Difference between revisions of "Journal:Laboratory diagnosis of COVID-19 in China: A review of challenging cases and analysis"
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==Introduction== | ==Introduction== | ||
Soon after [[coronavirus disease 2019]] (COVID-19) fully emerged in China at the beginning of 2020, the Chinese government immediately implemented strong measures to contain the outbreak. With great efforts, the COVID-19 cases have stabilized in China as a whole to date, albeit a small number of imported cases that intermittently emerge. However, an [[epidemic] began to rapidly spread around the world from April to date. As of August 21, 2020 (6:48pm CEST), there had been a total of 22,536,278 confirmed cases worldwide, with the largest cumulative number of COVID-19 confirmed cases (''n'' = 5,477,305) in the United States of America (USA), followed by Brazil (''n'' = 3,456,652), and India (''n'' = 2.905,823).<ref name="WHOCoronaDash">{{cite web |url=https://covid19.who.int/table |title=WHO Coronavirus Disease (COVID-19) Dashboard |author=World Health Oranization |publisher=World Health Organization |date=2020}}</ref> | |||
Some challenging cases of COVID-19 diagnosis were encountered in China and elsewhere, involving inconsistent [[laboratory]] testing results, mainly caused by false-negative [[Reverse transcription polymerase chain reaction|real-time reverse transcription-polymerase chain reaction]] (qRT-PCR) detection. In this review, we summarize and discuss some possible causes of false-negative results, including how to resolve the diagnostic dilemma. We also review and discuss the advantages and disadvantages of the different lab assays for diagnosing COVID-19, including different molecular techniques and [[wikipedia:Serology|serological assays]], and the value of combining qRT-PCR assays with serological testing. In brief, it is crucial to select appropriate diagnostic methods according to the phase of infection, or to use a combination of different methods and other clinical parameters in confirming the infection status of individuals. | |||
==SARS-CoV-2 etiological characteristics and genome organization== | |||
There are four genera under the subfamily [[coronavirus]] (CoVs)<ref name="ChanGenomic20">{{cite journal |title=Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan |journal=Emerging Microbes and Infections |author=Chan, H. F.-W.; Kok, J.-H.; Zhu, Z. et al. |volume=9 |issue=1 |pages=221–36 |year=2020 |doi=10.1080/22221751.2020.1719902 |pmid=31987001 |pmc=PMC7067204}}</ref>, including α, β, γ, and δ. The [[severe acute respiratory syndrome coronavirus 2]] (SARS-CoV-2) virus, responsible for COVID-19, belongs to the β CoV genus, the seventh member of the family of CoVs possessing a single-stranded<ref name="ChanGenomic20" /><ref name="ZhuANovel20">{{cite journal |title=A Novel Coronavirus from Patients with Pneumonia in China, 2019 |journal=New England Journal of Medicine |author=Zhu, N.; Zhang, D.; Wang, W. et al. |volume=382 |issue=8 |pages=727–33 |year=2020 |doi=10.1056/NEJMoa2001017 |pmid=31978945 |pmc=PMC7092803}}</ref>, positive-sense RNA [[Genomics|genome]]. The genome of the SARS-CoV-2 virus consists of about 29,000 bases.<ref name="ChanGenomic20" /><ref name="WangDevelop20">{{cite journal |title=Development of research and application of nucleic acid detection of 2019 novel coronavirus |journal=Chinese Journal of Clinical Laboratory Science |author=Wang, X.; Shi, J.; Ding, W. et al. |volume=38 |pages=81–84 |year=2020 |doi=10.13602/j.cnki.jcls.2020.02.01}}</ref> Studies show that there are at least 12 coding regions, including open reading frames (ORF) 1 ab, S, 3, E, M, 7, 8, 9, 10b, N, 13, and 14.<ref name="WangDevelop20" /><ref name="LuGenomic20">{{cite journal |title=Genomic characterisation and epidemiology of 2019 novel coronavirus: Implications for virus origins and receptor binding |journal=Lancet |author=Lu, R.; Zhao, X.; Li, J. et al. |volume=395 |issue=10224 |pages=565–74 |year=2020 |doi=10.1016/S0140-6736(20)30251-8 |pmid=32007145 |pmc=PMC7159086}}</ref> Among them, ORF 1 ab is the region of the ''RdRp'' gene which codes for RNA polymerase and is responsible for viral nucleic acid replication.<ref name="HuangClinical20">{{cite journal |title=Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China |journal=Lancet |author=Huang, C.; Wang, Y.; Li, X. et al. |volume=395 |issue=10223 |pages=497–506 |year=2020 |doi=10.1016/S0140-6736(20)30183-5 |pmid=31986264 |pmc=PMC7159299}}</ref> | |||
