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Zhang G, Zhang Y, Ba L, Liu L, Su T, Sun Y, Dian Z. Epidemiological changes in respiratory pathogen transmission among children with acute respiratory infections during the COVID-19 pandemic in Kunming, China. BMC Infect Dis 2024; 24:826. [PMID: 39143516 PMCID: PMC11323578 DOI: 10.1186/s12879-024-09733-y] [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: 05/28/2024] [Accepted: 08/07/2024] [Indexed: 08/16/2024] Open
Abstract
BACKGROUND Acute respiratory infections are a leading cause of morbidity and mortality in children. However, studies on the prevalence of respiratory viruses among children with acute respiratory infections in Kunming, China, are lacking. Therefore, we aimed to investigate the epidemiological characteristics of respiratory pathogens among children with acute respiratory infections in Kunming during the coronavirus disease 2019 pandemic. METHODS Nasopharyngeal swab samples were collected from 4956 children with acute respiratory infections at Yunnan Provincial First People's Hospital between January 2020 and December 2022, patients with COVID-19 were excluded from the study. Multiplex reverse transcription polymerase chain reaction was used to detect respiratory pathogens. RESULTS The frequency of respiratory pathogens among children was significantly lower in 2020 than in 2021 and 2022. The following pathogens had the highest prevalence rates (in descending order) from 2020 to 2022: HRV > RSV > PIV > ADV > MP; HRV > RSV > HADV > PIV > MP and HRV > Mp > HADV > H3N2 > HMPV. The overall frequency of respiratory pathogens exhibited an inverted U-shape with increasing age among the children. Human bocavirus, human parainfluenza virus, and human respiratory syncytial virus were the dominant respiratory viruses in children aged ≤ 3 years, whereas Mycoplasma pneumoniae was the dominant respiratory pathogen in children aged > 3 years. HRV has the highest prevalence and is the main pathogen of mixed infection. The prevalence of the influenza A virus has decreased significantly, whereas HRSV and Mp are found to be seasonal. CONCLUSIONS Our findings offer an objective evaluation of transmission dynamics and epidemiological shifts in respiratory pathogens during the coronavirus disease 2019 pandemic in Kunming, serving as a basis for informed decision-making, prevention, and treatment strategies.
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Affiliation(s)
- Guiqian Zhang
- Department of Clinical Laboratory, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
- Yunnan Provincial Key Laboratory of Clinical Virology, The First People's Hospital of Yunnan Province, Kunming, China
| | - Yu Zhang
- Department of Clinical Laboratory, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Limei Ba
- Department of Clinical Laboratory, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Luping Liu
- Department of Clinical Laboratory, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Ting Su
- Department of Clinical Laboratory, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Yi Sun
- Department of Clinical Laboratory, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China
| | - Ziqin Dian
- Department of Clinical Laboratory, The First People's Hospital of Yunnan Province, The Affiliated Hospital of Kunming University of Science and Technology, Kunming, China.
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Zhao MC, Wen C, Sun L, Duan SX, Zang KX, Wang L, Cui XW. Epidemiology and Clinical Characteristics of Seasonal Human Coronaviruses in Children Hospitalized in Hebei Province, China Before and During the COVID-19 Pandemic. Risk Manag Healthc Policy 2023; 16:1801-1807. [PMID: 37705991 PMCID: PMC10497059 DOI: 10.2147/rmhp.s423077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/19/2023] [Indexed: 09/15/2023] Open
Abstract
Background This study aimed to assess the impact of the COVID-19 pandemic on the prevalence and clinical characteristics of seasonal human coronavirus (HCoV) infections among children hospitalized in Hebei, China. Methods We examined nasopharyngeal aspirate (NPA) specimens for seasonal HCoVs from January 2018 to December 2021, at the Children's Hospital of Hebei Province. We used a GeXP-based multiplex reverse transcription PCR assay for the detection of 11 common respiratory viruses (including seasonal HCoVs), chlamydia, and Mycoplasma pneumoniae. The demographic and clinical characteristics of children who tested positive for seasonal HCoVs were recorded and analyzed. Results A total of 377 (1.96%) of the 19,248 specimens from 2018 to 2019 and 263 (1.96%) of the 13,426 specimens from 2020 to 2021 exhibited seasonal HCoVs. Compared to 2018 and 2019, the positive rate of seasonal HCoVs was lower from January to July of 2020 and increased beginning in August 2020, peaking in the autumn and winter. In 2020-2021, nasal blockage and swollen adenoids were detected more frequently in children who tested positive for seasonal HCoVs. During 2018-2019, however, the duration of fever was significantly longer, and cough and dyspnea were more prominent among children who had fallen ill. In addition, seasonal HCoV-positive patients in 2018-2019 were more likely to experience complications, had a higher risk of severe community-acquired pneumonia (CAP), and had a tendency to require a longer hospital stay than patients in 2020-2021. Conclusion According to our findings, there were significant changes in the epidemiology of seasonal HCoVs in Hebei, China during the COVID-19 pandemic, and children infected with seasonal HCoVs usually experienced milder clinical symptoms during the pandemic than before it.
