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Reduced clinical severity during 2022 Shanghai Spring epidemic of SARS-CoV-2 omicron BA.2 variant infection——an integrated account of virus pathogenicity and vaccination effectiveness

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National Science Review 2024年第4期11卷 24-27页

作者： Xingyue Wu Yao Chen Kangli Cao Yao Shen Xueling Wu Yilin Yang Zhongshu Kuang Qingrun Li Zhenzhen Lu Yichen Jia Mian Shao Guorong Gu Xiangwei Wang Ye Yao Ying Wang Shaodie Chen Zhigao Yu Wei Wei Longfei Ding Lulu Lan Tianwen Gu Xiangyu Long Jian Sun Lingyu Xing Jiayuan Shen Yi Han Yue Luo Sucheng Mu Mengna Lin Xiaoyan Zhang Rong Zeng Jianqing Xu Guoping Zhao Lihong Huang Zhenju Song Department of Emergency Medicine Clinical Center for Bio-Therapy Department of Biostatistics and Department of UrologyShanghai Key Laboratory of Lung Inflammation and Injury Zhongshan Hospital Fudan University Department of respiratory and Critical Care Medicine Shanghai Pudong Hospital Fudan University Department of Pulmonology Renji Hospital Shanghai Jiao Tong University School of Medicine Key laboratory of Systems Biology Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of Sciences Shanghai Public Health Clinical Center Fudan University Department of Biostatistics School of Public Health Key Laboratory of Public Health Safety of Ministry of Education and Shanghai Institute of Infectious Disease and Biosecurity School of Public Health Fudan University Shanghai Institute of Immunology Department of Immunology and Microbiology Shanghai Institute of Virology Key Laboratory of Cell Differentiation and Apoptosis of Chinese Ministry of EducationSchool of Medicine Shanghai Jiao Tong University State Key laboratory of Genetic Engineering Fudan Microbiome CenterSchool of Life Sciences Fudan University Bio-Med Big Data Center Shanghai Institute of Nutrition and Health Chinese Academy of Sciences

The emergence of SARS-Co V-2 variant of concern omicron BA.2 led to high infection incidence rates as well as reduced severity of COVID-19 during the Shanghai Spring epidemic of 2022 [1]. We assessed the role of viral pathogenicity and the effectiveness of inactivated vaccines in a retrospective observational study including 10 258 confirmed COVID-19cases identified between April and June of 2022, from four COVID-19 designated hospitals located in two areas of Shanghai, namely the West Bund and the East Bund, where the populations’ demographic characteristics varied significantly (Table S1, Fig. S1).

关键词： REPLICATION

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Individual virome analysis reveals the general co-infection of mammal-associated viruses with SARS-related coronaviruses in bats

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Virologica Sinica 2024年第4期39卷 565-573页

作者： Hao-Rui Si Ke Wu Jia Su Tian-Yi Dong Yan Zhu Bei Li Ying Chen Yang Li Zheng-Li Shi Peng Zhou Wuhan Institute of Virology Chinese Academy of SciencesWuhan 43000China Guangzhou National laboratory Guangzhou International Bio IslandGuangzhou 510005China University of Chinese Academy of Sciences Beijing 100000China State Key laboratory of respiratory Disease The First Affiliated Hospital of Guangzhou Medical SchoolGuangzhou 510005China

Bats are the natural reservoir hosts for SARS-related coronavirus(SARSr-CoV)and other highly pathogenic ***,it is conceivable that an individual bat may harbor multiple ***,there is limited knowledge on the overall co-circulation of microorganisms in ***,we conducted a 16-year monitoring of bat viruses in south and central China and identified 238 SARSr-CoV positive samples across nine bat species from ten provinces or administrative *** these,76 individual samples were selected for further metagenomics *** found a complex microenvironment characterized by the general cocirculation of microbes from two different sources:mammal-associated viruses or environment-associated *** later includes commensal bacteria,enterobacteria-related phages,and insect or fungal viruses of food *** showed that 25%(19/76)of the samples contained at least one another mammal-associated virus,notably alphacoronaviruses(13/76)such as AlphaCoV/YN2012,HKU2-related CoV and AlphaCoV/Rf-HuB2013,along with viruses from other ***,we observed three viruses co-circulating within a single bat,comprising two coronavirus species and one *** analysis also revealed the potential presence of pathogenic bacteria or fungi in ***,we obtained 25 viral genomes from the 76 bat SARSr-CoV positive samples,some of which formed new evolutionary ***,our study reveals the complex microenvironment of bat microbiome,facilitating deeper investigations into their pathogenic potential and the likelihood of cross-species transmission.

