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Journal of Medical Microbiology logo Journal of Medical Microbiology

Volume 69, Issue 5

Logic in the time of coronavirus Open Access

Read Tim Inglis’ coronastream blog

Abstract

Much has happened here since the local news media trumpeted the first Australian COVID-19 fatality, and stirred up a medieval fear of contagion. We now need to take a step back to examine the logic underlying the use of our limited COVID-19 countermeasures. Emerging infectious diseases by their nature, pose new challenges to the diagnostic-treatment-control nexus, and push our concepts of causality beyond the limits of the conventional Koch-Henle approach to aetiology. We need to use contemporary methods of assessing causality to ensure that clinical, laboratory and public health measures draw on a rational, evidence-based approach to argumentation. The purpose of any aetiological hypothesis is to derive actionable insights into this latest emerging infectious disease. This review is an introduction to a conversation with medical microbiologists, which will be supported by a moderated blog.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): coronavirus , countermeasures , COVID-19 , principles of aetiology and SARS-CoV-2
© 2020 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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/content/journal/jmm/10.1099/jmm.0.001191
2020-04-22
2025-04-21
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References

  1. Inglis TJJ. Principia aetiologica: taking causality beyond Koch's postulates. J Med Microbiol 2007; 56:1419–1422 [View Article][PubMed][PubMed]
     [Google Scholar]
  2. Wu A, Peng Y, Huang B, Ding X, Wang X et al. Genome composition and divergence of the novel coronavirus (2019-nCoV) originating in China. Cell Host Microbe 2020; 27:pii: S1931-3128(20)30072-X328 [View Article][PubMed][PubMed]
     [Google Scholar]
  3. Wu Y, Ho W, Huang Y, Jin D-Y, Li S et al. SARS-CoV-2 is an appropriate name for the new coronavirus. Lancet 2020; 395:pii: S0140-6736(20)30557-2950 [View Article][PubMed][PubMed]
     [Google Scholar]
  4. Young BE, Ong SWX, Kalimuddin S, Low JG, Tan SY et al. Epidemiologic features and clinical course of patients infected with SARS-CoV-2 in Singapore. JAMA 2020 [View Article][PubMed][PubMed]
     [Google Scholar]
  5. YH X, Dong JH, WM A, XY L, Yin XP et al. Clinical and computed tomographic imaging features of novel coronavirus pneumonia caused by SARS-CoV-2. J Infect 2020pii: S0163-4453(20)30100-6
     [Google Scholar]
  6. Lipsitch M, Swerdlow DL, Finelli L. Defining the Epidemiology of Covid-19 - Studies Needed. N Engl J Med 2020; 382:1194–1196 [View Article][PubMed][PubMed]
     [Google Scholar]
  7. Lauer SA, Grantz KH, Bi Q, Jones FK, Zheng Q et al. The incubation period of coronavirus disease 2019 (COVID-19) from publicly reported confirmed cases: estimation and application. Ann Intern Med 2020 [View Article]
     [Google Scholar]
  8. Linton NM, Kobayashi T, Yang Y, Hayashi K, Akhmetzhanov AR et al. Incubation period and other epidemiological characteristics of 2019 novel coronavirus infections with right truncation: a statistical analysis of publicly available case data. J Clin Med 2020; 9:pii: E538.538 [View Article][PubMed][PubMed]
     [Google Scholar]
  9. Lauer SA, Grantz KH, Bi Q, Jones FK, Zheng Q et al. The incubation period of coronavirus disease 2019 (COVID-19) from publicly reported confirmed cases: estimation and application. Ann Intern Med 2020 [View Article][PubMed][PubMed]
     [Google Scholar]
  10. Nishiura H, Linton NM, Akhmetzhanov AR. Serial interval of novel coronavirus (COVID-19) infections. Int J Infect Dis 2020; 93:pii: S1201-9712(20)30119-3284–286 [View Article][PubMed][PubMed]
     [Google Scholar]
  11. Wang Y, You XY, Wang YJ, Peng LP, Du ZC et al. [Estimating the basic reproduction number of COVID-19 in Wuhan, China]. Zhonghua Liu Xing Bing Xue Za Zhi 2020; 41:476–479 [View Article][PubMed][PubMed]
