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Klivleyeva N, Lukmanova G, Glebova T, Shamenova M, Ongarbayeva N, Saktaganov N, Baimukhametova A, Baiseiit S, Ismagulova D, Kassymova G, Rachimbayeva A, Murzagaliyeva A, Xetayeva G, Isabayeva R, Sagatova M. Spread of Pathogens Causing Respiratory Viral Diseases Before and During CoVID-19 Pandemic in Kazakhstan. Indian J Microbiol 2023; 63:129-138. [PMID: 37168842 PMCID: PMC9972336 DOI: 10.1007/s12088-023-01064-x] [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: 09/22/2022] [Accepted: 02/11/2023] [Indexed: 03/06/2023] Open
Abstract
Analyze clinical samples collected and determine the etiology of viral pathogens and the dynamics of their spread. Acute respiratory viral infections remain one of the key health problems worldwide. They constitute etiologically independent diseases, with similar clinical infection manifestations and a single mechanism for the transmission of pathogens. 4712 nasopharyngeal swabs were collected from people before and during the COVID-19 pandemic with acute respiratory infections that tested negative for COVID-19 and were examined in this study. The collected samples were screened by a real-time polymerase chain reaction on a Rotor-Gene Q6 plex instrument. Statistical processing of the results, tabular, and graphical data were analyzed in the MS Excel. The largest number of the nasopharyngeal swabs were collected from children under 17 years of age (60.75%). In 702 samples (9.85%) pathogens of respiratory infections of non-influenza etiology were detected, including adenovirus, bocavirus, coronavirus, metapneumovirus, paramyxovirus types I–IV, respiratory syncytial virus, and rhinovirus. At the same time, both before and during the COVID-19 pandemic, different influenza virus variants co-circulation (A/H1N1, A/H3N2, and type B) were discovered, with a predominance of viruses with the antigenic formula A/H1N1. The results of the study indicate the need for continuous monitoring of the viral pathogens spread, which will expand the existing knowledge of the viral etiology of respiratory diseases and highlight the importance of viruses in the respiratory infections occurrence.
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Affiliation(s)
- Nailya Klivleyeva
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | - Galina Lukmanova
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | - Tatyana Glebova
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | - Mira Shamenova
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | - Nuray Ongarbayeva
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | - Nurbol Saktaganov
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | - Assem Baimukhametova
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | - Sagadat Baiseiit
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | - Dariya Ismagulova
- The Laboratory of Viral Biochemistry, The Research and Production Center for Microbiology and Virology LLP, 105 Bogenbai Batyr Street, Almaty, Kazakhstan
| | | | - Almagul Rachimbayeva
- The Almaty Branch of National Center for Expertise, 3 Zhibek Zholy Avenue, Almaty, Kazakhstan
| | - Ardak Murzagaliyeva
- The West Kazakhstan Marat Ospanov Medical University, 68 Maresyev Street, Aktobe, Kazakhstan
| | - Gulzakira Xetayeva
- The Children’s City Clinical Infectious Diseases Hospital, SOPE On REM, ChCCIDH, 299a Baizakova Street, Almaty, Kazakhstan
| | - Rauna Isabayeva
- The Communal State Enterprise Regional Region Clinical Hospital (CSE RCH) of Karaganda Regional Health Department, 41/43 Erubaev Street, Karaganda, Kazakhstan
| | - Madisha Sagatova
- The East Kazakhstan Regional Branch of National Center for Expertise, 17 Independence Avenue, Ust-Kamenogorsk, Kazakhstan
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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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3
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Gazeau P, Vallet S, Ansart S, Beauruelle C, Tran-Minoui A, Payan C, Pilorgé L. Rapid multiplex PCR assays in patients with respiratory viral infections: is semi-quantitative data useful? A pilot study. Braz J Microbiol 2021; 52:1173-1179. [PMID: 34105111 PMCID: PMC8187131 DOI: 10.1007/s42770-021-00536-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 05/26/2021] [Indexed: 11/29/2022] Open
Abstract
Viral respiratory rapid multiplex PCR assays FilmArray® (FA) and ePlex® (eP) provide qualitative results which may not reflect clinical relevance. In a pilot study, we report retrospectively whether the semi-quantitative PCR assay R-GENE® would have facilitated clinical interpretation. Forty-four patients were hospitalized for various respiratory manifestations; all of them have benefited from a respiratory sample during acute symptoms. Among the 44 patients, FA detected 23 positive samples including 31 viruses, 26 of them gave high or moderate R-GENE® scores (cycle threshold < 35), and all but one were consistent with clinical history. Semi-quantitative scores would have allowed for critical interpretation of the results; those are a key additional element for an optimal exploitation of the rapid multiplex PCR assays power.