关键词： Bat microbiome SARS-related coronavirus Co-infection Alphacoronavirus

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Lung microbiome:new insights into the pathogenesis of respiratory diseases

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Signal Transduction and Targeted Therapy 2024年第2期9卷 652-678页

作者： Ruomeng Li Jing Li Xikun Zhou Department of Biotherapy Cancer Center and State Key Laboratory of BiotherapyWest China HospitalSichuan UniversityChengdu 610041China State Key laboratory of Oral Diseases National Clinical Research Center for Oral DiseasesChinese Academy of Medical Sciences Research Unit of Oral Carcinogenesis and ManagementWest China Hospital of StomatologySichuan UniversityChengduSichuan 610041China

The lungs were long thought to be sterile until technical advances uncovered the presence of the lung microbial *** microbiome of healthy lungs is mainly derived from the upper respiratory tract(URT)microbiome but also has its own characteristic *** selection mechanisms in the lung,including clearance by coughing,pulmonary macrophages,the oscillation of respiratory cilia,and bacterial inhibition by alveolar surfactant,keep the microbiome transient and mobile,which is different from the microbiome in other *** pulmonary bacteriome has been intensively studied recently,but relatively little research has focused on the mycobiome and *** up-to-date review retrospectively summarizes the lung microbiome’s history,composition,and *** focus on the interaction of the lung microbiome with the oropharynx and gut microbiome and emphasize the role it plays in the innate and adaptive immune *** importantly,we focus on multiple respiratory diseases,including asthma,chronic obstructive pulmonary disease(COPD),fibrosis,bronchiectasis,and *** impact of the lung microbiome on coronavirus disease 2019(COVID-19)and lung cancer has also been comprehensively ***,by summarizing the therapeutic potential of the lung microbiome in lung diseases and examining the shortcomings of the field,we propose an outlook of the direction of lung microbiome research.

关键词： respiratory diseases Lung

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Aryl hydrocarbon receptor:Linking environment to aging process in elderly patients with asthma

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Chinese Medical Journal 2024年第4期137卷 382-393页

作者： Tianrui Yang Rongjun Wan Wei Tu Sai Nithin Avvaru Peisong Gao Division of Allergy and Clinical Immunology Department of MedicineJohns Hopkins University School of MedicineBaltimoreMD 21224USA Department of Geriatric Medicine The First People’s Hospital of Yunnan ProvinceKunmingYunnan 650032China Department of respiratory Medicine Xiangya HospitalCentral South UniversityChangshaHunan 410008China The State Key laboratory of respiratory Disease for Allergy Shenzhen Key Laboratory of Allergy and ImmunologyShenzhen University School of MedicineShenzhenGuangdong 518055China

Aging is a significant risk factor for various diseases,including asthma,and it often leads to poorer clinical outcomes,particularly in elderly *** is recognized that age-related diseases are due to a time-dependent accumulation of cellular damage,resulting in a progressive decline in cellular and physiological functions and an increased susceptibility to chronic *** effects of aging affect not only the elderly but also those of younger ages,posing significant challenges to global ***,understanding the molecular mechanisms associated with aging in different diseases is *** intriguing factor is the aryl hydrocarbon receptor(AhR),which serves as a cytoplasmic receptor and ligand-activated transcription factor and has been linked to the aging ***,we review the literature on several major hallmarks of aging,including mitochondrial dysfunction,cellular senescence,autophagy,mitophagy,epigenetic alterations,and microbiome ***,we provide an overview of the impact of AhR on these hallmarks by mediating responses to environmental exposures,particularly in relation to the immune ***,we explore how aging hallmarks affect clinical characteristics,inflammatory features,exacerbations,and the treatment of *** is suggested that AhR signaling may potentially play a role in regulating asthma phenotypes in elderly populations as part of the aging process.

