Analysis of pathogen detection results of upper respiratory tract specimens from fever clinic patients

Objective: To explore the pathogen composition and distribution characteristics of pathogens in respiratory samples from patients with fever of unknown origin. Methods: A total of 96 respiratory samples of patients with unknown cause fever with respiratory symptoms were collected from four hospitals above grade II in Shijiazhuang area (Hebei Provincial Hospital of Traditional Chinese Medicine, Luancheng District People's Hospital, Luquan District People's Hospital, Shenze County Hospital) from January to April 2020, and multiplex-fluorescent polymerase chain reaction(PCR)was used to detect influenza A virus, influenza B virus, enterovirus, parainfluenza virus I/II/III/IV, respiratory adenovirus, human metapneumovirus, respiratory syncytial virus, human rhinovirus, human bocavirus, COVID-19, Mycoplasma pneumoniae, Chlamydia pneumoniae, Legionella pneumophila, Pseudomonas aeruginosa, Streptococcus pneumoniae, Klebsiella pneumoniae, Group A streptococcus, Haemophilus influenzae, Staphylococcus aureus nucleic acid detection, the results were analyzed for chi-square. Results: A total of 8 pathogens were detected in the upper respiratory tract samples of 96 fever patients, including 1 kind of virus, 6 kinds of bacterias, and Mycoplasma pneumoniae. There were 12 viruses including influenza virus and parainfluenza virus, Legionella pneumophila and Chlamydia pneumoniae were not detected. The pathogen detection rates in descending order were Streptococcus pneumoniae (58/96, 60.42%), Haemophilus influenzae(38/96, 39.58%), Klebsiella pneumoniae (14/96, 14.58%), Staphylococcus aureus (10/96, 10.42%), Mycoplasma pneumoniae (8/96, 8.33%), Pseudomonas aeruginosa (6/96, 6.25%), Group A streptococcus (4/96, 4.17%) and human rhinovirus (2/96, 2.08%). The proportions of single-pathogen infection and multi-pathogen mixed infection in fever clinic patients were similar, 41.67% (40/96) and 45.83% (44/96), respectively, and 12.50% (12/96)of the cases had no pathogens detected. The infection rate of Mycoplasma pneumoniae in female patients with fever (21.43%) was higher than that in male patients with fever (2.94%) (P < 0.05). There was no statistical difference between the distribution of of other pathogens and gender and age(P > 0.05). Conclusions: The upper respiratory tract pathogens were mainly bacterial infections, and occasional human rhinovirus and Mycoplasma pneumonia infections. In clinical diagnosis and treatment, comprehensive consideration should be given to the pathogen detection.

An outbreak of school influenza complicated with Mycoplasma pneumoniae infection

Objective: To describe the clinical features, causal agent and transmission mode of a fever outbreak in a school in Shanghai. Methods: Field epidemiological approaches including case definition development, searching for contacts, distribution of diseases description, environmental sampling and laboratory testing. Results: A total of 16 influenza-like cases were included, all concentrated in the one class of grade two, including 15 students and 1 teacher. Among student cases, the incidence rate was 36.59%(15/41), the average age was 7.4 years, the incidence rate was 36.84%(7/19) for boys, 36.36%(8/22) for girls. The clinical course was 5-15 days, with the median of 9 days, and 18.75%(3/16) of the cases stayed studying while sick. The nasopharyngeal swab specimens in 16 cases all tested positive for influenza B, of which 11 tested positive for mycoplasma pneumoniae and 1 case also tested positive for coronavirus OC43. Body temperature, number of mononuclear cells, and treatment time of patients infected with Influenza B and mycoplasma pneumoniae were higher than those of patients infected with influenza B alone(P < 0.05). The outbreak lasted for 12 days, all sick students were treated and discharged from hospital, with no severe cases or death, and the outbreak was effectively controlled. Conclusion: This campus cluster outbreak caused by influenza B and mycoplasma pneumoniae. Patients with influenza B with mycoplasma pneumoniae have severe symptoms and a long course of illness, suggesting the importance of early management of the epidemic.