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Affiliation(s)
- Meng-Chuan Zhao
- Department of Laborotory Medicine, Children’s Hospital of Hebei Province, Shijiazhuang, People’s Republic of China
| | - Chan Wen
- Department of Medical, Children’s Hospital of Hebei Province, Shijiazhuang, People’s Republic of China
| | - Ling Sun
- Department of Medical, Children’s Hospital of Hebei Province, Shijiazhuang, People’s Republic of China
| | - Su-xia Duan
- Department of Laborotory Medicine, Children’s Hospital of Hebei Province, Shijiazhuang, People’s Republic of China
| | - Ke-xin Zang
- Hebei Medical University, Shijiazhuang, People’s Republic of China
| | - Le Wang
- Department of Laborotory Medicine, Children’s Hospital of Hebei Province, Shijiazhuang, People’s Republic of China
| | - Xiao-Wei Cui
- Children’s Hospital of Hebei Province, Shijiazhuang, People’s Republic of China
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Cao XQ, Gu XL, Zhang L, Xu J, Han HJ, Yu XJ. Molecular detection of Rickettsia, Anaplasma, and Bartonella in ticks from free-ranging sheep in Gansu Province, China. Ticks Tick Borne Dis 2023; 14:102137. [PMID: 36738629 DOI: 10.1016/j.ttbdis.2023.102137] [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: 08/18/2022] [Revised: 01/18/2023] [Accepted: 01/22/2023] [Indexed: 02/05/2023]
Abstract
Ticks pose a serious threat to public health as carriers and often vectors of zoonotic pathogens. There are few systematic studies on the prevalence and genetic diversity of tick-borne bacterial pathogens in Western China. In this study, 465 ticks were collected from free-ranging sheep in Gansu Province in China. Ticks were divided into 113 pools and tick DNA was extracted from these ticks. PCR assays were performed using specific primers to screen for tick-borne pathogens as well as sequence analysis based on the 16S rRNA (rrs), ompB, gltA, ompA genes for Rickettsia, rrs, groEL genes for Anaplasma, and ssrA and rpoB genes for Bartonella. The PCR results showed that the minimum infection rates with Rickettsia, Anaplasma, and Bartonella were 16.8% (78/465), 18.9% (88/465), and 0.9% (4/465), respectively. Sequence analysis based on the concatenated sequences of rrs-ompB-gltA-ompA indicated that the Rickettsia species identified in the ticks belonged to Rickettsia raoultii, Rickettsia slovaca, and Rickettsia sibirica, respectively; phylogenetic analysis based on the groEL gene showed that all Anaplasma strains identified were Anaplasma ovis; and phylogenetic analysis based on the ssrA and rpoB genes indicated that all Bartonella strains in the ticks belonged to Bartonella melophagi. The results of this study showed that ticks in Gansu Province harbored multiple pathogens that may cause rickettsial diseases and bartonellosis. These diseases were neglected in the area and physicians and public health workers need to pay attention to their diagnoses to prevent human infection.
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Affiliation(s)
- Xiao-Qian Cao
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, Hubei, China
| | - Xiao-Lan Gu
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, Hubei, China
| | - Li Zhang
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, Hubei, China
| | - Jiao Xu
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, Hubei, China
| | - Hui-Ju Han
- School of Public Health, Shandong First Medical University & Shandong Academy of Medical Sciences, Ji'nan, Shandong, China.
| | - Xue-Jie Yu
- State Key Laboratory of Virology, School of Public Health, Wuhan University, Wuhan, Hubei, China.