关键词： Aging Environment Reactive oxygen species Senescence Aryl hydrocarbon receptor Asthma

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Alteration of the respiratory microbiome in COVID-19 patients with different severities

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Journal of Genetics and Genomics 2022年第3期49卷 258-261页

作者： Zhengtu Li Yinhu Li Linghua Li Xiaoneng Mo Shaoqiang Li Mingzhou Xie Yangqing Zhan Ye Lin Zhun Li Min Xie Zhaoming Chen Airu Zhu Ruosu Ying Le Yu Jin cun Zhao Shuai Cheng Li Weiping Cai Feng Ye State Key laboratory of respiratory Disease National Clinical Research Center for Respiratory DiseaseGuangzhou Institute of Respiratory HealthThe First Affiliated Hospital of Guangzhou Medical UniversityNational Center for Respiratory MedicineGuangzhouGuangdong 510120China Department of Computer Sciences City University of Hong KongHong Kong 999077China Guangzhou Eighth People's Hospital Guangzhou Medical UniversityGuangzhouGuangdong 510060China Beijing YuanShengKangTai(ProtoDNA)Genetech Co.Ltd. Beijing100190China

Coronavirus disease 2019(COVID-19) is rampant worldwide and has affected more than 215 countries and regions. According to the World Health Organization's report, there were 226,018,919 COVID-19 cases and 4,654,898 deaths as of March 14, 2021, although300,002,228 vaccines have been administered globally. COVID-19patients have different clinical phenotypes and can be divided into asymptomatic, normal, mild, severe, and critical patients.

关键词： patients respiratory clinical

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Comparison of Composition and Diversity of Bacterial microbiome in Human Upper and Lower respiratory Tract

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Chinese Medical Journal 2017年第9期130卷 1122-1124页

作者： Zhi-Hong Feng Qin Li Si-Ran Liu Xiao-Nan Du Chen Wang Xiu-Hong Nie Wei Wang Sun Ying Department of respiratory Medicine Beijing Xuanwu Hospital Capital Medical University Beijing 100053 China Department of Immunology and The Research Centre of microbiome School of Basic Medical Sciences Capital Medical University Beijing 100069 China Department of respiratory Disease Capital Medical University Beijing 100069 China China-Japan Friendship Hospital National Clinical Research Center for Respiratory Diseases Beijing 100029 China

INTRODUCTIONmicrobiome residing in the airways and parenchymal tissues, as a biological barrier of respiratory tract, plays an important role in maintaining the normal functions of individual＇s respiratory system and preventing the invasion and colonization of exogenous pathogens.H1 Changes of microbial community may result in the occurrence and progression of infectious pneumonia and acute exacerbation of chronic diseases, through disordering commensal microorganisms and increasing invasive ability of pathogens.F21 Traditional methods for detecting bacteria normally rely on culture technique, which have a number of critical problems, including time-consuming and relatively low positive rate of detection. In the last 1 0 years, 16S rRNA gene sequencing technique has been thought to be more comprehensive and reliable than those of culture-dependent methods for monitoring bacterial microbiome in skin, organs, and tracts quantitatively and qualitatively.E31 In this case, choosing credible samples are critical to evaluate the community composition of microbiome in the host tracts, including respiratory tract. In the present study, we aimed to compare the composition and diversity of bacterial community structure in different samples collected from the individuals＇ airways using 16S rRNA gene sequencing technique.

关键词： 16S rRNA Gene Sequencing Bronchoalveolar Lavage Fluid Microbiota respiratory Tract Sputum

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Human Pharyngeal microbiome May Play A Protective Role in respiratory Tract Infections

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Genomics, Proteomics & Bioinformatics 2014年第3期12卷 144-150页

作者： Zhancheng Gao Yu Kang Jun Yu Lufeng Ren Department of respiratory and Critical Care Medicine Peking University People's Hospital CAS Key laboratory of Genome Sciences and Information Beijing Institute of Genomics Chinese Academy of Sciences

The human pharyngeal microbiome, which resides at the juncture of digestive and respiratory tracts, may have an active role in the prevention of respiratory tract infections, similar to the actions of the intestinal microbiome against enteric infections. Recent studies have demonstrated that the pharyngeal microbiome comprises an abundance of bacterial species that interacts with the local epithelial and immune cells, and together, they form a unique micro-ecological system. Most of the microbial species in microbiomes are obligate symbionts constantly adapting to their unique surroundings. Indigenous commensal species are capable of both maintaining dominance and evoking host immune responses to eliminate invading species. Temporary damage to the pharyngeal microbiome due to the impaired local epithelia is also considered an important predisposing risk factor for infections. Therefore, reinforcement of microbiome homeostasis to prevent invasion of infection-prone species would provide a novel treatment strategy in addition to antibiotic treatment and vaccination. Hence continued research efforts on evaluating probiotic treatment and developing appropriate procedures are necessary to both prevent and treat respiratory infections.

