COVID-19 diagnostic study of choice: Difference between revisions

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*World Health Organization recommends two-step gene testing by NAAT for diagnosis of coronavirus illness. The first step is screening for coronavirus illness with Envelope(E) gene assay followed by a confirmatory test with RNA dependent RNA polymerase (RdRP) gene assay.<ref name="pmid31992387">{{cite journal| author=Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DK | display-authors=etal| title=Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. | journal=Euro Surveill | year= 2020 | volume= 25 | issue= 3 | pages=  | pmid=31992387 | doi=10.2807/1560-7917.ES.2020.25.3.2000045 | pmc=6988269 | url=https://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&tool=sumsearch.org/cite&retmode=ref&cmd=prlinks&id=31992387  }} </ref>
*World Health Organization recommends two-step gene testing by NAAT for diagnosis of coronavirus illness. The first step is screening for coronavirus illness with Envelope(E) gene assay followed by a confirmatory test with RNA dependent RNA polymerase (RdRP) gene assay.<ref name="pmid31992387">{{cite journal| author=Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DK | display-authors=etal| title=Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR. | journal=Euro Surveill | year= 2020 | volume= 25 | issue= 3 | pages=  | pmid=31992387 | doi=10.2807/1560-7917.ES.2020.25.3.2000045 | pmc=6988269 | url=https://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&tool=sumsearch.org/cite&retmode=ref&cmd=prlinks&id=31992387  }} </ref>
*The RdRp/Hel gene assay has the highest sensitivity and specificity for the diagnosis of coronavirus illness in comparison with spike and nucleocapsid genes. It has the lowest limit of detection in vitro.<ref name="pmid32132196">{{cite journal| author=Chan JF, Yip CC, To KK, Tang TH, Wong SC, Leung KH | display-authors=etal| title=Improved Molecular Diagnosis of COVID-19 by the Novel, Highly Sensitive and Specific COVID-19-RdRp/Hel Real-Time Reverse Transcription-PCR Assay Validated In Vitro and with Clinical Specimens. | journal=J Clin Microbiol | year= 2020 | volume= 58 | issue= 5 | pages=  | pmid=32132196 | doi=10.1128/JCM.00310-20 | pmc=7180250 | url=https://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&tool=sumsearch.org/cite&retmode=ref&cmd=prlinks&id=32132196  }} </ref>
*The RdRp/Hel gene assay has the highest sensitivity and specificity for the diagnosis of coronavirus illness in comparison with spike and nucleocapsid genes. It has the lowest limit of detection in vitro.<ref name="pmid32132196">{{cite journal| author=Chan JF, Yip CC, To KK, Tang TH, Wong SC, Leung KH | display-authors=etal| title=Improved Molecular Diagnosis of COVID-19 by the Novel, Highly Sensitive and Specific COVID-19-RdRp/Hel Real-Time Reverse Transcription-PCR Assay Validated In Vitro and with Clinical Specimens. | journal=J Clin Microbiol | year= 2020 | volume= 58 | issue= 5 | pages=  | pmid=32132196 | doi=10.1128/JCM.00310-20 | pmc=7180250 | url=https://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&tool=sumsearch.org/cite&retmode=ref&cmd=prlinks&id=32132196  }} </ref>
*The NAAT can have false-negative results. A study was done in a hospital in China where 51 coronavirus suspected patients had RT-PCR tests and chest CT scans. 36 patients had positive first RT-PCR tests. 15 patients had negative tests with CT scan findings were highly suggestive of viral pneumonia. Serial testing by RT-PCR was positive in these patients.<ref name="FangZhang2020">{{cite journal|last1=Fang|first1=Yicheng|last2=Zhang|first2=Huangqi|last3=Xie|first3=Jicheng|last4=Lin|first4=Minjie|last5=Ying|first5=Lingjun|last6=Pang|first6=Peipei|last7=Ji|first7=Wenbin|title=Sensitivity of Chest CT for COVID-19: Comparison to                    RT-PCR|journal=Radiology|year=2020|pages=200432|issn=0033-8419|doi=10.1148/radiol.2020200432}}</ref>