Exposure of wild Caspian seals (Pusa caspica) to parasites, bacterial and viral pathogens, evaluated via molecular and serological assays

Disease surveillance of marine mammal populations is essential to understand the causes of strandings, identify potential threats to animal health, and to support development of conservation strategies. Here we report the first large multi-pathogen screening of prevalence for viruses, bacteria and parasites in a sample of 177 live, healthy, wild Caspian seals (Pusa caspica), captured and released during satellite telemetry studies 2007-2017. Employing molecular and serological assays we assess prevalence of pathogens known to be of significance for marine mammal health worldwide, and evaluate the results in relation to Caspian seal health and conservation. RT-PCR, and PCR assays find evidence for infection by Canine Distemper Virus (CDV), Phocine herpes virus, phocine adenovirus and Influenza A at prevalences of 5%, 6.4%, 21.7%, and 4% respectively. The genomes of CDV isolates collected in 2008 showed 99.59% identity with the 2000 Caspian seal CDV epizootic strain. A partial coding sequence for the Us2 gene from the Caspian seal herpes virus was identical to PhHV-1 isolate PB84, previously reported from a harbor seal (Phoca vitulina), while amplicon sequences for the adenovirus polymerase gene indicated a novel strain. ELISA assays detected exposure to Influenza A (55% of tested samples), adenovirus (25%), coronavirus (6%), CDV (8%), herpes virus (94%), Toxoplasma gondii (2.6%) and heartworm (1%). Hemagglutination inhibition (HI) tests detected exposure to Influenza B at a prevalence of 20%, and Leptospira microscopic agglutination tests detected suspected exposure to Leptospira serovars in 9% of tested samples. Overall, the risks, profile and prevalence of pathogens in Caspian seals appear comparable to other wild phocid seal populations. Our results suggest Caspian seals have exposure pathways to pathogens with epizootic potential or ability to cause significant morbidity, and that disease impacts could reduce the resilience of the population to other conservation threats. Caspian seals are listed as Endangered by the International Union for Conservation of Nature (IUCN), and we recommend that resources are invested to support further surveillance programs and to understand how anthropogenic pressures may influence future disease risks. A translated version of this is available in Russian and Kazakh in the Supplementary Material (Presentation 1 and Presentation 2)

Establishment of multi-target rapid detection method of upper repiratory susceptible viruses based on digital microfluidic technology

Objective: Provide a digital microfluidic RT-qPCR chip for rapid detection of several upper respiratory diseases. Methods: Several specific primer-probe sets were designed according to the conserved sequences of 2019 novel corona virus(2019-n COV), influenza A virus(Flu A), influenza B virus(Flu B), severe acute respiratory syndrome corona virus(SARS-Co V), Middle East respiratory syndrome corona virus(MERS-Co V), and then packaged into a digital microfluidic chip which allowed simultaneous detection of five upper respiratory tract pathogens with the help of reverse transcription quantitative PCR(RT-q PCR)technology. In the meanwhile, the detection limit, specificity and sensitivity of this digital microfluidic chip were evaluated base on the clinical specimens, plasmids and unrelated pathogens. Results: The established digital microfluidic RT-q PCR chip for 2019-n COV, Flu A, Flu B,SARS-Co V,MERS-Co V had a detection limit of 12 copies/reaction, while the detection limit of the RT-q PCR method without digital microfluidics was 15 copy/reaction;the detection limit of the two methods was basically the same. For nucleic acid samples extracted from clinical samples, the detection results of digital microfluidic RT-q PCR chips were all negative without non-specific amplification. At the same time, the RT-qPCR method and the digital microfluidic RT-qPCR chip method were used to carry out clinical comparative tests of 5 items in 20 clinical samples, total 100 tests. The results showed that the sensitivity of the digital microfluidic RT-q PCR chip reached 94%, the specificity was 100%. SPSS was used to analyze the consistency of the two methods, and the results showed that the two methods had a high degree of consistency(Kappa=0.962, P<0.05). Conclusion: Based on digital microfluidic RT-q PCR chip technology,a multi-target rapid detection method of upper respiratory tract susceptible virus was established, which could provide a new detection method for early clinical identification of respiratory pathogens.

Advances in molecular diagnostic tests for community-acquired pneumonia

The use of a timely and appropriate antibiotic therapy, which requires early and accurate microorganisms' detection in pneumonia. Currently, the identification of microorganisms in pneumonia is limited by the low sensitivity and long response time of standard culture-based diagnostic tools. For this reason, treatment in pneumonia is empirical. An inadequate empirical treatment is related to poor outcomes in patients with pneumonia. The microbiological diagnosis is key to improve the outcomes in patient with pneumonia. Over the past years there was a significant advance in the molecular diagnosis of infectious diseases including pneumonia. Also the impact of the COVID-19 pandemic has impacted the development and application of these new molecular techniques. This review summarizes the advances in molecular diagnosis of community-acquired pneumonia.Copyright © 2022 EDIZIONI MINERVA MEDICA.

Fu-Zheng-Xuan-Fei formula promotes macrophage polarization and Th17/Treg cell homeostasis against the influenza B virus (Victoria strain) infection.

