新冠病毒实验室常见检测方法Routine laboratory testing methods for SARS-CoV-2
余静怡,余方友
摘要(Abstract):
新型冠状病毒肺炎(COVID-19)是由新型严重急性呼吸系统综合症冠状病毒2(SARS-CoV-2)引起的呼吸系统疾病,已对全球健康构成重大威胁。鉴于目前无症状感染的出现,且近期出现的Delta新冠变异株传播力强、感染潜伏期短、致病性强、发病进程快等特点,实验室高效诊断技术与方法的重要性日益突出,快速、简便、大规模的检测对控制新冠病毒的传播、患者的管理等方面起到关键作用。本文就SARS-CoV-2的相关实验室检测技术与方法进行综述,为临床医生、公共卫生与感染预防和控制提供诊断支持。
关键词(KeyWords): 新型冠状病毒;等温扩增技术;CRISPR-Cas系统;下一代测序;实时荧光定量聚合酶链式反应
基金项目(Foundation):
作者(Author): 余静怡,余方友
参考文献(References):
- [1] CDC.Interim Clinical Guidance for Management of Patients with Confirmed Coronavirus Disease (COVID-19)[EB/OL].(2021-02-16)[2021-10-05].https://www.cdc.gov/coronavirus/2019-ncov/hcp/clinical-guidance-management-patients.html.
- [2] Bhimraj A,Morgan RL,Shumaker AH,et al.Infectious diseases society of America guidelines on the treatment and management of patients with COVID-19[J].Clin Infect Dis,2020:ciaa478.
- [3] Safiabadi Tali SH,LeBlanc JJ,Sadiq Z,et al.Tools and techniques for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2)/COVID-19 detection[J].Clin Microbiol Rev,2021,34(3):e00228-e00220.
- [4] Stegeman I,Ochodo EA,Guleid F,et al.Routine laboratory testing to determine if a patient has COVID-19[J].Cochrane Database Syst Rev,2020,11(11):CD013787.
- [5] Charlton CL,Babady E,Ginocchio CC,et al.Practical guidance for clinical microbiology laboratories:viruses causing acute respiratory tract infections[J].Clin Microbiol Rev,2018,32(1):e00042-e00018.
- [6] Sutjipto S,Lee PH,Tay JY,et al.The effect of sample site,illness duration,and the presence of pneumonia on the detection of SARS-CoV-2 by real-time reverse transcription PCR[J].Open Forum Infect Dis,2020,7(9):ofaa335.
- [7] Huang YB,Chen SB,Yang ZF,et al.SARS-CoV-2 viral load in clinical samples from critically ill patients[J].Am J Respir Crit Care Med,2020,201(11):1435-1438.
- [8] Liu R,Han H,Liu F,et al.Positive rate of RT-PCR detection of SARS-CoV-2 infection in 4880 cases from one hospital in Wuhan,China,from Jan to Feb 2020[J].Clin Chim Acta,2020,505:172-175.
- [9] Wang WL,Xu YL,Gao RQ,et al.Detection of SARS-CoV-2 in different types of clinical specimens[J].JAMA,2020,323(18):1843-1844.
- [10] Garnett L,Bello A,Tran KN,et al.Comparison analysis of different swabs and transport mediums suitable for SARS-CoV-2 testing following shortages[J].J Virol Methods,2020,285:113947.
- [11] Palmas G,Moriondo M,Trapani S,et al.Nasal swab as preferred clinical specimen for COVID-19 testing in children[J].Pediatr Infect Dis J,2020,39(9):e267-e270.
- [12] Jamal AJ,Mozafarihashjin M,Coomes E,et al.Sensitivity of nasopharyngeal swabs and saliva for the detection of severe acute respiratory syndrome coronavirus 2[J].Clin Infect Dis,2021,72(6):1064-1066.
- [13] Foladori P,Cutrupi F,Segata N,et al.SARS-CoV-2 from faeces to wastewater treatment:what do we know?A review[J].Sci Total Environ,2020,743:140444.
- [14] van Doorn AS,Meijer B,Frampton CMA,et al.Systematic review with meta-analysis:SARS-CoV-2 stool testing and the potential for faecal-oral transmission[J].Aliment Pharmacol Ther,2020,52(8):1276-1288.
- [15] James AS,Alawneh JI.COVID-19 infection diagnosis:potential impact of isothermal amplification technology to reduce community transmission of SARS-CoV-2[J].Diagnostics (Basel),2020,10(6):399.