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Li W, Wang X, Cui W, Yuan L, Hu X. Clinical Evaluation of a Multiplex PCR Assay for Simultaneous Detection of 18 Respiratory Pathogens in Patients with Acute Respiratory Infections. Pathogens 2022; 12:pathogens12010021. [PMID: 36678368 PMCID: PMC9862116 DOI: 10.3390/pathogens12010021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022] Open
Abstract
Reliable diagnostics are necessary to identify influenza infections, and coronavirus disease 2019 (COVID-19) highlights the need to develop highly specific and sensitive viral detection methods to distinguish severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory pathogens to prevent their further spread. In this prospective study, 1070 clinical respiratory samples were collected from patients with acute respiratory infections from January 2019 to February 2021 to evaluate the diagnostic performance of a multiplex probe amplification (MPA) assay, designed to screen 18 pathogens, mainly those causing acute respiratory infections. Ninety-six positive samples and twenty negative samples for the 18 respiratory pathogens defined by the MPA assay and reverse transcription polymerase chain reaction (RT-PCR) were further confirmed by reference next-generation sequencing (NGS). The sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of the MPA assay were 95.00%, 93.75%, 98.96% and 75.00%, respectively. Additionally, the co-infection rate for these positive samples were 25% (24/95). The MPA assay demonstrated a highly concordant diagnostic performance with NGS in the diagnosis of 18 respiratory pathogens and might play an important role in clinical respiratory pathogen diagnosis.
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Affiliation(s)
- Wenmin Li
- Division of Laboratory Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Xiaoxiao Wang
- Division of Laboratory Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Wenhao Cui
- Division of Laboratory Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
| | - Leyong Yuan
- Department of Clinical Laboratory, Southern University of Science and Technology Hospital, Shenzhen 518055, China
- Correspondence: (L.Y.); (X.H.)
| | - Xuejiao Hu
- Division of Laboratory Medicine, Guangdong Provincial People’s Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China
- Correspondence: (L.Y.); (X.H.)
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Zhao MC, Jiang Y, Li GX, Tie YQ, Zheng YH, Li JF, Zhang WC, Duan SX, Zhai Y, Li YL, Zhang DJ, Zeng XP, Wu Y, Guo YH, Feng ZS. Simultaneous detection of 9 respiratory pathogens using a newly developed multiplex real-time PCR panel based on an automatic molecular detection and analysis system. Diagn Microbiol Infect Dis 2022; 104:115801. [DOI: 10.1016/j.diagmicrobio.2022.115801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2022] [Revised: 07/18/2022] [Accepted: 08/20/2022] [Indexed: 11/03/2022]
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Zhao L, Li G, Wang J, Zhao M, Wang L, Feng Z, Ma X. Development and evaluation of a panel of multiplex one-tube nested real time PCR assay for simultaneous detection of 14 respiratory viruses in five reactions. J Med Virol 2020; 92:3073-3080. [PMID: 31981228 PMCID: PMC7228275 DOI: 10.1002/jmv.25686] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 01/20/2020] [Indexed: 11/10/2022]
Abstract
Multiplex real-time quantitative polymerase chain reaction (mRT-qPCR) assay is commonly used to detect respiratory viruses, however, the sensitivity is limited for most reports. A panel of locked nucleic acid based multiplex closed one-tube nested real-time PCR (mOTNRT-PCR) assay consisting of five separate internally controlled RT-qPCR assays was developed for detection of 14 respiratory viruses. The sensitivity and reproducibility of mOTNRT-PCR panel were evaluated using plasmid standards and the specificity was evaluated using clinical samples. The clinical performance of mOTNRT-PCR panel was further evaluated with 468 samples collected from patients with an acute respiratory infection and compared with individual real-time PCR (RT-qPCR) assay. The analytical sensitivities of mOTNRT-PCR panel ranged from 2 to 20 copies/reaction, and no cross-reaction with common respiratory viruses was observed. The coefficients of variation of intra-assay and inter-assay were between 0.35% and 8.29%. Totally 35 clinical samples detected by mOTNRT-PCR assay panel were missed by RT-qPCR and confirmed true positive by sequencing of nested PCR products. The mOTNRT-PCR assay panel provides a more sensitive and high-throughput method for the detection of 14 respiratory viruses.