ETHNOPHARMACOLOGICAL RELEVANCE: Fu-Zheng-Xuan-Fei formula (FF) is a prescription that has been clinically used through the basic theory of traditional Chinese medicine (TCM) for treating viral pneumonia. Although FF possesses a prominent clinical therapeutic effect, seldom pharmacological studies have been reported on its anti-influenza B virus (IBV) activity. AIM OF THE STUDY: Influenza is an acute infectious respiratory disease caused by the influenza virus, which has high annual morbidity and mortality worldwide. With a global decline in the COVID-19 control, the infection rate of influenza virus is gradually increasing. Therefore, it is of great importance to develop novel drugs for the effective treatment of influenza virus. Apart from conventional antiviral drugs, TCM has been widely used in the clinical treatment of influenza in China. Therefore, studying the antiviral mechanism of TCM can facilitate the scientific development of TCM. MATERIALS AND METHODS: Madin-Darby canine kidney cells (MDCK) and BALB/c mice were infected with IBV, and FF was added to evaluate the anti-IBV effects of FF both in vitro and in vivo by Western blotting, immunofluorescence, flow cytometry, and pathological assessment. RESULTS: It was found that FF exhibited anti-viral activity against IBV infection both in vivo and in vitro, while inducing macrophage activation and promoting M1 macrophage polarization. In addition, FF effectively regulated the signal transducer and activator of transcription (STAT) signaling pathway-mediated Th17/Treg balance to improve the lung tissue damage caused by IBV infection-induced inflammation. The findings provided the scientific basis for the antiviral mechanism of FF against IBV infection. CONCLUSIONS: This study shows that FF is a potentially effective antiviral drug against IBV infection.

RSV circulation during SARS-CoV-2 pandemic era: what happened in Italy

Background: In the northern hemisphere, Respiratory Syncytial Virus (RSV) is more frequently detected from December to February. In Italy, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) presented a peak in incidence from the end of December 2021 to February 2022. Aim(s): To evaluate how SARS-CoV-2 pandemic has influenced RSV circulation. Method(s): We evaluated 389 children, aged 0-18 years, admitted for respiratory tract infections from September 2021 to January 2022 throughout Italy, from the north to the south. Children underwent nasal washing from 1 to 3 days after hospitalization. A (RT)-PCR was developed for detecting 15 respiratory viruses, including RSV, influenza virus A and B, human coronavirus OC43, 229E, NL-63 and HUK1, adenovirus, rhinovirus, parainfluenza virus 1-3, human bocavirus and human metapneumovirus. Result(s): We detected a virus in 338 children (86.9%): RSV was found in 267 (68.7%), other viruses in 71 (18.3%). 51 children (13.1%) resulted negative. Dividing our observational period in two-week timeframes, we found that RSV showed an early peak from October to the first half of December 2021 compared to its usual seasonality. In a previous study, we have demonstrated that RSV circulation was incredibly low from September 2020 to January 2021, in contrast with what we found in the same period in 2021-2022. Comparing RSV and SARS-CoV-2 incidences, we found that these two viruses spread in opposite ways: when SARS-CoV-2 present an incidence peak, RSV circulation reduced and viceversa. Conclusion(s): The relationship between RSV and SARS-CoV-2 showed that viral interference plays a crucial role in their epidemiology.

The Circulation of Common Respiratory Viruses and Their Co-infection with Severe Acute Respiratory Syndrome Coronavirus 2 Before and After Coronavirus Disease of 2019 Vaccination

Background: Respiratory viruses play important roles in respiratory tract infections;they are the major cause of diseases such as the common cold, bronchiolitis, pneumonia, etc., in humans that circulate more often in the cold seasons. During the COVID-19 pandemic, many strict public health measures, such as hand hygiene, the use of face masks, social distancing, and quarantines, were implemented worldwide to control the pandemic. Besides controlling the COVID-19 pandemic, these introduced measures might change the spread of other common respiratory viruses. Moreover, with COVID-19 vaccination and reducing public health protocols, the circulation of other respiratory viruses probably increases in the community. Objective(s): This study aims to explore changes in the circulation pattern of common respiratory viruses during the COVID-19 pan-demic. Method(s): In the present study, we evaluated the circulation of seven common respiratory viruses (influenza viruses A and B, rhi-novirus, and seasonal human Coronaviruses (229E, NL63, OC43, and HKU1) and their co-infection with SARS-CoV-2 in suspected cases of COVID-19 in two time periods before and after COVID-19 vaccination. Clinical nasopharyngeal swabs of 400 suspected cases of COVID-19 were tested for SARS-CoV-2 and seven common respiratory viruses by reverse transcription real-time polymerase chain reaction. Result(s): Our results showed common respiratory viruses were detected only in 10% and 8% of SARS-CoV-2-positive samples before and after vaccination, respectively, in which there were not any significant differences between them (P-value = 0.14). Moreover, common viral respiratory infections were found only in 12% and 32% of SARS-CoV-2-negative specimens before and after vaccination, respectively, in which there was a significant difference between them (P-value = 0.041). Conclusion(s): Our data showed a low rate of co-infection of other respiratory viruses with SARS-CoV-2 at both durations, before and after COVID-19 vaccination. Moreover, the circulation of common respiratory viruses before the COVID-19 vaccination was lower, probably due to non-pharmaceutical interventions (NPI), while virus activity (especially influenza virus A) was significantly in-creased after COVID-19 vaccination with reducing strict public health measures.Copyright © 2023, Author(s).