- [16] Chu DKW,Pan Y,Cheng SMS,et al.Molecular diagnosis of a novel coronavirus (2019-nCoV) causing an outbreak of pneumonia[J].Clin Chem,2020,66(4):549-555.
- [17] VanGuilder HD,Vrana KE,Freeman WM.Twenty-five years of quantitative PCR for gene expression analysis[J].BioTechniques,2008,44(5):619-626.
- [18] LeBlanc JJ,Gubbay JB,Li Y,et al.Real-time PCR-based SARS-CoV-2 detection in Canadian laboratories[J].J Clin Virol,2020,128:104433.
- [19] Udugama B,Kadhiresan P,Kozlowski HN,et al.Diagnosing COVID-19:the disease and tools for detection[J].ACS Nano,2020,14(4):3822-3835.
- [20] Ben-Assa N,Naddaf R,Gefen T,et al.Direct on-the-spot detection of SARS-CoV-2 in patients[J].Exp Biol Med (Maywood),2020,245(14):1187-1193.
- [21] Hogan CA,Sahoo MK,Pinsky BA.Sample pooling as a strategy to detect community transmission of SARS-CoV-2[J].JAMA,2020,323(19):1967-1969.
- [22] Carter LJ,Garner LV,Smoot JW,et al.Assay techniques and test development for COVID-19 diagnosis[J].ACS Cent Sci,2020,6(5):591-605.
- [23] Qian C,Wang R,Wu H,et al.Nicking enzyme-assisted amplification (NEAA) technology and its applications:a review[J].Anal Chim Acta,2019,1050:1-15.
- [24] Parida M,Sannarangaiah S,Dash PK,et al.Loop mediated isothermal amplification (LAMP):a new generation of innovative gene amplification technique;perspectives in clinical diagnosis of infectious diseases[J].Rev Med Virol,2008,18(6):407-421.
- [25] Mautner L,Baillie CK,Herold HM,et al.Rapid point-of-care detection of SARS-CoV-2 using reverse transcription loop-mediated isothermal amplification (RT-LAMP)[J].Virol J,2020,17(1):160.
- [26] Soroka M,Wasowicz B,Rymaszewska A.Loop-mediated isothermal amplification (LAMP):the better sibling of PCR?[J].Cells,2021,10(8):1931.
- [27] Yoo HM,Kim IH,Kim S.Nucleic acid testing of SARS-CoV-2[J].Int J Mol Sci,2021,22(11):6150.
- [28] Broughton JP,Deng XD,Yu GX,et al.CRISPR-cas12-based detection of SARS-CoV-2[J].Nat Biotechnol,2020,38(7):870-874.
- [29] Ding X,Yin K,Li ZY,et al.Ultrasensitive and visual detection of SARS-CoV-2 using all-in-one dual CRISPR-Cas12a assay[J].Nat Commun,2020,11(1):4711.
- [30] LaManna CM,Pyhtila B,Barrangou R.Sharing the CRISPR toolbox with an expanding community[J].CRISPR J,2020,3(4):248-252.
- [31] Chen JS,Ma EB,Harrington LB,et al.CRISPR-Cas12a target binding unleashes indiscriminate single-stranded DNase activity[J].Science,2018,360(6387):436-439.
- [32] Russo A,Minichini C,Starace M,et al.Current status of laboratory diagnosis for COVID-19:a narrative review[J].Infect Drug Resist,2020,13:2657-2665.
- [33] Gootenberg JS,Abudayyeh OO,Lee JW,et al.Nucleic acid detection with CRISPR-Cas13a/C2c2[J].Science,2017,356(6336):438-442.
- [34] Kellner MJ,Koob JG,Gootenberg JS,et al.SHERLOCK:nucleic acid detection with CRISPR nucleases[J].Nat Protoc,2019,14(10):2986-3012.
- [35] Azhar M,Phutela R,Kumar M,et al.Rapid and accurate nucleobase detection using FnCas9 and its application in COVID-19 diagnosis[J].Biosens Bioelectron,2021,183:113207.
- [36] Rauch JN,Valois E,Solley SC,et al.A scalable,easy-to-deploy protocol for Cas13-based detection of SARS-CoV-2 genetic material[J].J Clin Microbiol,2021,59(4):e02402-e02420.
- [37] Ding X,Yin K,Li Z,et al.All-in-one dual CRISPR-Cas12a (AIOD-CRISPR) assay:a case for rapid,ultrasensitive and visual detection of novel coronavirus SARS-CoV-2 and HIV virus[J].bioRxiv,2020:2020.03.19.998724.21.
- [38] Metzker ML.Sequencing technologies-the next generation[J].Nat Rev Genet,2010,11(1):31-46.