===The comparison of chest CT scan and RT PCR in diagnosing Covid-19 illness===
*There are research studies that compared the accuracy, sensitivity, and specificity of chest CT scans with RT-PCR in diagnosing coronavirus illness.
*The RT-PCR test is the reference standard for the comparison.
*A retrospective study was performed by Ai et al. in 1049 suspected patients at the largest hospital in Wuhan, China. <ref name="pmid32101510">{{cite journal| author=Ai T, Yang Z, Hou H, Zhan C, Chen C, Lv W | display-authors=etal| title=Correlation of Chest CT and RT-PCR Testing in Coronavirus Disease 2019 (COVID-19) in China: A Report of 1014 Cases. | journal=Radiology | year= 2020 | volume=  | issue=  | pages= 200642 | pmid=32101510 | doi=10.1148/radiol.2020200642 | pmc=7233399 | url=https://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&tool=sumsearch.org/cite&retmode=ref&cmd=prlinks&id=32101510  }} </ref> Gietema et al. did a prospective study on 193 symptomatic patients in a hospital in Netherland.<ref name="pmid32645053">{{cite journal| author=Gietema HA, Zelis N, Nobel JM, Lambriks LJG, van Alphen LB, Oude Lashof AML | display-authors=etal| title=CT in relation to RT-PCR in diagnosing COVID-19 in The Netherlands: A prospective study. | journal=PLoS One | year= 2020 | volume= 15 | issue= 7 | pages= e0235844 | pmid=32645053 | doi=10.1371/journal.pone.0235844 | pmc= | url=https://www.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pubmed&tool=sumsearch.org/cite&retmode=ref&cmd=prlinks&id=32645053  }} </ref> The results from both these studies are tabulated below:
=== Diagnostic Criteria ===
=== Diagnostic Criteria ===
The diagnostic criteria for suspected and confirmed cases of [[coronavirus]] disease 2019 ([[COVID-19]]) is tabulated below:<ref name="ChenZhou2020">{{cite journal|last1=Chen|first1=Nanshan|last2=Zhou|first2=Min|last3=Dong|first3=Xuan|last4=Qu|first4=Jieming|last5=Gong|first5=Fengyun|last6=Han|first6=Yang|last7=Qiu|first7=Yang|last8=Wang|first8=Jingli|last9=Liu|first9=Ying|last10=Wei|first10=Yuan|last11=Xia|first11=Jia'an|last12=Yu|first12=Ting|last13=Zhang|first13=Xinxin|last14=Zhang|first14=Li|title=Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study|journal=The Lancet|volume=395|issue=10223|year=2020|pages=507–513|issn=01406736|doi=10.1016/S0140-6736(20)30211-7}}</ref><ref>{{Cite web|url=http://www.nhc.gov.cn/xcs/zhengcwj/202002/de2d62a5711c41ef9b2c4b6f4d1f2136.shtml|title=C.N.H. Commission
The diagnostic criteria for suspected and confirmed cases of [[coronavirus]] disease 2019 ([[COVID-19]]) is tabulated below:<ref name="ChenZhou2020">{{cite journal|last1=Chen|first1=Nanshan|last2=Zhou|first2=Min|last3=Dong|first3=Xuan|last4=Qu|first4=Jieming|last5=Gong|first5=Fengyun|last6=Han|first6=Yang|last7=Qiu|first7=Yang|last8=Wang|first8=Jingli|last9=Liu|first9=Ying|last10=Wei|first10=Yuan|last11=Xia|first11=Jia'an|last12=Yu|first12=Ting|last13=Zhang|first13=Xinxin|last14=Zhang|first14=Li|title=Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study|journal=The Lancet|volume=395|issue=10223|year=2020|pages=507–513|issn=01406736|doi=10.1016/S0140-6736(20)30211-7}}</ref><ref>{{Cite web|url=http://www.nhc.gov.cn/xcs/zhengcwj/202002/de2d62a5711c41ef9b2c4b6f4d1f2136.shtml|title=C.N.H. Commission

Revision as of 10:34, 12 July 2020

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Editor-In-Chief: C. Michael Gibson, M.S., M.D. [1] ; Associate Editor(s)-in-Chief: Sabawoon Mirwais, M.B.B.S, M.D.[2]

Overview

The diagnostic criteria for suspected and confirmed cases of coronavirus disease 2019 (COVID-19) are tabulated in the section below.

