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Altawalah H, Alfouzan W, Al-Fadalah T, Zalzala MA, Ezzikouri S. Viral etiology of severe lower respiratory tract infections in SARS-CoV-2 negative hospitalized patients during the COVID-19 pandemic in Kuwait. Heliyon 2024; 10:e29855. [PMID: 38681623 PMCID: PMC11046192 DOI: 10.1016/j.heliyon.2024.e29855] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 04/15/2024] [Accepted: 04/16/2024] [Indexed: 05/01/2024] Open
Abstract
Background The prevalence of respiratory infections is largely underexplored in Kuwait. The aim of our study is to determine the etiology of infections from patients who are SARS-CoV-2 negative hospitalized with severe lower respiratory tract infections (LRTIs) in Kuwait during the coronavirus disease 2019 (COVID-19) pandemic. Methods We conducted an observational cross-sectional study among severe LRTI patients between September 2021 and March 2022. Respiratory samples from 545 non-COVID-19 severe LRTIs patients were prospectively evaluated with FTD Respiratory 21 Plus® real-time PCR, targeting 20 different viruses and 1 atypical bacterial pathogen. Results Among all 545 hospitalized cases, 411 (75.4 %) tested positive for at least one respiratory pathogen. The most common were rhinovirus (HRV) (32.7 %), respiratory syncytial virus (RSV) (20.9 %), metapneumovirus (HMPV) (14.1 %), bocavirus (13.2 %), and influenza A (12.7 %). The proportion of pathogens detected was highest in the under-5 age group, while HKU1 (44.4 %) predominated in the elderly (>50 years). Conclusion Our study reveals a high prevalence of respiratory viruses in severe acute lower respiratory tract infections among non-COVID-19 hospitalized patients in Kuwait. HRV remains the main etiology affecting the country, particularly in infants. These results underscore the necessity of employing multiplex PCR for accurate diagnosis and describing the epidemiology of infections among severe lower respiratory tract infections. This will facilitate the use of specific antiviral therapy and help avoid excessive or inappropriate antibiotic therapy.
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Affiliation(s)
- Haya Altawalah
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, 24923, Kuwait
- Virology Unit, Yacoub Behbehani Center, Sabah Hospital, Ministry of Health, Kuwait, Kuwait
| | - Wadha Alfouzan
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, 24923, Kuwait
- Laboratory Medicine, Farwania Hospital, Ministry of Health, Farwania, Kuwait
| | - Talal Al-Fadalah
- Qualities and Accreditation Directorate, Ministry of Health, Kuwait, Kuwait
| | - Mariam Ali Zalzala
- Department of Microbiology, Faculty of Medicine, Kuwait University, Safat, 24923, Kuwait
| | - Sayeh Ezzikouri
- Virology Unit, Viral Hepatitis Laboratory, Institut Pasteur du Maroc, Casablanca, Morocco
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Hong YJ, Jung BK, Kim JK. Epidemiological Characterization of Respiratory Pathogens Using the Multiplex PCR FilmArray™ Respiratory Panel. Diagnostics (Basel) 2024; 14:734. [PMID: 38611647 PMCID: PMC11011807 DOI: 10.3390/diagnostics14070734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2024] [Revised: 03/25/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
Various pathogens can cause upper respiratory tract infections, presenting challenges in accurate diagnosis due to similar symptomatology. Therefore, rapid and precise diagnostic tests are crucial for effective treatment planning. Traditional culture-based methods for diagnosis are limited by their reliance on skilled personnel and lengthy processing times. In contrast, multiplex polymerase chain reaction (PCR) techniques offer enhanced accuracy and speed in identifying respiratory pathogens. In this study, we aimed to assess the efficacy of the FilmArray™ Respiratory Panel (RP), a multiplex PCR test capable of simultaneously screening 20 pathogens. This retrospective analysis was conducted at Dankook University Hospital, South Korea, between January 2018 and December 2022. Samples from patients with upper respiratory tract infections were analyzed. Results revealed adenovirus as the most prevalent pathogen (18.9%), followed by influenza virus A (16.5%), among others. Notably, a 22.5% co-infection rate was observed. The FilmArray™ RP method successfully identified 20 pathogens within 2 h, facilitating prompt treatment decisions and mitigating unnecessary antibiotic prescriptions. This study underscores the utility of multiplex PCR in respiratory pathogen identification, offering valuable insights for epidemiological surveillance and diagnosis.
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Affiliation(s)
- Young Jun Hong
- Department of Biomedical Laboratory Science, College of Health Sciences, Dankook University, Cheonan 31116, Republic of Korea;
| | - Bo Kyeung Jung
- Department of Laboratory Medicine, College of Medicine, Dankook University, Cheonan 31116, Republic of Korea;
| | - Jae Kyung Kim
- Department of Biomedical Laboratory Science, College of Health Sciences, Dankook University, Cheonan 31116, Republic of Korea;
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Feng Y, He T, Zhang B, Yuan H, Zhou Y. Epidemiology and diagnosis technologies of human metapneumovirus in China: a mini review. Virol J 2024; 21:59. [PMID: 38454484 PMCID: PMC10921660 DOI: 10.1186/s12985-024-02327-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 02/26/2024] [Indexed: 03/09/2024] Open
Abstract
Human metapneumovirus (HMPV) is a newly identified pathogen causing acute respiratory tract infections in young infants worldwide. Since the initial document of HMPV infection in China in 2003, Chinese scientists have made lots of efforts to prevent and control this disease, including developing diagnosis methods, vaccines and antiviral agents against HMPV, as well as conducting epidemiological investigations. However, effective vaccines or special antiviral agents against HMPV are currently not approved, thus developing early diagnosis methods and knowing its epidemiological characteristics will be beneficial for HMPV control. Here, we summarized current research focused on the epidemiological characteristics of HMPV in China and its available detection methods, which will be beneficial to increase the public awareness and disease control in the future.
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Affiliation(s)
- Yuan Feng
- Xiangtan Central Hospital, Xiangtan, 411100, Hunan, China
| | - Tao He
- Xiangtan Maternal and Child Health Hospital, Xiangtan, 411100, China
| | - Bo Zhang
- Xiangtan Central Hospital, Xiangtan, 411100, Hunan, China
| | - Haibin Yuan
- Xiangtan Central Hospital, Xiangtan, 411100, Hunan, China
| | - Yinfei Zhou
- Xiangtan Central Hospital, Xiangtan, 411100, Hunan, China.
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4
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Hong S, Li D, Wei Y, Zheng Y, Cai J, Zheng H, Zhang X, Deng Y, Han D, Wang J, Chen L, Li S, Qiu W, Ren M, Zou L. Epidemiology of respiratory pathogens in patients with acute respiratory tract infection in Xiamen, China: A retrospective survey from 2020 to 2022. Heliyon 2023; 9:e22302. [PMID: 38053876 PMCID: PMC10694312 DOI: 10.1016/j.heliyon.2023.e22302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 11/08/2023] [Accepted: 11/09/2023] [Indexed: 12/07/2023] Open
Abstract
Acute respiratory tract infections (ARTI) are caused by respiratory pathogens and range from asymptomatic infections to severe respiratory diseases. These diseases can be life threatening with high morbidity and mortality worldwide. Under the pandemic of coronavirus disease 2019 (COVID-19), little has been reported about the pathogen etiologies and epidemiology of patients suffering from ARTI of all age in Xiamen. Region-specific surveillance in individuals with ARTI of all ages was performed in Xiamen from January 2020 to October 2022. Here, we observed the epidemiological characteristics of thirteen pathogens within ARTI patients and further revealed the difference of that between upper respiratory tract infections (URTI) and lower respiratory tract infections (LRTI). In total 56.36 % (2358/4184) of the ARTI patients were positive for at least one respiratory pathogen. Rhinovirus (RVs, 29.22 %), influenza A (FluA, 19.59 %), respiratory syncytial virus (RSV, 18.36 %), metapneumovirus (MPV, 13.91 %), and adenovirus (ADV, 10.31 %) were the five leading respiratory pathogens. Respiratory pathogens displayed age- and season-specific patterns, even between URTI and LRTI. Compared with other groups, a higher proportion of FluA (52.17 % and 68.75 %, respectively) infection was found in the adult group and the elder group, while the lower proportion of RVs (14.11 % and 11.11 %) infection was also observed in them. Although ARTI cases circulated throughout the year, RVs, FluB, and BoV peaked in autumn, and FluA circulated more in summer. Besides, the co-infectious rate was 8.7 % with the most common for RVs. Logistic regression analyses revealed the correlations between respiratory pathogens and disease types. These results are essential for replenishing epidemiological characteristics of common respiratory pathogens that caused ARTI in Xiamen during the epidemic of COVID-19, and a better understanding of it might optimize the local prevention and clinical control.
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Affiliation(s)
- Shan Hong
- Department of Pediatrics, The Fifth Hospital of Xiamen, Xiamen, Fujian, China
| | - Dan Li
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang, China
| | - Yanli Wei
- Department of General Practice, The Fifth Hospital of Xiamen, Xiamen, Fujian, China
| | - Yilin Zheng
- Department of Pediatrics, The Fifth Hospital of Xiamen, Xiamen, Fujian, China
| | - Jiading Cai
- Department of General Practice, The Fifth Hospital of Xiamen, Xiamen, Fujian, China
| | - Heping Zheng
- Department of Intensive Care Unit, The Fifth Hospital of Xiamen, Xiamen, Fujian, China
| | - Xuan Zhang
- Key Laboratory of Digital Technology in Medical Diagnostics of Zhejiang Province, Dian Diagnostics Group Co., Ltd., Hangzhou, Zhejiang, China
| | - Yulin Deng
- Department of Pediatrics, The Fifth Hospital of Xiamen, Xiamen, Fujian, China
| | - Dandan Han
- Department of Pediatrics, The Fifth Hospital of Xiamen, Xiamen, Fujian, China
| | - Jia Wang
- Department of Pediatrics, The Fifth Hospital of Xiamen, Xiamen, Fujian, China
| | - Linlin Chen
- Department of Pediatrics, The Fifth Hospital of Xiamen, Xiamen, Fujian, China
| | - Shujing Li
- Department of Pediatrics, The Fifth Hospital of Xiamen, Xiamen, Fujian, China
| | - Weiping Qiu
- Department of General Practice, The Fifth Hospital of Xiamen, Xiamen, Fujian, China
| | - Min Ren
- Department of Pediatrics, The Fifth Hospital of Xiamen, Xiamen, Fujian, China
| | - Liangneng Zou
- Department of General Practice, The Fifth Hospital of Xiamen, Xiamen, Fujian, China
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Zhang L, Xiao Y, Xiang Z, Chen L, Wang Y, Wang X, Dong X, Ren L, Wang J. Statistical Analysis of Common Respiratory Viruses Reveals the Binary of Virus-Virus Interaction. Microbiol Spectr 2023; 11:e0001923. [PMID: 37378522 PMCID: PMC10433823 DOI: 10.1128/spectrum.00019-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Accepted: 06/09/2023] [Indexed: 06/29/2023] Open
Abstract
Respiratory viruses may interfere with each other and affect the epidemic trend of the virus. However, the understanding of the interactions between respiratory viruses at the population level is still very limited. We here conducted a prospective laboratory-based etiological study by enrolling 14,426 patients suffered from acute respiratory infection (ARI) in Beijing, China during 2005 to 2015. All 18 respiratory viruses were simultaneously tested for each nasal and throat swabs collected from enrolled patients using molecular tests. The virus correlations were quantitatively evaluated, and the respiratory viruses could be divided into two panels according to the positive and negative correlations. One included influenza viruses (IFVs) A, B, and respiratory syncytial virus (RSV), while the other included human parainfluenza viruses (HPIVs) 1/3, 2/4, adenovirus (Adv), human metapneumovirus (hMPV), and enterovirus (including rhinovirus, named picoRNA), α and β human coronaviruses (HCoVs). The viruses were positive-correlated in each panel, while negative-correlated between panels. After adjusting the confounding factors by vector autoregressive model, positive interaction between IFV-A and RSV and negative interaction between IFV-A and picoRNA are still be observed. The asynchronous interference of IFV-A significantly delayed the peak of β human coronaviruses epidemic. The binary property of the respiratory virus interactions provides new insights into the viral epidemic dynamics in human population, facilitating the development of infectious disease control and prevention strategies. IMPORTANCE Systematic quantitative assessment of the interactions between different respiratory viruses is pivotal for the prevention of infectious diseases and the development of vaccine strategies. Our data showed stable interactions among respiratory viruses at human population level, which are season irrelevant. Respiratory viruses could be divided into two panels according to their positive and negative correlations. One included influenza virus and respiratory syncytial virus, while the other included other common respiratory viruses. It showed negative correlations between the two panels. The asynchronous interference between influenza virus and β human coronaviruses significantly delayed the peak of β human coronaviruses epidemic. The binary property of the viruses indicated transient immunity induced by one kind of virus would play role on subsequent infection, which provides important data for the development of epidemic surveillance strategies.
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Affiliation(s)
- Lulu Zhang
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Yan Xiao
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Zichun Xiang
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Lan Chen
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Ying Wang
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Xinming Wang
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Xiaojing Dong
- Santa Clara University, Santa Clara, California, USA
| | - Lili Ren
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
| | - Jianwei Wang
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People’s Republic of China
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Zhang L, Xiao Y, Zhang G, Li H, Zhao J, Chen M, Chen F, Liu L, Li Y, Peng L, Zhao F, Yang D, Wen Z, Wu L, Wu S, Sun Y, Wang Y, Chen L, Wang X, Wang L, Li W, Qiu H, Chen Y, Gao Z, Ren L, Wang J. Identification of priority pathogens for aetiological diagnosis in adults with community-acquired pneumonia in China: a multicentre prospective study. BMC Infect Dis 2023; 23:231. [PMID: 37059987 PMCID: PMC10103676 DOI: 10.1186/s12879-023-08166-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 03/15/2023] [Indexed: 04/16/2023] Open
Abstract
BACKGROUND Community-acquired pneumonia (CAP) is a major public health challenge worldwide. However, the aetiological and disease severity-related pathogens associated with CAP in adults in China are not well established based on the detection of both viral and bacterial agents. METHODS A multicentre, prospective study was conducted involving 10 hospitals located in nine geographical regions in China from 2014 to 2019. Sputum or bronchoalveolar lavage fluid (BALF) samples were collected from each recruited CAP patient. Multiplex real-time PCR and bacteria culture methods were used to detect respiratory pathogens. The association between detected pathogens and CAP severity was evaluated. RESULTS Among the 3,403 recruited eligible patients, 462 (13.58%) had severe CAP, and the in-hospital mortality rate was 1.94% (66/3,403). At least one pathogen was detected in 2,054 (60.36%) patients, with two or more pathogens were co-detected in 725 patients. The ten major pathogens detected were Mycoplasma pneumoniae (11.05%), Haemophilus influenzae (10.67%), Klebsiella pneumoniae (10.43%), influenza A virus (9.49%), human rhinovirus (9.02%), Streptococcus pneumoniae (7.43%), Staphylococcus aureus (4.50%), adenovirus (2.94%), respiratory syncytial viruses (2.35%), and Legionella pneumophila (1.03%), which accounted for 76.06-92.52% of all positive detection results across sampling sites. Klebsiella pneumoniae (p < 0.001) and influenza viruses (p = 0.005) were more frequently detected in older patients, whereas Mycoplasma pneumoniae was more frequently detected in younger patients (p < 0.001). Infections with Klebsiella pneumoniae, Staphylococcus aureus, influenza viruses and respiratory syncytial viruses were risk factors for severe CAP. CONCLUSIONS The major respiratory pathogens causing CAP in adults in China were different from those in USA and European countries, which were consistent across different geographical regions over study years. Given the detection rate of pathogens and their association with severe CAP, we propose to include the ten major pathogens as priorities for clinical pathogen screening in China.