- [39] John G,Sahajpal NS,Mondal AK,et al.Next-generation sequencing (NGS) in COVID-19:a tool for SARS-CoV-2 diagnosis,monitoring new strains and phylodynamic modeling in molecular epidemiology[J].Curr Issues Mol Biol,2021,43(2):845-867.
- [40] Bloom JS,Sathe L,Munugala C,et al.Swab-Seq:a high-throughput platform for massively scaled up SARS-CoV-2 testing[J].medRxiv,2021:2020.08.04.20167874.
- [41] Bhoyar RC,Jain A,Sehgal P,et al.High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing[J].PLoS One,2021,16(2):e0247115.
- [42] Nasir JA,Kozak RA,Aftanas P,et al.A comparison of whole genome sequencing of SARS-CoV-2 using amplicon-based sequencing,random hexamers,and bait capture[J].Viruses,2020,12(8):895.
- [43] Xiao MF,Liu XQ,Ji JK,et al.Multiple approaches for massively parallel sequencing of SARS-CoV-2 genomes directly from clinical samples[J].Genome Med,2020,12(1):57.
- [44] Lou B,Li TD,Zheng SF,et al.Serology characteristics of SARS-CoV-2 infection after exposure and post-symptom onset[J].Eur Respir J,2020,56(2):2000763.
- [45] Candel FJ,Barreiro P,Román JS,et al.Recommendations for use of antigenic tests in the diagnosis of acute SARS-CoV-2 infection in the second pandemic wave:attitude in different clinical settings[J].Rev Esp Quimioter,2020,33(6):466-484.
- [46] Cui FY,Zhou HS.Diagnostic methods and potential portable biosensors for coronavirus disease 2019[J].Biosens Bioelectron,2020,165:112349.
- [47] Seo G,Lee G,Kim MJ,et al.Rapid detection of COVID-19 causative virus (SARS-CoV-2) in human nasopharyngeal swab specimens using field-effect transistor-based biosensor[J].ACS Nano,2020,14(4):5135-5142.
- [48] Mak GC,Cheng PK,Lau SS,et al.Evaluation of rapid antigen test for detection of SARS-CoV-2 virus[J].J Clin Virol,2020,129:104500.
- [49] Krüttgen A,Cornelissen CG,Dreher M,et al.Comparison of the SARS-CoV-2 rapid antigen test to the real star Sars-CoV-2 RT PCR kit[J].J Virol Methods,2021,288:114024.
- [50] Li DD,Li JM.Immunologic testing for SARS-CoV-2 infection from the antigen perspective[J].J Clin Microbiol,2021,59(5):e02160-e02120.
- [51] Suthar MS,Zimmerman MG,Kauffman RC,et al.Rapid generation of neutralizing antibody responses in COVID-19 patients[J].Cell Rep Med,2020,1(3):100040.
- [52] Espejo AP,Akgun Y,Al Mana AF,et al.Review of current advances in serologic testing for COVID-19[J].Am J Clin Pathol,2020,154(3):293-304.
- [53] Liu WB,Liu L,Kou GM,et al.Evaluation of nucleocapsid and spike protein-based enzyme-linked immunosorbent assays for detecting antibodies against SARS-CoV-2[J].J Clin Microbiol,2020,58(6):e00461-e00420.
- [54] Okba NMA,Müller MA,Li WT,et al.Severe acute respiratory syndrome coronavirus 2-specific antibody responses in coronavirus disease patients[J].Emerg Infect Dis,2020,26(7):1478-1488.
- [55] To KKW,Tsang OTY,Leung WS,et al.Temporal profiles of viral load in posterior oropharyngeal saliva samples and serum antibody responses during infection by SARS-CoV-2:an observational cohort study[J].Lancet Infect Dis,2020,20(5):565-574.
- [56] Cinquanta L,Fontana DE,Bizzaro N.Chemiluminescent immunoassay technology:what does it change in autoantibody detection?[J].Auto Immun Highlights,2017,8(1):9.
- [57] Li ZT,Yi YX,Luo XM,et al.Development and clinical application of a rapid IgM-IgG combined antibody test for SARS-CoV-2 infection diagnosis[J].J Med Virol,2020,92(9):1518-1524.
- [58] Pisanic N,Randad PR,Kruczynski K,et al.COVID-19 serology at population scale:SARS-CoV-2-specific antibody responses in saliva[J].J Clin Microbiol,2020,59(1):e02204-e02220.
扩展功能
本文信息
服务与反馈
本文关键词相关文章
本文作者相关文章
中国知网
分享