Analysis of drug resistance gene in Mycoplasma pneumoniae and 13 pathogens in bronchoalveolar lavage fluid of children with Mycoplasma pneumoniae pneumonia. TT -.

Objective To investigate drug resistance gene in Mycoplasma pneumoniae (MP) and the distribution of 13 respiratory pathogens in bronchoalveolar lavage fluid(BALF) of children with Mycoplasma pneumoniae pneumonia(MPP). Methods A total of 100 BALF of children with MPP in Peking University Third Hospital and Peking University First Hospital from January 2018 to January 2019 were collected. Fluorogenic quantitative PCR was used to detect nucleic acid and it's drug resistance gene of MP and multiple PCR method was adopted to detect influenza A virus, influenza A virus - H1 N1, influenza A virus - H3 N2, influenza B, human parainfluenza virus, adenovirus, human bocavirus, human rhino virus, Chlamydia pneumoniae, human metapneumovirus, MP, human corona virus, and respiratory syncytial virus gene, and the results were compared by using Chi square test. Results In 100 BALF samples, MP and drug resistance gene were detected by fluorogenic quantitative PCR. Totally, 83 cases (83. 00%) were MP positive and 78 cases (93. 98%) were drug resistant. All of them had the point mutations A2063G in V region of 23S rRNA domain. A total of 13 kinds of respiratory pathogens were detected by multiplex PCR method, and 89 cases (89. 00%) were positive. Totally, 79 cases (79. 00%) were MP positive, of which 74 cases (74. 00%) detected only MP, and 5 cases (5. 00%) detected MP combined with other pathogens. Other pathogens were detected in 10 cases (10. 00%). The virus detection rate of 0-4 years old group was higher than that of > 4-6 years old group (P - 0. 042) and > 6 years old group (P =0. 002), and the differences were statistically significant. Conclusions MP can be detected in most BALF samples of MPP children, the drug resistance phenomenon is serious, and the main point mutation is A2063G. There were other respiratory pathogens and 2 or 3 pathogens were detected in a small number of BALF samples.Copyright © 2022 Authors. All rights reserved.

Antiviral effects of Atractyloside A on the influenza B virus (Victoria strain) infection.

Influenza viruses pose a serious threat to human health, infecting hundreds of millions of people worldwide each year, resulting in a significant increase in global morbidity and mortality. Influenza activity has declined at the onset of the COVID-19 pandemic, but the genetic diversity of B/Victoria lineage viruses has increased significantly during this period. Therefore, the prevention and treatment of the influenza B Victoria strain virus should continue to attract research attention. In this study, we found that Atractyloside A (AA), one of the effective components in Atractylodes lancea (Thunb.) DC shows potential antiviral properties. This study shows that AA not only possesses anti-influenza B virus infection effects in vivo and in vitro but also can regulate macrophage polarization to the M2 type, which can effectively attenuate the damage caused by influenza B virus infection. Therefore, Atractyloside A may be an effective natural drug against B/Victoria influenza infection.