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Affiliation(s)
- Pierre Gazeau
- Unité Des Maladies Infectieuses Et Tropicales, Centre Hospitalier Régional Et Universitaire de Brest, Brest, France
| | - Sophie Vallet
- Unité de Virologie, Département de Bactériologie-Virologie-Parasitologie-Mycologie-Hygiène, Pôle de Biologie-Pathologie, Centre Hospitalier Régional Et Universitaire de Brest, Brest, France.,Univ Brest, Inserm, EFS, UMR 1078, GGB Génétique, Génomique Fonctionnelle Et Biotechnologies, Brest, France
| | - Séverine Ansart
- Unité Des Maladies Infectieuses Et Tropicales, Centre Hospitalier Régional Et Universitaire de Brest, Brest, France.,Laboratoire de traitement de l'information médicale, LaTIM-UMR 1101, INSERM, Université de Bretagne Occidentale, Brest, France
| | - Clémence Beauruelle
- Univ Brest, Inserm, EFS, UMR 1078, GGB Génétique, Génomique Fonctionnelle Et Biotechnologies, Brest, France.,Unité de Bactériologie, Département de Bactériologie-Virologie-Parasitologie-Mycologie-Hygiène, Pôle de Biologie-Pathologie, Centre Hospitalier Régional Et Universitaire de Brest, Brest, France
| | - Adissa Tran-Minoui
- Unité de Virologie, Département de Bactériologie-Virologie-Parasitologie-Mycologie-Hygiène, Pôle de Biologie-Pathologie, Centre Hospitalier Régional Et Universitaire de Brest, Brest, France
| | - Christopher Payan
- Unité de Virologie, Département de Bactériologie-Virologie-Parasitologie-Mycologie-Hygiène, Pôle de Biologie-Pathologie, Centre Hospitalier Régional Et Universitaire de Brest, Brest, France.,Univ Brest, Inserm, EFS, UMR 1078, GGB Génétique, Génomique Fonctionnelle Et Biotechnologies, Brest, France
| | - Léa Pilorgé
- Unité de Virologie, Département de Bactériologie-Virologie-Parasitologie-Mycologie-Hygiène, Pôle de Biologie-Pathologie, Centre Hospitalier Régional Et Universitaire de Brest, Brest, France.
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4
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Uhteg K, Carroll KC, Mostafa HH. Coronavirus Detection in the Clinical Microbiology Laboratory: Are We Ready for Identifying and Diagnosing a Novel Virus? Clin Lab Med 2020; 40:459-472. [PMID: 33121615 PMCID: PMC7414311 DOI: 10.1016/j.cll.2020.08.004] [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] [Indexed: 11/27/2022]
Abstract
Endemic species of coronavirus (HCoV-OC43, HCoV-229E, HCoV-NL63, and HCoV-HKU1) are frequent causes of upper respiratory tract infections. Three highly pathogenic coronaviruses have been associated with outbreaks and epidemics and have challenged clinical microbiology laboratories to quickly develop assays for diagnosis. Their initial characterization was achieved by molecular methods. With the great advance in metagenomic whole-genome sequencing directly from clinical specimens, diagnosis of novel coronaviruses could be quickly implemented into the workflow of managing cases of pneumonia of unknown cause, which will markedly affect the time of the initial characterization and accelerate the initiation of outbreak control measures.