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Affiliation(s)
- Lulu Zhang
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.9 Dong Dan San Tiao, Dongcheng District, Beijing, 100730, P.R. China
| | - Yan Xiao
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.9 Dong Dan San Tiao, Dongcheng District, Beijing, 100730, P.R. China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences, Peking Union Medical College, No.9 Dong Dan San Tiao, Dongcheng District, Beijing, 100730, P.R. China
| | - Guoliang Zhang
- Shenzhen Third People's Hospital, Shenzhen, 518112, P.R. China
| | - Hongru Li
- Fujian Provincial Hospital, Fujian, 350001, P.R. China
| | - Jianping Zhao
- Tongji Hospital, Tongji Medical College of Hust, Wuhan, 430030, P.R. China
| | - Mingwei Chen
- The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, 710061, P.R. China
| | - Fuhui Chen
- The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| | - Ling Liu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, P.R. China
| | - Yalun Li
- Department of Respiratory and Critical Care Medicine, Lung Cancer Treatment Center, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Liping Peng
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, 130021, China
| | - Feng Zhao
- Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, P.R. China
| | - Donghong Yang
- Peking University People's Hospital, No.11 Xizhimen South Dajie, Xicheng District, Beijing, 100044, P.R. China
| | - Zhongmei Wen
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, 130021, China
| | - Lei Wu
- Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, P.R. China
| | - Shuo Wu
- Xijing Hospital, Fourth Military Medical University, Xi'an, 710032, P.R. China
| | - Yajiao Sun
- The Second Affiliated Hospital of Harbin Medical University, Harbin, 150001, P.R. China
| | - Ying Wang
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.9 Dong Dan San Tiao, Dongcheng District, Beijing, 100730, P.R. China
| | - Lan Chen
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.9 Dong Dan San Tiao, Dongcheng District, Beijing, 100730, P.R. China
| | - Xinming Wang
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.9 Dong Dan San Tiao, Dongcheng District, Beijing, 100730, P.R. China
| | - Lihui Wang
- Department of Respiratory Medicine, The First Hospital of Jilin University, Changchun, 130021, China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, Lung Cancer Treatment Center, West China Hospital, Sichuan University, Chengdu, 610041, P.R. China
| | - Haibo Qiu
- Jiangsu Provincial Key Laboratory of Critical Care Medicine, Department of Critical Care Medicine, School of Medicine, Zhongda Hospital, Southeast University, Nanjing, 210009, P.R. China
| | - Yusheng Chen
- Fujian Provincial Hospital, Fujian, 350001, P.R. China
| | - Zhancheng Gao
- Peking University People's Hospital, No.11 Xizhimen South Dajie, Xicheng District, Beijing, 100044, P.R. China.
| | - Lili Ren
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.9 Dong Dan San Tiao, Dongcheng District, Beijing, 100730, P.R. China.
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences, Peking Union Medical College, No.9 Dong Dan San Tiao, Dongcheng District, Beijing, 100730, P.R. China.
| | - Jianwei Wang
- Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, No.9 Dong Dan San Tiao, Dongcheng District, Beijing, 100730, P.R. China.
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences, Peking Union Medical College, No.9 Dong Dan San Tiao, Dongcheng District, Beijing, 100730, P.R. China.
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7
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Fan Y, Li D, Wang P, Ren L, Chen X. Case-control study of relationship of infection by respiratory viruses with acute otitis media in Chinese children. Heliyon 2023; 9:e14422. [PMID: 36967868 PMCID: PMC10036650 DOI: 10.1016/j.heliyon.2023.e14422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2022] [Revised: 02/12/2023] [Accepted: 03/06/2023] [Indexed: 03/13/2023] Open
Abstract
Background Acute otitis media (AOM) may occur as a complication of viral upper respiratory infection (URI) in children. Our objective was to examine children with URI + AOM or URI alone to determine the association of infection by different common respiratory viruses with AOM. Methods Nasopharyngeal swabs were collected from March 2014 to February 2015. Quantitative PCR was then used to identify the following 10 common respiratory viruses: respiratory syncytial virus (RSV); parainfluenza viruses 1-4 (PIVs); influenza virus type A (IFVA); influenza virus type B; human rhinovirus (HRV); enterovirus; human metapneumovirus; human coronavirus OC43, 229E, NL63, and HKU1; adenovirus; and human bocavirus. Results We examined 255 children with URIs (mean age: 32.9 ± 18.7 months), and 164 (64.1%) of them tested positive for at least one respiratory virus. The most common viruses were RSV (44, 24.3%), PIVs (28, 15.5%), and IFVA (25, 13.8%). Positivity for RSV was significantly greater in the URI + AOM group than in the URI group, but these groups did not differ in infection rates for the other 9 viruses. There were also significant seasonal differences in positivity for RSV, IFVA, HRV,HBoV, PIVs and EV. Conclusion Our results indicated a relationship between infection by common respiratory viruses and AOM in children from Beijing. A URI with RSV significantly increased the risk of AOM in these children.
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Affiliation(s)
- Yue Fan
- Department of Otolaryngology-Head and Neck Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, No. 1 Shuaifuyuan, Wangfujing, Beijing, 100730, China
| | - Dongdong Li
- Department of Otolaryngology-Head and Neck Surgery, Xin Jiang Karamay Central Hospital, 834000, China
| | - Pu Wang
- Department of Otolaryngology-Head and Neck Surgery, Beijing Tiantan Hospital, Capital Medical University, Beijing, 100070, China
| | - Lili Ren
- National Health Commission of the People's Republic of China Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
- Corresponding author. Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.
| | - Xiaowei Chen
- Department of Otolaryngology-Head and Neck Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical Science and Peking Union Medical College, No. 1 Shuaifuyuan, Wangfujing, Beijing, 100730, China
- Corresponding author.
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8
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Cao J, Xiao Y, Zhang M, Huang L, Wang Y, Liu W, Wang X, Wu J, Huang Y, Wang R, Zhou L, Li L, Zhang Y, Ren L, Qian K, Wang J. Deep Learning of Dual Plasma Fingerprints for High-Performance Infection Classification. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2023; 19:e2206349. [PMID: 36470664 DOI: 10.1002/smll.202206349] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/17/2022] [Indexed: 06/17/2023]
Abstract
Infection classification is the key for choosing the proper treatment plans. Early determination of the causative agents is critical for disease control. Host responses analysis can detect variform and sensitive host inflammatory responses to ascertain the presence and type of the infection. However, traditional host-derived inflammatory indicators are insufficient for clinical infection classification. Fingerprints-based omic analysis has attracted increasing attention globally for analyzing the complex host systemic immune response. A single type of fingerprints is not applicable for infection classification (area under curve (AUC) of 0.550-0.617). Herein, an infection classification platform based on deep learning of dual plasma fingerprints (DPFs-DL) is developed. The DPFs with high reproducibility (coefficient of variation <15%) are obtained at low sample consumption (550 nL native plasma) using inorganic nanoparticle and organic matrix assisted laser desorption/ionization mass spectrometry. A classifier (DPFs-DL) for viral versus bacterial infection discrimination (AUC of 0.775) and coronavirus disease 2019 (COVID-2019) diagnosis (AUC of 0.917) is also built. Furthermore, a metabolic biomarker panel of two differentially regulated metabolites, which may serve as potential biomarkers for COVID-19 management (AUC of 0.677-0.883), is constructed. This study will contribute to the development of precision clinical care for infectious diseases.
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Affiliation(s)
- Jing Cao
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering and Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore, 117583, Singapore
| | - Yan Xiao
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Mengji Zhang
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering and Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Lin Huang
- Country Department of Clinical Laboratory Medicine, Shanghai Chest Hospital, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
| | - Ying Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Wanshan Liu
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering and Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Xinming Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Jiao Wu
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering and Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Yida Huang
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering and Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Ruimin Wang
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering and Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Li Zhou
- Beijing health biotech co. Ltd, Beijing, 100193, P. R. China
| | - Lin Li
- Beijing health biotech co. Ltd, Beijing, 100193, P. R. China
| | - Yong Zhang
- Department of Biomedical Engineering, Faculty of Engineering, National University of Singapore, Singapore, 117583, Singapore
| | - Lili Ren
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
| | - Kun Qian
- State Key Laboratory for Oncogenes and Related Genes, School of Biomedical Engineering and Institute of Medical Robotics, Shanghai Jiao Tong University, Shanghai, 200030, P. R. China
- Division of Cardiology, Renji Hospital, School of Medicine, Shanghai Jiao Tong University, 160 Pujian Road, Shanghai, 200127, P. R. China
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
- Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, P. R. China
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9
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Luo M, Gong C, Zhang Y, Wang X, Liu Y, Luo Q, Li M, Li A, Wang Y, Dong M, Xu W, Huang F. Comparison of infections with respiratory syncytial virus between children and adults: a multicenter surveillance from 2015 to 2019 in Beijing, China. Eur J Clin Microbiol Infect Dis 2022; 41:1387-1397. [PMID: 36197575 PMCID: PMC9533982 DOI: 10.1007/s10096-022-04492-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2022] [Accepted: 09/05/2022] [Indexed: 11/28/2022]
Abstract
The objective of this study is to investigate the epidemiological and clinical characteristics of the acute respiratory tract infections (ARTI) caused by respiratory syncytial virus (RSV) among the population of all age categories in Beijing, China. Outpatients and inpatients with ARTI were enrolled from 35 sentinel hospitals in Beijing between March 2015 and February 2019. They were interviewed and their medical records were collected using a standardized form. Their respiratory specimens were collected and tested for the nucleic acid of RSV. The RSV-positive specimens were further genotyped into RSV-A and RSV-B groups. A total of 29,923 cases were included in this study. RSV was detected in 623 (2%, 623/29923) patients, with 391 (62.8%) genotypd as RSV-A, 126 (20.2%) as RSV-B, and 106 (17.0%) untyped. The RSV epidemic season usually occurred between October and March covering approximately 90% of annual RSV infections. The RSV-infected children aged < 5 years accounted for 52.2% of the total RSV infections with cough and fever as the most common manifestations. The RSV-infected elderly adults aged ≥ 60 years have the second largest proportion (25.2%) with dyspnea and lymphocytopenia as the most common manifestations and showed an elevated rate of hospitalization, an increased rate of ICU admission, an extended length of hospital stay, and an elevated mortality compared to the RSV-infected children. The RSV infections aged ≥ 60 years old, as the second largest population of the total annual RSV infections, usually developed worse outcomes than children and should be taken seriously.
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Affiliation(s)
- Ming Luo
- Institute for Immunization and Prevention, Beijing Center for Disease Prevention and Control & Beijing Research Center for Preventive Medicine, 16th Hepingli Middle Road, Dongcheng District, Beijing, 100013, China
| | - Cheng Gong
- Institute for Immunization and Prevention, Beijing Center for Disease Prevention and Control & Beijing Research Center for Preventive Medicine, 16th Hepingli Middle Road, Dongcheng District, Beijing, 100013, China
| | - Yan Zhang
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155th Changbai Road, Changping District, Beijing, 102206, China
| | - Xue Wang
- Institute for Immunization and Prevention, Beijing Center for Disease Prevention and Control & Beijing Research Center for Preventive Medicine, 16th Hepingli Middle Road, Dongcheng District, Beijing, 100013, China
| | - Yang Liu
- Tongzhou Center for Disease Prevention and Control, 1st Luhe Middle School North Road, Tongzhou District, Beijing, 101100, China
| | - Qing Luo
- Institute for Immunization and Prevention, Beijing Center for Disease Prevention and Control & Beijing Research Center for Preventive Medicine, 16th Hepingli Middle Road, Dongcheng District, Beijing, 100013, China.,College of Public Health, Capital Medical University, No.10 West, You'anmen Avenue, Fengtai District, Beijing, 100069, China
| | - Maozhong Li
- Institute for Immunization and Prevention, Beijing Center for Disease Prevention and Control & Beijing Research Center for Preventive Medicine, 16th Hepingli Middle Road, Dongcheng District, Beijing, 100013, China
| | - Aihua Li
- Institute for Immunization and Prevention, Beijing Center for Disease Prevention and Control & Beijing Research Center for Preventive Medicine, 16th Hepingli Middle Road, Dongcheng District, Beijing, 100013, China
| | - Yiting Wang
- Institute for Immunization and Prevention, Beijing Center for Disease Prevention and Control & Beijing Research Center for Preventive Medicine, 16th Hepingli Middle Road, Dongcheng District, Beijing, 100013, China
| | - Mei Dong
- Institute for Immunization and Prevention, Beijing Center for Disease Prevention and Control & Beijing Research Center for Preventive Medicine, 16th Hepingli Middle Road, Dongcheng District, Beijing, 100013, China
| | - Wenbo Xu
- National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 155th Changbai Road, Changping District, Beijing, 102206, China.
| | - Fang Huang
- Institute for Immunization and Prevention, Beijing Center for Disease Prevention and Control & Beijing Research Center for Preventive Medicine, 16th Hepingli Middle Road, Dongcheng District, Beijing, 100013, China.
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10
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Molecular Evidence of Coinfection with Acute Respiratory Viruses and High Prevalence of SARS-CoV-2 among Patients Presenting Flu-Like Illness in Bukavu City, Democratic Republic of Congo. CANADIAN JOURNAL OF INFECTIOUS DISEASES AND MEDICAL MICROBIOLOGY 2022; 2022:1553266. [PMID: 35411212 PMCID: PMC8994514 DOI: 10.1155/2022/1553266] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Accepted: 03/23/2022] [Indexed: 01/08/2023]
Abstract
The coronavirus disease 2019 (COVID-19) is caused by severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), with clinical manifestation cases that are almost similar to those of common respiratory viral infections. This study determined the prevalence of SARS-CoV-2 and other acute respiratory viruses among patients with flu-like symptoms in Bukavu city, Democratic Republic of Congo. We screened 1352 individuals with flu-like illnesses seeking treatment in 10 health facilities. Nasopharyngeal swab specimens were collected to detect SARS-CoV-2 using real-time reverse transcription-polymerase chain reaction (RT-PCR), and 10 common respiratory viruses were detected by multiplex reverse transcription-polymerase chain reaction assay. Overall, 13.9% (188/1352) of patients were confirmed positive for SARS-CoV-2. Influenza A 5.6% (56/1352) and Influenza B 0.9% (12/1352) were the most common respiratory viruses detected. Overall, more than two cases of the other acute respiratory viruses were detected. Frequently observed symptoms associated with SARS-CoV-2 positivity were shivering (47.8%; OR = 1.8; CI: 0.88–1.35), cough (89.6%; OR = 6.5, CI: 2.16–28.2), and myalgia and dizziness (59.7%; OR = 2.7; CI: 1.36–5.85). Moreover, coinfection was observed in 12 (11.5%) specimens. SARS-CoV-2 and influenza A were the most cooccurring infections, accounting for 33.3% of all positive cases. This study demonstrates cases of COVID-19 infections cooccurring with other acute respiratory infections in Bukavu city during the ongoing outbreak of COVID-19. Therefore, testing for respiratory viruses should be performed in all patients with flu-like symptoms for effective surveillance of the transmission patterns in the COVID-19 affected areas for optimal treatment and effective disease management.
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11
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Calzado-Dacasin C, Foronda JL, Arguelles VL, Daga CM, Quimpo MT, Lupisan S, Dapat C, Saito M, Okamoto M, Albano PM, Oshitani H. Serotype Identification of Human Adenoviruses Associated with Influenza-Like Illnesses in the Philippines from 2006-2012 by Microneutralization and Molecular Techniques. Int J Infect Dis 2022; 117:326-333. [PMID: 35150916 DOI: 10.1016/j.ijid.2022.02.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Revised: 02/03/2022] [Accepted: 02/03/2022] [Indexed: 11/17/2022] Open
Abstract
OBJECTIVES Human adenoviruses (HAdV) are known to cause a wide range of diseases including acute respiratory infections, conjunctivitis, and acute gastroenteritis. In this study, we aimed to determine the serotypes of HAdV in patients with influenza-like illness (ILI) in the Philippines from 2006-2012 and to describe the demographic and epidemiological characteristics of patients who tested positive for HAdV. METHODS Between 2006 and 2012, the Philippine National Influenza Centre detected HAdV in 1294 samples of patients with ILI. Serotype determination was done in select samples using microneutralization, polymerase chain reaction (PCR), and sequencing methods. RESULTS A total of 8 serotypes were identified (HAdV 1-7 and 11), with HAdV-2 (27.8%), and HAdV-3 (27.8%) being the most prevalent. The majority of HAdV infections were found in children below 5 years of age (79.9%). CONCLUSIONS The identification of HAdV circulating serotypes may serve as guide for designing disease intervention and control strategies and will provide important information regarding the contribution of this virus to respiratory infections, particularly in children, which remain a public health burden in the Philippines.