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Affiliation(s)
- Li Zhao
- Department of Blood TransfusionChildren's Hospital of Hebei ProvinceShijiazhuangHebeiChina
| | - Gui‐xia Li
- Institute of Pediatric ResearchChildren's Hospital of Hebei ProvinceShijiazhuangHebeiChina
| | - Ji Wang
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
| | - Meng‐chuan Zhao
- Institute of Pediatric ResearchChildren's Hospital of Hebei ProvinceShijiazhuangHebeiChina
| | - Le Wang
- Institute of Pediatric ResearchChildren's Hospital of Hebei ProvinceShijiazhuangHebeiChina
| | - Zhi‐shan Feng
- Department of Laboratory MedicineHebei General HospitalShijiazhuangHebeiChina
| | - Xue‐jun Ma
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and PreventionChinese Center for Disease Control and PreventionBeijingChina
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Multiplex Tests for Respiratory Tract Infections: The Direct Utility of the FilmArray Respiratory Panel in Emergency Department. Can Respir J 2020; 2020:6014563. [PMID: 32774562 PMCID: PMC7397412 DOI: 10.1155/2020/6014563] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 06/29/2020] [Indexed: 12/31/2022] Open
Abstract
Background The FilmArray Respiratory Panel with multiplex targets for respiratory pathogens has been widely used and verified in clinical trials in special test settings. However, it is necessary to evaluate the panel's performance at the point of care directly, in nonspecific test settings. Methods Patients with respiratory tract infections were enrolled from among emergency department visitors, and all steps, including the collection of specimens and testing, were performed by our clinicians. Results Among 270 patients, 196 (72.6%) patients were found to have one or more pathogens. For signal pathogen detection, influenza A virus had the highest rate of detection; 45 (16.7%) of the patients had two or more respiratory pathogens codetected, and most of the multiplex pathogens were rhinovirus/enterovirus codetected with Bordetella pertussis (17.8%). The information provided by the FilmArray had an impact on the prescription of antimicrobials, and there were differences in the rates of antibiotic prescriptions and anti-influenza prescriptions among patients. Conclusions Use of the FilmArray by clinical staff was successfully implemented in the emergency department for the first time in China. The FilmArray has the potential for point-of-care testing in nonspecific settings.
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Zhao MC, Guo YH, Qiu FZ, Wang L, Yang S, Feng ZS, Li GX. Molecular and clinical characterization of human adenovirus associated with acute respiratory tract infection in hospitalized children. J Clin Virol 2019; 123:104254. [PMID: 31901884 PMCID: PMC7106522 DOI: 10.1016/j.jcv.2019.104254] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 12/01/2019] [Accepted: 12/21/2019] [Indexed: 01/22/2023]
Abstract
3.71% of children with ARTI exhibited HAdV positive. HAdV-2, HAdV-3 and HAdV-7 were the predominant types identified from ARTI children. 74.85% of HAdV were co-detected with other respiratory pathogens, most commonly HRV. The co-detection rate of HAdV-C was significant higher than those of HAdV-B. HAdV-7 positive children may not present more severe clinical outcome.
