Status and problems of SARS-CoV-2 nucleic acid detection

doi:10.3969/j.issn.1673-8640.2021.05.019

Abstract

Abstract:

The ongoing outbreak of corona virus disease 2019（COVID-19） has posed a challenge for worldwide public health. The detection of severe acute respiratory syndrome coronavirus 2（SARS-CoV-2） nucleic acid plays an important role of diagnosis,therapy,prevention and control of COVID-19. In clinical practice,false negative results may mislead clinical decision-making,leading to the spread of the epidemic,while false positive results may cause unnecessary social panic. This review focuses on the interfering factors and the status and problems of SARS-CoV-2 nucleic acid detection,so as to provide a reference for the standardization and accuracy for SARS-CoV-2 nucleic acid detection in clinical laboratory.

Key words: Severe acute respiratory syndrome coronavirus 2, Corona virus disease 2019, Nucleic acid detection, False negativity, False positivity, Sample inactivation, Sample pooling

CLC Number:

R446.1

HUANG Fei, ZHANG Chunyan, GUO Wei, PAN Baishen, WANG Beili. Status and problems of SARS-CoV-2 nucleic acid detection[J]. Laboratory Medicine, 2021, 36(5): 554-559.

References 40

[1]	WU D, WU T, LIU Q, et al. The SARS-CoV-2 outbreak:what we know[J]. J Infect Dis, 2020,94:44-48.
[2]	PETERSEN E, KOOPMANS M, GO U, et al. Comparing SARS-CoV-2 with SARS-CoV and influenza pandemics[J]. Lancet Infect Dis, 2020,20(9):e238-e244. DOI URL
[3]	国家卫生健康委办公厅. 新型冠状病毒肺炎诊疗方案（第七版）[EB/OL]. (2020-03-03)[2020-07-04]. http://www.nhc.gov.cn/yzygj/s7653p/202003/46c9294a7dfe4cef80dc7f5912eb1989/files/ce3e6945832a438eaae415350a8ce964.pdf.
[4]	YOUNES N, AL-SADEQ D W, AL-JIGHEFEE H, et al. Challenges in laboratory diagnosis of the novel coronavirus SARS-CoV-2[J]. Viruses, 2020,12(6):582. DOI URL
[5]	XIAO F, SUN J, XU Y, et al. Infectious SARS-CoV-2 in feces of patient with severe COVID-19[J]. Emerg Infect Dis, 2020,26(8):1920-1922. DOI URL
[6]	CHEUNG K S, HUNG I F N, CHAN P P Y, et al. Gastrointestinal manifestations of SARS-CoV-2 infection and virus load in fecal samples from a Hong Kong cohort:systematic review and meta-analysis[J]. Gastroenterology, 2020,159(1):81-95. DOI URL
[7]	WONG M C, HUANG J, LAI C, et al. Detection of SARS-CoV-2 RNA in fecal specimens of patients with confirmed COVID-19:a meta-analysis[J]. J Infect, 2020,81(2):e31-e38.
[8]	AZZI L, CARCANO G, GIANFAGNA F, et al. Saliva is a reliable tool to detect SARS-CoV-2[J]. J Infect, 2020,81(1):e45-e50. DOI URL
[9]	WANG W, XU Y, GAO R, et al. Detection of SARS-CoV-2 in different types of clinical specimens[J]. JAMA, 2020,323(18):1843-1844.
[10]	CHAN J F W, YIP C C Y, TO K K W, et al. Improved molecular diagnosis of COVID-19 by the novel,highly sensitive and specific COVID-19- RdRp/Hel real-time reverse transcription-polymerase chain reaction assay validated in vitro and with clinical specimens[J]. J Clin Microbiol, 2020,58(5):e00310-20.
[11]	LU R, ZHAO X, LI J, et al. Genomic characterisation and epidemiology of 2019 novel coronavirus:implications for virus origins and receptor binding[J]. Lancet, 2020,395(10224):565-574. DOI URL
[12]	SUNGNAK W, HUANG N, BÉCAVIN C, et al. SARS-CoV-2 entry factors are highly expressed in nasal epithelial cells together with innate immune genes[J]. Nat Med, 2020,26(5):681-687. DOI URL
[13]	WALSH K A, JORDAN K, CLYNE B, et al. SARS-CoV-2 detection,viral load and infectivity over the course of an infection[J]. J Infect, 2020,81(3):357-371. DOI URL
[14]	Center for Disease Control and Prevention. Interim guidelines for collecting and handling of clinical specimens for COVID-19 testing[EB/OL]. (2021-02-26)[2021-02-28]. https://www.cdc.gov/coronavirus/2019-ncov/lab/guidelines-clinical-specimens.html.
[15]	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(第二版)[EB/OL].(2020-01-23)[2020-01-25]. http://www.gov.cn/xinwen/2020-01/23/content_5471768.htm.
[16]	CHEN H, WU R, XING Y, et al. Influence of different inactivation methods on severe acute respiratory syndrome coronavirus 2 RNA copy number[J]. J Clin Microbiol, 2020, 58(8):e0095820.
