|
|
|
| Nucleic Acid Detection of the SARS-CoV-2 |
| ZHANG Yong-zhuo, WANG Jing, FU Bo-qiang, HUANG Xiang, DONG Lian-hua, NIU Chun-yan, YANG Jia-yi |
| National Institute of Metrology, Beijing 100029, China |
|
|
|
|
Abstract The ongoing global Corona Virus Disease (COVID-19) outbreak is a public health emergency of international concern. It is very important to speed up the diagnosis and confirmation detection of suspected cases and quickly distinguish the disease of COVID-19 from other diseases. The novel coronavirus pneumonia diagnosis and treatment plan issued by National Health Committee of the People’s Republic of China has stipulated the nucleic acid detection of the 2019-Novel Coronavirus(2019-nCoV/SARS-CoV-2). The detection methods of nucleic acid PCR and sequencing, including real time quantitative Polymerase Chain Reaction(PCR), digital PCR detection and gene sequencing method were described to virus nucleic acid detection. A long time monitoring and biometrology standard system related to biosafety were prospected.
|
|
Received: 29 February 2020
|
|
|
|
|
|
1 LuoG X, GaoS J. Global Health Concern Stirred by Emerging Viral Infections[J]. Journal of Medical Virology, 2020,92:399-340.
2 LuR J, ZhaoX, LiJ, et al. Genomic Characterization and Epidemiology of 2019 Novel Coronavirus: Implications for Virus Origins and Receptor Binding[J]. The Lancet,2020 ,395（10224）:565-574.
3 ChenY, LiuQ Y, GuoD Y. Emerging Coronaviruses: Genome Structure, Replication, and Pathogenesis[J]. J Med Virol,2020, 92(4):418-423.DOI:10.1002/jmv.25681.
4 WuF, ZhaoS, YuB, et al. A new coronavirus associated with human respiratory disease in China[J]. Nature,2020. DOI:10.1038/s41586-020-2008-3.
5 ChanJ F, YuanS F, KokK H, et al. A familial cluster of pneumonia associated with the 2019 novel coronavirus indicating person-to-person transmission: a study of a family cluster[J]. The Lancet,2020 , 395(10223):514-523.
6 LiX G, ZaiJ J, WangX M, et al. Potential of large ‘first generation’ human-to-human transmission of 2019-nCoV[J]. Journal of Medical Virology,2020,92:448-454.
7 ChenL J, LiuW Y, ZhangQ, et al. RNA Based mNGS Approach Identifies a Novel Human Coronavirus from Two Individual Pneumonia Cases in 2019 Wuhan Outbreak[J]. Emerg Microbes Infect, 2020,9(1):313-319. doi: 10.1080/22221751.2020.1725399.
8 PhanT. Novel coronavirus: From discovery to clinical diagnostics[J]. Infect Genet Evol, 2020, 79: 104211.
9 XieX Z, ZhongZ, ZhaoW, et al. Chest CT for Typical 2019-nCoV Pneumonia: Relationship to Negative RT-PCR Testing[J]. Radiology, Published Online:Feb 12 2020. https://doi.org/10.1148/radiol.2020200343.
10 LagiF, PolliniS, ZammarchiL. Clinical role of viral identification by a polymerase chain reaction-based diagnostic panel in adults hospitalized with community-acquired pneumonia[J]. Internal and Emergency Medicine, 2020. https://doi.org/10.1007/s11739-020-02282-7.
11 CormanV M, LandtO, KaiserM, et al. Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR[J]. Euro Surveill,2020, 25(3): 2000045.
12 中华人民共和国国家卫生健康委员会.新型冠状病毒肺炎诊疗方案（试行第七版）[EB/OL].http://www.nhc.gov.cn/yzygj.
13 CDC.Real-Time RT-PCR Panel for Detection 2019-Novel Coronavirus[EB/OL].https://www.cdc.gov/ coronavirus/2019-ncov/lab/rt-pcr-detection-instructions.html.
14 中国疾病预防控制中心病毒预防控制所. 新型冠状病毒核酸检测引物和探针序列.[EB/OL].http://ivdc.chinacdc.cn/kyjz/202001/t20200121_211337.html.
15 BurnsM, BurrellA, FoyC. The applicability of digital PCR for the assessment of detection limits in GMO analysis[J]. Eur Food Res Technol, 2010, 231(3): 353-362.
16 CorbisierP, BhatS, PartisL, et al.Absolute quantification of genetically modified MON810 maize (Zea mays L.) by digital polymerase chain reaction[J]. Anal Bioanal Chem, 2009, 396(6): 2143-2150.
17 HeyriesK A, TropiniC, VanInsbergheM, et al. Megapixel digital PCR[J]. Nat Methods, 2011, 8(8): 649-651.
18 TerryC F, ShanahanD J, BallamL D, et al. Real-time detection of genetically modified soya using Lightcycler and ABI 7700 platforms with TaqMan, Scorpion, and SYBR Green I chemistries[J]. Journal of AOAC International, 2002, 85(4): 938-944.