The structural proteins include<ref name="WangDevelop20" />: | |||
* a spike (S), crucially associated with virus transmission capacity, binding to angiotensin-converting enzyme 2 (ACE2) receptors on the cell surface to get into the host cell; | |||
* an envelope protein (E), responsible for the formation of virus envelopes and virus particles; | |||
* a membrane protein (M), responsible for membrane proteins encoded; and | |||
* a nucleocapsid (N), having recognition with the host RNA of the virus genome. | |||
These functional proteins play an essential role in genome maintenance and virus replication. Beyond these, several accessory proteins also help in virus replication, including ORF3, ORF6, ORF7a, ORF7b, ORF8, and ORF9b.<ref name="ChanGenomic20" /> The amplication fragments and loci of genes coding these proteins are shown in Fig. 1. | |||
Revision as of 22:58, 16 November 2020
| Full article title | Laboratory diagnosis of COVID-19 in China: A review of challenging cases and analysis |
|---|---|
| Journal | Journal of Microbiology, Immunology and Infection |
| Author(s) | Jing, Ran; Kudinha, Timothy; Zhou, Meng-Lan; Xiao, Meng; Wang, He; Yang, Wen-Hang; Xu, Ying-Chun; Hsueh, Po-Ren |
| Author affiliation(s) |
Chinese Academy of Medical Sciences, Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Charles Sturt University, NSW Health Pathology, National Taiwan University College of Medicine |
| Primary contact | Email: tkudinha at yahoo dot com |
| Year published | 2020 |
| Volume and issue | In Press |
| DOI | 10.1016/j.jmii.2020.10.004 |
| ISSN | 1684-1182 |
| Distribution license | Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International |
| Website | https://www.sciencedirect.com/science/article/pii/S1684118220302498 |
| Download | https://www.sciencedirect.com/science/article/pii/S1684118220302498/pdfft (PDF) |
 |
This article should be considered a work in progress and incomplete. Consider this article incomplete until this notice is removed. |
Abstract
Since the initial emergence of coronavirus disease 2019 (COVID-19) in Wuhan, Hubei province, China, a rapid spread of the disease occurred around the world, becoming an international global health concern at the pandemic level. In the face of this medical challenge threatening humans, the development of rapid and accurate methods for early screening and diagnosis of COVID-19 became crucial to containing the emerging public health threat, and preventing further spread within the population. Despite the large number of COVID-19 confirmed cases in China, some problematic cases with inconsistent laboratory testing results were reported. Specifically, a high false-negative rate of 41% on severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) detection by real-time reverse transcription polymerase chain reaction (qRT-PCR) assays was observed in China. Although serological testing has been applied worldwide as a complementary method to help identify SARS-CoV-2, several limitations on its use have been reported in China. Therefore, the separate use of qRT-PCR and serological testing in the diagnosis of COVID-19 in China and elsewhere presents considerable challenges, but when used in combination, these methods can be valuable tools in the fight against COVID-19. In this review, we give an overview of the advantages and disadvantages of different molecular techniques for SARS-CoV-2 detection that are currently used in several labs, including qRT-PCR, gene sequencing, loop-mediated isothermal amplification (LAMP), nucleic acid mass spectrometry (MS), and gene editing techniques based on the clustered regularly interspaced short palindromic repeats (CRISPR/Cas13) system. Then we mainly review and analyze some causes of false-negative qRT-PCR results, and how to resolve some of the diagnostic dilemmas.