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Affiliation(s)
- Catherine Calzado-Dacasin
- Department of Virology, Research Institute for Tropical Medicine, Muntinlupa, Philippines; Graduate School, University of Santo Tomas, Manila, Philippines.
| | - Janiza Lianne Foronda
- Department of Virology, Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Vina Lea Arguelles
- Department of Virology, Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Chona Mae Daga
- Department of Epidemiology and Biostatistics, Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Marie Therese Quimpo
- Department of Virology, Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Socorro Lupisan
- Department of Virology, Research Institute for Tropical Medicine, Muntinlupa, Philippines
| | - Clyde Dapat
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan
| | - Mariko Saito
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan; RITM-Tohoku Collaborating Research Center on Emerging and Re-emerging Infectious Diseases, Muntinlupa, Philippines
| | - Michiko Okamoto
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan; RITM-Tohoku Collaborating Research Center on Emerging and Re-emerging Infectious Diseases, Muntinlupa, Philippines
| | - Pia Marie Albano
- Graduate School, University of Santo Tomas, Manila, Philippines; Department of Biological Sciences, College of Science, University of Santo Tomas, Manila, Philippines
| | - Hitoshi Oshitani
- Department of Virology, Tohoku University Graduate School of Medicine, Sendai, Japan; RITM-Tohoku Collaborating Research Center on Emerging and Re-emerging Infectious Diseases, Muntinlupa, Philippines
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12
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Guo L, Wang Y, Kang L, Hu Y, Wang L, Zhong J, Chen H, Ren L, Gu X, Wang G, Wang C, Dong X, Wu C, Han L, Wang Y, Fan G, Zou X, Li H, Xu J, Jin Q, Cao B, Wang J. Cross-reactive antibody against human coronavirus OC43 spike protein correlates with disease severity in COVID-19 patients: a retrospective study. Emerg Microbes Infect 2021; 10:664-676. [PMID: 33734013 PMCID: PMC8023607 DOI: 10.1080/22221751.2021.1905488] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Revised: 03/11/2021] [Accepted: 03/15/2021] [Indexed: 02/08/2023]
Abstract
Seasonal human coronaviruses (HCoVs) including HCoV-229E, -OC43, -NL63, and -HKU1 widely spread in global human populations. However, the relevance of humoral response against seasonal HCoVs to COVID-19 pathogenesis is elusive. In this study, we profiled the temporal changes of IgG antibody against spike proteins (S-IgG) of SARS-CoV-2 and seasonal HCoVs in 838 plasma samples collected from 344 COVID-19 patients. We tested the antigenic cross-reactivities of S protein between SARS-CoV-2 and seasonal HCoVs and evaluated the correlations between the levels of HCoV-OC43 S-IgG and the disease severity in COVID-19 patients. We found that SARS-CoV-2 S-IgG titres mounted until days 22-28, whereas HCoV-OC43 antibody titres increased until days 15-21 and then plateaued until day 46. However, IgG titres against HCoV-NL63, -229E, and -HKU1 showed no significant increase. A two-way cross-reactivity was identified between SARS-CoV-2 and HCoV-OC43. Neutralizing antibodies against SARS-CoV-2 were not detectable in healthy controls who were positive for HCoV-OC43 S-IgG. HCoV-OC43 S-IgG titres were significantly higher in patients with severe disease than those in mild patients at days 1-21 post symptom onset (PSO). Higher levels of HCoV-OC43 S-IgG were also observed in patients requiring mechanical ventilation. At days 1-10 PSO, HCoV-OC43 S-IgG titres correlated to disease severity in the age group over 60. Our data indicate that there is a correlation between cross-reactive antibody against HCoV-OC43 spike protein and disease severity in COVID-19 patients.
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Affiliation(s)
- Li Guo
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Key Laboratory of Respiratory Disease Pathogenomics and Christophe Mérieux Laboratory, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Yeming Wang
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, China–Japan Friendship Hospital, Beijing, People’s Republic of China
| | - Liang Kang
- Jin Yin-tan Hospital, Wuhan, People’s Republic of China
| | - Yongfeng Hu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Linghang Wang
- Emergency Department of Infectious Diseases of Beijing Ditan Hospital, Capital Medical University, Beijing, People’s Republic of China
| | - Jingchuan Zhong
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Hong Chen
- The Second Affiliated Hospital of Harbin Medical University, Harbin, People’s Republic of China
| | - Lili Ren
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Key Laboratory of Respiratory Disease Pathogenomics and Christophe Mérieux Laboratory, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Xiaoying Gu
- Institute of Clinical Medical Sciences, China–Japan Friendship Hospital, Beijing, People’s Republic of China
| | - Geng Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Conghui Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Xiaojing Dong
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Chao Wu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Lianlian Han
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Ying Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Guohui Fan
- Institute of Clinical Medical Sciences, China–Japan Friendship Hospital, Beijing, People’s Republic of China
| | - Xiaohui Zou
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, China–Japan Friendship Hospital, Beijing, People’s Republic of China
| | - Haibo Li
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, China–Japan Friendship Hospital, Beijing, People’s Republic of China
- Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, People’s Republic of China
| | - Jiuyang Xu
- Tsinghua University School of Medicine, Beijing, People’s Republic of China
| | - Qi Jin
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
| | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, China–Japan Friendship Hospital, Beijing, People’s Republic of China
- Institute of Respiratory Medicine, Chinese Academy of Medical Science, Beijing, People’s Republic of China
- Department of Respiratory Medicine, Capital Medical University, Beijing, People’s Republic of China
| | - Jianwei Wang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
- Key Laboratory of Respiratory Disease Pathogenomics and Christophe Mérieux Laboratory, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, People’s Republic of China
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13
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Shao N, Liu B, Xiao Y, Wang X, Ren L, Dong J, Sun L, Zhu Y, Zhang T, Yang F. Genetic Characteristics of Human Parainfluenza Virus Types 1-4 From Patients With Clinical Respiratory Tract Infection in China. Front Microbiol 2021; 12:679246. [PMID: 34335501 PMCID: PMC8320325 DOI: 10.3389/fmicb.2021.679246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2021] [Accepted: 06/17/2021] [Indexed: 11/27/2022] Open
Abstract
Human parainfluenza viruses (HPIV1–4) cause acute respiratory tract infections, thereby impacting human health worldwide. However, there are no current effective antivirals or licensed vaccines for infection prevention. Moreover, sequence information for human parainfluenza viruses (HPIVs) circulating in China is inadequate. Therefore, to shed light on viral genetic diversity and evolution, we collected samples from patients infected with HPIV1–4 in China from 2012 to 2018 to sequence the viruses. We obtained 24 consensus sequences, comprising 1 for HPIV1, 2 for HPIV2, 19 for HPIV3, and 2 for HPIV4A. Phylogenetic analyses classified the 1 HPIV1 into clade 2, and the 2 HPIV4 sequences into cluster 4A. Based on the hemagglutinin-neuraminidase (HN) gene, a new sub-cluster was identified in one of the HPIV2, namely G1c, and the 19 HPIV3 sequences were classified into the genetic lineages of C3f and C3a. The results indicated that HPIV1–4 were co-circulated in China. Further, the lineages of sub-cluster C3 of HPIV3 were co-circulated in China. A recombination analysis indicated that a putative recombination event may have occurred in the HN gene of HPIV3. In the obtained sequences of HPIV3, we found that two amino acid substitution sites (R73K in the F protein of PUMCH14028/2014 and A281V in the HN protein of PUMCH13961/2014) and a negative selection site (amino acid position 398 in the F protein) corresponded to the previously reported neutralization-related sites. Moreover, amino acid substitution site (K108E) corresponded to the negative selection site (amino acid position 108) in the 10 F proteins of HPIV3. However, no amino acid substitution site corresponded to the glycosylation site in the obtained HPIV3 sequences. These results might help in studying virus evolution, developing vaccines, and monitoring HPIV-related respiratory diseases.
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Affiliation(s)
- Nan Shao
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Bo Liu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yan Xiao
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xinming Wang
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lili Ren
- NHC Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jie Dong
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Lilian Sun
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Yafang Zhu
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ting Zhang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Fan Yang
- NHC Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
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14
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Han Z, Rao J, Xie Z, Wang C, Xu B, Qian S, Wang Y, Zhu J, Yang B, Xu F, Lei X, Guo F, Zhao Z, Ren L, Wang J. Chemokine (C-X-C Motif) Ligand 4 Is a Restrictor of Respiratory Syncytial Virus Infection and an Indicator of Clinical Severity. Am J Respir Crit Care Med 2020; 202:717-729. [PMID: 32543879 DOI: 10.1164/rccm.201908-1567oc] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Rationale: Respiratory syncytial virus (RSV) is the leading cause of childhood respiratory infections worldwide; however, no vaccine is available, and treatment options are limited. Identification of host factors pivotal to viral replication may inform the development of novel therapies, prophylaxes, or diagnoses.Objectives: To identify host factors involved in RSV replication and to evaluate their potential for disease management.Methods: A gain-of-function screening was performed on the basis of a genome-wide human complementary DNA library screen for host factors involved in RSV replication. The antiviral mechanism of CXCL4 (chemokine [C-X-C motif] ligand 4) was analyzed. Its clinical role was evaluated via nasopharyngeal aspirates and plasma samples from patients with RSV infection and different disease severities.Measurements and Main Results: Forty-nine host factors restricting RSV replication were identified by gain-of-function screening, with CXCL4 showing the strongest antiviral effect, which was secretion dependent. CXCL4 blocked viral attachment through binding to the RSV main receptor heparan sulfate, instead of through interacting with RSV surface proteins. Intranasal pretreatment with CXCL4 alleviated inflammation in RSV-infected mice, as shown by decreased concentrations of tumor necrosis factor and viral load in BAL fluid samples as well as by viral nucleocapsid protein histological staining in lungs. Compared with non-RSV infections, RSV infections induced elevated CXCL4 concentrations both in plasma and airway samples from mice and pediatric patients. The airway CXCL4 concentration was correlated with viral load and disease severity in patients (P < 0.001).Conclusions: Our results suggest that CXCL4 is an RSV restriction factor that can block viral entry and serve as an indicator of clinical severity in RSV infections.
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Affiliation(s)
- Zibo Han
- National Health Commission Key Laboratory of Systems Biology of Pathogens and.,Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Jian Rao
- National Health Commission Key Laboratory of Systems Biology of Pathogens and.,Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Zhengde Xie
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases.,Key Laboratory of Major Diseases in Children, Ministry of Education, and.,Laboratory of Infection and Virology, Beijing Pediatric Research Institute, National Clinical Research Center for Respiratory Diseases and National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, People's Republic of China; and.,Research Unit of Critical Infection in Children and
| | - Conghui Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and.,Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Baoping Xu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases.,Key Laboratory of Major Diseases in Children, Ministry of Education, and.,Laboratory of Infection and Virology, Beijing Pediatric Research Institute, National Clinical Research Center for Respiratory Diseases and National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, People's Republic of China; and.,Research Unit of Critical Infection in Children and
| | - Suyun Qian
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases.,Key Laboratory of Major Diseases in Children, Ministry of Education, and.,Laboratory of Infection and Virology, Beijing Pediatric Research Institute, National Clinical Research Center for Respiratory Diseases and National Center for Children's Health, Beijing Children's Hospital, Capital Medical University, Beijing, People's Republic of China; and.,Research Unit of Critical Infection in Children and
| | - Yingying Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and.,Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Junlin Zhu
- National Health Commission Key Laboratory of Systems Biology of Pathogens and.,Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Bin Yang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and.,Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Fengwen Xu
- National Health Commission Key Laboratory of Systems Biology of Pathogens and
| | - Xiaobo Lei
- National Health Commission Key Laboratory of Systems Biology of Pathogens and.,Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China
| | - Fei Guo
- National Health Commission Key Laboratory of Systems Biology of Pathogens and
| | - Zhendong Zhao
- National Health Commission Key Laboratory of Systems Biology of Pathogens and
| | - Lili Ren
- National Health Commission Key Laboratory of Systems Biology of Pathogens and.,Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
| | - Jianwei Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and.,Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, People's Republic of China.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences, Beijing, People's Republic of China
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15
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Jung SM, Lee H, Yang Y, Nishiura H. Quantifying the causal impact of funding bedside antigen testing on the incidence of respiratory syncytial virus infection in Japan: a difference-in-differences study. ANNALS OF TRANSLATIONAL MEDICINE 2020; 8:1441. [PMID: 33313186 PMCID: PMC7723552 DOI: 10.21037/atm-20-423] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND To estimate the causal impact of a change in the national health insurance policy to cover the cost of respiratory syncytial virus (RSV) antigen testing on the incidence of RSV infection by age-groups, we analyzed the sentinel datasets of RSV infection in Japan from 2009-2017. METHODS The causal effect of introducing RSV antigen testing on increasing the reported incidence of RSV infection was quantified using a quasi-experimental difference-in-differences (DID) design and influenza as a control group. RESULTS Examining sentinel and virus surveillance datasets, only clinically mild cases have selectively increased from 2012/13. The median estimated incidences of influenza and RSV infection among children aged 0-4 years, the age group that dominates cases of both diseases, were estimated at 5,607 and 1,761 per 100,000 individuals, respectively. Exploring sentinel datasets, only the incidence of RSV infection abruptly increased from 2012/13. Using an age-dependent model, the estimated causal effect on the increase in RSV annual incidence was greatest among children aged 5-9 years, with an estimated additional 1,912 cases per 100,000 individuals (95% CI: 418-3,406). CONCLUSIONS Owing to financial support of bedside RSV antigen testing from 2012/13, the incidence of RSV infection has been elevated. The recent increasing trend in RSV infection incidence should not be directly perceived as an increase in natural infections with RSV.
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Affiliation(s)
- Sung-Mok Jung
- Graduate School of Medicine, Hokkaido University, Sapporo-shi, Hokkaido, Japan.,CREST, Japan Science and Technology Agency, Saitama, Japan.,Kyoto University School of Public Health, Kyoto, Japan
| | - Hyojung Lee
- Graduate School of Medicine, Hokkaido University, Sapporo-shi, Hokkaido, Japan.,CREST, Japan Science and Technology Agency, Saitama, Japan.,National Institute for Mathematical Sciences, Daejeon, Korea
| | - Yichi Yang
- Graduate School of Medicine, Hokkaido University, Sapporo-shi, Hokkaido, Japan
| | - Hiroshi Nishiura
- Graduate School of Medicine, Hokkaido University, Sapporo-shi, Hokkaido, Japan.,CREST, Japan Science and Technology Agency, Saitama, Japan.,Kyoto University School of Public Health, Kyoto, Japan
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Liu J, Wang M, Zhao Z, Lin X, Zhang P, Yue Q, Zhang T, Meng Y. Viral and bacterial coinfection among hospitalized children with respiratory tract infections. Am J Infect Control 2020; 48:1231-1236. [PMID: 32113661 PMCID: PMC7132732 DOI: 10.1016/j.ajic.2020.01.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 01/15/2020] [Accepted: 01/15/2020] [Indexed: 01/26/2023]
Abstract
BACKGROUND The epidemiology of Mycoplasma pneumoniae (MP) and local dominant etiologies of pathogens that cause respiratory tract infections (RTIs) among central China children (≤14 years old) hospitalized are poorly understood. METHODS A total of 10,429 specimens were analyzed, and IgM antibodies against 9 respiratory pathogens including MP were detected using indirect immunofluorescence assay from serum. RESULTS It showed that 59.3% of the enrolled children were positive for at least 1 pathogen; highest detection rates included those between 3 and <6 years of age (70.4%), female (63.2%), and who were hospitalized in 2014 (80.9%). The most predominant pathogen was MP (45.6%), followed by Parainfluenza viruses (PIVs) (22.6%) and influenza B viruses (IFVB) (14.7%). Coinfection was observed in 2,907 specimens (27.9%); the coinfection combination containing MP and PIVs had the highest detection rate of 15%, followed by MP and IFVB as well as IFVB and PIVs. CONCLUSIONS MP was the most commonly detected bacteria among hospitalized children, which should be included in the differential diagnosis for hospitalized children with RTI. These findings will contribute to the effective prevention and therapeutic approaches of pathogens among local children suffering from RTI.
