Microbiology

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This page collects observations, interpretations, and consequences for action about Microbiology in general of SARS-CoV2. Please observe the structure of the page, when you add your content. Please use references where possible. Remember to find the relevant page. For example, if your observation is about Sources, please use that page, instead of posting your content here. If you have specific microbiological topics that warrant a separate page, please create one.

What is already known[edit]

  • Laboratory surge capacity is a critical success factor in pandemic preparedness
  • ECDC has surveyed laboratory capacity in the EU (EULabCap) and reported in 2016. [1]
    • Outbreak Assistance Laboratories in the Netherlands were found in 2009 to have sufficient capacity to process xxx samples per month of BSL3 respiratory pathogens, in addition to the routine diagnostics.[2]

Observation[edit]

  • Large differences exist between EU countries in numbers of Corona tests performed per capita (ref)
  • Since 11 March, the Netherlands indicated that not all COVID19 suspect cases could be tested, due to limited capacity. The bottleneck are reagents, according to labs. By 7 March, 6000 tests had been performed [3], after which no data on testing were shared.
  • Between 11 and 20 march, the calculated case fatality of COVID19 in the Netherlands increased from 0.99% to 3.54% (calculated by day as number of cumulative deaths divided by number of cumulative confirmed cases). https://twitter.com/iTrainEU/status/1241048616615260166
  • There are not clear criteria on who should be tested. Even inside the country sometimes different practices are followed. For example, in Greece the national public health organization has requested people that recover from the disease to be sent home after at least 5 days without symptoms and without being tested. Hospitals did not comply, and test cases once before they leave or even twice (with 10 days interval).

Analysis and interpretation[edit]

  • The increasing case fatality suggests that an increasing amount of COVID19 goes undetected, which is supported by the statement that testing is increasingly restricted.
  • As a result, the strategy can no longer comply with the WHO recommendation to test broadly, in order to identify each new case, isolate, treat and trace all contacts.
  • Existing lab capacity surveys may have looked at ‘theoretical capacity’, but clearly did not take into account dependency on supply of reagents.
  • Most corona diagnostics depend on automated, high-throughput devices, which use proprietary materials. If any of those materials get out of stock, machines doe not work, even when alternative (non proprietary) materials are used.
  • Manual alternatives exist, but that requires specially trained lab personnel.

Consequences for action[edit]

  • In future, laboratory capacity surveys should not only take into account if labs are qualitatively able to perform the tests, but the quantitative capacity is important as well. This should include an analysis of dependencies, such as of external supply chains and amount of competent staff to scale up manual testing, if necessary.
  • maybe a central european management of available resources to keep a minimum capacity in all countries in such a huge public health emergency? proposal how this mechanism can work and under which prerequisities
  • come up with a list of criteria regarding testing and priorities at each phase of the outbreak given specific scenarios on the available resources...improvision to be avoided, consistency of testing among countries
  • different indicators should be used for following up the evolvement of the epidemic. Reporting only hospitalised cases / cases in ICUs and deaths could be more a more aproppriate approach after a specific point during the epidemic in order to avoid misunderstandings regarding the burden of disease in different regions of the world

References[edit]

  1. European Centre for Disease Prevention and Control. European Centre for Disease Prevention and Control. EU Laboratory Capability Monitoring System (EULabCap) – Report on 2016 survey of EU/EEA country capabilities and capacities. Stockholm: ECDC; 2018
  2. Asten, L. van, Lubben, M. van der, Wijngaard, C. van den, Pelt, W. van, Verheij, R., Jacobi, A., Overduin, P., Meijer, A., Luijt, D., Claas, E., Hermans, M., Melchers, W., Rossen, J., Schuurman, R., Woffs, P., Boucher, C., Schirm, J., Kroes, L., Leenders, S., Galama, J., Peeters, M., Loon, A. van, Stobberingh, E., Schutten, M., Koopmans, M. Strengthening the diagnostic capacity to detect Bio Safety Level 3 organisms in unusual respiratory viral outbreaks. Journal of Clinical Virology: 2009, 45(3), 185-190
  3. https://ourworldindata.org/coronavirus-testing-source-data