Keywords: SARS-CoV-2, COVID-19, qRT-PCR, serology testing, challenging cases
Introduction
Soon after coronavirus disease 2019 (COVID-19) fully emerged in China at the beginning of 2020, the Chinese government immediately implemented strong measures to contain the outbreak. With great efforts, the COVID-19 cases have stabilized in China as a whole to date, albeit a small number of imported cases that intermittently emerge. However, an [[epidemic] began to rapidly spread around the world from April to date. As of August 21, 2020 (6:48pm CEST), there had been a total of 22,536,278 confirmed cases worldwide, with the largest cumulative number of COVID-19 confirmed cases (n = 5,477,305) in the United States of America (USA), followed by Brazil (n = 3,456,652), and India (n = 2.905,823).[1]
Some challenging cases of COVID-19 diagnosis were encountered in China and elsewhere, involving inconsistent laboratory testing results, mainly caused by false-negative real-time reverse transcription-polymerase chain reaction (qRT-PCR) detection. In this review, we summarize and discuss some possible causes of false-negative results, including how to resolve the diagnostic dilemma. We also review and discuss the advantages and disadvantages of the different lab assays for diagnosing COVID-19, including different molecular techniques and serological assays, and the value of combining qRT-PCR assays with serological testing. In brief, it is crucial to select appropriate diagnostic methods according to the phase of infection, or to use a combination of different methods and other clinical parameters in confirming the infection status of individuals.
SARS-CoV-2 etiological characteristics and genome organization
There are four genera under the subfamily coronavirus (CoVs)[2], including α, β, γ, and δ. The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) virus, responsible for COVID-19, belongs to the β CoV genus, the seventh member of the family of CoVs possessing a single-stranded[2][3], positive-sense RNA genome. The genome of the SARS-CoV-2 virus consists of about 29,000 bases.[2][4] Studies show that there are at least 12 coding regions, including open reading frames (ORF) 1 ab, S, 3, E, M, 7, 8, 9, 10b, N, 13, and 14.[4][5] Among them, ORF 1 ab is the region of the RdRp gene which codes for RNA polymerase and is responsible for viral nucleic acid replication.[6]
The structural proteins include[4]:
- a spike (S), crucially associated with virus transmission capacity, binding to angiotensin-converting enzyme 2 (ACE2) receptors on the cell surface to get into the host cell;
- an envelope protein (E), responsible for the formation of virus envelopes and virus particles;
- a membrane protein (M), responsible for membrane proteins encoded; and
- a nucleocapsid (N), having recognition with the host RNA of the virus genome.
These functional proteins play an essential role in genome maintenance and virus replication. Beyond these, several accessory proteins also help in virus replication, including ORF3, ORF6, ORF7a, ORF7b, ORF8, and ORF9b.[2] The amplication fragments and loci of genes coding these proteins are shown in Fig. 1.
References
- ↑ World Health Oranization (2020). "WHO Coronavirus Disease (COVID-19) Dashboard". World Health Organization. https://covid19.who.int/table.
- ↑ 2.0 2.1 2.2 2.3 Chan, H. F.-W.; Kok, J.-H.; Zhu, Z. et al. (2020). "Genomic characterization of the 2019 novel human-pathogenic coronavirus isolated from a patient with atypical pneumonia after visiting Wuhan". Emerging Microbes and Infections 9 (1): 221–36. doi:10.1080/22221751.2020.1719902. PMC PMC7067204. PMID 31987001. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7067204.
- ↑ Zhu, N.; Zhang, D.; Wang, W. et al. (2020). "A Novel Coronavirus from Patients with Pneumonia in China, 2019". New England Journal of Medicine 382 (8): 727–33. doi:10.1056/NEJMoa2001017. PMC PMC7092803. PMID 31978945. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7092803.
- ↑ 4.0 4.1 4.2 Wang, X.; Shi, J.; Ding, W. et al. (2020). "Development of research and application of nucleic acid detection of 2019 novel coronavirus". Chinese Journal of Clinical Laboratory Science 38: 81–84. doi:10.13602/j.cnki.jcls.2020.02.01.
- ↑ Lu, R.; Zhao, X.; Li, J. et al. (2020). "Genomic characterisation and epidemiology of 2019 novel coronavirus: Implications for virus origins and receptor binding". Lancet 395 (10224): 565–74. doi:10.1016/S0140-6736(20)30251-8. PMC PMC7159086. PMID 32007145. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159086.
- ↑ Huang, C.; Wang, Y.; Li, X. et al. (2020). "Clinical features of patients infected with 2019 novel coronavirus in Wuhan, China". Lancet 395 (10223): 497–506. doi:10.1016/S0140-6736(20)30183-5. PMC PMC7159299. PMID 31986264. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7159299.
Notes
This presentation is faithful to the original, with only a few minor changes to presentation, spelling, and grammar. In some cases important information was missing from the references, and that information was added. Otherwise, no other changes were made in conformance with the "NoDerivatives" portion of the document license.
