Corona Detective - Revision history

Rachel: /* Recommendation + next steps */

2023-11-20T17:13:45Z

Recommendation + next steps

Rachel: /* Introduction */

2023-09-29T08:29:19Z

Introduction

Rachel: /* Recommendation + next steps */

2023-02-12T13:57:26Z

Recommendation + next steps

Rachel: /* Recommendation + next steps */

2023-02-12T13:56:13Z

Recommendation + next steps

Rachel at 10:29, 1 January 2022

2022-01-01T10:29:42Z

Rachel at 20:05, 16 December 2021

2021-12-16T20:05:58Z

Rachel: /* Recommendation + next steps */

2021-12-04T15:32:16Z

Recommendation + next steps

Rachel: /* The Corona Detective Project */

2021-12-04T15:29:09Z

The Corona Detective Project

Rachel: /* The Corona Detective Project */

2021-12-04T15:11:08Z

The Corona Detective Project

Rachel: /* The Corona Detective Project */

2021-10-06T10:15:47Z

The Corona Detective Project

@@ Line 108: / Line 108: @@
 ==Recommendation + next steps ==
-(The following is from January 2022) Organising reliable GMP batches for independent validation  by regulators has been a great difficulty, with it being hard to reach agreements at such a distance with no actual meetings.  Additionally, it seems likely that licensing agreements are needed, as not only did extension of LAMP patent get approved, but there is a patent for the QUASR detection method depicted above (from the Sandia national labs in the states...).
+(The following was from January 2022) Organising reliable GMP batches for independent validation  by regulators has been a great difficulty, with it being hard to reach agreements at such a distance with no actual meetings.  Additionally, it seems likely that licensing agreements are needed, as not only did extension of LAMP patent get approved, but there is a patent for the QUASR detection method depicted above (from the Sandia national labs in the states...).
 Currently, we are in discussion with people in Ghana as those moronic variants get spread... (yes, sorry, sometimes only humor can help us realise - if people already knew more when this started and were strict the first 2 months, we might not be here 2 years later! -almost, yes...)
@@ Line 114: / Line 114: @@
-Now, more than a year later (Feb 2023), we are learning to live with Covid-19, but our PoP batch of reactions from Canada's freeze-drying company EVIK, has still not finished providing amazing data.  Here in Switzerland, clinical validations with left over RNA extracts were about 97% concordant for positive and 100% for negative samples.  We await results from our colleagues in Ghana, and also 96 reactions are in Chile, for further tests versus batches made with 'homebrew' enzymes and clinical tests (perhaps also with colleagues in Brazil).
+More than a year later (Feb 2023), we are learning to live with Covid-19, but our PoP batch of reactions from Canada's freeze-drying company EVIK, has still not finished providing amazing data.  Here in Switzerland, clinical validations with left over RNA extracts were about 97% concordant for positive and 100% for negative samples.  We await results from our colleagues in Ghana, and also 96 reactions are in Chile, for further tests versus batches made with 'homebrew' enzymes and clinical tests (perhaps also with colleagues in Brazil).
 The compiled results may help for the next pandemic and make open science innovation more acceptable in its early phases?
+Now, the experiments for Corona Detective are basically done (July 2023), and perhaps another publication could be made...
 ''(Ce qui suit date de janvier 2022) L'organisation de lots BPF fiables pour une validation indépendante par les régulateurs a été une grande difficulté, car il est difficile de parvenir à des accords à une telle distance sans réunions réelles. En outre, il semble probable que des accords de licence soient nécessaires, car non seulement l'extension du brevet LAMP a été approuvée, mais il existe également un brevet pour la méthode de détection QUASR décrite ci-dessus (des laboratoires nationaux Sandia aux États-Unis...).''
@@ Line 127: / Line 127: @@
 ''Les résultats compilés pourraient être utiles pour la prochaine pandémie et rendre l'innovation scientifique ouverte plus acceptable dans ses premières phases ?''
 [[Category:Work In Progress]]
 [[Category:Manual]]