Diagnostic Study of Choice

Study of Choice

  • The Nucleic acid amplification test by the reverse transcriptase-polymerase chain reaction (RT-PCR) is the gold standard test for detecting coronavirus illness. These tests are highly specific for detecting coronavirus illness.[1]

Diagnostic Results

  • The NAAT detects viral gene sequence specific for coronavirus. The genes detected by NAAT include nucleocapsid(N), envelope(E), spike(S), and RNA dependent RNA polymerase (RdRP) in the open reading frame. [2]
  • The turnaround time for these tests is variable depending upon the specific testing kit and laboratory performing it.[3]
  • The diagnosis of coronavirus illness requires detection of at least two genes specific for SAR Cov-2 by RT-PCR. In the United States, the Center for disease control and prevention recommends testing for two nucleocapsid proteins N1 and N2.[4]
  • World Health Organization recommends two-step gene testing by NAAT for diagnosis of coronavirus illness. The first step is screening for coronavirus illness with Envelope(E) gene assay followed by a confirmatory test with RNA dependent RNA polymerase (RdRP) gene assay.[5]
  • The RdRp/Hel gene assay has the highest sensitivity and specificity for the diagnosis of coronavirus illness in comparison with spike and nucleocapsid genes. It has the lowest limit of detection in vitro.[6]
  • The NAAT can have false-negative results. A study was done in a hospital in China where 51 coronavirus suspected patients had RT-PCR tests and chest CT scans. 36 patients had positive first RT-PCR tests. 15 patients had negative tests with CT scan findings were highly suggestive of viral pneumonia. Serial testing by RT-PCR was positive in these patients.[7]

The comparison of chest CT scan and RT PCR in diagnosing Covid-19 illness

  • There are research studies that compared the accuracy, sensitivity, and specificity of chest CT scans with RT-PCR in diagnosing coronavirus illness.
  • The RT-PCR test is the reference standard for the comparison.
  • A retrospective study was performed by Ai et al. in 1049 suspected patients at the largest hospital in Wuhan, China. [8] Gietema et al. did a prospective study on 193 symptomatic patients in a hospital in Netherland.[9] The results from both these studies are tabulated below:

Diagnostic Criteria

The diagnostic criteria for suspected and confirmed cases of coronavirus disease 2019 (COVID-19) is tabulated below:[10][11][12][13][14][15]

Case Diagnostic Criteria
Suspected Case Anyone with a history of epidemiology and any two of the clinical manifestations or anyone without epidemiological history and three of the clinical manifestations is considered to be a suspected case:

1) Epidemiological history:

  • Within 14 days before the disease onset, there is a travel history or living history in Wuhan or other areas with local cases
  • Within 14 days before the disease onset, there is contact with patients who had a fever or respiratory symptoms from Wuhan or other areas with local cases
  • Clustering of patients or contact with patients infected with the SARS-CoV-2


2) Clinical manifestations:

  • Fever and/or respiratory symptoms
  • With the above-mentioned imaging characteristics of pneumonia
  • The total number of leukocytes in the early stage of the disease is normal or decreased, or the lymphocyte count is decreased
Confirmed Case Any suspected case with one of the following pathogenic features is reclassified as a confirmed case:

Ongoing diagnostic Trials

  • A researcher at Israel’s Ben-Gurion University of the Negev (BGU) has developed a test that identifies those carrying the COVID-19 virus in less than a minute. And it is both affordable and works with greater than 90% accuracy to boot[16]