Background Human adenovirus (HAdV) is a common pathogen in children that can cause acute respiratory tract infection (ARTI), but the molecular epidemiological and clinical information relating to HAdV among hospitalized children with ARTI are few reported in China. Objectives To evaluate the epidemiological, clinical, and molecular characteristics of HAdV infections among hospitalized children with ARTI in Hebei, Northern China from June 2017 to May 2018. Study design A 12-month longitudinal, retrospective study on HAdV, typed by nested polymerase chain reaction targeting the hexon gene’s hypervariable region (typing was merely performed by sequencing of the hexon neutralization epitope and thus genotypes could not be identified unequivocally), associated with ARTI was performed. The epidemiological and clinical data of different types of HAdV were analyzed using statistical product and service solutions (SPSS) 21.0 software. Results HAdV was detected in 330 (3.71%) of the 8906 specimens, with most (88.48%, 292/330) HAdV-positives cases detected among children < 3 years old. HAdV were detected throughout the year with a higher prevalence in spring. 11 types were identified, with HAdV-2 (33.33%, 110/330) as the predominant type, followed by HAdV-3 (21.21%, 70/330) and HAdV-7 (13.94%, 46/330). Of the 330 HAdV-positive specimens, 247 (74.85%) were co-detected with other respiratory pathogens, most commonly rhinovirus (HRV) (58.7%, 145/247). Additionally, patients with HAdV-7 positive had longer duration of fever than HAdV-2 or -3 positive patients. Conclusions During the study period, HAdV-2, HAdV-3 and HAdV-7 were the predominant types identified from children with ARTI in Hebei Province. Pediatric patients with HAdV-7 positive may not present more severe clinical outcome except a longer duration of fever.
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Affiliation(s)
- Meng-Chuan Zhao
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Affiliated to Hebei Medical University, 133 Jianhua South Street, Shijiazhuang, Hebei Province, 050031, China.
| | - Ying-Hui Guo
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Affiliated to Hebei Medical University, 133 Jianhua South Street, Shijiazhuang, Hebei Province, 050031, China.
| | - Fang-Zhou Qiu
- Department of Laboratory Medicine, Tianjin Children's Hospital, 238 Longyan Road, Tianjin, 30074, China.
| | - Le Wang
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Affiliated to Hebei Medical University, 133 Jianhua South Street, Shijiazhuang, Hebei Province, 050031, China.
| | - Shuo Yang
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Affiliated to Hebei Medical University, 133 Jianhua South Street, Shijiazhuang, Hebei Province, 050031, China.
| | - Zhi-Shan Feng
- Department of Laboratory Medicine, People's Hospital of Hebei Province, 384 Heping West Road, Shijiazhuang, Hebei Province, 050051, China.
| | - Gui-Xia Li
- Institute of Pediatric Research, Children's Hospital of Hebei Province, Affiliated to Hebei Medical University, 133 Jianhua South Street, Shijiazhuang, Hebei Province, 050031, China.
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Zhao MC, Wang L, Qiu FZ, Zhao L, Guo WW, Yang S, Feng ZS, Li GX. Impact and clinical profiles of Mycoplasma pneumoniae co-detection in childhood community-acquired pneumonia. BMC Infect Dis 2019; 19:835. [PMID: 31601192 PMCID: PMC6788033 DOI: 10.1186/s12879-019-4426-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 08/29/2019] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Increasing number of hospitalized children with community acquired pneumonia (CAP) is co-detected with Mycoplasma pneumoniae (Mp). The clinical characteristics and impact of Mp co-detected with other bacterial and/or viral pathogens remain poorly understood. The purpose of this study was to evaluate the demographic and clinical features of CAP children with Mp mono-detection and Mp co-detection. METHODS A total of 4148 hospitalized children with CAP were recruited from January to December 2017 at the Children's Hospital of Hebei Province, affiliated to Hebei Medical University. A variety of respiratory viruses, bacteria and Mp were detected using multiple modalities. The demographic and clinical features of CAP children with Mp mono-detection and Mp co-detection were recorded and analyzed. RESULTS Among the 110 CAP children with Mp positive, 42 (38.18%) of them were co-detected with at least one other pathogen. Co-detection was more common among children aged ≤3 years. No significant differences were found in most clinical symptoms, complications, underlying conditions and disease severity parameters among various etiological groups, with the following exceptions. First, prolonged duration of fever, lack of appetite and runny nose were more prevalent among CAP children with Mp-virus co-detection. Second, Mp-virus (excluding HRV) co-detected patients were more likely to present with prolonged duration of fever. Third, patients co-detected with Mp-bacteria were more likely to have abnormal blood gases. Additionally, CAP children with Mp-HRV co-detection were significantly more likely to report severe runny nose compared to those with Mp mono-detection. CONCLUSION Mp co-detection with viral and/or bacterial pathogens is common in clinical practice. However, there are no apparent differences between Mp mono-detection and Mp co-detections in terms of clinical features and disease severity.