Etiologies of medically attended acute respiratory infections among young Ecuadorian children prior to the start of the 2020 SARS-CoV-2 pandemic

Background. Data regarding respiratory pathogen epidemiology in the tropical country of Ecuador are limited. Here, we describe the temporal patterns and etiologies of medically attended acute respiratory infections among Ecuadorean children during the 20-month period preceding the onset of the 2020 SARS-CoV-2 pandemic. Methods. Children < 5 years old presenting to a designated outpatient clinic with at least 2 new symptoms consistent with an acute respiratory infection are eligible for enrollment. Informed consent is obtained. Demographic and clinical details are collected. A nasopharyngeal sample is collected for diagnostic testing of 22 target pathogen groups using Biofire's Respiratory Panel v1.7 multiplex polymerase chain reaction assay. Results. Of the 820 subjects enrolled between July 15, 2018 and March 15, 2020, 655 (80%) tested positive for at least one pathogen. The detection of pathogens was more likely from samples collected from children enrolled in Quito (85%) compared to Machala (76%) (p < 0.05). The most frequently detected pathogen groups were rhinovirus/ enterovirus (46%), parainfluenza virus (14%), respiratory syncytial virus (RSV) (12%), and influenza virus (10%). Two or more pathogen groups were codetected in 174 (27%) of the respiratory samples. Pathogen specific seasonal patterns were not observed for rhinovirus/enterovirus, adenovirus, or atypical bacteria at either site. Samples collected in Quito were positive for the detection of RSV spanning a 32-week period between November and June. In contrast, detection of RSV from samples collected in Machala spanned only a 17- week period between February and May. In Quito, influenza viruses were detected between August and February, with influenza A activity preceding that of influenza B. In Machala, the detection of influenza B virus coincided with the dry season, while detection of influenza A virus was clustered in the rainy period between January and March. Conclusion. The specific etiologies and seasonality of acute respiratory tract infections among Ecuadorean children < 5 years of age differ by site of enrollment. Such differences in regional data can be used to optimize regional implementation of existing and soon-to-be available public health prevention measures.

Relationships Between Community Virus Activity and Cardiorespiratory Rehospitalizations From Post-Acute Care.

OBJECTIVES: Quantify the relationship between increasing influenza and respiratory syncytial virus (RSV) community viral activity and cardiorespiratory rehospitalizations among older adults discharged to skilled nursing facilities (SNFs). DESIGN: Retrospective cohort. SETTING AND PARTICIPANTS: Adults aged ≥65 years who were hospitalized and then discharged to a US SNF between 2012 and 2015. METHODS: We linked Medicare Provider Analysis and Review claims to Minimum Data Set version 3.0 assessments, PRISM Climate Group data, and the Centers for Disease Control and Prevention viral testing data. All data were aggregated to US Department of Health and Human Services regions. Negative binomial regression models quantified the relationship between increasing viral activity for RSV and 3 influenza strains (H1N1pdm09, H3N2, and B) and cardiorespiratory rehospitalizations from SNFs. Incidence rate ratios described the relationship between a 5% increase in circulating virus and the rates of rehospitalization for cardiorespiratory outcomes. Analyses were repeated using the same model, but influenza and RSV were considered "in season" or "out of season" based on a 10% positive testing threshold. RESULTS: Cardiorespiratory rehospitalization rates increased by approximately 1% for every 5% increase in circulating influenza A(H3N2), influenza B, and RSV, but decreased by 1% for every 5% increase in circulating influenza A(H1N1pdm09). When respiratory viruses were in season (vs out of season), cardiorespiratory rehospitalization rates increased by approximately 6% for influenza A(H3N2), 3% for influenza B, and 5% for RSV, but decreased by 6% for influenza A(H1N1pdm09). CONCLUSIONS AND IMPLICATIONS: The respiratory season is a particularly important period to implement interventions that reduce cardiorespiratory hospitalizations among SNF residents. Decreasing viral transmission in SNFs through practices such as influenza vaccination for residents and staff, use of personal protective equipment, improved environmental cleaning measures, screening and testing of residents and staff, surveillance of viral activity, and quarantining infected individuals may be potential strategies to limit viral infections and associated cardiorespiratory rehospitalizations.

The Impact of COVID-19 Pandemic Social Distancing and Mask Mandates on the Prevalence of Influenza and RSV During Their Peak Season