Antibody response

  • Most recovering from #COVID19 do not have high levels of neutralizing antibodies BUT antibodies to the receptor binding domain (RBD) of the spike protein with potent antiviral activity were found in all individuals tested & may be tx target[17]
  • 8 weeks after hospital discharge, 40% of asymptomatic patients have no antibodies, and 12.9% of those who were symptomatic had no #COVID19 antibodies[18]

References

  1. ↑ Nalla AK, Casto AM, Huang MW, Perchetti GA, Sampoleo R, Shrestha L; et al. (2020). "Comparative Performance of SARS-CoV-2 Detection Assays Using Seven Different Primer-Probe Sets and One Assay Kit". J Clin Microbiol. 58 (6). doi:10.1128/JCM.00557-20. PMC 7269385 Check |pmc= value (help). PMID 32269100 Check |pmid= value (help).
  2. ↑ Tang YW, Schmitz JE, Persing DH, Stratton CW (2020). "Laboratory Diagnosis of COVID-19: Current Issues and Challenges". J Clin Microbiol. 58 (6). doi:10.1128/JCM.00512-20. PMC 7269383 Check |pmc= value (help). PMID 32245835 Check |pmid= value (help).
  3. ↑ Lieberman JA, Pepper G, Naccache SN, Huang ML, Jerome KR, Greninger AL (2020). "Comparison of Commercially Available and Laboratory Developed Assays for in vitro Detection of SARS-CoV-2 in Clinical Laboratories". J Clin Microbiol. doi:10.1128/JCM.00821-20. PMID 32350048 Check |pmid= value (help).
  4. ↑ Holshue ML, DeBolt C, Lindquist S, Lofy KH, Wiesman J, Bruce H; et al. (2020). "First Case of 2019 Novel Coronavirus in the United States". N Engl J Med. 382 (10): 929–936. doi:10.1056/NEJMoa2001191. PMC 7092802 Check |pmc= value (help). PMID 32004427 Check |pmid= value (help).
  5. ↑ Corman VM, Landt O, Kaiser M, Molenkamp R, Meijer A, Chu DK; et al. (2020). "Detection of 2019 novel coronavirus (2019-nCoV) by real-time RT-PCR". Euro Surveill. 25 (3). doi:10.2807/1560-7917.ES.2020.25.3.2000045. PMC 6988269 Check |pmc= value (help). PMID 31992387.
  6. ↑ Chan JF, Yip CC, To KK, Tang TH, Wong SC, Leung KH; et al. (2020). "Improved Molecular Diagnosis of COVID-19 by the Novel, Highly Sensitive and Specific COVID-19-RdRp/Hel Real-Time Reverse Transcription-PCR Assay Validated In Vitro and with Clinical Specimens". J Clin Microbiol. 58 (5). doi:10.1128/JCM.00310-20. PMC 7180250 Check |pmc= value (help). PMID 32132196 Check |pmid= value (help).
  7. ↑ Fang, Yicheng; Zhang, Huangqi; Xie, Jicheng; Lin, Minjie; Ying, Lingjun; Pang, Peipei; Ji, Wenbin (2020). "Sensitivity of Chest CT for COVID-19: Comparison to RT-PCR". Radiology: 200432. doi:10.1148/radiol.2020200432. ISSN 0033-8419.
  8. ↑ Ai T, Yang Z, Hou H, Zhan C, Chen C, Lv W; et al. (2020). "Correlation of Chest CT and RT-PCR Testing in Coronavirus Disease 2019 (COVID-19) in China: A Report of 1014 Cases". Radiology: 200642. doi:10.1148/radiol.2020200642. PMC 7233399 Check |pmc= value (help). PMID 32101510 Check |pmid= value (help).
  9. ↑ Gietema HA, Zelis N, Nobel JM, Lambriks LJG, van Alphen LB, Oude Lashof AML; et al. (2020). "CT in relation to RT-PCR in diagnosing COVID-19 in The Netherlands: A prospective study". PLoS One. 15 (7): e0235844. doi:10.1371/journal.pone.0235844. PMID 32645053 Check |pmid= value (help).