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Affiliation(s)
- Meng-chuan Zhao
- Institute of Pediatric Research, Children’s Hospital of Hebei Province, affiliated to Hebei Medical University, 133 Jianhua South Street, Shijiazhuang, 050031 Hebei Province China
| | - Le Wang
- Institute of Pediatric Research, Children’s Hospital of Hebei Province, affiliated to Hebei Medical University, 133 Jianhua South Street, Shijiazhuang, 050031 Hebei Province China
| | - Fang-zhou Qiu
- Graduate School of Hebei Medical University, 361 Zhongshan East Road, Shijiazhuang, 050017 Hebei Province China
| | - Li Zhao
- Graduate School of Hebei Medical University, 361 Zhongshan East Road, Shijiazhuang, 050017 Hebei Province China
| | - Wei-wei Guo
- Institute of Pediatric Research, Children’s Hospital of Hebei Province, affiliated to Hebei Medical University, 133 Jianhua South Street, Shijiazhuang, 050031 Hebei Province China
| | - Shuo Yang
- Institute of Pediatric Research, Children’s Hospital of Hebei Province, affiliated to Hebei Medical University, 133 Jianhua South Street, Shijiazhuang, 050031 Hebei Province China
| | - Zhi-shan Feng
- Department of Laboratory Medicine, People’s Hospital of Hebei Province, 384 Heping West Road, Shijiazhuang, 050051 Hebei Province China
| | - Gui-xia Li
- Institute of Pediatric Research, Children’s Hospital of Hebei Province, affiliated to Hebei Medical University, 133 Jianhua South Street, Shijiazhuang, 050031 Hebei Province China
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Xi Y, Xu CZ, Xie ZZ, Zhu DL, Dong JM, Xiao G. Development of a reverse transcription recombinase polymerase amplification assay for rapid detection of human respiratory syncytial virus. Mol Cell Probes 2019; 45:8-13. [PMID: 30922817 DOI: 10.1016/j.mcp.2019.03.005] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Revised: 03/19/2019] [Accepted: 03/19/2019] [Indexed: 02/06/2023]
Abstract
Respiratory syncytial virus (RSV) is one of the most important causative agents that causing respiratory tract infection in children and associated with high morbidity and mortality. A diagnostic method would be a robust tool for identification of RSV infection, especially in the resource-limited settings. Recombinase polymerase amplification (RPA) is a novel isothermal amplification technique which has been widely employed to detect human/animal pathogens. In present study, a probe-based reverse transcription RPA (RT-RPA) assay was established for the detection of RSV. The primers and probe were designed based on the sequences of the conserved nucleocapsid (N) gene. The minimal detection limit of the RT-RPA assay for the detection of RSV B was 19 copies of RNA molecules at 95% probability, whereas the detection limit for RSV A was 104 copies molecule. The assay was RSV-specific since it had no non-specific reactions with other common human pathogens. The clinical performance of the RT-RPA assay was validated using 188 nasopharyngeal aspirates (NPAs). The nucleic acid extraction of the samples was performed by use of the magnetic bead-based kit which didn't require the heavy and expensive centrifuge. The coincidence rates between RT-RPA and qRT-PCR for the clinical samples was 96%, indicating the RT-RPA assay had good diagnostic performance on clinical samples. The real-time RT-RPA assay combined with the manual genome extraction method make it potential to detect clinical samples in field, providing a possible solution for RSV diagnosis in remote rural areas in developing countries.
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Affiliation(s)
- Yun Xi
- Department of Clinical Laboratory, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China.