Background: Influenza and bronchiolitis are serious infections especially among vulnerable pediatric populations. Earlier studies have suggested that the transmission of influenza viruses can be reduced by face masking and social distancing measures. In response to the COVID-19 pandemic, Ohio adopted various measures including school closing, travel restrictions, social distancing, and face masking in March, 2020. These measures have created a unique opportunity to study the impact of social distancing measures on the spread of potentially serious viral infections such as influenza and respiratory syncytial viral (RSV) infections of children in our locality. Methods: This is a retrospective cohort study conducted at Akron Children's hospital in Northeast Ohio where the peak respiratory season extends from October to April. The primary outcome was to evaluate the prevalence of influenza A and B and RSV infections before and after implementation of social distancing measures. Prevalence of SARS-CoV-2 was also tracked for comparison. Viral assay data were collected between October 1, 2020 through April 30th, 2021 (during the pandemic and social distancing implementation) and compared with two pre-COVID19 respiratory seasons: 2018-19 and 2019-20. Results from all patients who received viral testing as a part of their medical care were included. Viral tests included rapid antigen tests for Influenza A/B and RSV (Quidel SoFIA), Respiratory Film Array (BioFire, includes flu, RSV, and SARS-CoV-2 targets), and single target tests for SARS-CoV-2 from multiple vendors (see Table 1). Results: There was a dramatic increase in viral testing in the 2020-2021 respiratory season. With most of the new test targeting SARS-CoV-2, Flu and RSV antigen tests decreased significantly but were replaced in part by Respiratory FilmArray use (Table 1). Pre-COVID-19, the peak incidence of RSV occurred in December for the 2018-19 (28.9%, average of 8.8%) and 2019- 20 (24.7%, average of 8.8%) seasons. After social distancing measures, the incidence and positivity rate for RSV was 0% until March 14, 2021 when the first RSV case was detected in our locality, concurrent with relaxation of social distancing measures. Pre-COVID 19, the peak incidence of Influenza A virus occurred during February in the seasons 2018-19 (40.9%;average of 13.6%) and 2019-20 (24.1%, average of 6.1%). Influenza B had a low incidence throughout 2018-2019 (average of 0.3%) with a peak during January in the 2019-2020 season (24.0%, average of 6.8%). During the 2020-2021 season, we detected only two isolated cases of Influenza B virus and no cases of Influenza A virus through April 30, 2021 (Figure-1). Conclusion: Social distancing and mask mandates can be effective tools to decrease the rates of potentially serious infections such as Influenza and RSV in the pediatric population. Travel restrictions and school closures likely had an affect but were not evaluated during this study.

Surveillance of influenza B severe hospitalized cases during 10 seasons in Catalonia: Does the lineage make a difference?

Influenza B viruses circulate in two lineages (B/Victoria and B/Yamagata). Although classically affecting children, recently it has shown a high rate of infection and increased hospitalization in the elderly. To describe and analyze the clinical and epidemiological characteristics of severe hospitalized laboratory-confirmed influenza B virus (SHLCI-B) cases in Catalonia associated with mismatch from Influenza B virus strain included in the trivalent influenza vaccine (TIV). SHLCI-B was registered by the influenza sentinel surveillance system of Catalonia (PIDIRAC) during ten surveillance seasons from 2010 to 2020. Variables age, comorbidities, and vaccination status were recorded. Vaccine effectiveness was estimated as (1-OR) for intensive care unit (ICU) admission. Statistical significance was established at p < 0.05. A total of 1159 SHLCI-B were registered, of these 68.2% (791) corresponded to the 2017-2018 season; 21.8% (253) were admitted to ICU and 13.8% (160) were exitus; 62.5% (725) cases occurred in those aged >64 years; most frequent risk factor was cardiovascular disease (35.1%, 407) followed by chronic pulmonary obstructive disease-COPD (24.6%, 285) and diabetes (24.1%, 279). In four seasons, the predominant circulating lineage was B/Victoria, in two seasons the B/Yamagata lineage and four seasons had no IBV activity. Four seasons presented discordance with the strain included within the TIV. Vaccine effectiveness (VE) to prevent ICU admission was 31% (95% confidence interval [CI]: 4%-51%; p = 0.03); being 29% (95% CI: -3% to 51%) in discordant and 43% (95% CI:-43% to 77%) in concordant seasons. Significant differences were observed in the number of affected aged > 64 years (odds ratio [OR] = 2.5; 95% CI: 1.9-3.4; p < 0.001) and in patients with heart disease (OR = 2.40 95% CI: 1.7-3.4; p < 0.001), COPD (OR = 1.6 95% CI: 1.1-2.3; p = 0.01), and diabetes (OR = 1.5 95% CI: 1.1-2.1; p = 0.04) between discordant and concordant seasons. The increase in hospitalization rate in people> 64 years of age and those presenting comorbidities in seasons with circulating influenza B virus belonging to a lineage discordant with the strain included in the TIV and the decrease of VE to prevent ICU admissions evidence the vital need to administer the quadrivalent influenza vaccine regardless of the findings of predominant circulation in the previous season.