@@ Line 51: / Line 51: @@
 ===Context===
 When the pandemic began, RA (as CSO of AGiR!) of course began some corona virus 'sequence gazing' ...
-Thomas Landrain's visit to Hackuarium was put off by 'lockdown' - but a big collaboration developed in the platform of his Just One Giant Lab (JOGL).
+Thomas Landrain's visit to Hackuarium was put off by 'lockdown' - but a big collaboration developed in the platform of his Just One Giant Lab (JOGL), where we developed an 'Open Covid Initiative'.
-RA got Guy and Fran in too, and one thing led to [https://app.jogl.io/project/181 another]...  Here is our [https://www.youtube.com/watch?v=Tdfws3g3R2s 'teaser' video] from when we were semi-finalists for the xprize!
+RA got Guy and Fran in too, and one thing led to [https://app.jogl.io/project/181 another]...  Indeed, as part of the nuclear amplification working group in JOGL, we also made sure to [https://docs.google.com/document/d/1ldQ1aRxHjuj-U7kNqwWlkwwwW54U6ls8xMI9l0LBFrQ/edit?usp=sharing highlight biosecurity], and the best practices for making and testing such diagnostic methods.
 The first 'workshop' of this [https://app.jogl.io/project/181/coronadetective method to detect the virus] causing Covid-19, inspired by the [https://gmodetective.com/ GMO Detective], was held on the evening of 9June21, and was virtual, as part of the [https://bbkopenscience.com/streaming/ BBK open science festival]!<br>
 We had 4 labs (here, in Paris, in Bilbao, and in Zurich) running tests that day.  <br>Happily, all 4 cities had great positive control results and no people positive... whew.  (hope for video stream link ...)
 The latest [http://wiki.hackuarium.ch/w/File:CoronaDetective_simpleUSERprotocol.pdf 'simple' protocol is available here], and your input is welcome.<br>
@@ Line 61: / Line 65: @@
 With our Colombian colleagues we also discussed the method virtually also, as the 2nd of a 3-part series of talks (Oct2020, as announced in the flyer, Charla #2).
 === People===

@@ Line 87: / Line 87: @@
-Now, more than a year later (Feb 2023), we are learning to live with Covid-19, but our PoP batch of reactions from Canada's freeze-drying company EVIK, has still not finished providing amazing data.  Here in Switzerland, clinical validations with left over RNA extracts were about 97% concordant for positive and 100% for negative samples.  We await results from our colleagues in Ghana, and also 96 reactions are in Chile, for further tests versus batches made with 'homebrew' enzyme batches and clinical tests (perhaps also with colleagues in Brazil).  The compiled results may help for the next pandemic and make open science innovation more acceptable in its early phases?
@@ Line 94: / Line 98: @@
 ''Actuellement, nous sommes en discussion avec des personnes au Ghana alors que ces variantes débiles se répandent... (oui, désolé, parfois seul l'humour peut nous aider à réaliser - si les gens en savaient déjà plus quand cela a commencé et étaient stricts les 2 premiers mois, nous ne serions peut-être pas là 2 ans plus tard ! -presque, oui...)''
-''Aujourd'hui, plus d'un an plus tard (février 2023), nous apprenons à vivre avec Covid-19, mais notre lot de réactions PoP de la société canadienne de lyophilisation EVIK, n'a toujours pas fini de fournir des données étonnantes. Ici en Suisse, les validations cliniques avec les extraits d'ARN restants étaient concordantes à 97 % pour les échantillons positifs et à 100 % pour les échantillons négatifs. Nous attendons les résultats de nos collègues au Ghana, et aussi 96 réactions au Chili, pour des tests supplémentaires par rapport aux lots fabriqués avec des lots d'enzymes "maison" et des tests cliniques (peut-être aussi avec des collègues au Brésil). Les résultats compilés pourraient être utiles pour la prochaine pandémie et rendre l'innovation scientifique ouverte plus acceptable dans ses premières phases ?''
+''Aujourd'hui, plus d'un an plus tard (février 2023), nous apprenons à vivre avec Covid-19, mais notre lot de réactions PoP de la société canadienne de lyophilisation EVIK, n'a toujours pas fini de fournir des données étonnantes. Ici en Suisse, les validations cliniques avec les extraits d'ARN restants étaient concordantes à 97 % pour les échantillons positifs et à 100 % pour les échantillons négatifs. Nous attendons les résultats de nos collègues au Ghana, et aussi 96 réactions au Chili, pour des tests supplémentaires par rapport aux lots fabriqués avec des lots d'enzymes "faites-maison" et des tests cliniques (peut-être aussi avec des collègues au Brésil).''
 [[Category:Work In Progress]]
 [[Category:Manual]]