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Affiliation(s)
- Junxiao Liu
- Department of Medical Laboratory, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan, China; Department of Gynecology, Luoyang Clinical Research Center of Obstetrics, Gynecology and Reproductive Medicine, Luoyang Central Hospital, Luoyang, Henan, China.
| | - Mengli Wang
- Department of Medical Laboratory, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan, China
| | - Zhihong Zhao
- Department of Blood Transfusion, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan, China
| | - Xiao Lin
- Department of Technology, Beijing Zhifang Science and Technology Development Limited Company, Luoyang, Henan, China
| | - Pei Zhang
- Department of Gynecology, Luoyang Clinical Research Center of Obstetrics, Gynecology and Reproductive Medicine, Luoyang Central Hospital, Luoyang, Henan, China; Department of Gynecology, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan, China
| | - Qingfen Yue
- Department of Gynecology, Luoyang Clinical Research Center of Obstetrics, Gynecology and Reproductive Medicine, Luoyang Central Hospital, Luoyang, Henan, China; Department of Gynecology, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan, China
| | - Ting Zhang
- Department of Medical Laboratory, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan, China
| | - Yujuan Meng
- Department of Medical Laboratory, Luoyang Central Hospital Affiliated to Zhengzhou University, Luoyang, Henan, China
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17
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Si Y, Zhao Z, Chen R, Zhong H, Liu T, Wang M, Song X, Li W, Ying B. Epidemiological surveillance of common respiratory viruses in patients with suspected COVID-19 in Southwest China. BMC Infect Dis 2020; 20:688. [PMID: 32957928 PMCID: PMC7503430 DOI: 10.1186/s12879-020-05392-x] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 09/02/2020] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND The outbreak of coronavirus disease 2019 (COVID-19) caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is currently the peak season of common respiratory viral infections. However, the clinical symptoms of most SARS-CoV-2 infected patients are not significantly different from those of common respiratory viral infections. Therefore, knowing the epidemiological patterns of common respiratory viruses may be valuable to improve the diagnostic and therapeutic efficacy of patients with suspected COVID-19, especially in Southwest China (a mild epidemic area). METHODS A total of 2188 patients with clinically suspected of COVID-19 in Southwest China were recruited from January 21 to February 29, 2020. Nasopharyngeal swabs, throat swabs and sputum specimens were collected to detect SARS-CoV-2 by using real-time reverse transcription-polymerase chain reaction (RT-PCR) and other 12 viruses via PCR fragment analysis combined with capillary electrophoresis. Clinical characteristics and laboratory test findings were acquired from electronic medical records. All data were analyzed to unravel the epidemiological patterns. RESULTS Only 1.1% (24/2188) patients with suspected COVID-19 were eventually confirmed to have SARS-CoV-2 infection, and the most frequently observed symptoms were fever (75.0%, 18/24) and cough (20.8%, 5/24). The overall detection rate of other respiratory pathogens was 10.3% (226/2188). Among them, human rhinovirus (3.2%, 71/2188), human parainfluenza viruses (1.6%, 35/2188), influenza B virus (1.2%, 26/2188) and mycoplasma pneumonia (1.2%, 26/2188) were the predominantly detected pathogens in this study. Moreover, the co-infection was observed in 22 specimens. Notably, one COVID-19 case had a coexisting infection with human parainfluenza virus (4.2%, 1/24) and bocavirus was the most common virus tending to occur in co-infection with other respiratory pathogens. CONCLUSIONS This study reveals the epidemiological features of common respiratory viruses and their clinical impact during the ongoing outbreak of COVID-19 in a mild epidemic area. The findings highlight the importance of understanding the transmission patterns of the common respiratory virus in COVID-19 regions, which can provide information support for the development of appropriate treatment plans and health policies, while eliminating unnecessary fear and tension.
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Affiliation(s)
- Yanjun Si
- Department of Laboratory Medicine, West China Hospital, Sichuan University, 37 Guoxue Alley in the wuhou District, Chengdu, Sichuan, China
| | - Zhenzhen Zhao
- Department of Laboratory Medicine, West China Hospital, Sichuan University, 37 Guoxue Alley in the wuhou District, Chengdu, Sichuan, China
| | - Rong Chen
- Department of Clinical Laboratory, The First People's Hospital of Shuangliu District, Chengdu/ West China (Airport) Hospital Sichuan University, Chengdu, Sichuan, China
| | - Huiyu Zhong
- Department of Laboratory Medicine, West China Hospital, Sichuan University, 37 Guoxue Alley in the wuhou District, Chengdu, Sichuan, China
| | - Tangyuheng Liu
- Department of Laboratory Medicine, West China Hospital, Sichuan University, 37 Guoxue Alley in the wuhou District, Chengdu, Sichuan, China
| | - Minjin Wang
- Department of Laboratory Medicine, West China Hospital, Sichuan University, 37 Guoxue Alley in the wuhou District, Chengdu, Sichuan, China
| | - Xingbo Song
- Department of Laboratory Medicine, West China Hospital, Sichuan University, 37 Guoxue Alley in the wuhou District, Chengdu, Sichuan, China
| | - Weimin Li
- Department of Respiratory and Critical Care Medicine, West China Hospital, Sichuan University, 37 Guoxue Alley in the wuhou District, Chengdu, Sichuan, China.
| | - Binwu Ying
- Department of Laboratory Medicine, West China Hospital, Sichuan University, 37 Guoxue Alley in the wuhou District, Chengdu, Sichuan, China.
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Gao M, Yao X, Mao W, Shen C, Zhang Z, Huang Q, Cui D, Sun H, Zou W. Etiological analysis of virus, mycoplasma pneumoniae and chlamydia pneumoniae in hospitalized children with acute respiratory infections in Huzhou. Virol J 2020; 17:119. [PMID: 32738914 PMCID: PMC7395355 DOI: 10.1186/s12985-020-01380-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 07/02/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Acute respiratory infections are a common disease in children with high mortality and morbidity. Multiple pathogens can cause acute respiratory infections. A 2-year survey of hospitalized children was conducted to understand the epidemic situation, seasonal spread of pathogens and the improvement of clinical diagnosis, treatment and prevention of disease in Huzhou, China. METHODS From September 2017 to August 2019, 3121 nasopharyngeal swabs from hospitalized children with acute respiratory infections were collected, and real-time PCR was used to detect various pathogens. Then, pathogen profiles, frequency and seasonality were analyzed. RESULTS Of the 3121 specimens, 14.45% (451/3121) were positive for at least one pathogen. Of the single-pathogen infections, RSV (45.61%, 182/399) was the most frequent pathogen, followed by PIVs (14.79%, 59/399), ADV (14.54%, 58/399), MP (10.78%, 43/399), and IAV (5.26%, 21/399). Of the 52 coinfections, RSV + PIVs viruses were predominantly identified and accounted for 40.38% (21/52) of cases. RSV was the most frequent pathogen in all four groups. The highest positive rate of the pathogens occurred in the winter (21.26%), followed by autumn (14.98%), the summer (14.11%) and the spring (12.25%). CONCLUSION Viruses are the main pathogens in hospitalized children with acute respiratory infections in Huzhou city, Zhejiang Province, China. Among the pathogens, RSV had the highest detection rate, and MP is also a common pathogen among children with acute respiratory infections. This study provided a better understanding of the distribution of pathogens in children of different ages and seasons, which is conducive to the development of more reasonable treatment strategies and prevention and control measures.
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Affiliation(s)
- Min Gao
- Department of Clinical Laboratory, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, 313000, China
| | - Xing Yao
- Hepatobiliary and Pancreatic Surgery, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, 313000, China
| | - Wei Mao
- Department of Respiratory Diseases, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, 313000, China
| | - Cuifen Shen
- Department of Clinical Laboratory, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, 313000, China
| | - Zongxin Zhang
- Department of Clinical Laboratory, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, 313000, China
| | - Qiuling Huang
- Department of Pediatrics, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, 313000, China
| | - Dawei Cui
- Department of Blood Transfusion, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China
| | - Haiyan Sun
- Department of Clinical Laboratory, Shaoxing Second Hospital, Shaoxing, 312000, Zhejianeg Province, China
| | - Weihua Zou
- Department of Clinical Laboratory, Huzhou Central Hospital, Affiliated Central Hospital Huzhou University, Huzhou, 313000, China.
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Liu Y, Wang Y, Wang X, Xiao Y, Chen L, Guo L, Li J, Ren L, Wang J. Development of two TaqMan real-time reverse transcription-PCR assays for the detection of severe acute respiratory syndrome coronavirus-2. BIOSAFETY AND HEALTH 2020; 2:232-237. [PMID: 32838286 PMCID: PMC7375968 DOI: 10.1016/j.bsheal.2020.07.009] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2020] [Revised: 07/18/2020] [Accepted: 07/20/2020] [Indexed: 11/01/2022] Open
Abstract
The outbreak of coronavirus disease 2019 (COVID-19) in Wuhan, China, was caused by a novel coronavirus (CoV), named severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). The rapid detection of viral nucleic acids is critical for the early identification of infected cases. We have developed two TaqMan real-time reverse transcription-PCR assays to detect SARS-CoV-2. The designed primers target the nucleocapsid (N) and open reading frame (ORF) 1b gene regions, where the probes discriminate SARS-CoV-2 from other human and animal CoVs. The sensitivities are one genomic copy per reaction for the N gene assay and ten copies for the ORF 1b gene assay. The overall linear detection ranges are 1-106 and 10-106 copies per reaction for the N gene assay and the ORF 1b gene assay, respectively. Surveillance of 23 suspected COVID-19 patients demonstrated that SARS-CoV-2 could be detected from 100% (23/23) and 62.5% (16/23) of clinical specimens by the N gene assay and the ORF 1b gene assay, respectively. All of the samples not detected by the ORF 1b gene assay were throat swabs, indicating a lower viral load in the upper respiratory tract and the relatively lower sensitivity of the ORF 1b gene assay. The assays developed in the present study offer alternative diagnostic tests for COVID-19.
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Affiliation(s)
- Yiwei Liu
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Yingying Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Xinming Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Yan Xiao
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Lan Chen
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Li Guo
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China
| | - Jianguo Li
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan 030006, China
| | - Lili Ren
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
| | - Jianwei Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing 100730, China.,Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100730, China
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20
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Qin S, Zhang W, Chen F, Luo F, Zhou Q, Ke P, Chen C. Antibodies against atypical pathogens and respiratory viruses detected by Pneumoslide IgM test in adults with community-acquired pneumonia in Guangzhou City. J Clin Lab Anal 2020; 34:e23419. [PMID: 32537759 PMCID: PMC7521227 DOI: 10.1002/jcla.23419] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 04/21/2020] [Accepted: 05/18/2020] [Indexed: 12/17/2022] Open
Abstract
Background To detect the serum antibodies against respiratory viruses and atypical pathogens in adults with community‐acquired pneumonia (CAP) in Guangzhou City (Guangdong province, China). Methods A retrospective study was carried out with samples from 685 adults who were admitted with CAP and 108 non‐CAP control patients. Atypical pathogens and respiratory viruses in serum were detected using the Pneumoslide IgM test from Vircell, Spain. All patients were divided into 6 groups according to age: 18‐24, 25‐44, 45‐59, 60‐74, 75‐89, and >90. Results The total positive rate of CAP was 35.4%, which was highest in the 18‐24 age group (P < .05). The highest positive rate, 17.11%, was observed for Mycoplasma pneumoniae (MP). The mean age of MP‐infected patients was higher than that of the controls (P < .05). The positive rates for influenza B (INFB), Legionella pneumophila (LP1), Coxiella burnetii (COX), influenza A (INFA), parainfluenza virus (PIV), respiratory syncytial virus (RSV), Chlamydophila pneumoniae (CP), and adenovirus (ADV) were 5.56%, 3.07%, 2.63%, 2.34%, 1.90%, 1.61, 0.88%, and 0.29%, respectively. There were 4.37% of patients with CAP having multiple infections. The main symptoms observed in the 685 CAP patients were cough and sputum production, in 78.4% and 67.4%. Fever was followed by 54% of CAP patients. Dyspnea (39.1%), anorexia (36.8%), increased thirst (26.7%), chills (18.7), headache (14.6%), and nausea (13.1%) were also frequently observed in the CAP patients. Conclusions MP infection was the most common in adult CAP patients in Guangzhou City with the highest positive rate in the 18‐24 age groups.
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Affiliation(s)
- Sheng Qin
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Weizheng Zhang
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Fu Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Fudong Luo
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Qiang Zhou
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Peifeng Ke
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
| | - Cha Chen
- Department of Laboratory Medicine, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou, China
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21
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Ding Q, Xu L, Zhu Y, Xu B, Chen X, Duan Y, Xie Z, Shen K. Comparison of clinical features of acute lower respiratory tract infections in infants with RSV/HRV infection, and incidences of subsequent wheezing or asthma in childhood. BMC Infect Dis 2020; 20:387. [PMID: 32473625 PMCID: PMC7260463 DOI: 10.1186/s12879-020-05094-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2019] [Accepted: 05/15/2020] [Indexed: 12/17/2022] Open
Abstract
Background To compare the clinical characteristics of acute lower respiratory tract infections (ALRTIs) caused by respiratory syncytial virus (RSV) and human rhinovirus (HRV) and to explore the relationship between the development of recurrent wheezing/asthma and RSV/ HRV infections in infancy. Methods Retrospective study was conducted to compare the clinical characteristics of acute lower respiratory tract infections (ALRTIs). Hospitalized patients with ALRTIs from March 2007 to December 2016 were screened. Single RSV cases (s-RSV), single HRV cases (s-HRV), and cases who had co-infection with the two viruses were enrolled. Follow-up was performed to determine whether either specific respiratory virus infection was related to subsequent development of recurrent wheezing/asthma. Results The s-RSV children were the youngest (P = 0.021), they experienced the most serious condition (P < 0.001) and respiratory failure (P < 0.001), they also required highest demand of oxygen therapy (P < 0.001). And in s-RSV group, the incidence of development of recurrent wheezing was significantly higher in subgroup with the family history of wheezing than that without (P < 0.001). Conclusion The s-RSV cases suffered from the worst severity of illness, respiratory failure and required highest demand of oxygen therapy. Recurrent wheezing was more common in s-RSV group with family history of wheezing than those without.
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Affiliation(s)
- Qin Ding
- Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Lili Xu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Yun Zhu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Baoping Xu
- Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Xiangpeng Chen
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Yali Duan
- Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China
| | - Zhengde Xie
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China.
| | - Kunling Shen
- Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, 100045, China.
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22
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Al-Romaihi HE, Smatti MK, Al-Khatib HA, Coyle PV, Ganesan N, Nadeem S, Farag EA, Al Thani AA, Al Khal A, Al Ansari KM, Al Maslamani MA, Yassine HM. Molecular epidemiology of influenza, RSV, and other respiratory infections among children in Qatar: A six years report (2012-2017). Int J Infect Dis 2020; 95:133-141. [PMID: 32278934 PMCID: PMC7194828 DOI: 10.1016/j.ijid.2020.04.008] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 03/23/2020] [Accepted: 04/02/2020] [Indexed: 01/11/2023] Open
Abstract
Throughout a five years period, HRV, RSV, and influenza viruses were responsible for two-thirds of acute respiratory infections among children in Qatar. RSV, influenza, and HMPV circulated in winter, whereas HRV was highly active during other seasons. RSV is more prevalent among infants, while influenza circulates more among children above five years of age. Influenza–RSV co-infections are significantly associated with age. Gender-dependent differences affect infection rates.
Background Studies on the etiology of respiratory infections among children in Qatar and surrounding countries are limited. Objectives To describe the prevalence and seasonality of RSV, influenza, and other respiratory pathogens among children in Qatar. Methods We retrospectively collected and analyzed data of 33,404 children (<15 years) presented with influenza-like illness from 2012 to 2017. Results At least one respiratory pathogen was detected in 26,138 (78%) of patients. Together, human rhinoviruses (HRV), respiratory syncytial virus (RSV), and influenza viruses comprised nearly two-thirds of all cases, affecting 24%, 19.7%, and 18.5%, respectively. A prevalence of 5-10% was recorded for adenovirus, parainfluenza viruses (PIVs), human bocavirus (HboV), and human coronaviruses (HCoVs). Human metapneumovirus (HMPV), enteroviruses, M. pneumonia, and parechovirus had prevalences below 5%. While RSV, influenza, and HMPV exhibited strong seasonal activity in the winter, HRV was active during low RSV and influenza circulation. The burden of RSV exceeds that of influenza among young age groups, whereas influenza correlated positively with age. Further, HRV, adenovirus, influenza, and RSV infection rates varied significantly between male and females. Conclusion This comprehensive multi-year study provides insights into the etiology of ILI among children in Qatar, which represents the Gulf region. Our results reinforce the significance of active surveillance of respiratory pathogens to improve infection prevention and control strategies, particularly among children.
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Affiliation(s)
| | - Maria K Smatti
- Biomedical Research Center, Qatar University, Doha, Qatar.
| | - Hebah A Al-Khatib
- College of Health and Life Sciences, Hamad Bin Khalifa University, Doha, Qatar.
| | | | | | | | | | - Asmaa A Al Thani
- Biomedical Research Center, Qatar University, Doha, Qatar; College of Health Sciences-QU health, Qatar University, Doha, Qatar.
| | | | | | | | - Hadi M Yassine
- Biomedical Research Center, Qatar University, Doha, Qatar; College of Health Sciences-QU health, Qatar University, Doha, Qatar.