Analysis of the prevalence of common respiratory pathogens in children in Beijing in 2020

Objective To investigate the changes in epidemiological characteristics of common respiratory pathogens in children in Beijing during COVID-19 epidemic.Methods A total of 9 728 serum samples were collected from cases of acute respiratory infections in Beijing Children′s Hospital from January 2020 to December 2020.Indirect immunofluorescence antibody test was performed to detect IgM antibodies against eight common respiratory pathogens and the test results were statistically analyzed.The eight common respiratory pathogens were influenza virus A (FluA), influenza virus B (FluB), respiratory syncytial virus (RSV), adenovirus (ADV), parainfluenza virus (PIV), Mycoplasma pneumoniae (Mp), Chlamydia pneumoniae (Cp) and Legionella pneumophila (Lp).Results The detection rate of respiratory pathogens in 9 728 cases was 41.71% (4 058/9 728) and respiratory viruses (FluA, FluB, RSV, ADV and PIV) accounted for 46.18% (2 343/5 074) of all detected pathogens.Mp, FluB and FluA accounted for 84.73% (4 299/5 074)of all detected pathogens, and the detection rates were 24.27% (2 361/9 728), 11.49% (1 118/9 728) and 8.43% (820/9 728), respectively.There were 846 cases positive for two kinds of pathogens, and the most common co-infection was Mp and FluB.The detection rates in male and female were 37.56% (2 089/5 562) and 47.26% (1 969/4 166), respectively.There were significant differences in the total detection rate and the positive rates of PIV and Mp between different sexes (P<0.05).The detection rate in school-age children (6-12 years old) was the highest (52.26%, 1 535/2 937).The detection rates of respiratory pathogens in different months ranged from 30.12% (203/674) to 49.81% (268/538) with higher rates in autumn and winter [42.45% (1 304/3 072) and 43.29% (1 618/3 738)].The detection rates of FluA and FluB were higher in summer [11.46% (195/1 701)] and winter [14.63% (547/3738)], respectively.Most of RSV infection occurred in summer [1.35% (23/1 701)], and Mp could be detected all year round, especially in winter and spring [27.21% (1 017/3 738) and 25.64% (312/1 217)].The detection rate of respiratory pathogens in outpatient group was higher than that in inpatient group [46.48% (1 583/3 406) vs 39.15% (2 475/6 322)].The detection rate in severe cases was 26.10% (71/272).The detection rates of total pathogens, FluB and Mp were higher in outpatients than in inpatients and the differences were statistically significant (P<0.05).The detection rates of FluA, PIV and ADV were higher in inpatients than in outpatients and the differences were statistically significant (P < 0.05).The detection rates of total pathogens, FluB and Mp in mild cases were significantly higher than those in severe cases and the differences were statistically significant (P<0.05).The detection rate of RSV in severe cases was significantly higher than that in mild cases and the difference was statistically significant (P<0.05).Conclusions The protective measures taken during the period of regular prevention and control of COVID-19 epidemic could better prevent the spread of respiratory viruses, having a certain impact on the population susceptible to respiratory pathogens and typical seasonal patterns, but had little effect on the prevention and control of Mp.New protective measures needed to be studied to prevent Mp infection in children during epidemical season.

The relationship between viruses and clinical findings in hospitalized children diagnosed with acute lower respiratory tract infection

Objective: In this retrospective study, we aimed to identify viral agents in children hospitalized with ALRTI and to show the relationship between viral agents and clinical characteristics. Material and Methods: Two hundred and fifty five children (55.7% male) who were diagnosed with ALRTI and hospitalized between March 2016 and February 2017 were included in the study. Clinical characteristics of the patients who were examined to detect respiratory tract viruses with PCR analysis in nasopharyngeal swab samples were evaluated by using medical records. The patients were divided into three groups according to their age: under two years old, between 2-6 years old, and between 6-18 years old. Newborns were not included in the study.

Simultaneous detection of respiratory infectious diseases using immunoprecipitation and liquid chromatography-tandem mass spectrometry