[17]	PAN Y, LONG L, ZHANG D, et al. Potential false-negative nucleic acid testing results for severe acute respiratory syndrome coronavirus 2 from thermal inactivation of samples with low viral loads[J]. Clin Chem, 2020,66(6):794-801. DOI URL
[18]	JUREKA A S, SILVAS J A, BASLER C F. Propagation,inactivation,and safety testing of SARS-CoV-2[J]. Viruses, 2020,12(6):622. DOI URL
[19]	LI L, LI X, GUO Z, et al. Influence of storage conditions on SARS-CoV-2 nucleic acid detection in throat swabs[J]. J Infect Dis, 2020 , 222(2):203-205. DOI URL
[20]	BAIN W, LEE J S, WATSON A M, et al. Practical guidelines for collection,manipulation and inactivation of SARS-CoV-2 and COVID-19 clinical specimens[J]. Curr Protoc Cytom, 2020,93(1):e77.
[21]	SHI J, HAN D, ZHANG R, et al. Molecular and serological assays for SARS-CoV-2:insights from genome and clinical characteristics[J]. Clin Chem, 2020,66(8):1030-1046. DOI URL
[22]	ZHU N, ZHANG D, WANG W, et al. A novel coronavirus from patients with pneumonia in China,2019[J]. N Engl J Med, 2020,382(8):727-733. DOI URL
[23]	REN L L, WANG Y M, WU Z Q, et al. Identification of a novel coronavirus causing severe pneumonia in human:a descriptive study[J]. Chin Med J(Engl), 2020,133(9):1015-1024.
[24]	ZHOU P, YANG X L, WANG X G, et al. A pneumonia outbreak associated with a new coronavirus of probable bat origin[J]. Nature, 2020,579(7798):270-273. DOI URL
[25]	CORMAN V M, LANDT O, KAISER M, et al. Detection of 2019 novel coronavirus(2019-nCoV) by real-time RT-PCR[J]. Euro Surveill, 2020,25(3):2000045.
[26]	国家卫生健康委临床检验中心. 全国新型冠状病毒核酸检测室间质量评价结果报告[EB/OL].(2020-04-12)[2020-04-12]. ttp://www.360doc.cn/mip/905407789.html.
[27]	MERINDOL N, PÉPIN G, MARCHAND C, et al. SARS-CoV-2 detection by direct rRT-PCR without RNA extraction[J]. J Clin Virol, 2020,128:104423. DOI URL
[28]	FUKUMOTO T, IWASAKI S, FUJISAWA S, et al. Efficacy of a novel SARS-CoV-2 detection kit without RNA extraction and purification[J]. Int J Infect Dis, 2020,98:16-17. DOI URL
[29]	国务院应对新型冠状病毒肺炎疫情联防联控机制医疗救治组. 关于印发新冠病毒核酸筛查稀释混样检测技术指引的通知[EB/OL].(2020-07-21)[2020-07-23]. http://www.gov.cn/xinwen/2020-07/23/content_5529372.htm.
[30]	NOTOMI T, OKAYAMA H, MASUBUCHI H, et al. Loop-mediated isothermal amplification of DNA[J]. Nucleic Acids Res, 2000,28(12):E63. DOI URL
[31]	KEIGHTLEY M C, SILLEKENS P, SCHIPPERS W, et al. Real-time NASBA detection of SARS-associated coronavirus and comparison with real-time reverse transcription-PCR[J]. J Med Virol, 2005,77(4):602-608. DOI URL
[32]	WANG W K, FANG C T, CHEN H L, et al. Detection of severe acute respiratory syndrome coronavirus RNA in plasma during the course of infection[J]. J Clin Microbiol, 2005,43(2):962-965. DOI URL
[33]	KELLNER M J, KOOB J G, GOOTENBERG J S, et al. SHERLOCK:nucleic acid detection with CRISPR nucleases[J]. Nat Protoc, 2019,14(10):2986-3012. DOI URL
[34]	GOOTENBERG J S, ABUDAYYEH O O, KELLNER M J, et al. Multiplexed and portable nucleic acid detection platform with Cas13,Cas12a,and Csm6[J]. Science, 2018,360(6387):439-444. DOI URL
[35]	国务院应对新型冠状病毒肺炎疫情联防联控机制综合组. 关于加快推进新冠病毒核酸检测的实施意见[EB/OL].(2020-06-08)[2020-06-10]. http://www.gov.cn/xinwen/2020-06/08/content_5518067.htm.
[36]	剑走偏锋?“武汉大会战”背后的检测之道[EB/OL]. (2020-05-29)[2020-06-05]. http://www.zhaoyq.com/article-1310.html.
[37]	ABDALHAMID B, BILDER C R, MCCUTCHEN E L, et al. Assessment of specimen pooling to conserve SARS CoV-2 testing resources[J]. Am J Clin Pathol, 2020,153(6):715-718. DOI URL
[38]	HOGAN C A, SAHOO M K, PINSKY B A. Sample pooling as a strategy to detect community transmission of SARS-CoV-2[J]. JAMA, 2020,323(19):1967-1969. DOI URL
[39]	国务院应对新型冠状病毒肺炎疫情联防联控机制医疗救治组. 关于印发新冠病毒核酸10合1混采检测技术规范的通知[EB/OL].( 2020- 08- 17)[2020-08-19]. http://www.gov.cn/xinwen/2020-08/19/content_5535756.htm.
[40]	YELIN I, AHARONY N, TAMAR E S, et al. Evaluation of COVID-19 RT-qPCR test in multi-sample pools[J]. Clin Infect Dis, 2020,71(16):2073-2078. DOI URL