| | - Chang-Zhi Xu
- Department of Clinical Laboratory, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Zhi-Zhi Xie
- Department of Clinical Laboratory, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Dong-Lin Zhu
- Department of Clinical Laboratory, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Jie-Ming Dong
- Department of Clinical Laboratory, The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Gang Xiao
- Department of Clinical Laboratory, The Third Affiliated Hospital of Southern Medical University, Guangzhou, China
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Feng ZS, Zhao L, Wang J, Qiu FZ, Zhao MC, Wang L, Duan SX, Zhang RQ, Chen C, Qi JJ, Fan T, Li GX, Ma XJ. A multiplex one-tube nested real time RT-PCR assay for simultaneous detection of respiratory syncytial virus, human rhinovirus and human metapneumovirus. Virol J 2018; 15:167. [PMID: 30376870 PMCID: PMC6208169 DOI: 10.1186/s12985-018-1061-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 09/19/2018] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Respiratory syncytial virus (RSV), human Rhinovirus (HRV) and human Metapneumo Virus (HMPV) are important viral pathogens causing acute respiratory tract infections in the hospitalized patients. Sensitive and accurate detection of RSV, HRV and HMPV is necessary for clinical diagnosis and treatment. RESULTS A locked nucleic acid (LNA)-based multiplex closed one-tube nested real-time RT-PCR (mOTNRT-PCR) assay was developed for simultaneous detection of RSV, HRV and HMPV. The sensitivity, specificity, reproducibility and clinical performance of mOTNRT-PCR were evaluated and compared with individual real time PCR (RT-qPCR) assay using clinical samples. The analytical sensitivity of mOTNRT-PCR assay was 5 copies/reaction for RSV, HRV and HMPV, respectively, and no cross-reaction with other common respiratory viruses was observed. The coefficients of variation (CV) of intra-assay and inter-assay were between 0.51 to 3.67%. Of 398 nasopharyngeal aspirates samples tested, 109 (27.39%), 150 (37.69%) and 44 (11.06%) were positive for RSV, HRV and HMPV, respectively, whereas 95 (23.87%), 137 (34.42%) and 38 (9.55%) were positive for RSV, HRV and HMPV, respectively, by individual RT-qPCR assay. Thirty three samples that were positive by mOTNRT-PCR but negative by RT-qPCR were confirmed as true positives by sequencing using reported traditional two-step nested PCR assay. CONCLUSION mOTNRT-PCR assay reveals extremely higher sensitivity than that of RT-qPCR assay for detecting RSV, HRV and HMPV in clinical settings.
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Affiliation(s)
- Zhi-Shan Feng
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China
| | - Li Zhao
- Hebei Medical University, Shijiazhuang, 050031, Hebei, China.,Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Street, Chang ping District, Beijing, 102206, China
| | - Ji Wang
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Street, Chang ping District, Beijing, 102206, China
| | - Fang-Zhou Qiu
- Hebei Medical University, Shijiazhuang, 050031, Hebei, China.,Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Street, Chang ping District, Beijing, 102206, China
| | - Meng-Chuan Zhao
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China
| | - Le Wang
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China
| | - Su-Xia Duan
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China
| | - Rui-Qing Zhang
- Hebei Medical University, Shijiazhuang, 050031, Hebei, China.,Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Street, Chang ping District, Beijing, 102206, China
| | - Chen Chen
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Street, Chang ping District, Beijing, 102206, China
| | - Ju-Ju Qi
- Hebei Medical University, Shijiazhuang, 050031, Hebei, China.,Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Street, Chang ping District, Beijing, 102206, China
| | - Tao Fan
- Hebei Medical University, Shijiazhuang, 050031, Hebei, China.,Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Street, Chang ping District, Beijing, 102206, China
| | - Gui-Xia Li
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China.
| | - Xue-Jun Ma
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Street, Chang ping District, Beijing, 102206, China.
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12
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Zhao L, Wang J, Li GX, Qiu FZ, Chen C, Zhao MC, Wang L, Duan SX, Feng ZS, Ma XJ. A highly sensitive 1-tube nested real-time RT-PCR assay using LNA-modified primers for detection of respiratory syncytial virus. Diagn Microbiol Infect Dis 2018; 93:101-106. [PMID: 30266400 PMCID: PMC7126397 DOI: 10.1016/j.diagmicrobio.2018.09.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2018] [Revised: 07/23/2018] [Accepted: 09/03/2018] [Indexed: 12/31/2022]
Abstract
Respiratory syncytial virus (RSV) causes serious respiratory tract infection worldwide. The relatively low RSV load makes it difficult to detect in frail, elderly, and severely immune-compromised patients. In the present study, we developed a locked nucleic acid–-based 1-tube nested real-time RT-PCR (OTNRT-PCR) assay with the advantages of extremely high sensitivity, facile operability, and less likelihood of cross-contamination. The sensitivity, specificity, and clinical performance of the OTNRT-PCR assay were compared in parallel with a conventional TaqMan probe-based real-time PCR (qRT-PCR) assay and a traditional 2-step nested RT-PCR assay. The limit of detection of the OTNRT-PCR assay was 1.02 × 10−1 TCID50/mL, equivalent to the traditional 2-step nested RT-PCR assay and 25-fold lower than the qRT-PCR assay. Of 616 nasopharyngeal aspirates tested, 143 RSV-negative samples by qRT-PCR were confirmed as positive by sequencing the OTNRT-PCR products. We therefore conclude that OTNRT-PCR is more sensitive than qRT-PCR for detection of RSV in clinical samples.