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23
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Yu J, Qian S, Liu C, Xiao Y, Xu T, Wang Y, Su H, Chen L, Yuan B, Wang X, Xu B, Yang Y, Shen K, Xie Z, Ren L, Wang J. Viral etiology of life-threatening pediatric pneumonia: A matched case-control study. Influenza Other Respir Viruses 2020; 14:452-459. [PMID: 32267084 PMCID: PMC7262399 DOI: 10.1111/irv.12738] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Revised: 03/06/2020] [Accepted: 03/09/2020] [Indexed: 12/15/2022] Open
Abstract
Background Pediatric pneumonia remains a significant health challenge, while the viral risk factors for adverse outcomes in pediatric pneumonia are not yet fully clear. Methods A matched case‐control study of pediatric patients with pneumonia was carried out in Beijing, China, between 2007 and 2015. The study enrolled 334 intensive care unit patients who developed life‐threatening diseases and 522 controls matched to the sex, age, ethnicity, admission dates, and residing district of the cases suffered from pneumonia. Nasopharyngeal aspirates were taken from all participants and tested by PCR for 18 common respiratory viruses. Results At least, one virus was detected in 257 (77%) of the cases and 409 (78%) of the controls. We observed no difference in the prevalence of 17 respiratory viruses between cases and controls but found a higher frequency of influenza A virus (IFV‐A) in the cases than in the controls (7% vs 4%, P = .036). After adjusting for comorbid conditions and a history of reactive airway diseases, IFV‐A was associated with an increase in life‐threatening pneumonia (adjusted odds ratio = 2.55, 95% CI = 1.24‐5.24). Young age and congenital heart disease (aOR = 10.16‐10.27, P < .001) were also independent risk factors. Conclusions The prevention of IFV infection is critical in decreasing the risk of life‐threatening pneumonia in children.
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Affiliation(s)
- Jianxing Yu
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Suyun Qian
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Chunyan Liu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Yan Xiao
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Teng Xu
- Vision Medicals, Guangzhou, China
| | - Ying Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Hang Su
- The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Lan Chen
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Bin Yuan
- The University of Texas Health Science Center at San Antonio, San Antonio, TX, USA
| | - Xinming Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Baoping Xu
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Yan Yang
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Kunling Shen
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Zhengde Xie
- Beijing Key Laboratory of Pediatric Respiratory Infection Diseases, Key Laboratory of Major Diseases in Children, Ministry of Education, National Clinical Research Center for Respiratory Diseases, National Key Discipline of Pediatrics (Capital Medical University), Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, National Center for Children's Health, Beijing, China
| | - Lili Ren
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
| | - Jianwei Wang
- National Health Commission Key Laboratory of Systems Biology of Pathogens and Christophe Merieux Laboratory, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, China
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Abstract
Respiratory syncytial virus (RSV) is the most common pathogen associated with acute lower respiratory tract infections in young children. RSV is also a major viral pathogen causing severe lung disease in the adult population, particularly among the elderly. We conducted a review of adult RSV studies published from January 1970 to February 2017 to determine the burden of disease among adults worldwide. There were no restrictions on health care setting or definition of RSV infection. A total of 1530 published studies were identified, 95 of which were included in this review. The incidence rates of hospitalised RSV acute respiratory tract infection (ARI) in adults >65 years old ranged from 7.3 to 13.0/105 population in Africa and Asia and from 190 to 254/105 population in the USA. Higher incidence rates (195–1790/105 population) were observed in adults ≥50 years old for outpatient or emergency visits in the USA. Of all ARI patients, RSV accounted for 1–10% in adults and 2–14% in patients with chronic diseases or transplantation. Given the limitations in the existing data, significant efforts should be made to generate evidence on the burden of RSV infections in adults and to estimate the potential impact of future preventive interventions.
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Yu J, Liu C, Xiao Y, Xiang Z, Zhou H, Chen L, Shen K, Xie Z, Ren L, Wang J. Respiratory Syncytial Virus Seasonality, Beijing, China, 2007-2015. Emerg Infect Dis 2019; 25:1127-1135. [PMID: 31107230 PMCID: PMC6537707 DOI: 10.3201/eid2506.180532] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
During July 2007-June 2015, we enrolled 4,225 hospitalized children with pneumonia in a study to determine the seasonality of respiratory syncytial virus (RSV) infection in Beijing, China. We defined season as the period during which >10% of total PCRs performed each week were RSV positive. We identified 8 distinctive RSV seasons. On average, the season onset occurred at week 41 (mid-October) and lasted 33 weeks, through week 20 of the next year (mid-May); 97% of all RSV-positive cases occurred during the season. RSV seasons occurred 3-5 weeks earlier and lasted ≈6 weeks longer in RSV subgroup A-dominant years than in RSV subgroup B-dominant years. Our analysis indicates that monitoring such RSV subgroup shifts might provide better estimates for the onset of RSV transmission. PCR-based tests could be a flexible or complementary way of determining RSV seasonality in locations where RSV surveillance is less well-established, such as local hospitals throughout China.
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Li HJ, Du J, Yang YN, Cui Y, Xi L, Wang S, Liu YQ, Zhang GF, Cui F, Lu QB. Outbreak of Human Parainfluenza Virus Type 1 in a Kindergarten from China, 2018. J PEDIAT INF DIS-GER 2019; 15:25-30. [PMID: 32300276 PMCID: PMC7117075 DOI: 10.1055/s-0039-1695039] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2019] [Accepted: 07/12/2019] [Indexed: 01/05/2023]
Abstract
Objective
We reported an outbreak of human parainfluenza virus type 1 (HPIV1) in a kindergarten and explored the genetic characteristics of HPIV1
hemagglutinin-neuraminidase
(HN) and
fusion
(F) genes to provide more evidence about HPIV1 outbreaks.
Methods
Suspected cases were the children with an influenza-like illness during June 20 to 26, 2018. Nasopharyngeal swabs were collected and screened to determine the presence of respiratory pathogens by real-time fluorescent quantitative polymerase chain reaction. The HN and F gene sequences of HPIV-positive samples were further amplified and sequenced to confirm the HPIV genotype and identify genetic characteristics. A phylogenetic tree, based on the HN and F genes, was reconstructed by maximum likelihood method.
Results
Fourteen children in the outbreak were diagnosed as upper respiratory tract infection. The most common symptom was cough (10/14), followed by rhinorrhea (5/14), sore throat (4/14), headache (1/14), and abdominal pain (1/14). Eight patients were positive for HPIV1 and negative for other pathogens. Phylogenetic tree demonstrated that the eight strains from the year 2018 in our study located in the clade 2.3. Two specific substitutions (N333S and I509M) in the amino acids of the F protein and two substitutions (V19A and L436I) in the HN protein were different from other strains in the clade 2.
Conclusion
HPIV1 was attributed to the outbreak, which may be related to the genetic variations of HPIV1.
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Affiliation(s)
- Hong-Jun Li
- Institute for Infectious Diseases and Endemic Diseases Prevention and Control, Beijing Tongzhou Center for Diseases Prevention and Control, Beijing, People's Republic of China
| | - Juan Du
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, People's Republic of China
| | - Yan-Na Yang
- Institute for Infectious Diseases and Endemic Diseases Prevention and Control, Beijing Tongzhou Center for Diseases Prevention and Control, Beijing, People's Republic of China
| | - Yan Cui
- Institute for Infectious Diseases and Endemic Diseases Prevention and Control, Beijing Tongzhou Center for Diseases Prevention and Control, Beijing, People's Republic of China
| | - Lu Xi
- Institute for Infectious Diseases and Endemic Diseases Prevention and Control, Beijing Tongzhou Center for Diseases Prevention and Control, Beijing, People's Republic of China
| | - Shuai Wang
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, People's Republic of China
| | - Ya-Qiong Liu
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, People's Republic of China
| | - Guo-Feng Zhang
- Institute for Infectious Diseases and Endemic Diseases Prevention and Control, Beijing Tongzhou Center for Diseases Prevention and Control, Beijing, People's Republic of China
| | - Fuqiang Cui
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, People's Republic of China
| | - Qing-Bin Lu
- Department of Laboratorial Science and Technology, School of Public Health, Peking University, Beijing, People's Republic of China
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Zhao Y, Lu R, Shen J, Xie Z, Liu G, Tan W. Comparison of viral and epidemiological profiles of hospitalized children with severe acute respiratory infection in Beijing and Shanghai, China. BMC Infect Dis 2019; 19:729. [PMID: 31429710 PMCID: PMC6701130 DOI: 10.1186/s12879-019-4385-5] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2018] [Accepted: 08/15/2019] [Indexed: 12/16/2022] Open
Abstract
Background No comparison data have been reported on viral and epidemiological profiles of hospitalized children with severe acute respiratory infection (SARI) in Beijing or Shanghai, China. Methods We collected 700 nasopharyngeal aspirates (NPA) from hospitalized children with SARI in Beijing (northern China) and Shanghai (southern China). Multiple respiratory viruses (including 15 common viruses) were screened by validated polymerase chain reaction (PCR) or real-time reverse transcription-PCR assays and confirmed by sequencing. Demographic data and the distribution of viral infections were also examined. Results Of 700 samples, 547 (78.1%) tested positive for viral infections. The picornaviruses (PIC), which included rhinovirus (RV) and enterovirus (EV), were the most common (34.0%), followed by respiratory syncytial virus (RSV) (28.3%), human bocavirus (HBoV) (19.1%), adenovirus (ADV) (13.7%), human coronaviruses (HCoV) (10.7%), influenza A and B (8.9%), parainfluenza virus (PIV 1–3) (7.9%), and human metapneumovirus (HMPV) (5.0%). PIC (RV/EV) and RSV were the most prevalent etiological agents of SARI in both cities. The total and age-matched prevalence of RSV, HCoV, and hMPV among SARI children under 5 years old were significantly higher in Beijing than in Shanghai. Different age and seasonal distribution patterns of the viral infections were found between Beijing and Shanghai. Conclusions Viral infection was tested and shown to be the most prevalent etiological agent among children with SARI in either the Beijing or the Shanghai area, while showing different patterns of viral and epidemiological profiles. Our findings provide a better understanding of the roles of geographic location and climate in respiratory viral infections in hospitalized children with SARI.
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Affiliation(s)
- Yanjie Zhao
- Key Laboratory of Laboratory Medicine, Ministry of Education, and Institute of Medical Virology, Wenzhou Medical University, Zhejiang, China.,National Institute for Viral Disease Control and Prevention, China CDC, 155Changbai Road, Beijing, 102206, Changping District, China
| | - Roujian Lu
- National Institute for Viral Disease Control and Prevention, China CDC, 155Changbai Road, Beijing, 102206, Changping District, China
| | - Jun Shen
- Children's Hospital of Fudan University, Shanghai, China
| | - Zhengde Xie
- Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, Beijing, 100045, China
| | - Gaoshan Liu
- Key Laboratory of Laboratory Medicine, Ministry of Education, and Institute of Medical Virology, Wenzhou Medical University, Zhejiang, China
| | - Wenjie Tan
- Key Laboratory of Laboratory Medicine, Ministry of Education, and Institute of Medical Virology, Wenzhou Medical University, Zhejiang, China. .,National Institute for Viral Disease Control and Prevention, China CDC, 155Changbai Road, Beijing, 102206, Changping District, China.
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28
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Al-Romaihi HE, Smatti MK, Ganesan N, Nadeem S, Farag E, Coyle PV, Nader JD, Al-Khatib HA, Elmagboul EB, Al Dhahry S, Al-Marri SA, Al Thani AA, Al Khal A, Al Maslamani MA, Yassine HM. Epidemiology of respiratory infections among adults in Qatar (2012-2017). PLoS One 2019; 14:e0218097. [PMID: 31194775 PMCID: PMC6563968 DOI: 10.1371/journal.pone.0218097] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2019] [Accepted: 05/24/2019] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Limited data is available about the etiology of influenza like illnesses (ILIs) in Qatar. OBJECTIVES This study aimed at providing preliminary estimates of influenza and other respiratory infections circulating among adults in Qatar. METHODS We retrospectively collected data of about 44,000 patients who visited Hamad General Hospital clinics, sentinel sites, and all primary healthcare centers in Qatar between 2012 and 2017. All samples were tested for influenza viruses, whereas about 38,000 samples were tested for influenza and a panel of respiratory viruses using Fast Track Diagnostics (FTD) RT-PCR kit. RESULTS Among all ILIs cases, 20,278 (46.5%) tested positive for at least one respiratory pathogen. Influenza virus was predominating (22.6%), followed by human rhinoviruses (HRVs) (9.5%), and human coronaviruses (HCoVs) (5%). A detection rate of 2-3% was recorded for mycoplasma pneumonia, adenoviruses, human parainfluenza viruses (HPIVs), respiratory syncytial virus (RSV), and human metapneumovirus (HMPV). ILIs cases were reported throughout the year, however, influenza, RSV, and HMPV exhibited strong seasonal peaks in the winter, while HRVs circulated more during fall and spring. Elderly (>50 years) had the lowest rates of influenza A (13.9%) and B (4.2%), while presenting the highest rates of RSV (3.4%) and HMPV (3.3%). While males had higher rates of HRVs (11.9%), enteroviruses (1.1%) and MERS CoV (0.2%), females had higher proportions of influenza (26.3%), HPIVs (3.2%) and RSV (3.6%) infections. CONCLUSION This report provides a comprehensive insight about the epidemiology of ILIs among adults in the Qatar, as a representative of Gulf States. These results would help in improvement and optimization of diagnostic procedures, as well as control and prevention of the respiratory infections.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | - Asmaa A. Al Thani
- Biomedical Research Center, Qatar University, Doha, Qatar
- College of Health Sciences, QU Health, Qatar University, Doha, Qatar
| | | | | | - Hadi M. Yassine
- Biomedical Research Center, Qatar University, Doha, Qatar
- College of Health Sciences, QU Health, Qatar University, Doha, Qatar
- * E-mail: (MAA); (HMY)
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The Prevalence of Respiratory Viruses Among Patients with Influenza-Like Illness in Zahedan, Southeastern Iran. ARCHIVES OF CLINICAL INFECTIOUS DISEASES 2019. [DOI: 10.5812/archcid.77089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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30
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Seynaeve D, Augusseau-Rivière B, Couturier P, Morel-Baccard C, Landelle C, Bosson JL, Gavazzi G, Mallaret MR. Outbreak of Human Metapneumovirus in a Nursing Home: A Clinical Perspective. J Am Med Dir Assoc 2019; 21:104-109.e1. [PMID: 31101588 PMCID: PMC7105973 DOI: 10.1016/j.jamda.2019.03.015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2018] [Revised: 03/12/2019] [Accepted: 03/15/2019] [Indexed: 01/26/2023]
Abstract
Objectives To describe a human metapneumovirus (hMPV) outbreak occurring in a nursing home for older adults and to identify the risk factors associated with the clinical infection. Design A retrospective, case-controlled study. Setting and participants A French nursing home for older adults between December 27, 2014 and January 20, 2015. Probable cases were residents presenting at least 1 respiratory symptom or 1 constitutional symptom. Confirmed cases identified in the same way as probable cases but with a positive RT-PCR test for hMPV. Controls were residents with no symptoms of respiratory infection. Measures Identification of hMPV was realized on nasal swab samples by RT-PCR. Results Seventy-eight older people were resident at the time of the outbreak. Three of the 4 tested were positive for hMPV by RT-PCR and negative for 13 other viruses or bacteria. All probable infected residents presented cough; other symptoms were scarcer. An inflammatory response was present, with median C-reactive protein at 50 mg/L. The median duration of the illness was 7 days. The rate of infection among residents was high (51%), with 5 hospitalizations (12.5%) and 1 death (2.5%). In multivariate analysis, vaccination against influenza virus appeared to emerge as associated with a probable hMPV infection, but this might be an artifact, as the proportion of unvaccinated residents was low (15%). A clear infected population profile was hard to define, although limited autonomy and low ADL score may play a role. Basic hygiene precautions were reinforced, but droplet precautions seemed difficult to apply rigorously to this population. Conclusions/Implications Clinical and biological presentations were nonspecific. The rate of infection was high, highlighting the need for the rapid introduction of strict precautions to contain the infection.