关键词： respiratory tract infections Pharyngeal microbiome Homeostasis Probiotics Restoration balance ofmicrobiome

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Impact of inhaled corticosteroid use on elderly chronic pulmonary disease patients with community acquired pneumonia

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Chinese Medical Journal 2024年第2期137卷 241-243页

作者： Xiudi Han Hong Wang Liang Chen Yimin Wang Hui Li Fei Zhou Xiqian Xing Chunxiao Zhang Lijun Suo Jinxiang Wang Guohua Yu Guangqiang Wang Xuexin Yao Hongxia Yu Lei Wang Meng Liu Chunxue Xue Bo Liu Xiaoli Zhu Yanli Li Ying Xiao Xiaojing Cui Lijuan Li Xuedong Liu Bin Cao Department of Pulmonary and Critical Care Medicine Qingdao Municipal HospitalQingdaoShandong 266011China Department of Nosocomial Infection Qingdao Municipal HospitalQingdaoShandong 266011China Department of Infectious Diseases Nanjing Lishui People’s HospitalNanjingJiangsu 211213China Department of Pulmonary and Critical Care Medicine National Clinical Research Center of Respiratory DiseasesCenter for Respiratory DiseasesChina-Japan Friendship HospitalBeijing 100020China Department of respiratory Medicine Yan’an Hospital Affiliated to Kunming Medical UniversityKunmingYunnan 652199China Department of respiratory Medicine Beijing Huimin HospitalBeijing 100054China Department of Pulmonary and Critical Care Medicine Zibo Municipal HospitalZiboShandong 255000China Department of respiratory Medicine Beijing Luhe HospitalCapital Medical UniversityBeijing 101149China Department of Pulmonary and Critical Care Medicine Weifang No.2 People’s HospitalWeifangShandong 261599China Department of respiratory Medicine Shandong University Affiliated Qilu Hospital(Qingdao)QingdaoShandong 266035China Department of respiratory Medicine the 2nd Hospital of Beijing CorpsChinese Armed Police ForcesBeijing 100044China Department of Infectious Disease Qingdao University Medical College Affiliated Yantai Yuhuangding HospitalYantaiShandong 100191China Department of respiratory Medicine Rizhao Chinese Medical Hospital Affiliated to Shandong Chinese Medical UniversityRizhaoShandong 276800China Department of respiratory Medicine Beijing Hospital of Traditional Chinese Medicine Affiliated to Capital Medical UniversityBeijing 100010China Department of Occupational Medicine and Toxicology Beijing Chao-Yang HospitalCapital Medical UniversityBeijing 100020China

To the Editor:With an aging global population,the incidences of community-acquired pneumonia(CAP)and chronic obstructive pulmonary disease(COPD)have signicantly increased.[1]Previous studies have conrmed that COPD and asthma are independently associated with the prevalence of *** use of inhaled corticosteroid(ICS),the cornerstone of treatment for asthma,COPD with frequent acute exacerbations,and asthma-COPD overlap(ACO)may induce changes in the local lung microbiome and abnormal lung immunity,ultimately,causing a signicantly increased risk of ***,in cases of pneumonia,the effect of the use of ICS on CAP mortality remains *** data from one study favored the prior use of ICS,which was associated with a signicantly lower short-term mortality rate,[2]other studies have identied no impact on *** date,data on the impact of the use of ICS on mortality,prehospitalization or during hospitalization,are scarce,particularly in the older ***,this multicenter,retrospective study explored the association between the use of ICS during hospitalization and short-term mortality in older patients with CAP and those with chronic pulmonary disease(CPD).

关键词： pneumonia patients immunity

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Alterations in nasal microbiota of patients with amyotrophic lateral sclerosis

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Chinese Medical Journal 2024年第2期137卷 162-171页

作者： Kaixiong Liu Qifu Guo Ying Ding Li Luo Jianchai Huang Qijie Zhang Department of respiratory and Critical Care Medicine The First Affiliated HospitalFujian Medical UniversityFuzhouFujian 350005China Department of Respiratory and Critical Care MedicineNational Regional Medical CenterBinhai Campus of The First Affiliated HospitalFujian Medical UniversityFuzhouFujian 350212China Department of Neurology Fujian Institute of NeurologyThe First Affiliated HospitalFujian Medical UniversityFuzhouFujian 350005China Department of NeurologyNational Regional Medical CenterBinhai Campus of The First Affiliated HospitalFujian Medical UniversityFuzhouFujian 350212China