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Affiliation(s)
- Li Zhao
- Hebei Medical University, Shijiazhuang, 050031, Hebei, China; Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Ji Wang
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Gui-Xia Li
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China.
| | - Fang-Zhou Qiu
- Hebei Medical University, Shijiazhuang, 050031, Hebei, China; Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Chen Chen
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
| | - Meng-Chuan Zhao
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China.
| | - Le Wang
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China.
| | - Su-Xia Duan
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China; Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China.
| | - Zhi-Shan Feng
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China.
| | - Xue-Jun Ma
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, 102206, China.
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13
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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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14
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Qiu FZ, Shen XX, Zhao MC, Zhao L, Duan SX, Chen C, Qi JJ, Li GX, Wang L, Feng ZS, Ma XJ. A triplex quantitative real-time PCR assay for differential detection of human adenovirus serotypes 2, 3 and 7. Virol J 2018; 15:81. [PMID: 29716642 PMCID: PMC5930744 DOI: 10.1186/s12985-018-0983-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2018] [Accepted: 04/11/2018] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Human adenovirus (HAdV) serotypes 2, 3 and 7 are more prevalent than other serotypes and have been associated with severe pneumonia in pediatric children. Molecular typing of HAdV is not routinely performed in clinical diagnostic laboratories as it is time-consuming and labor-intensive. METHODS In the present study, we developed a triplex quantitative real-time PCR assay (tq-PCR) in a single closed tube for differential detection and quantitative analysis of HAdV serotypes 2, 3 and 7. The sensitivity, specificity, reproducibility and clinical performance of tq-PCR were evaluated. RESULTS The analytical sensitivity of the tq-PCR was 100 copies/reaction for each of HAdV serotypes 2, 3 and 7, and no cross-reaction with other common respiratory viruses or HAdV serotypes 1,4,5,6,31,55 and 57 was observed. The coefficients of variation (CV) of intra-assay and inter-assay were between 0.6% to 3.6%. Of 138 previously-defined HAdV-positive nasopharyngeal aspirates samples tested, the detection agreement between tq-PCR and nested PCR was 96.38% (133/138). CONCLUSION The proposed tq-PCR assay is a sensitive, specific and reproducible method and has the potential for clinical use in the rapid and differential detection and quantitation of HAdV serotypes 2, 3 and 7.
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Affiliation(s)
- Fang-Zhou Qiu
- Hebei Medical University, Shijiazhuang, 050031, Hebei, China.,Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Street, Chang ping District, Beijing, 102206, China
| | - Xin-Xin Shen
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Street, Chang ping District, Beijing, 102206, China
| | - Meng-Chuan Zhao
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China
| | - Li Zhao
- Hebei Medical University, Shijiazhuang, 050031, Hebei, China.,Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Street, Chang ping District, Beijing, 102206, China
| | - Su-Xia Duan
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Street, Chang ping District, Beijing, 102206, China.,Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China
| | - Chen Chen
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Street, Chang ping District, Beijing, 102206, China
| | - Ju-Ju Qi
- Hebei Medical University, Shijiazhuang, 050031, Hebei, China.,Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Street, Chang ping District, Beijing, 102206, China
| | - Gui-Xia Li
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China
| | - Le Wang
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China
| | - Zhi-Shan Feng
- Children's Hospital of Hebei Province, Shijiazhuang, 050031, Hebei, China.
| | - Xue-Jun Ma
- Key Laboratory for Medical Virology, National Health and Family Planning Commission, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No. 155 Changbai Street, Chang ping District, Beijing, 102206, China.
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