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Affiliation(s)
- Damien Seynaeve
- Service d'Hygiène Hospitalière et de Gestion des Risques, CHU Grenoble Alpes, Grenoble Cedex, France.
| | | | - Pascal Couturier
- Clinique Universitaire de Médecine Gériatrique, CHU Grenoble Alpes, Grenoble Cedex, France
| | | | - Caroline Landelle
- Service d'Hygiène Hospitalière et de Gestion des Risques, CHU Grenoble Alpes, Grenoble Cedex, France; Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, Grenoble Cedex, France
| | - Jean-Luc Bosson
- Pôle de Santé Publique, CHU Grenoble Alpes, Grenoble Cedex, France; Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, Grenoble Cedex, France
| | - Gaëtan Gavazzi
- Clinique Universitaire de Médecine Gériatrique, CHU Grenoble Alpes, Grenoble Cedex, France; Université Grenoble Alpes, GREPI EA 7408, Grenoble Cedex, France
| | - Marie-Reine Mallaret
- Service d'Hygiène Hospitalière et de Gestion des Risques, CHU Grenoble Alpes, Grenoble Cedex, France; Université Grenoble Alpes, CNRS, Grenoble INP, TIMC-IMAG, Grenoble Cedex, France
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31
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Application of next generation sequencing technology on contamination monitoring in microbiology laboratory. BIOSAFETY AND HEALTH 2019; 1:25-31. [PMID: 32501441 PMCID: PMC7148601 DOI: 10.1016/j.bsheal.2019.02.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/07/2019] [Accepted: 02/21/2019] [Indexed: 12/25/2022] Open
Abstract
The surveillance and prevention of pathogenic microbiological contamination are the most important tasks of biosafety management in the lab. There is an urgent need to establish an effective and unbiased method to evaluate and monitor such contamination. This study aims to investigate the utility of next generation sequencing (NGS) method to detect possible contamination in the microbiology laboratory. Environmental samples were taken at multiple sites at the lab including the inner site of centrifuge rotor, the bench used for molecular biological tests, the benches of biosafety cabinets used for viral culture, clinical sample pre-treatment and nucleic acids extraction, by scrubbing the sites using sterile flocked swabs. The extracted total nucleic acids were used to construct the libraries for deep sequencing according to the protocol of Ion Torrent platform. At least 1G raw data was obtained for each sample. The reads of viruses and bacteria accounted for 0.01 ± 0.02%, and 77.76 ± 12.53% of total reads respectively. The viral sequences were likely to be derived from gene amplification products, the nucleic acids contaminated in fetal bovine serum. Reads from environmental microorganisms were also identified. Our results suggested that NGS method was capable of monitoring the nucleic acids contaminations from different sources in the lab, demonstrating its promising utility in monitoring and assessing the risk of potential laboratory contamination. The risk of contamination from reagents, remnant DNA and environment should be considered in data analysis and results interpretation.
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32
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Wen X, Huang Q, Tao H, Zou W, Gao M, Guo H, Yao X, Cui D, Wang X. Clinical characteristics and viral etiologies of outpatients with acute respiratory infections in Huzhou of China: a retrospective study. BMC Infect Dis 2019; 19:32. [PMID: 30621623 PMCID: PMC6325799 DOI: 10.1186/s12879-018-3668-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Accepted: 12/28/2018] [Indexed: 01/06/2023] Open
Abstract
BACKGROUND Viruses are commonly found in patients with acute respiratory infections (ARIs). However, the viral etiologies and clinical characteristics of outpatients with ARIs are poorly understood in China. Here, we identified the viral etiologies in outpatients with ARIs in Huzhou, China. RESULTS Our results indicated that of 426 outpatients, 246 were positive for viruses. Of them, 221 were positive for a single virus, including influenza A, which comprised H3N2 (28.5%) and pandemic H1N1 (2009) (19.0%), enterovirus (10.4%), and influenza B (8.6%). Other single viruses were detected at less than 8.0%. Twenty-five patients were positively coinfected with two viruses. The prevalent viruses in coinfections were rhinovirus and H3N2 virus (28.0%). Viruses were major pathogens in young children (< 5 years) (75.0%). Coinfections were prevalent in older adults (11.9%) and young children (9.5%). Virus-positive outpatients presented higher temperatures and more sore throat, fatigue and shortness of breath than virus-negative outpatients. ARIs and most virus detections peaked during the winter, but enteroviruses emerged between April and September. CONCLUSION Viruses are major agents of ARIs among outpatients in Huzhou, China. There was a variation in the distribution of viruses across different age groups and seasons. These findings are beneficial for planning prevention and treatment services for outpatients with ARIs.
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Affiliation(s)
- Xiaohong Wen
- The First People's Hospital Affiliated to Huzhou University, Huzhou, 313000, China
| | - Qiuling Huang
- Department of Clinical Laboratory, Huzhou Central Hospital, Huzhou, 313000, China
| | - Hong Tao
- Department of Laboratory & Pharmacy, Suzhou Vocational Health College, Suzhou, 215009, China
| | - Weihua Zou
- Department of Clinical Laboratory, Huzhou Central Hospital, Huzhou, 313000, China
| | - Min Gao
- Department of Clinical Laboratory, Huzhou Central Hospital, Huzhou, 313000, China
| | - Huihui Guo
- The First People's Hospital Affiliated to Huzhou University, Huzhou, 313000, China
| | - Xing Yao
- Department of Clinical Laboratory, Huzhou Central Hospital, Huzhou, 313000, China
| | - Dawei Cui
- Department of Blood Transfusion, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, 310003, China.
| | - Xiang Wang
- The First People's Hospital Affiliated to Huzhou University, Huzhou, 313000, China.
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Lai K, Shen H, Zhou X, Qiu Z, Cai S, Huang K, Wang Q, Wang C, Lin J, Hao C, Kong L, Zhang S, Chen Y, Luo W, Jiang M, Xie J, Zhong N. Clinical Practice Guidelines for Diagnosis and Management of Cough-Chinese Thoracic Society (CTS) Asthma Consortium. J Thorac Dis 2018; 10:6314-6351. [PMID: 30622806 PMCID: PMC6297434 DOI: 10.21037/jtd.2018.09.153] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 09/10/2018] [Indexed: 12/26/2022]
Affiliation(s)
- Kefang Lai
- State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
| | - Huahao Shen
- The Second Hospital Affiliated to Medical College of Zhejiang University, Hangzhou 310009, China
| | - Xin Zhou
- Shanghai Jiaotong University Affiliated Shanghai No. 1 People’s Hospital, Shanghai 200080, China
| | - Zhongmin Qiu
- Tongji Affiliated Tongji Hospital, Shanghai 200065, China
| | - Shaoxi Cai
- Southern Medical University Affiliated Nanfang Hospital, Guangzhou 510515, China
| | - Kewu Huang
- Capital Medical University Affiliated Beijing Chaoyang Hospital, Beijing 100020, China
| | | | - Changzheng Wang
- Xinqiao Hospital, Third Military Medical University, Chongqing 400037, China
| | - Jiangtao Lin
- China-Japan Friendship Hospital, Beijing 100029, China
| | - Chuangli Hao
- Children’s Hospital of Soochow University, Suzhou 215025, China
| | - Lingfei Kong
- The First Hospital of China Medical University, Shenyang 110001, China
| | - Shunan Zhang
- China-Japan Friendship Hospital, Beijing 100029, China
| | - Yaolong Chen
- Evidence-based Medical Center of Lanzhou University, Lanzhou 730000, China
| | - Wei Luo
- State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
| | - Mei Jiang
- State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
| | - Jiaxing Xie
- State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
| | - Nanshan Zhong
- State Key Laboratory of Respiratory Diseases, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou Institute of Respiratory Health, Guangzhou 510120, China
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Khani H, Tabarraei A, Moradi A. Survey of Coronaviruses Infection among Patients with Flu-like Symptoms in the Golestan Province, Iran. MEDICAL LABORATORY JOURNAL 2018. [DOI: 10.29252/mlj.12.6.1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
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35
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Liu P, Lu L, Xu M, Zhong H, Jia R, Su L, Cao L, Dong Z, Dong N, Zhou L, Xu J. A novel multiplex PCR for virus detection by melting curve analysis. J Virol Methods 2018; 262:56-60. [PMID: 30267725 PMCID: PMC7113878 DOI: 10.1016/j.jviromet.2018.09.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 09/21/2018] [Accepted: 09/25/2018] [Indexed: 12/23/2022]
Abstract
Taqman probe based melting curve analysis can detect and distinguish six respiratory viruses simultaneously. The multiplex PCR established here has a good analytical sensitivity and specificity. The accordance rate between the multiplex PCR and direct fluorescent antibody testing was high. Taqman probe based melting curve analysis is well suited to multiple virus detection.
Background Rapid and accurate laboratory diagnoses of viral infections are crucial for the management and treatment of patients with viral infections. Conventional methods for virus detection are labourious, time consuming, and only a single virus can be analysed in one assay. Objectives The objective of this study was to develop a novel real-time PCR method for multiple virus detection by melting curve analysis using Taqman probes in a single reaction. Study design As a model, six respiratory viruses were detected in one tube using three fluorophores. The specificity was assessed by cross-reaction tests with other common respiratory pathogens. The analytical sensitivity was assessed by testing the limit of detection of the assay using artificial plasmids as the positive template. The clinical evaluation of the established assay was evaluated for the detection of respiratory viruses in clinical samples, and the results were compared with direct fluorescent antibody testing (DFA). Results The six respiratory viruses were clearly distinguished by their respective melting temperature values in the corresponding fluorescence detection channels. No cross reactions were observed by cross reaction tests. The detection limits of this assay were 2 to 2 × 103 copies per reaction for each virus. The clinical evaluation of this assay was demonstrated by analysing 352 clinical samples, and 67(19.0%) samples were positive for at least one virus. The accordance rate between the established PCR and DFA testing was high, and ranged from 94.57% to 100%. Conclusions Taqman probe-based melting curve analysis is well suited for detection of multiple viruses in clinical and research laboratories because of its high throughput, reliability, and cost savings.
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Affiliation(s)
- Pengcheng Liu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Lijuan Lu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Menghua Xu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Huaqing Zhong
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Ran Jia
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Liyun Su
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Lingfeng Cao
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Zuoquan Dong
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Niuniu Dong
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Linfu Zhou
- Medical Biotechnology Laboratory, Zhejiang University, Hangzhou, China.
| | - Jin Xu
- Department of Clinical Laboratory, Children's Hospital of Fudan University, Shanghai, China.
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Kadjo HA, Adjogoua E, Dia N, Adagba M, Abdoulaye O, Daniel S, Kouakou B, Ngolo DC, Coulibaly D, Ndahwouh TN, Dosso M. DETECTION OF NON-INFLUENZA VIRUSES IN ACUTE RESPIRATORY INFECTIONS IN CHILDREN UNDER FIVE-YEAR-OLD IN COTE D'IVOIRE (JANUARY - DECEMBER 2013). Afr J Infect Dis 2018; 12:78-88. [PMID: 30109291 PMCID: PMC6085743 DOI: 10.21010/ajid.v12i2.13] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2017] [Revised: 05/04/2018] [Accepted: 05/07/2018] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Influenza sentinel surveillance in Cote d'Ivoire showed that 70% of Acute Respiratory Infections (ARI) cases remained without etiology. This work aims to describe the epidemiological, clinical, and virological pattern of ARI that tested negative for influenza virus, in children under five years old. MATERIALS AND METHODS one thousand and fifty nine samples of patients presenting influenza Like Illness (ILI) or Severe Acute Respiratory Infections (SARI) symptoms were tested for other respiratory viruses using multiplex RT-PCR assays targeting 10 respiratory viruses. RESULTS The following pathogens were detected as follows, hRV 31,92% (98/307), hRSV 24.4% (75/329), PIV 20.5% (63/307), HCoV 229E 12,05% (37/307), hMPV 6.2% (19/307), HCoVOC43 1.0% (3/307) and EnV 1.0% (3/307). Among the 1,059 specimens analyzed, 917 (86.6%) were ILI samples and 142 (23.4%) were SARI samples. The proportion of children infected with at least one virus was 29.8% (273/917) in ILI cases and 23.9% (34/142) in SARI cases. The most prevalent viruses, responsible for ILI cases were hRV with 35.89% (98/273) and hRSV in SARI cases with 41.2% (14/34) of cases. Among the 1,059 patients, only 22 (2.1%) children presented risk factors related to the severity of influenza virus infection. CONCLUSION This study showed that respiratory viruses play an important role in the etiology of ARI in children. For a better understanding of the epidemiology of ARI and improved case management, it would be interesting in this context to expand the surveillance of influenza to other respiratory viruses.
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Affiliation(s)
- Herve A. Kadjo
- Pasteur Institute of Cote d’Ivoire, Abidjan, Cote d’Ivoire
| | | | | | - Marius Adagba
- Pasteur Institute of Cote d’Ivoire, Abidjan, Cote d’Ivoire
| | | | - Saraka Daniel
- Pasteur Institute of Cote d’Ivoire, Abidjan, Cote d’Ivoire
| | - Bertin Kouakou
- Pasteur Institute of Cote d’Ivoire, Abidjan, Cote d’Ivoire
| | - David C. Ngolo
- Pasteur Institute of Cote d’Ivoire, Abidjan, Cote d’Ivoire
| | | | - Talla Nzussouo Ndahwouh
- Noguchi Memorial Institute for Medical Research (NMIMR) University of Ghana, Legon, Accra, Ghana
| | - Mireille Dosso
- Pasteur Institute of Cote d’Ivoire, Abidjan, Cote d’Ivoire
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Ge X, Guo Y, Chen J, Hu R, Feng X. Epidemiology and Seasonality of Respiratory Viruses Detected from Children with Respiratory Tract Infections in Wuxi, East China. Med Sci Monit 2018; 24:1856-1862. [PMID: 29599424 PMCID: PMC5892462 DOI: 10.12659/msm.908483] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Background Respiratory tract infections (RTIs) are the major causes of mortality and morbidity in children and lead to hospitalization in developing countries. However, little is known about the epidemiology and seasonality of respiratory viruses in the pediatric population in Wuxi, East China. Material/Methods We included all patients 14 years of age and below who presented with signs and symptoms of RTIs between January 2010 and December 2016. During this period, a total of 2160 children treated in Wuxi No. 2 People’s Hospital were involved in our study. The clinical and sociodemographic data were recorded to describe the frequency and seasonality. Respiratory specimens were tested by multiplex real-time PCR assays for virus identification. Results More than 30% (35.19%, 760 samples) of the specimens showed evidence of infection with viruses, including respiratory syncytial virus (368 samples), influenza virus A (114 samples), influenza virus B (115 samples), parainfluenza virus I (29 samples), parainfluenza virus II (39 samples), parainfluenza virus III (13 samples), and adenovirus (82 samples); 48.99% of the children infected with viruses were under 12 months of age. Viruses were detected throughout all the year, with a peak in winter. Conclusions Our study found that RSV is the most important cause of RTIs in our region during winter. Our data provide a comprehensive understanding of the epidemiology and seasonality of virus, which may help to reduce the use of antibiotics and implement an effective approach for prevention, control, and treatment of RTIs, especially during its peak season.
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Affiliation(s)
- Xiaoli Ge
- Neonate Department, Children's Hospital of Soochow University, Suzhou, Jiangsu, China (mainland).,Department of Pediatrics, Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China (mainland)
| | - Yi Guo
- Department of Pediatrics, Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China (mainland)
| | - JuanJuan Chen
- Department of Pediatrics, Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China (mainland)
| | - Renjing Hu
- Department of Laboratory Medicine, Wuxi Second People's Hospital of Nanjing Medical University, Wuxi, Jiangsu, China (mainland)
| | - Xing Feng
- Neonate Department, Children's Hospital of Soochow University, Suzhou, Jiangsu, China (mainland)
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Kim JM, Jung HD, Cheong HM, Lee A, Lee NJ, Chu H, Lee JY, Kim SS, Choi JH. Nation-wide surveillance of human acute respiratory virus infections between 2013 and 2015 in Korea. J Med Virol 2018; 90:1177-1183. [PMID: 29488229 PMCID: PMC7166751 DOI: 10.1002/jmv.25069] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 12/21/2017] [Indexed: 01/08/2023]
Abstract
The prevalence of eight respiratory viruses detected in patients with acute respiratory infections (ARIs) in Korea was investigated through analysis of data recorded by the Korea Influenza and Respiratory Viruses Surveillance System (KINRESS) from 2013 to 2015. Nasal aspirate and throat swabs specimens were collected from 36 915 patients with ARIs, and viral nucleic acids were detected by real‐time (reverse‐transcription) polymerase chain reaction for eight respiratory viruses, including human respiratory syncytial viruses (HRSVs), influenza viruses (IFVs), human parainfluenza viruses (HPIVs), human coronaviruses (HCoVs), human rhinovirus (HRV), human adenovirus (HAdV), human bocavirus (HBoV), and human metapneumovirus (HMPV). The overall positive rate of patient specimens was 49.4% (18 236/36 915), 5% of which carried two or more viruses simultaneously. HRV (15.6%) was the most predominantly detected virus, followed by IFVs (14.6%), HAdV (7.5%), HPIVs (5.8%), HCoVs (4.2%), HRSVs (3.6%), HBoV (1.9%), and HMPV (1.6%). Most of the ARIs were significantly correlated with clinical symptoms of fever, cough, and runny nose. Although HRV and HAdV were frequently detected throughout the year in patients, other respiratory viruses showed apparent seasonality. HRSVs and IFVs were the major causative agents of acute respiratory diseases in infants and young children. Overall, this study demonstrates a meaningful relationship between viral infection and typical manifestations of known clinical features as well as seasonality, age distribution, and co‐infection among respiratory viruses. Therefore, these data could provide useful information for public health management and to enhance patient care for primary clinicians.