     [Google Scholar]
  12. Zhu N, Zhang D, Wang W, Li X, Yang B et al. A novel coronavirus from patients with pneumonia in China, 2019. N Engl J Med 2020; 382:727–733 [View Article][PubMed][PubMed]
     [Google Scholar]
  13. Chen Z-L, Zhang Q, Lu Y, Guo Z-M, Zhang X et al. Distribution of the COVID-19 epidemic and correlation with population emigration from Wuhan, China. Chin Med J 20201 [View Article][PubMed][PubMed]
     [Google Scholar]
  14. Tian S, Hu N, Lou J, Chen K, Kang X et al. Characteristics of COVID-19 infection in Beijing. J Infect 2020pii: S0163-4453(20)30101-8
     [Google Scholar]
  15. Spiteri G, Fielding J, Diercke M, Campese C, Enouf V et al. First cases of coronavirus disease 2019 (COVID-19) in the who European region, 24 January to 21 February 2020. Euro Surveill 2020; 25: [View Article][PubMed][PubMed]
     [Google Scholar]
  16. Li K, Wu J, Wu F, Guo D, Chen L et al. The clinical and chest CT features associated with severe and critical COVID-19 pneumonia. Invest Radiol 20201 [View Article][PubMed][PubMed]
     [Google Scholar]
  17. Ai T, Yang Z, Hou H, Zhan C, Chen C et al. Correlation of chest CT and RT-PCR testing in coronavirus disease 2019 (COVID-19) in China: a report of 1014 cases. Radiology 2020; 42:200642 [View Article][PubMed][PubMed]
     [Google Scholar]
  18. Yan R, Zhang Y, Li Y, Xia L, Guo Y et al. Structural basis for the recognition of SARS-CoV-2 by full-length human ACE2. Science 2020; 367:pii: eabb27621448 [View Article][PubMed][PubMed]
     [Google Scholar]
  19. Hoffmann M, Kleine-Weber H, Schroeder S, Krüger N, Herrler T et al. SARS-CoV-2 cell entry depends on ACE2 and TMPRSS2 and is blocked by a clinically proven protease inhibitor. Cell 2020pii: S0092-8674(20)30229-4 [View Article][PubMed][PubMed]
     [Google Scholar]
  20. Shang J, Wan Y, Liu C, Yount B, Gully K et al. Structure of mouse coronavirus spike protein complexed with receptor reveals mechanism for viral entry. PLoS Pathog 2020; 16:e1008392 [View Article][PubMed][PubMed]
     [Google Scholar]
  21. Fang Y, Nie Y, Penny M. Transmission dynamics of the COVID‐19 outbreak and effectiveness of government interventions: a data‐driven analysis. J Med Virol 2020; 2: [View Article][PubMed][PubMed]
     [Google Scholar]
  22. Hellewell J, Abbott S, Gimma A, Bosse NI, Jarvis CI et al. Centre for the mathematical modelling of infectious diseases COVID-19 Working group, Funk S, Eggo RM. feasibility of controlling COVID-19 outbreaks by isolation of cases and contacts. Lancet Glob Health 2020pii: S2214-109X(20)30074-7
     [Google Scholar]
  23. Lim J, Jeon S, Shin HY, Kim MJ, Seong YM et al. Case of the index patient who caused tertiary transmission of COVID-19 infection in Korea: the application of Lopinavir/Ritonavir for the treatment of COVID-19 infected pneumonia monitored by quantitative RT-PCR. J Korean Med Sci 2020; 35:e79 [View Article][PubMed][PubMed]
     [Google Scholar]
  24. Multicenter collaboration group of Department of Science and Technology of Guangdong Province and Health Commission of Guangdong Province for chloroquine in the treatment of novel coronavirus pneumonia [Expert consensus on chloroquine phosphate for the treatment of novel coronavirus pneumonia]. Chinese Journal of Tuberculosis and Respiratory Disease 2020; 43:E019 [View Article][PubMed][PubMed]
     [Google Scholar]
  25. Cortegiani A, Ingoglia G, Ippolito M, Giarratano A, Einav S. A systematic review on the efficacy and safety of chloroquine for the treatment of COVID-19. J Crit Care 202010:S0883-9441(20)30390-7 [View Article][PubMed][PubMed]
     [Google Scholar]
  26. Ahmed SF, Quadeer AA, McKay MR. Preliminary identification of potential vaccine targets for the COVID-19 coronavirus (SARS-CoV-2) based on SARS-CoV immunological studies. Viruses 2020; 12:pii: E254 [View Article][PubMed][PubMed]
     [Google Scholar]
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