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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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Xiao Y, Li Z, Wang X, Wang Y, Wang Y, Wang G, Ren L, Li J. Comparison of three TaqMan real-time reverse transcription-PCR assays in detecting SARS-CoV-2. J Virol Methods 2020; 288:114030. [PMID: 33275927 PMCID: PMC7706421 DOI: 10.1016/j.jviromet.2020.114030] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Revised: 09/30/2020] [Accepted: 11/25/2020] [Indexed: 02/03/2023]
Abstract
Quick and accurate detection of SARS-CoV-2 is critical for COVID-19 control. Dozens of real-time reverse transcription PCR (qRT-PCR) assays have been developed to meet the urgent need of COVID-19 control. However, methodological comparisons among the developed qRT-PCR assays are limited. In the present study, we evaluated the sensitivity, specificity, amplification efficiency, and linear detection ranges of three qRT-PCR assays, including the assays developed by our group (IPBCAMS), and the assays recommended by WHO and China CDC (CCDC). The three qRT-PCR assays exhibited similar sensitivities, with the limit of detection (LoD) at about 10 copies per reaction (except the ORF 1b gene assay in CCDC assays with a LoD at about 100 copies per reaction). No cross reaction with other respiratory viruses were observed in all of the three qRT-PCR assays. Wide linear detection ranges from 106 to 101 copies per reaction and acceptable reproducibility were obtained. By using 25 clinical specimens, the N gene assay of IPBCAMS assays and CCDC assays performed better (with detection rates of 92 % and 100 %, respectively) than that of the WHO assays (with a detection rate of 60 %), and the ORF 1b gene assay in IPBCAMS assays performed better (with a detection rate of 64 %) than those of the WHO assays and the CCDC assays (with detection rates of 48 % and 20 %, respectively). In conclusion, the N gene assays of CCDC assays and IPBCAMS assays and the ORF 1b gene assay of IPBCAMS assays were recommended for qRT-PCR screening of SARS-CoV-2.
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Affiliation(s)
- 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, PR China
| | - Zhen Li
- Key Laboratory of Medical Molecular Cell Biology of Shanxi Province, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, PR 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, PR 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, PR China
| | - Ying 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, PR China
| | - Geng 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, PR 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, PR China; Key Laboratory of Respiratory Disease Pathogenomics, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100730, PR China.
| | - Jianguo Li
- Key Laboratory of Medical Molecular Cell Biology of Shanxi Province, Institutes of Biomedical Sciences, Shanxi University, Taiyuan, 030006, PR China; The Provincial Key Laboratories for Prevention and Treatment of Major Infectious Diseases, Shanxi, Taiyuan, 030006, PR China.
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7
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Liu Y, Yu J, Wang X, Dong J. MicroRNA-345-5p regulates depression by targeting suppressor of cytokine signaling 1. Brain Behav 2020; 10:e01653. [PMID: 32730696 PMCID: PMC7507044 DOI: 10.1002/brb3.1653] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 03/28/2020] [Accepted: 03/30/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND/AIMS MicroRNA(miR)-345-5p plays a key role in various cellular functions. However, the function of miR-345-5p in resistant depression (TRD) is unclear. The aim of this study was to evaluate the role and mechanism of miR-345-5p in the treatment of resistance depression (TRD). METHODS RT-qPCR was used to detect the expression of miR-345-5p in BV-2 microglia. CCK-8 method and flow cytometry were used for cell viability and apoptosis of microglia. Target gene prediction and screening, and luciferase reporter assays were used to verify the downstream target gene of miR-345-5p. Western blot was used to analyze the protein expression of related proteins. RESULTS miR-345-5p increased the cell viability of BV-2 microglia and the expression level of pro-inflammatory cytokines. In addition, the conditioned medium of microglia treated with miR-345-5p reduced the cell viability of HT22 hippocampal cells and caused S-phase arrest. The miR-345-5p-treated microglia induced apoptosis by regulating the expression levels of Bax, Bcl-2, pro-caspase-3, and cleaved caspase-3. Furthermore, SOCS1 was a direct target of miR-345-5p, and overexpression of SOCS1 was able to reverse the proapoptotic effect of miR-345-5p on activation of microglia on hippocampal neurons. CONCLUSION miR-345-5p induced inflammatory damage in hippocampal neurons by activating microglia. MiR-345-5p may be an effective target for TRD therapy.
