those with documented prior SARSCoV- 2 infection (n=493), prior COVID-19 vaccine, but no SARS-CoV-2 infection (n=1,568), or no prior SARS-CoV-2 infection or vaccination (n=2,874). We conducted a retrospective review of all individuals at Boston Medical Center that underwent a comprehensive respiratory panel polymerase chain reaction (CRP-PCR) test from November 30, 2020 to October 8, 2021 to estimate infection incidence. A subset within each group was assessed for coronavirus specific humoral and cellular immune responses, via pseudovirus neutralization and peptide stimulation T cell assays. Comparisons among the three groups were done using Chi-square and multi-variate Cox-proportional hazards models. Result(s): Incidence of symptomatic ccCoV was lower in those individuals with documented prior SARS-CoV-2 infection (1.0%) compared to those with COVID-19 vaccination (2.9%) or no prior SARS-CoV-2 exposure (1.8%, p = 0.01). Rhinovirus/enterovirus incidence was similar in all three groups (range 6.2 - 8.7%). Individuals with prior SARS-CoV-2 infection and those with previous COVID-19 vaccination had similar plasma neutralization against SARS-CoV-2, OC43, and 229E spike bearing pseudoviruses. SARS-CoV-2 (p = 0.01) and OC43 nucleocapsid (p = 0.02), but not spike specific peptides, yielded higher T cell responses in individuals with a prior SARS-CoV-2 infection as compared to those with COVID-19 vaccination or no prior SARS-CoV-2 exposure. Conclusion(s): Prior SARS-CoV-2 infection, but not COVID-19 vaccination, protects against subsequent related but different ccCoV symptomatic infection. This protection against symptomatic ccCoVs may be mediated by cellular responses to non-spike proteins. Future pan-coronavirus vaccines could be improved by including both spike and non-spike antigens.

A nosocomial outbreak caused by human rhinovirus species A type 61 in a welfare facility in Gunma Prefecture, Japan.

The human rhinovirus (HRV) is generally considered as the common cold and its mild symptoms' main cause. However, HRV are also implicated in severe respiratory infections. This study reports on a nosocomial outbreak of bronchitis and pneumonia caused by HRV in a hospital during the COVID-19 epidemic in September 2022 in Gunma Prefecture, Japan. Patients continued to become infected for 9 days. During this outbreak, all 15 residents had respiratory symptoms, and HRV-A was detected in 12 of the 12 samples and phylogenetic analysis showed that it was classified into HRV-A type 61. HRV and COVID-19 or other respiratory infections cannot be differentiated from clinical symptoms; therefore, a surveillance system to monitor them may be needed.

Rhino- and Rs-Viruses in the Covid-19 Pandemic

Acute respiratory viral infections are distributed across the globe and are the most numerous human diseases caused by several hundreds of diverse viruses. Human rhinovirus is one of the most common respiratory pathogens worldwide, causing more than half of all acute respiratory viral infection cases. Seasonal human coronaviruses account for 10-15% of common cold cases;respiratory syncytial (RS) virus is the most common cause of respiratory hospitalization in infants;influenza viruses, adenoviruses, human parainfluenza virus, metapneumoviruses, and some other pathogens are also widespread. It is believed that viral common colds are mostly self-limited, causing mild infections that usually resolve within 8-10 days. However, the role of common seasonal respiratory viruses in total respiratory morbidity should not be underestimated. It turned out that during extraordinary conditions of pandemics, they behave differently. This was clearly demonstrated in the last 2009 influenza pandemic. Whereas some viruses lost relevance under the burden of a new aggressive pandemic strain, others, e.g., rhinovirus, continued to fight for existence and not only circulated along with the pandemic pathogen, but delayed its spread in some cases. For instance, the data from some European countries pointed out that the circulation of the H1N1pdm09 influenza A pandemic virus was interrupted by the annual rhinovirus outbreak. Ten years after the H1N1pdm09 influenza pandemic, a new virus outbreak emerged - the COVID-19 pandemic has begun. This pandemic, caused by the SARS-CoV-2 virus, has disrupted well-established pathogenetic and epidemiological relationships. The level of circulation of many respiratory pathogens has changed dramatically. For instance, global influenza activity has been at a much lower level than expected for the second year from now. In many regions of the world, the flu season has not been started yet. But what is interesting is that rhinoviruses together with RS-virus again showed their unique ability to compete with highly pathogenic and aggressive pathogens. Along with profoundly reduced circulation of many other seasonal respiratory viruses, rhinovirus, and RS-virus are the most frequently detected viruses. In this review, we have brought together the main biological characteristics of such genetically distinct viruses such as rhinovirus, influenza A virus, RS-virus, and SARS-CoV-2. We focused on their main similarities and discrepancies in the attempt to understand why they behave so differently in extreme pandemic conditions as well as what allows rhinoviruses and RS-viruses to coexist with SARS-CoV-2, which in turn almost fully replaced the influenza virus.