Background-aim: With recent emergences in new infectious diseases and their variants, there is a need to develop a faster and more specific analytical tool to detect different respiratory infectious diseases such as SARS-CoV-2 or influenza viruses. Not only their symptoms are similar at early stages, but also, they are both enveloped viruses with several common biological properties, often leading to challenges in disease identification. Among different viral components, nucleocapsid protein or nucleoprotein (NP) is highly conserved, less post-translational modifications possessed, and mostly specific for each infectious disease virus types. Therefore, targeting NP could be more advantageous to the method development, achieving much simpler and robust method with minimal subsequent modifications. This study describes a targeted approach for simultaneous detection of NPs from different respiratory infectious diseases using immunoprecipitation (IP) and liquid chromatography-tandem mass spectrometry (LC-MS/MS). Multiple viruses, SARS-CoV-2, influenza virus A and B types, respiratory syncytial virus, and human coronavirus (HCoV-229E), were selected to show that this method can distinguish different disease viruses. Methods: Sample collected via nasopharyngeal swabs in viral transport media was directly subjected to IP using Thermo Scientific™ Pierce™ MS-Compatible IP Kit (Streptavidin). The IP purified samples were then digested using SMART Digest™ Trypsin Kits and analyzed by Thermo Scientific™ Vanquish™ MD HPLC system hyphenated to Thermo Scientific™ TSQ Altis MD mass spectrometer. Data processing was performed using TraceFinder™ LDT software 1.0. Results: Combining IP and LC-MS/MS resulted in a highly targeted approach with the high sensitivity and specificity. The method detected sub tens to hundreds amol of peptides on LC column. Also, it simplified the overall sample preparation process eliminating prior protein precipitation and post sample clean-up. Since the NPs mostly remain unchanged or less modified regardless of variants, the method doesn’t need tremendous alterations once established. Conclusions: This targeted approach can be applied to other enveloped viruses’ detection. Automated IP method is available with KingFisher system so it could lead to a faster turn-around time and higher throughput of the method.

Using amino acid features to identify the pathogenicity of influenza B virus.

BACKGROUND: Influenza B virus can cause epidemics with high pathogenicity, so it poses a serious threat to public health. A feature representation algorithm is proposed in this paper to identify the pathogenicity phenotype of influenza B virus. METHODS: The dataset included all 11 influenza virus proteins encoded in eight genome segments of 1724 strains. Two types of features were hierarchically used to build the prediction model. Amino acid features were directly delivered from 67 feature descriptors and input into the random forest classifier to output informative features about the class label and probabilistic prediction. The sequential forward search strategy was used to optimize the informative features. The final features for each strain had low dimensions and included knowledge from different perspectives, which were used to build the machine learning model for pathogenicity identification. RESULTS: The 40 signature positions were achieved by entropy screening. Mutations at position 135 of the hemagglutinin protein had the highest entropy value (1.06). After the informative features were directly generated from the 67 random forest models, the dimensions for class and probabilistic features were optimized as 4 and 3, respectively. The optimal class features had a maximum accuracy of 94.2% and a maximum Matthews correlation coefficient of 88.4%, while the optimal probabilistic features had a maximum accuracy of 94.1% and a maximum Matthews correlation coefficient of 88.2%. The optimized features outperformed the original informative features and amino acid features from individual descriptors. The sequential forward search strategy had better performance than the classical ensemble method. CONCLUSIONS: The optimized informative features had the best performance and were used to build a predictive model so as to identify the phenotype of influenza B virus with high pathogenicity and provide early risk warning for disease control.

Antiviral potential of garlic (Allium sativum) and its organosulfur compounds: A systematic update of pre-clinical and clinical data.

BACKGROUND: Garlic (Allium sativum L.) is a common herb consumed worldwide as functional food and traditional remedy for the prevention of infectious diseases since ancient time. Garlic and its active organosulfur compounds (OSCs) have been reported to alleviate a number of viral infections in pre-clinical and clinical investigations. However, so far no systematic review on its antiviral effects and the underlying molecular mechanisms exists. SCOPE AND APPROACH: The aim of this review is to systematically summarize pre-clinical and clinical investigations on antiviral effects of garlic and its OSCs as well as to further analyse recent findings on the mechanisms that underpin these antiviral actions. PubMed, Cochrane library, Google Scholar and Science Direct databases were searched and articles up to June 2020 were included in this review. KEY FINDINGS AND CONCLUSIONS: Pre-clinical data demonstrated that garlic and its OSCs have potential antiviral activity against different human, animal and plant pathogenic viruses through blocking viral entry into host cells, inhibiting viral RNA polymerase, reverse transcriptase, DNA synthesis and immediate-early gene 1(IEG1) transcription, as well as through downregulating the extracellular-signal-regulated kinase (ERK)/mitogen activated protein kinase (MAPK) signaling pathway. The alleviation of viral infection was also shown to link with immunomodulatory effects of garlic and its OSCs. Clinical studies further demonstrated a prophylactic effect of garlic in the prevention of widespread viral infections in humans through enhancing the immune response. This review highlights that garlic possesses significant antiviral activity and can be used prophylactically in the prevention of viral infections.

Evaluation of multiplex combined real-time PCR detection kit for nucleic acid detection of 22 respiratory pathogens

Objective: To evaluate the detection consistency and power of a multiplex combined real-time PCR detection kits, and provide reference for the prevention and control of influenza plus SARS-CoV-2 infection.