  10. ↑ Chen, Nanshan; Zhou, Min; Dong, Xuan; Qu, Jieming; Gong, Fengyun; Han, Yang; Qiu, Yang; Wang, Jingli; Liu, Ying; Wei, Yuan; Xia, Jia'an; Yu, Ting; Zhang, Xinxin; Zhang, Li (2020). "Epidemiological and clinical characteristics of 99 cases of 2019 novel coronavirus pneumonia in Wuhan, China: a descriptive study". The Lancet. 395 (10223): 507–513. doi:10.1016/S0140-6736(20)30211-7. ISSN 0140-6736.
  11. ↑ "C.N.H. Commission Notice on prevention and control of pneumonia in children and pregnant women with new coronavirus infection China National Health Commission, Beijing (2020) (in Chinese)". line feed character in |title= at position 18 (help)
  12. ↑ "Technology, M.e.g.o.T.h.a.t.T.M.C.o.H.U.o.S.a. A rapid guideline for the diagnosis and treatment of pneumonia with new coronavirus infection (Third edition)".
  13. ↑ "Union Hospital T.M.C., Huazhong University of Science and Technology., Wuhan union hospital manage the 2019 new coronavirus infection strategies and instructions (in Chinese)". line feed character in |title= at position 15 (help)
  14. ↑ "[Diagnosis and clinical management of 2019 novel coronavirus infection: an operational recommendation of Peking Union Medical College Hospital (V2.0)]". Zhonghua Nei Ke Za Zhi (in Chinese). 59 (3): 186–188. February 2020. doi:10.3760/cma.j.issn.0578-1426.2020.03.003. PMID 32023681 Check |pmid= value (help).
  15. ↑ "Clinical management of severe acute respiratory infection when novel coronavirus (nCoV) infection is suspected".
  16. ↑ https://www.bioworld.com/articles/435285-Israels-ben-Gurion-university-develops-one-minute-coronavirus-test.html. Missing or empty |title= (help)
  17. ↑ Robbiani, Davide F.; Gaebler, Christian; Muecksch, Frauke; Lorenzi, Julio C. C.; Wang, Zijun; Cho, Alice; Agudelo, Marianna; Barnes, Christopher O.; Gazumyan, Anna; Finkin, Shlomo; Hägglöf, Thomas; Oliveira, Thiago Y.; Viant, Charlotte; Hurley, Arlene; Hoffmann, Hans-Heinrich; Millard, Katrina G.; Kost, Rhonda G.; Cipolla, Melissa; Gordon, Kristie; Bianchini, Filippo; Chen, Spencer T.; Ramos, Victor; Patel, Roshni; Dizon, Juan; Shimeliovich, Irina; Mendoza, Pilar; Hartweger, Harald; Nogueira, Lilian; Pack, Maggi; Horowitz, Jill; Schmidt, Fabian; Weisblum, Yiska; Michailidis, Eleftherios; Ashbrook, Alison W.; Waltari, Eric; Pak, John E.; Huey-Tubman, Kathryn E.; Koranda, Nicholas; Hoffman, Pauline R.; West, Anthony P.; Rice, Charles M.; Hatziioannou, Theodora; Bjorkman, Pamela J.; Bieniasz, Paul D.; Caskey, Marina; Nussenzweig, Michel C. (2020). "Convergent antibody responses to SARS-CoV-2 in convalescent individuals". Nature. doi:10.1038/s41586-020-2456-9. ISSN 0028-0836.
  18. ↑ Long, Quan-Xin; Tang, Xiao-Jun; Shi, Qiu-Lin; Li, Qin; Deng, Hai-Jun; Yuan, Jun; Hu, Jie-Li; Xu, Wei; Zhang, Yong; Lv, Fa-Jin; Su, Kun; Zhang, Fan; Gong, Jiang; Wu, Bo; Liu, Xia-Mao; Li, Jin-Jing; Qiu, Jing-Fu; Chen, Juan; Huang, Ai-Long (2020). "Clinical and immunological assessment of asymptomatic SARS-CoV-2 infections". Nature Medicine. doi:10.1038/s41591-020-0965-6. ISSN 1078-8956.
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