Virological profile of upper respiratory tract infections in children under 5 years of age- a cross sectional study in a tertiary care hospital in North India.

OBJECTIVE: To study the virological profile of URI among children under 5 years of age. Since, it is very difficult to distinguish between various viral etiologies solely on the basis of symptoms, this study was attempted to generate evidence that majority of URI are caused due to viral illness and no antibiotics should be prescribed in the management of the same. METHODS: This observational study was conducted over a period of one year (June 2021-May 2022) in a tertiary care teaching hospital in New Delhi. A total of 180 children between the age of 0-5 years with symptoms of URI were included. Nasopharyngeal swabs were taken and processed for detection of viruses using multiplex RT PCR. RESULTS: Presence of viruses were detected in 136 (75.6%) samples. A single virus was identified in 113 samples, whereas 21 were found to harbour two viruses and 2 were carrying three viruses. The most common virus isolated was Human Rhinovirus (HRV- 55.8%) followed by Respiratory Syncytial Virus (RSV- 23.5%). In samples showing coinfection with two viruses, most common was Human Corona Virus (HCoV)- NL63, 229E, OC43, HKU1. None of the patients were given antibiotics. None of the patients required any hospital admission for severe respiratory illness. CONCLUSIONS: Viruses are a major cause of URI in children under five years of age, with the most prevalent organisms being HRV and RSV. Antibiotic prescriptions in URI are not warranted.

Acute bronchiolitis during the COVID-19 pandemic.

Introduction: The autumn and winter bronchiolitis epidemics have virtually disappeared in the first year of the COVID-19 pandemic.Our objectives were characterised bronchiolitis during fourth quarter of 2020 and the role played by SARS-CoV-2. Methods: Prospective multi-centre study performed in Madrid (Spain) between October and December 2020 including all children admitted with acute bronchiolitis. Clinical data were collected and multiplex PCR for respiratory viruses were performed. Results: Thirty-three patients were hospitalised with bronchiolitis during the study period: 28 corresponded to rhinovirus (RV), 4 to SARS-CoV-2, and 1 had both types of infection. SAR-CoV-2 bronchiolitis were comparable to RV bronchiolitis except for a shorter hospital stay. A significant decrease in the admission rate for bronchiolitis was found and no RSV was isolated. Conclusion: SARS-CoV-2 infection rarely causes acute bronchiolitis and it is not associated with a severe clinical course. During COVID-19 pandemic period there was a marked decrease in bronchiolitis cases.

Introducción: La epidemia de bronquiolitis de otoño e invierno prácticamente desapareció durante el primer año de la pandemia de COVID-19.Nuestros objetivos eran caracterizar la bronquiolitis durante el cuarto trimestre de 2020 y determinar el papel desempeñado por el virus SARS-CoV-2. Métodos: Estudio multicéntrico prospectivo realizado en Madrid (España) entre los meses de octubre y diciembre de 2020, que incluyó a todos los niños ingresados con bronquiolitis aguda. Se recogieron los datos clínicos y se realizó una PCR múltiple para virus respiratorios. Resultados: Se hospitalizó a treinta y tres pacientes con bronquiolitis durante el periodo del estudio: 28 correspondieron a rinovirus, 4 a SARS-CoV-2 y uno presentaba ambos tipos de infección. Las bronquiolitis por SAR-CoV-2 fueron comparables a las bronquiolitis por rinovirus, salvo por una estancia hospitalaria más corta. Se detectó una reducción significativa en la tasa de ingresos por bronquiolitis y no se aisló VSR. Conclusión: Es raro que la infección por SARS-CoV-2 cause bronquiolitis aguda y no se asocia a una evolución clínica grave. Durante la pandemia de COVID-19 se produjo un descenso pronunciado de los casos de bronquiolitis.