19 傅博强,王晶,唐治玉,等．核酸定量测量技术研究进展[J].中国计量,2013,(3):82-85. FuB Q, WangJ, TangZ Y, et al. The Progress of Quantitative Measurement Techniques of Nucleic Acid[J].China Metrology, 2013,(3):82-85.
20 SandersR, HuggettJ F, BushellC A, et al. Evaluation of Digital PCR for Absolute DNA Quantification[J]. Anal Chem, 2011, 83 (17): 6474-6484.
21 董莲华, 隋志伟, 王晶, 等. 数字PCR方法准确测量质粒DNA拷贝浓度[J].计量学报,2017,38(2):247-251. DongL H, SuiZ W, WangJ, et al. Accurate Plasmid DNA Copy Concentration Quantification by Digital PCR[J].Acta Metrologica Sinica, 2017, 38(2): 247-251.
22 董莲华,王晶,傅博强,等. 数字PCR和下一代测序方法用于KRAS基因突变检测中的可比性研究[J].计量学报,2018,39(3):436-441. DongL H, WangJ, FuB Q, et al. Comparability of Digital PCR and Next Generation Sequencing on Detection of KRAS Mutations Frequency[J].Acta Metrologica Sinica, 2018, 39(3): 436-441.
23 StrainM C, LadaS M, LuongT, et al. Highly Precise Measurement of HIV DNA by Droplet Digital PCR[J]. Plos One, 2013, 8(4): e55943.
24 AgapovaS, StephensonK, ManaryM, et al. Detection of Low-concentration Host mRNA Transcripts in Malawian Children at Risk for Environmental Enteropathy[J]. Journal of Pediatric Gastroenterology and Nutrition, 2013, 56(1):66-71.
25 SedlakR H, CookL, HuangM L, et al.Identification of Chromosomally Integrated Human Herpesvirus 6 by Droplet Digital PCR[J]. Clinical Chemistry, 2004,60(5):765-772.
26 RothrockM J, HiettK L, KiepperB H, et al. Quantification of Zoonotic Bacterial Pathogens within Commercial Poultry Processing Water Samples Using Droplet Digital PCR[J]. Advances in Microbiology,2013, 3(5):403-411.
27 中华医学会检验医学分会. 新型冠状病毒肺炎病毒核酸检测专家共识[J].中华医学杂志, 2020,100(00): E003. DOI: 10.3760/cma.j.issn.0376-2491.2020.0003. Branch of laboratory medicine of Chinese Medical Association. Expert consensus on novel coronavirus pneumonia virus nucleic acid detection[J].National Medical Journal of China,2020,100(00): E003. DOI: 10.3760/cma.j.issn.0376-2491.2020.0003
28 DongL H, ZhouJ B, NiuC Y, et al. Highly accurate and sensitive diagnostic detection of SARS-CoV-2 by digital PCR[J]. medRxiv,doi: https://doi.org/10.1101/2020.03.14.20036129.
29 SuoT, LiuX J, GuoM, et al. ddPCR: A more sensitive and accurate tool for SARS-CoV-2 detection in low viral load specimens[J]. medRxiv,doi: https://doi.org/10.1101/2020.02.29.20029439.
30 中华人民共和国国家卫生健康委员会.新型冠状病毒感染的肺炎实验室检测技术指南（第五版）[S].
31 GuW, MillerS, ChiuC Y. Clinical Metagenomic Next-Generation Sequencing for Pathogen Detection[J]. Annual review of pathology,2019 ,14:319-338.
32 GoodwinS, McphersonJ D, MccombieW R . Coming of Age: Ten Years of Next-Generation Sequencing Technologies[J]. Nature Reviews Genetics,2016, 17(6):333-351.
33 SalibaA E, WestermannA J, GorskiS A , et al. Single-cell RNA-seq: Advances and Future Challenges[J]. Nucleic Acids Research,2014, 42(14):8845-8860.
34 SchlabergR, ChiuC Y, MillerS, et al. Validation of Metagenomic Next-Generation Sequencing Tests for Universal Pathogen Detection[J]. Arch Pathol Lab Med,2017, 141(6):776-786.
35 ZhouP, YangX L, WangX G, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin[J]. Nature,2020: https:// doi.org/10.1038/s41586-020-2012-7(2020).
36 CohenJ, KupferschmidtK. Labs scramble to produce new coronavirus diagnostics[J]. Science,2020,367(6479):727.
37 ViehwegerA, KrautwurstS, LamkiewiczK, et al. Direct RNA nanopore sequencing of full-length coronavirus genomes provides novel insights into structural variants and enables modification analysis[J]. Genome Res,2019,29(9):1545-1554. |
|
|
|
2020, Vol. 41 