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Affiliation(s)
- Jeong-Min Kim
- Division of Emerging Infectious Disease and Vector Research, Cheongju-si, South Korea
| | - Hee-Dong Jung
- Division of Research Planning, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju-si, South Korea
| | | | - Anna Lee
- Division of Viral Disease, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Cheongju-si, South Korea
| | - Nam-Joo Lee
- Division of Viral Disease, Center for Laboratory Control of Infectious Diseases, Korea Centers for Disease Control and Prevention, Cheongju-si, South Korea
| | - Hyuk Chu
- Bacterial Disease Research, Cheongju-si, South Korea
| | - Joo-Yeon Lee
- Division of Emerging Infectious Disease and Vector Research, Cheongju-si, South Korea
| | | | - Jang-Hoon Choi
- Viral Disease Research, Center for Infectious Diseases Research, Korea National Institute of Health, Korea Centers for Disease Control and Prevention, Cheongju-si, South Korea
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Wei L, Xie Q, Hou JL, Tang H, Ning Q, Cheng J, Nan Y, Zhang L, Li J, Jiang J, McNabb B, Zhang F, Camus G, Mo H, Osinusi A, Brainard DM, Gong G, Mou Z, Wu S, Wang G, Hu P, Gao Y, Jia J, Duan Z. Ledipasvir/sofosbuvir for treatment-naive and treatment-experienced Chinese patients with genotype 1 HCV: an open-label, phase 3b study. Hepatol Int 2018; 12:126-132. [PMID: 29637511 PMCID: PMC5904238 DOI: 10.1007/s12072-018-9856-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 03/15/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Chronic hepatitis C virus (HCV) infection is a significant medical burden in China, affecting more than 10 million persons. In clinical trials and real-world settings, treatment with ledipasvir/sofosbuvir in patients with genotype 1 HCV infection resulted in high sustained virologic response rates. Ledipasvir/sofosbuvir may provide a highly effective, short-duration, single-tablet regimen for Chinese patients with HCV infection. METHODS Chinese patients with genotype 1 HCV infection who were HCV treatment naive or treatment experienced, without cirrhosis or with compensated cirrhosis, were treated with open-label ledipasvir/sofosbuvir for 12 weeks. The primary efficacy endpoint was sustained virologic response 12 weeks after completing treatment (SVR12). For treatment-naive patients, SVR12 was compared to a historical rate of 57%. The primary safety endpoint was adverse events leading to permanent discontinuation of study drug; serious adverse events were also evaluated. The presence of resistance-associated substitutions (RASs) was evaluated by viral sequencing. RESULTS All 206 enrolled patients achieved SVR12 (100%; 95% CI 98-100%), including 106 treatment-naive patients (100%; 95% CI 97-100%), which was superior to a historical SVR rate of 57% (p < 0.001). All patients with baseline NS5A and NS5B RASs (14 and 1% of patients, respectively) achieved SVR12. The most common adverse events were viral upper respiratory tract infection (17%), upper respiratory tract infection (14%), and cough (6%). There were no discontinuations due to adverse events; and no treatment-related serious adverse events were reported. CONCLUSION Ledipasvir/sofosbuvir is a well tolerated and highly effective treatment for Chinese patients with genotype 1 HCV, regardless of prior treatment experience, cirrhosis status, or the presence of pretreatment RASs.
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Affiliation(s)
- Lai Wei
- Beijing Key Lab for Hepatitis C and Immunologic Liver Disease, Peking University Hepatology Institute, Peking University People's Hospital, 11 Xizhimen S St, Xicheng District, Beijing, 100044, China.
| | - Qing Xie
- Ruijin Hospital, Shanghai Jiaotong University, Shanghai, China
| | - Jin Lin Hou
- Nanfang Hospital of Southern Medical University, Guangzhou, China
| | - Hong Tang
- West China Hospital, Sichuan University, Chengdu, China
| | - Qin Ning
- Tongji Hospital of Tongji Medical College, Huanzhong University of Science and Technology, Wuhan, China
| | - Jun Cheng
- Beijing Ditan Hospital Affiliated to Capital Medical University, Beijing, China
| | - Yuemin Nan
- The Third Hospital of Hebei Medical University, Hebei, China
| | - Lunli Zhang
- The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jun Li
- The First Affiliated Hospital with Nanjing Medical University, Nanjing, China
| | - Jianning Jiang
- The First Affiliated Hospital of Guangxi Medical University, Guangxi, China
| | | | | | | | | | | | | | - Guozhong Gong
- The Second Xiangya Hospital of Central South University, Changsha, China
| | | | - Shanming Wu
- Clinical Center of Shanghai Public Health, Shanghai, China
| | | | - Peng Hu
- The Second Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Yanhang Gao
- The First Hospital of Jilin University, Changchun, China
| | - Jidong Jia
- Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Zhongping Duan
- Beijing You-An Hospital, Capital Medical University, Beijing, China
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Xu W, Guo L, Dong X, Li X, Zhou P, Ni Q, Zhou X, Wagner AL, Li L. Detection of Viruses and Mycoplasma pneumoniae in Hospitalized Patients with Severe Acute Respiratory Infection in Northern China, 2015-2016. Jpn J Infect Dis 2018; 71:134-139. [PMID: 29491245 DOI: 10.7883/yoken.jjid.2017.412] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Severe acute respiratory infection (SARI) presents a huge disease and economic burden worldwide. The present study described the frequency and types of different infectious etiologies among hospitalized patients with SARI in Tianjin, China, during 2015 and 2016. Basic information, in addition to a throat or serum sample, was collected from SARI patients. Nine viruses were detected using reverse transcription polymerase chain reaction, and Mycoplasma pneumoniae was detected using the Serodia Myco II gelatin particle agglutination test. A total of 585 specimens from 2,290 SARI cases were collected. The most common infection (19.66%, 115/585) was M. pneumoniae, followed by influenza virus A/B (6.15%, 36/585), and respiratory syncytial virus (4.96%, 29/585). Identification of viral or M. pneumoniae infections was the highest in the pediatric medicine ward (74.84%, 119/159), followed by the intensive care unit (37.04%, 80/216) and respiratory medicine ward (34.29%, 72/210). M. pneumoniae was highest (38.71%, 24/62) in the 5-14-year age group. Influenza was the main infection in January 2015 and March 2016. The correlation coefficient for the proportion of hospitalized cases of SARI and the positive detection rate within the same week was 0.25. M. pneumoniae and influenza were the leading pathogens among hospitalized SARI patients. A continued surveillance of hospitalized cases of SARI can detect emerging diseases, such as avian influenza A (H7N9) virus and other respiratory disease outbreaks.
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Affiliation(s)
- Wenti Xu
- Department of Infectious Disease Control, Tianjin Centers for Disease Control and Prevention
| | - Liru Guo
- Department of Pathogen Test, Tianjin Centers for Disease Control and Prevention
| | - Xiaochun Dong
- Department of Infectious Disease Control, Tianjin Centers for Disease Control and Prevention
| | - Xiaoxia Li
- Department of Disease Prevention, Tianjin Third Center Hospital
| | - Penghui Zhou
- Department of Infectious Disease Control, Tianjin Centers for Disease Control and Prevention
| | - Qiang Ni
- Department of Disease Prevention, Tianjin Third Center Hospital
| | - Xinying Zhou
- Department of Pediatrics, Tianjin Third Center Hospital
| | | | - Lin Li
- Department of Infectious Disease Control, Tianjin Centers for Disease Control and Prevention
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Li X, Li J, Meng L, Zhu W, Liu X, Yang M, Yu D, Niu L, Shen X. Viral etiologies and epidemiology of patients with acute respiratory infections based on sentinel hospitals in Gansu Province, Northwest China, 2011-2015. J Med Virol 2018; 90:828-835. [PMID: 29388679 PMCID: PMC7166685 DOI: 10.1002/jmv.25040] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 01/17/2018] [Indexed: 01/01/2023]
Abstract
Understanding etiological role and epidemiological profile is needed to improve clinical management and prevention of acute respiratory infections (ARIs). A 5-year prospective study about active surveillance for outpatients and inpatients with ARIs was conducted in Gansu province, China, from January 2011 to November 2015. Respiratory specimens were collected from patients and tested for eight respiratory viruses using polymerase chain reaction (PCR) or reverse transcription polymerase chain reaction (RT-PCR). In this study, 2768 eligible patients with median age of 43 years were enrolled including pneumonia (1368, 49.2%), bronchitis (435, 15.7%), upper respiratory tract infection or URTI (250, 9.0%), and unclassified ARI (715, 25.8%). Overall, 29.2% (808/2768) were positive for any one of eight viruses, of whom 130 cases were identified with two or more viruses. Human rhinovirus (HRV) showed the highest detection rate (8.6%), followed by influenza virus (Flu, 7.3%), respiratory syncytial virus (RSV, 6.1%), human coronavirus (hCoV, 4.3%), human parainfluenza (PIV, 4.0%), adenovirus (ADV, 2.1%), human metapneumovirus (hMPV, 1.6%), and human bocavirus (hBoV, 0.7%). Compared with URTI, RSV was more likely identified in pneumonia (χ2 = 12.720, P < 0.001) and hCoV was more commonly associated with bronchitis than pneumonia (χ2 = 15.019, P < 0.001). In patients aged less than 5 years, RSV showed the highest detection rate and hCoV was the most frequent virus detected in adults and elderly. The clear epidemical seasons were observed in HRV, Flu, and hCoV infections. These findings could serve as a reference for local health authorities in drawing up further plans to prevent and control ARIs associated with viral etiologies.
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Affiliation(s)
- Xuechao Li
- Institution of Epidemiology and Health Statistics, School of Public Health, Lanzhou University, Gansu Province, P.R. China
| | - Juansheng Li
- Institution of Epidemiology and Health Statistics, School of Public Health, Lanzhou University, Gansu Province, P.R. China
| | - Lei Meng
- Centers' for Disease Control and Prevention, Gansu Province, P.R. China
| | - Wanqi Zhu
- Institution of Epidemiology and Health Statistics, School of Public Health, Lanzhou University, Gansu Province, P.R. China
| | - Xinfeng Liu
- Centers' for Disease Control and Prevention, Gansu Province, P.R. China
| | - Mei Yang
- Institution of Epidemiology and Health Statistics, School of Public Health, Lanzhou University, Gansu Province, P.R. China
| | - Deshan Yu
- Centers' for Disease Control and Prevention, Gansu Province, P.R. China
| | - Lixia Niu
- Institution of Epidemiology and Health Statistics, School of Public Health, Lanzhou University, Gansu Province, P.R. China
| | - Xiping Shen
- Institution of Epidemiology and Health Statistics, School of Public Health, Lanzhou University, Gansu Province, P.R. China
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Epidemiology of viral respiratory infections in Australian working-age adults (20–64 years): 2010–2013. Epidemiol Infect 2018; 146:619-626. [DOI: 10.1017/s0950268818000286] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
AbstractAcute respiratory infections cause significant morbidity and mortality accounting for 5.8 million deaths worldwide. In Australia, influenza-like illness (ILI), defined as cough, fever and fatigue is a common presentation in general practice and results in reduced productivity and lost working days. Little is known about the epidemiology of ILI in working-age adults. Using data from the ASPREN influenza surveillance network in Australia (2010–2013) we found that working-age adults made up 45.2% of all ILI notifications with 55% of samples positive for at least one respiratory virus. Viruses most commonly detected in our study included influenza A (20.6%), rhinovirus (18.6%), influenza B (6.2%), human meta-pneumovirus (3.4%), respiratory syncytial virus (3.1%), para-influenza virus (2.6%) and adenovirus (1.3%). We also demonstrated that influenza A is the predominant virus that increases ILI (by 1.2% per month for every positive influenza A case) in working-age adults during autumn–winter months while other viruses are active throughout the year. Understanding the epidemiology of viral respiratory infections through a year will help clinicians make informed decisions about testing, antibiotic and antiviral prescribing and when the beginning of the ‘flu season’ can be more confidently predicted.
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Yu J, Xie Z, Zhang T, Lu Y, Fan H, Yang D, Bénet T, Vanhems P, Shen K, Huang F, Han J, Li T, Gao Z, Ren L, Wang J. Comparison of the prevalence of respiratory viruses in patients with acute respiratory infections at different hospital settings in North China, 2012-2015. BMC Infect Dis 2018; 18:72. [PMID: 29422011 PMCID: PMC5806372 DOI: 10.1186/s12879-018-2982-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2017] [Accepted: 01/30/2018] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Acute respiratory infections (ARIs) are a great public health challenge globally. The prevalence of respiratory viruses in patients with ARIs attending at different hospital settings is fully undetermined. METHODS Laboratory-based surveillance for ARIs was conducted at inpatient and outpatient settings of 11 hospitals in North China. The first 2-5 patients with ARIs were recruited in each hospital weekly from 2012 through 2015. The presence of respiratory viruses was screened by PCR assays. The prevalence of respiratory viruses was determined and compared between patients at different hospital settings. RESULTS A total of 3487 hospitalized cases and 6437 outpatients/Emergency Department (ED) patients were enrolled. The most commonly detected viruses in the hospitalized cases were respiratory syncytial virus (RSV, 33.3%) in children less than two years old, adenoviruses (13.0%) in patients 15-34 years old, and influenza viruses (IFVs, 9.6%) in patients ≥65 years. IFVs were the most common virus in outpatient/ED patients across all age groups (22.7%). After controlling for the confounders caused by other viruses and covariates, adenoviruses (adjusted odds ratio [aOR]: 3.97, 99% confidence interval [99% CI]: 2.19-7.20) and RSV (aOR: 2.04, 99% CI: 1.34-3.11) were independently associated with increased hospitalization in children, as well as adenoviruses in adults (aOR: 2.14, 99% CI: 1.19-3.85). Additionally, co-infection of RSV with IFVs was associated with increased hospitalization in children (aOR: 12.20, 99% CI: 2.65-56.18). CONCLUSIONS A substantial proportion of ARIs was associated with respiratory viruses in North China. RSV, adenoviruses, and co-infection of RSV and IFVs were more frequent in hospitalized children (or adenoviruses in adults), which might predict the severity of ARIs. Attending clinicians should be more vigilant of these infections.
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Affiliation(s)
- Jianxing Yu
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, 100730, People's Republic of China
| | - Zhengde Xie
- Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, No. 56 Nan-li-shi Road, Beijing, 100045, People's Republic of China
| | - Tiegang Zhang
- Beijing Center for Disease Control and Prevention, No.16, Hepingli Middle Avenue of Dongcheng district, Beijing, 100013, People's Republic of China
| | - Yanqin Lu
- Shandong Medicinal Biotechnology Centre, Key Laboratory for Modern Medicine and Technology of Shandong Province, Shandong Academy of Medical Sciences, No. 18877 Jingshi Road, Jinan, Shandong, 250062, People's Republic of China
| | - Hongwei Fan
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, People's Republic of China
| | - Donghong Yang
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, People's Republic of China
| | - Thomas Bénet
- Service d'Hygiène, Epidémiologie et Prévention, Hôpital Edouard Herriot, Lyon, France.,Laboratoire des Pathogènes Emergents - Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), Institut National de la Santé et de la Recherche Médicale U1111, Centre National de la Recherche Scientifique, UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 21, Avenue Tony Garnier, 69007, Lyon, France
| | - Philippe Vanhems
- Service d'Hygiène, Epidémiologie et Prévention, Hôpital Edouard Herriot, Lyon, France.,Laboratoire des Pathogènes Emergents - Fondation Mérieux, Centre International de Recherche en Infectiologie (CIRI), Institut National de la Santé et de la Recherche Médicale U1111, Centre National de la Recherche Scientifique, UMR5308, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, 21, Avenue Tony Garnier, 69007, Lyon, France.,INSERM, F-CRIN, I-REIVAC, Lyon Collaborative Center, Lyon, France
| | - Kunling Shen
- Key Laboratory of Major Diseases in Children and National Key Discipline of Pediatrics (Capital Medical University), Ministry of Education, Beijing Pediatric Research Institute, Beijing Children's Hospital, Capital Medical University, No. 56 Nan-li-shi Road, Beijing, 100045, People's Republic of China
| | - Fang Huang
- Beijing Center for Disease Control and Prevention, No.16, Hepingli Middle Avenue of Dongcheng district, Beijing, 100013, People's Republic of China
| | - Jinxiang Han
- Shandong Medicinal Biotechnology Centre, Key Laboratory for Modern Medicine and Technology of Shandong Province, Shandong Academy of Medical Sciences, No. 18877 Jingshi Road, Jinan, Shandong, 250062, People's Republic of China
| | - Taisheng Li
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences & Peking Union Medical College, Beijing, 100730, People's Republic of China
| | - Zhancheng Gao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, 100044, People's Republic of China
| | - Lili Ren
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, 100730, People's Republic of China.
| | - Jianwei Wang
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing, 100730, People's Republic of China.