Background:Links between alterations in gut microbiota composition and amyotrophic lateral sclerosis(ALS)have previously been *** study aimed to examine the microbiota in the nasal cavity of ***:Sixty-six ALS patients and 40 healthy caregivers who live in close proximity with patients were *** throughput metagenomic sequencing of the 16S ribosomal deoxyribonucleic acid(rDNA)gene V3-V4 region of nasal microbiota was used to characterize the alpha and beta diversity and relative abundance of bacterial taxa,predict function,and conduct correlation analysis between specific taxa and clinical ***:The nasal microbiome of ALS patients showed lower alpha diversity than that of corresponding healthy family *** Gaiella,Sphingomonas,Polaribacter_1,Lachnospiraceae_NK4A136_group,Klebsiella,and Alistipes were differentially enriched in ALS patients compared to *** microbiota composition in ALS patients significantly differed from that in healthy subjects(unweighted UniFrac P=0.001),while Linear discriminant analysis Effect Size(LEfSe)analysis indicated that Bacteroidetes and Firmicutes dominated healthy nasal communities at the phylum level,whereas Actinobacteria was the predominant phylum and Thermoleophilia was the predominant class in ALS *** Faecalibacterium and Alistipes were positively correlated with ALS functional rating scale revised(ALSFRS-R;r_(s)=0.349,P=0.020 and r_(s)=0.393,P=0.008),while Prevotella-9 and Bacteroides operational taxonomic units(OTUs)were positively associated with lung function(FVC)in ALS patients(r_(s)=0.304,P=0.045,and r_(s)=0.300,P=0.048,respectively).Prevotella-1 was positively correlated with white blood cell counts(WBC,r_(s)=0.347,P=0.021),neutrophil percentage(Neu%,r_(s)=0.428,P=0.004),and neutrophil-to-lymphocyte ratio(NLR,r_(s)=0.411,P=0.006),but negatively correlated with lymphocyte percentage(Lym%,r_(s)=-0.408,P=0.006).In contrast,Streptococcus was negatively associa

关键词： Amyotrophic lateral sclerosis Nasal microbiota Dysbiosis Inflammation

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Severe respiratory syncytial virus disease

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Journal of Intensive Medicine 2024年第04期04卷 405-416页

作者： Peña-López Y. Sabater-Riera J. Raj P. microbiome Research laboratory (MRL) Department of Immunology University of Texas Southwestern Medical Center Dallas TX United States Pediatric Critical Care Department Hospital Universitari Vall d'Hebron Barcelona Spain Global Health eCore Vall d'Hebron Institute of Research Barcelona Spain Intensive Care Department Servei de Medicina Intensiva IDIBELL-Hospital Universitari de Bellvitge L´Hospitalet de Llobregat Barcelona Spain Bellvitge Biomedical Research Institute (IDIBELL) L'Hospitalet de Llobregat Barcelona Spain

The burden of respiratory syncytial virus (RSV) disease is widely recognized. Main risk factors for severe disease, such as extreme ages, chronic cardiopulmonary conditions, and immunosuppression, typically coincide with poorer outcomes. While the majority of RSV hospitalizations involve healthy children, a higher proportion of hospitalized adults with underlying conditions need intensive care. Presently, treatment primarily consists of supportive measures. RSV-induced wheezing should be distinguished from respiratory tract thickening, without response to bronchodilators. Obstructive RSV disease frequently overlaps with viral pneumonia. Non-invasive mechanical ventilation and high-flow oxygen therapy represented significant advancements in the management of severe RSV disease in children and may also hold considerable importance in specific phenotypes of RSV disease in adults. Most severe infections manifest with refractory hypoxemia necessitating more advanced ventilatory support and/or extracorporeal membrane oxygenation therapy. While bacterial co-infection rates are low, they have been associated with worse outcomes. Antibiotic prescription rates are high. Accurately diagnosing bacterial co-infections remains a challenge. Current evidence and antibiotic stewardship policies advise against indiscriminate antibiotic usage, even in severe cases. The role of currently developing antiviral therapies in severe RSV disease will be elucidated in the coming years, contingent upon the success of new vaccines and immune passive strategies involving nirsevimab. © 2024

关键词： ARDS Bronchiolitis Co-infection Pneumonia respiratory failure RSV

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