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Affiliation(s)
- Yulan Liu
- Psychiatric Department, Qingdao Mental Health Center, Qingdao university, Qingdao City, China
| | - Jun Yu
- Psychiatric Department, Qingdao Mental Health Center, Qingdao university, Qingdao City, China
| | - Xinrui Wang
- Psychiatric Department, Qingdao Mental Health Center, Qingdao university, Qingdao City, China
| | - Jicheng Dong
- Psychiatric Department, Qingdao Mental Health Center, Qingdao university, Qingdao City, China
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Zhang D, Lou X, Yan H, Pan J, Mao H, Tang H, Shu Y, Zhao Y, Liu L, Li J, Chen D, Zhang Y, Ma X. Respiratory virus associated with surgery in children patients. Respir Res 2019; 20:126. [PMID: 31208426 PMCID: PMC6580463 DOI: 10.1186/s12931-019-1086-y] [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: 03/11/2019] [Accepted: 05/29/2019] [Indexed: 11/25/2022] Open
Abstract
Background Viral respiratory infection (VRI) is a common contraindication to elective surgery. Asymptomatic shedding among pediatric surgery patients (PSPs) could potentially lead to progression of symptomatic diseases and cause outbreaks of respiratory diseases. The aim of this study is to investigate the incidence of infection among mild symptomatic PSP group and asymptomatic PSP group after surgical procedure. Methods We collected the induced sputum from enrolled 1629 children (under 18 years of age) with no respiratory symptom prior to pediatric surgery between March 2017 and February 2019. We tested 16 different respiratory virus infections in post-surgery mild symptomatic PSP group and asymptomatic PSP group using a quantitative real-time reverse transcriptase polymerase chain reaction (qRT-PCR) assay panel. We analyzed symptom data and quantitative viral load to investigate the association between viruses, symptoms and viral quantity in qRT-PCR-positive PSPs. Results Out of 1629 children enrolled, a total of 204 respiratory viruses were present in 171 (10.50%) PSPs including 47 patients with mild symptoms and 124 with no symptoms after surgery. Commonly detected viruses were human rhino/enterovirus (HRV/EV, 42.19%), parainfluenza virus 3 (PIV3, 24.48%), coronavirus (CoV NL63, OC43, HKU1, 11.46%), and respiratory syncytial virus (RSV, 9.9%). PIV3 infection with a higher viral load was frequently found in PSPs presenting with mild symptoms, progressing to pneumonia with radiographic evidence after surgery. HRV/EV were the most commonly detected pathogens in both asymptomatic and mild symptomatic PSPs. CoV (OC43, HKU1) infections with a higher viral load were mostly observed in asymptomatic PSPs progressing to alveolar or interstitial infiltration. Conclusions Our study suggested that PIV3 is a new risk factor for VRI in PSPs. Employing a more comprehensive, sensitive and quantitative method should be considered for preoperative testing of respiratory viruses in order to guide optimal surgical timing.
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Affiliation(s)
- Dan Zhang
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No.155 Changbai Road, Changping district, Beijing, 102206, China.,Institute of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, No. 3399 Binsheng Road, 310051, Binjiang district, Hangzhou, China
| | - Xiuyu Lou
- Institute of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, No. 3399 Binsheng Road, 310051, Binjiang district, Hangzhou, China
| | - Hao Yan
- Institute of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, No. 3399 Binsheng Road, 310051, Binjiang district, Hangzhou, China
| | - Junhang Pan
- Institute of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, No. 3399 Binsheng Road, 310051, Binjiang district, Hangzhou, China
| | - Haiyan Mao
- Institute of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, No. 3399 Binsheng Road, 310051, Binjiang district, Hangzhou, China
| | - Hongfeng Tang
- Department of Pathology, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yan Shu
- Department of Pathology, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Yun Zhao
- Department of Pathology, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Lei Liu
- Department of Pathology, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Junping Li
- Department of Pathology, The Children's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dong Chen
- Department of Laboratory Medicine, The Sixth People Hospital of Wenzhou, Wenzhou, China
| | - Yanjun Zhang
- Institute of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, No. 3399 Binsheng Road, 310051, Binjiang district, Hangzhou, China.
| | - Xuejun Ma
- NHC Key Laboratory of Medical Virology and Viral Diseases, National Institute for Viral Disease Control and Prevention, Chinese Center for Disease Control and Prevention, No.155 Changbai Road, Changping district, Beijing, 102206, China.
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Kuypers J. Impact of Rapid Molecular Detection of Respiratory Viruses on Clinical Outcomes and Patient Management. J Clin Microbiol 2019; 57:e01890-18. [PMID: 30651392 PMCID: PMC6440761 DOI: 10.1128/jcm.01890-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
To determine if rapid molecular testing for respiratory viruses in patients with respiratory illnesses can provide advantages to patients and hospitals, rigorous investigations on the impacts of using these assays are required. Well-conducted studies are needed to inform decisions about implementation of new rapid assays to replace standard molecular testing or to initiate testing in laboratories that are currently not doing molecular tests for respiratory viruses due to the complex nature of standard panels. In this issue of the Journal of Clinical Microbiology, N. Wabe et al. (J Clin Microbiol 57:e01727-18, 2019, https://doi.org/10.1128/JCM.01727-18) report the results of their evaluation of the impact of using a rapid molecular test for influenza A/influenza B and RSV on outcomes for adults hospitalized with respiratory illness. The median time from admission to test result of the rapid test was 7.5 h compared to 40.3 h for the standard PCR assay. Compared to the use of the standard molecular assay, use of a rapid test significantly shortened time in the hospital and reduced the number of other microbiology tests performed. The authors concluded that rapid PCR testing of adults hospitalized with respiratory illnesses could provide benefits to both the patients and the hospital. Patients were able to leave the hospital earlier and a greater proportion of them had received their test results before discharge, which would allow appropriate treatment to be provided more quickly.