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Oumei H, Xuefeng W, Jianping L, Kunling S, Rong M, Zhenze C, Li D, Huimin Y, Lining W, Zhaolan L, Xinmin L, Hua X, Zhiyan J, Yanning L, Yan H, Baoqing Z, Xiaochun F, Chunhui H, Yonghong J, Xue Z, Wei W, Zi W. Etiology of community-acquired pneumonia in 1500 hospitalized children. J Med Virol 2017; 90:421-428. [PMID: 28975629 PMCID: PMC7166354 DOI: 10.1002/jmv.24963] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2017] [Revised: 07/28/2017] [Accepted: 09/01/2017] [Indexed: 12/11/2022]
Abstract
Childhood community‐acquired pneumonia (CAP) is a common illness; however, comprehensive studies of hospitalizations for CAP among children in China based on prospective and multicenter data collection are limited. The aim of this investigation was to determine the respiratory pathogens responsible for CAP in hospitalized children. From January to December 2015, oropharyngeal swabs and blood serum were collected from hospitalized children with CAP symptoms ranging in age from 6 months to 14 years at 10 hospitals across China. We used immunofluorescence to detect antibodies for eight respiratory viruses and passive agglutination to detect specific IgM against Mycoplasma pneumoniae (M. pneumoniae). Of 1500 children presenting with CAP, 691 (46.1%) tested positive for at least one pathogen (virus or M. pneumoniae). M. pneumoniae (32.4%) was detected most frequently, followed by respiratory syncytial virus (11.5%), adenovirus (5.0%), influenza A virus (4.1 %), influenza B virus (3.4%), parainfluenza virus types 2 and 3 type (3.1 %), parainfluenza virus type 1 (2.9%), and human metapneumovirus (0.3%). Co‐infections were identified in 128 (18.5%) of the 691 cases. These data provide a better understanding of viral etiology and M. pneumoniae in CAP in children between 6 months and 14 years in China. More study of the etiologic investigations that would further aid the management of pneumonia is required. With effective immunization for RSV, ADV, and M. pneumoniae infections, more than one‐half of the pneumonia cases in this study could have been prevented.
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Affiliation(s)
- Hao Oumei
- Affiliated Hospital to Liaoning University Traditional Chinese Medicine, Shenyang, China
| | - Wang Xuefeng
- Affiliated Hospital to Liaoning University Traditional Chinese Medicine, Shenyang, China
| | - Liu Jianping
- Evidence-Based Medicine Centre, Beijing University of Chinese Medicine, Beijing, China
| | - Shen Kunling
- Beijing Children's Hospital to Capital Medical University, Beijing, China
| | - Ma Rong
- Affiliated Hospital to Tianjin University Traditional Chinese Medicine, Tianjin, China
| | - Cui Zhenze
- Dalian Children's Hospital, Dalian, China
| | - Deng Li
- Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Yan Huimin
- Beijing Children's Hospital to Capital Medical University, Beijing, China
| | - Wang Lining
- Affiliated Hospital to Guangxi University Traditional Chinese Medicine, Guangxi, China
| | - Liu Zhaolan
- Evidence-Based Medicine Centre, Beijing University of Chinese Medicine, Beijing, China
| | - Li Xinmin
- Affiliated Hospital to Tianjin University Traditional Chinese Medicine, Tianjin, China
| | - Xu Hua
- Affiliated Hospital to Guangzhou University Traditional Chinese Medicine, Guangzhou, China
| | - Jiang Zhiyan
- Long Hua Hospital to Shanghai University of Traditional Chinese, Shanghai, China
| | - Li Yanning
- Affiliated Hospital of Shandong University of Traditional Chinese, Shandong, China
| | - Huang Yan
- Dalian Children's Hospital, Dalian, China
| | - Zhang Baoqing
- Affiliated Hospital of Shandong University of Traditional Chinese, Shandong, China
| | - Feng Xiaochun
- Affiliated Hospital to Changchun University Traditional Chinese Medicine, Changchun, China
| | - He Chunhui
- Guangzhou Women and Children's Medical Center, Guangzhou, China
| | - Jiang Yonghong
- Long Hua Hospital to Shanghai University of Traditional Chinese, Shanghai, China
| | - Zhao Xue
- Affiliated Hospital to Liaoning University Traditional Chinese Medicine, Shenyang, China
| | - Wei Wei
- Affiliated Hospital to Liaoning University Traditional Chinese Medicine, Shenyang, China
| | - Wang Zi
- Affiliated Hospital to Liaoning University Traditional Chinese Medicine, Shenyang, China
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45
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Xiu L, Zhang C, Wu Z, Peng J. Establishment and Application of a Universal Coronavirus Screening Method Using MALDI-TOF Mass Spectrometry. Front Microbiol 2017; 8:1510. [PMID: 28848521 PMCID: PMC5552709 DOI: 10.3389/fmicb.2017.01510] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2017] [Accepted: 07/27/2017] [Indexed: 12/13/2022] Open
Abstract
There are four human coronaviruses (HCoVs), distributed worldwide, that are associated with a range of respiratory symptoms. The discovery of severe acute respiratory syndrome (SARS)-CoV and Middle East respiratory syndrome (MERS)-CoV shows that HCoVs pose a significant threat to human health. Our work aims to develop a sensitive method (mCoV-MS) which can not only identify known HCoVs accurately, but also have the ability to provide clues for the emerging HCoVs. The method was performed using a MassARRAY matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) system. We developed a 17-plex analysis to detect six HCoVs in Panel A and another 17-plex analysis to detect Alphacoronavirus and Betacoronavirus in Panel B. All tested primers and probes for the mCoV-MS method were effective, with no cross-reactivity observed with other common respiratory viruses. To confirm the usefulness of the mCoV-MS method we screened 384 pharyngeal and/or anal swab samples collected from bats/rodents, and 131 nasal and throat swabs from human patients. The results showed good concordance with the results of metagenomic analysis or PCR-sequencing. The validation test showed mCoV-MS method can detect potentially pathogenic CoVs in Alphacoronavirus and Betacoronavirus and provide convincingly phylogenetic evidences about unknown CoVs. The mCoV-MS method is a sensitive assay that is relatively simple to carry out. We propose that this method be used to complement next generation sequencing technology for large-scale screening studies.
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Affiliation(s)
- Leshan Xiu
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical CollegeBeijing, China
| | - Chi Zhang
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical CollegeBeijing, China
| | - Zhiqiang Wu
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical CollegeBeijing, China
| | - Junping Peng
- Ministry of Health Key Laboratory of Systems Biology of Pathogens, Institute of Pathogen Biology, Chinese Academy of Medical Sciences & Peking Union Medical CollegeBeijing, China
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46
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Xiang Z, Li L, Ren L, Guo L, Xie Z, Liu C, Li T, Luo M, Paranhos-Baccalà G, Xu W, Wang J. Seroepidemiology of enterovirus D68 infection in China. Emerg Microbes Infect 2017; 6:e32. [PMID: 28487560 PMCID: PMC5520479 DOI: 10.1038/emi.2017.14] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2016] [Revised: 02/13/2017] [Accepted: 02/13/2017] [Indexed: 11/21/2022]
Abstract
Human enterovirus 68 (EV-D68) is a rarely reported virus that has been linked to
respiratory disease. In recent years, reports about EV-D68 infection have markedly
increased worldwide. However, the epidemiological features of this emerging infection
are not well understood. To evaluate the emerging EV-D68 epidemic, we isolated the
circulating viral strain and investigated the seroprevalence of neutralizing
antibodies (NAbs) in Beijing between 2004 and 2011. We found that the titers of
EV-D68 NAbs were generally low in all age groups in sampled populations in 2004 but
significantly higher in 2009. From 2007 to 2011, the NAbs against EV-D68
significantly increased over time. These findings indicate that EV-D68 has spread
widely in the Chinese population in recent years, although only a limited number of
cases were reported.
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Affiliation(s)
- Zichun Xiang
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100730, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
| | - Linlin Li
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100730, China
| | - Lili Ren
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100730, China
| | - Li Guo
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100730, China
| | - Zhengde Xie
- Beijing Children's Hospital Affiliated to Capital University of Medical Sciences, Beijing 100045, China
| | - Chunyan Liu
- Beijing Children's Hospital Affiliated to Capital University of Medical Sciences, Beijing 100045, China
| | - Taisheng Li
- Peking Union Medical College Hospital, Beijing 100005, China
| | - Ming Luo
- Beijing Center for Diseases Control and Prevention, Beijing 100013, China
| | | | - Wenbo Xu
- WHO WPRO Regional Polio Reference Laboratory and Ministry of Health Key Laboratory for Medical Virology, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jianwei Wang
- MOH Key Laboratory of Systems Biology of Pathogens and Christophe Mérieux Laboratory, IPB, CAMS-Fondation Mérieux, Institute of Pathogen Biology (IPB), Chinese Academy of Medical Sciences (CAMS) & Peking Union Medical College, Beijing 100730, China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou 310003, China
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47
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Kaur A, Kumar N, Sengupta S, Mehta Y. Respiratory Multiplex Polymerase Chain Reaction: An Important Diagnostic Tool in Immunocompromised Patients. Indian J Crit Care Med 2017; 21:192-198. [PMID: 28515602 PMCID: PMC5416785 DOI: 10.4103/ijccm.ijccm_2_17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
Abstract
Background: Viruses and atypical pathogens can cause significant respiratory illness in immunocompromised patients. Multiplex polymerase chain reaction (MPCR) has improved the diagnostic yield of pathogens, and it is easier to identify the co-infections also. The present study was done to evaluate the performance of MPCR on bronchoalveolar lavage (BAL) samples in immunocompromised patients. Methods: Atotal of 177 BAL specimens collected over a 19 months period from immunocompromised patients with respiratory illness were analyzed with the MPCR and aerobic culture. Patients were divided into four according to the pathogens. Category V (only viral), Category NV (nonviral, i.e., bacteria and atypical), Category M (mixed, i.e., both viral and nonviral pathogen), and Category UK (unknown etiology). Results: MPCR identified the causative pathogen in 59.3% of patients while culture could identify only in 37.8% of patients. Most frequent etiological agent was Klebsiella pneumoniae (32%), followed by cytomegalovirus (21%), and Pneumocystis jirovecii (10%). Numbers of patients in each category were Category V (9.6%), Category NV (43.5%), Category M (19.8%), and Category UK (27.1%). Mortality was significantly higher in patients of Category M having mixed infections. Conclusion: MPCR is highly sensitive and rapid tool which can be considered in the routine diagnostic algorithm of respiratory illness in immunocompromised patients.
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Affiliation(s)
- Amarjeet Kaur
- Department of Microbiology, Medanta - The Medicity, Gurgaon, Haryana, India
| | - Navin Kumar
- Department of Microbiology, Medanta - The Medicity, Gurgaon, Haryana, India
| | - Sharmila Sengupta
- Department of Microbiology, Medanta - The Medicity, Gurgaon, Haryana, India
| | - Yatin Mehta
- Department of Critical Care and Anaesthesiology, Medanta - The Medicity, Gurgaon, Haryana, India
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48
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Dehority WN, Eickman MM, Schwalm KC, Gross SM, Schroth GP, Young SA, Dinwiddie DL. Complete genome sequence of a KI polyomavirus isolated from an otherwise healthy child with severe lower respiratory tract infection. J Med Virol 2016; 89:926-930. [PMID: 27704585 DOI: 10.1002/jmv.24706] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/04/2016] [Indexed: 11/11/2022]
Abstract
Unbiased, deep sequencing of a nasal specimen from an otherwise healthy 13-month-old boy hospitalized in intensive care revealed high gene expression and the complete genome of a novel isolate of KI polyomavirus (KIPyV). Further investigation detected minimal gene expression of additional viruses, suggesting that KIPyV was potentially the causal agent. Analysis of the complete genome of isolate NMKI001 revealed it is different from all previously reported genomes and contains two amino acid differences as compared to the closest virus isolate, Stockholm 380 (EF127908). J. Med. Virol. 89:926-930, 2017. © 2016 Wiley Periodicals, Inc.
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Affiliation(s)
- Walter N Dehority
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Megan M Eickman
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | - Kurt C Schwalm
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
| | | | | | | | - Darrell L Dinwiddie
- Department of Pediatrics, University of New Mexico Health Sciences Center, Albuquerque, New Mexico.,Clinical Translational Science Center, University of New Mexico Health Sciences Center, Albuquerque, New Mexico
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49
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Clinical and Epidemiologic Characteristics of Hospitalized Patients with Laboratory-Confirmed Respiratory Syncytial Virus Infection in Eastern China between 2009 and 2013: A Retrospective Study. PLoS One 2016; 11:e0165437. [PMID: 27802292 PMCID: PMC5089734 DOI: 10.1371/journal.pone.0165437] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2016] [Accepted: 10/11/2016] [Indexed: 01/10/2023] Open
Abstract
Respiratory syncytial virus (RSV) is a leading cause of morbidity and mortality worldwide in children aged <5 years and older adults with acute lower respiratory infections (ALRIs). However, few studies regarding the epidemiology of hospitalizations for RSV infection have been performed previously in China. Here, we aimed to describe the clinical and epidemiologic characteristics of hospitalized patients with laboratory-confirmed RSV infection in eastern China. Active surveillance for hospitalized ALRI patients using a broad case definition based on symptoms was performed from 2009–2013 in 12 sentinel hospitals in eastern China. Clinical and epidemiologic data pertaining to hospitalized patients of all ages with laboratory-confirmed RSV infection by PCR assay were collected and analyzed in this study. From 2009 to 2013, 1046 hospitalized patients with laboratory-confirmed RSV infection were enrolled in this study, and 14.7% of patients had subtype A, 24.2% of patients had subtype B, 23.8% of patients with subtype not performed, and 37.3% of patients had RSV coinfections with other viruses. RSV and influenza coinfections (33.3%) were the most common coinfections noted in this study. Moreover, young children aged <5 years (89.1%, 932/1046), particularly young infants aged <1 year (43.3%, 453/1046), represented the highest proportion of patients with RSV infections. In contrast, older adults aged ≥60 years (1.1%, 12/1046) represented the lowest proportion of patients with RSV infections among enrolled patients. The peak RSV infection period occurred mainly during autumn and winter, and 57% and 66% of patients exhibited symptoms such as fever (body temperature ≥38°C) and cough separately. Additionally, only a small number of patients were treated with broad-spectrum antiviral drugs, and most of patients were treated with antimicrobial drugs that were not appropriate for RSV infection. RSV is a leading viral pathogen and a common cause of viral infection in young children aged <5 years with ALRIs in eastern China. Effective vaccines and antiviral agents targeting RSV are needed to mitigate its large public health impact.
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50
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Indumathi CP, Gunanasekaran P, Kaveri K, Arunagiri K, Mohana S, Sheriff AK, SureshBabu BV, Padmapriya P, Senthilraja R, Fathima G. Isolation & molecular characterization of human parainfluenza virus in Chennai, India. Indian J Med Res 2016; 142:583-90. [PMID: 26658594 PMCID: PMC4743346 DOI: 10.4103/0971-5916.171287] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
Background & objectives: Human parainfluenza virus (HPIV) accounts for a significant proportion of lower respiratory tract infections in children as well as adults. This study was done to detect the presence of different subtypes of HPIV from patients having influenza like illness (ILI). Methods: Throat and nasal swabs from 232 patients with ILI who were negative for influenza viruses were tested by multiplex reverse transcription polymerase chain reaction(mRT-PCR) for the detection of human parainfluenza virus. All samples were inoculated in rhesus monkey kidney (LLC-MK2) cell line. Results: Of the 232 samples, 26(11.2%) were positive by mRT-PCR and nine (34.6%) showed cytopathic effect with syncytium formation for HPIV and all were HPIV-3 serotype, other serotypes like 1,2,4 were negative. The HPIV-3 strains (HN gene) were sequenced and analysed. Two novel mutations were identified at amino acid residues 295 and 297. Interpretation & conclusions: The mRT-PCR assay offers a rapid, sensitive and accurate diagnostic method for detection of HPIV which enables early detection and control. In our study there was a predominance of HPIV among 1-5 yr age group and the school going age group was less affected. Further studies need to be done to characterize HPIV isolated from different parts of the country.
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Affiliation(s)
| | | | - K Kaveri
- Department of Virology, King Institute of Preventive Medicine & Research, Chennai, India
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