Microbiology - Revision history

80.106.187.46: /* Consequences for action */

2020-03-24T11:58:18Z

‎Consequences for action

80.106.187.46: /* Observation */

2020-03-24T11:48:51Z

‎Observation

Arnold: /* Analysis and interpretation */

2020-03-23T22:25:52Z

‎Analysis and interpretation

Arnold: /* Observation */

2020-03-23T22:23:06Z

‎Observation

Arnold: /* Observation */

2020-03-23T22:20:38Z

‎Observation

Arnold: /* Observation */

2020-03-23T22:19:50Z

‎Observation

Arnold at 22:16, 23 March 2020

2020-03-23T22:16:23Z

Arnold: /* What is already known */

2020-03-23T21:57:43Z

‎What is already known

Arnold at 10:51, 16 March 2020

2020-03-16T10:51:38Z

Bosmana: Created page with "This page collects observations, interpretations, and consequences action about the epidemiology of SARS-CoV2 in general. Please observe the structure of the page, when you ad..."

2020-03-16T08:36:18Z

Created page with "This page collects observations, interpretations, and consequences action about the epidemiology of SARS-CoV2 in general. Please observe the structure of the page, when you ad..."

New page

This page collects observations, interpretations, and consequences action about the epidemiology of SARS-CoV2 in general. 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 [[transmission routes]], please use that page, instead of posting your content here.

=Topic 1=

==Obeservations==

==Analysis and interpretation==

==Consequences for action==

=References=

@@ Line 11: / Line 11: @@
 * 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 <Ref name=“Ourworldindata”> https://ourworldindata.org/coronavirus-testing-source-data</ref>, 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
 ==Analysis and interpretation==

@@ Line 13: / Line 13: @@
 ==Analysis and interpretation==
 * 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==
 * 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.
 =References=

@@ Line 10: / Line 10: @@
 * 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 <Ref name=“Ourworldindata”> https://ourworldindata.org/coronavirus-testing-source-data</ref>, 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). <nowiki>  <blockquote class="twitter-tweet"><p lang="en" dir="ltr">&gt; 1 week, NL says: <a href="https://twitter.com/hashtag/COVID19?src=hash&amp;ref_src=twsrc%5Etfw">#COVID19</a> test capacity is not enough.<br><br>Surprise to see <a href="https://twitter.com/hashtag/CaseFatality?src=hash&amp;ref_src=twsrc%5Etfw">#CaseFatality</a> increase?<br><br>No: it suggests we increasingly test severe cases, and miss lighter ones. <br>Absolute deaths keep increasing: spread continues to grow. <br><br>If we don&#39;t test, we can&#39;t control! <a href="https://twitter.com/rivm?ref_src=twsrc%5Etfw">@RIVM</a> <a href="https://t.co/JqP0H85Hka">pic.twitter.com/JqP0H85Hka</a></p>&mdash; Transmissible (@iTrainEU) <a href="https://twitter.com/iTrainEU/status/1241048616615260166?ref_src=twsrc%5Etfw">March 20, 2020</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
+* 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
 ==Analysis and interpretation==

@@ Line 10: / Line 10: @@
 * 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 <Ref name=“Ourworldindata”> https://ourworldindata.org/coronavirus-testing-source-data</ref>, 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). <blockquote class="twitter-tweet"><p lang="en" dir="ltr">&gt; 1 week, NL says: <a href="https://twitter.com/hashtag/COVID19?src=hash&amp;ref_src=twsrc%5Etfw">#COVID19</a> test capacity is not enough.<br><br>Surprise to see <a href="https://twitter.com/hashtag/CaseFatality?src=hash&amp;ref_src=twsrc%5Etfw">#CaseFatality</a> increase?<br><br>No: it suggests we increasingly test severe cases, and miss lighter ones. <br>Absolute deaths keep increasing: spread continues to grow. <br><br>If we don&#39;t test, we can&#39;t control! <a href="https://twitter.com/rivm?ref_src=twsrc%5Etfw">@RIVM</a> <a href="https://t.co/JqP0H85Hka">pic.twitter.com/JqP0H85Hka</a></p>&mdash; Transmissible (@iTrainEU) <a href="https://twitter.com/iTrainEU/status/1241048616615260166?ref_src=twsrc%5Etfw">March 20, 2020</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
+* 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). <nowiki>  <blockquote class="twitter-tweet"><p lang="en" dir="ltr">&gt; 1 week, NL says: <a href="https://twitter.com/hashtag/COVID19?src=hash&amp;ref_src=twsrc%5Etfw">#COVID19</a> test capacity is not enough.<br><br>Surprise to see <a href="https://twitter.com/hashtag/CaseFatality?src=hash&amp;ref_src=twsrc%5Etfw">#CaseFatality</a> increase?<br><br>No: it suggests we increasingly test severe cases, and miss lighter ones. <br>Absolute deaths keep increasing: spread continues to grow. <br><br>If we don&#39;t test, we can&#39;t control! <a href="https://twitter.com/rivm?ref_src=twsrc%5Etfw">@RIVM</a> <a href="https://t.co/JqP0H85Hka">pic.twitter.com/JqP0H85Hka</a></p>&mdash; Transmissible (@iTrainEU) <a href="https://twitter.com/iTrainEU/status/1241048616615260166?ref_src=twsrc%5Etfw">March 20, 2020</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>
 ==Analysis and interpretation==

@@ Line 10: / Line 10: @@
 * 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 <Ref name=“Ourworldindata”> https://ourworldindata.org/coronavirus-testing-source-data</ref>, after which no data on testing were shared.
 ==Analysis and interpretation==

← Older revision		Revision as of 21:57, 23 March 2020
Line 2:		Line 2:

	=What is already known=		=What is already known=
		+	* Laboratory surge capacity is a critical success factor in pandemic preparedness
		+	* ECDC has surveyed laboratory capacity in the EU (EULabCap) and reported in 2016. <Ref Name=“EULABCAP”> European Centre for Disease Prevention and Control. European Centre for Disease Prevention and Control. [https://www.ecdc.europa.eu/sites/default/files/documents/2016_EULabCap_EUreport_web_300418_final.pdf EU Laboratory Capability Monitoring System (EULabCap)] – Report on 2016 survey of EU/EEA country capabilities and capacities. Stockholm: ECDC; 2018</ref>
		+	**
		+	** 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.<Ref name=“LvAsten”> 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</ref>
		+
		+	==Observation==
		+	* Large differences exist between EU countries in numbers of Corona tests performed per capita (ref)
		+	*

	=Topic 1=		=Topic 1=

@@ Line 1: / Line 1: @@
-This page collects observations, interpretations, and consequences action about the epidemiology of SARS-CoV2 in general. 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 [[transmission routes]], please use that page, instead of posting your content here.
+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.
 =Topic 1=
+==Observations==
 ==Analysis and interpretation==
 ==Consequences for action==
 =References=