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Affiliation(s)
- Jane Kuypers
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, USA
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10
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Zhang D, Lou X, Yan H, Pan J, Mao H, Tang H, Shu Y, Zhao Y, Liu L, Li J, Chen J, Zhang Y, Ma X. Metagenomic analysis of viral nucleic acid extraction methods in respiratory clinical samples. BMC Genomics 2018; 19:773. [PMID: 30359242 PMCID: PMC6202819 DOI: 10.1186/s12864-018-5152-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Accepted: 10/09/2018] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND Numerous protocols for viral enrichment and genome amplification have been created. However, the direct identification of viral genomes from clinical specimens using next-generation sequencing (NGS) still has its challenges. As a selected viral nucleic acid extraction method may determine the sensitivity and reliability of NGS, it is still valuable to evaluate the extraction efficiency of different extraction kits using clinical specimens directly. RESULTS In this study, we performed qRT-PCR and viral metagenomic analysis of the extraction efficiency of four commonly used Qiagen extraction kits: QIAamp Viral RNA Mini Kit (VRMK), QIAamp MinElute Virus Spin Kit (MVSK), RNeasy Mini Kit (RMK), and RNeasy Plus Micro Kit (RPMK), using a mixed respiratory clinical sample without any pre-treatment. This sample contained an adenovirus (ADV), influenza virus A (Flu A), human parainfluenza virus 3 (PIV3), human coronavirus OC43 (OC43), and human metapneumovirus (HMPV). The quantity and quality of the viral extracts were significantly different among these kits. The highest threshold cycle(Ct)values for ADV and OC43 were obtained by using the RPMK. The MVSK had the lowest Ct values for ADV and PIV3. The RMK revealed the lowest detectability for HMPV and PIV3. The most effective rate of NGS data at 67.47% was observed with the RPMK. The other three kits ranged between 12.1-26.79% effectiveness rates for the NGS data. Most importantly, compared to the other three kits the highest proportion of non-host reads was obtained by the RPMK. The MVSK performed best with the lowest Ct value of 20.5 in the extraction of ADV, while the RMK revealed the best extraction efficiency by NGS analysis. CONCLUSIONS The evaluation of viral nucleic acid extraction efficiency is different between NGS and qRT-PCR analysis. The RPMK was most applicable for the metagenomic analysis of viral RNA and enabled more sensitive identification of the RNA virus genome in respiratory clinical samples. In addition, viral RNA extraction kits were also applicable for metagenomic analysis of the DNA virus. Our results highlighted the importance of nucleic acid extraction kit selection, which has a major impact on the yield and number of viral reads by NGS analysis. Therefore, the choice of extraction method for a given viral pathogen needs to be carefully considered.
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Affiliation(s)
- Dan Zhang
- 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, Changping District, Beijing, 102206, China.,Institute of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China
| | - Xiuyu Lou
- Institute of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China
| | - Hao Yan
- Institute of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China
| | - Junhang Pan
- Institute of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China
| | - Haiyan Mao
- Institute of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China
| | - Hongfeng Tang
- Department of Pathology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310013, China
| | - Yan Shu
- Department of Pathology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310013, China
| | - Yun Zhao
- Department of Pathology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310013, China
| | - Lei Liu
- Department of Pathology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310013, China
| | - Junping Li
- Department of Pathology, Children's Hospital, Zhejiang University School of Medicine, Hangzhou, 310013, China
| | - Jiang Chen
- College Of Medical Technology, Zhejiang Chinese Medical University, Hangzhou, 310013, China
| | - Yanjun Zhang
- Institute of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, 310051, China.
| | - Xuejun 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, Changping District, Beijing, 102206, China.
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