@@ Line 52: / Line 52: @@
 When the pandemic began, RA (as CSO of AGiR!) of course began some corona virus 'sequence gazing' ...
 Thomas Landrain's visit to Hackuarium was put off by 'lockdown' - but a big collaboration developed in the platform of his Just One Giant Lab (JOGL).
-RA got Guy and Fran in too, and one thing led to another...  Here is our [https://www.youtube.com/watch?v=Tdfws3g3R2s 'teaser' video] from when we were semi-finalists for the xprize!
+RA got Guy and Fran in too, and one thing led to [https://app.jogl.io/project/181 another]...  Here is our [https://www.youtube.com/watch?v=Tdfws3g3R2s 'teaser' video] from when we were semi-finalists for the xprize!
 The first 'workshop' of this [https://app.jogl.io/project/181/coronadetective method to detect the virus] causing Covid-19, inspired by the [https://gmodetective.com/ GMO Detective], was held on the evening of 9June21, and was virtual, as part of the [https://bbkopenscience.com/streaming/ BBK open science festival]!<br>
@@ Line 72: / Line 72: @@
 *the whole JOGL 'project nucleic amplification team' and Thomas Landrain for support!
 *you?
 ===Main Goals ===
@@ Line 83: / Line 82: @@
 ==Recommendation + next steps ==
-organising reliable GMP batches for independent validation  by regulators has been a great difficulty, with it being hard to reach agreements at such a distance with no actual meetings.  Additionally, it seems likely that licensing agreements are needed, as not only did extension of LAMP patent get approved, but there is a patent for the QUASR detection method depicted above (from the Sandia national labs in the states...).
+(The following is from January 2022) Organising reliable GMP batches for independent validation  by regulators has been a great difficulty, with it being hard to reach agreements at such a distance with no actual meetings.  Additionally, it seems likely that licensing agreements are needed, as not only did extension of LAMP patent get approved, but there is a patent for the QUASR detection method depicted above (from the Sandia national labs in the states...).
 Currently, we are in discussion with people in Ghana as those moronic variants get spread... (yes, sorry, sometimes only humor can help us realise - if people already knew more when this started and were strict the first 2 months, we might not be here 2 years later! -almost, yes...)
 [[Category:Work In Progress]]
 [[Category:Manual]]

@@ Line 1: / Line 1: @@
 This last pandemic year has brought together a lot of open collaborative research, including...
 [[File:CoronaDetectiveLogo.png|300px|thumb|]]
@@ Line 6: / Line 8: @@
 Here is our recent [[:File:SimplerOnePager Accurate Inexpensive Covid 19 Testing for Low Resource Settings.pdf|simple one page summary]] to seek more partners to help get this out where it is needed most!
-We have a new graphic to explain how the 'quenched fluorescence' detection method works.
+We have a new graphic, QuasrGraphic3 (below right), to explain how the amazing 'quenched fluorescence' detection method works, which provides such clear positive and negative endpoint results in Corona Detective reactions.

@@ Line 1: / Line 1: @@
 This last pandemic year has brought together a lot of open collaborative research, including...
 [[File:CoronaDetectiveLogo.png|300px|thumb|]]
-== The Corona Detective Project ==
+'''The Corona Detective Project'''
 [[File:Charla-rachel-2-final.jpg|thumb]]
 Here is our recent [[:File:SimplerOnePager Accurate Inexpensive Covid 19 Testing for Low Resource Settings.pdf|simple one page summary]] to seek more partners to help get this out where it is needed most!
@@ Line 26: / Line 14: @@
 <br>
-== Introduction ==
+==Introduction==
 This wiki page is under construction, to provide more information about this method for surveillance testing!
-=== Context ===
+===Context===
 When the pandemic began, RA (as CSO of AGiR!) of course began some corona virus 'sequence gazing' ...
 Thomas Landrain's visit to Hackuarium was put off by 'lockdown' - but a big collaboration developed in the platform of his Just One Giant Lab (JOGL).
 RA got Guy and Fran in too, and one thing led to another...  Here is our [https://www.youtube.com/watch?v=Tdfws3g3R2s 'teaser' video] from when we were semi-finalists for the xprize!
-=== People ===
+=== People===
 '''Contact and lead:'''
 *Rachel Aronoff - Founder and CSO of AGiR! Action for Genomic integrity through Research!
 '''Participants:'''
-* Tatiana Eliseeva
+*Tatiana Eliseeva
-* Guy Aidelberg
+*Guy Aidelberg
-* Fran Quero
+*Fran Quero
-* the whole JOGL 'project nucleic amplification team' and Thomas Landrain for support!
+*the whole JOGL 'project nucleic amplification team' and Thomas Landrain for support!
-* you?
+*you?
-=== Main Goals ===
+===Main Goals ===
 Surveillance screening for Covid-19
-=== Objectives ===
+===Objectives===
-*open science collaboration to develop a sensitive molecular diagnostic method
+* open science collaboration to develop a sensitive molecular diagnostic method
 *testing and validation
 *manufacturing at scale, to obtain regulator approval for surveillance screening (also of those with no symptoms)
-== Recommendation + next steps ==
+==Recommendation + next steps ==
-licensing agreements are needed! not only did extension of LAMP patent get approved, but there is a patent for the QUASR detection method depicted above. (from the Sandia national labs in the states...)
+organising reliable GMP batches for independent validation  by regulators has been a great difficulty, with it being hard to reach agreements at such a distance with no actual meetings.  Additionally, it seems likely that licensing agreements are needed, as not only did extension of LAMP patent get approved, but there is a patent for the QUASR detection method depicted above (from the Sandia national labs in the states...).
 [[Category:Work In Progress]]
 [[Category:Manual]]

@@ Line 14: / Line 14: @@
 Versions in [https://drive.google.com/file/d/1dh8CtQ7T2gQDi0DfiUOVVBhu_V2wJViS/view?usp=sharing French] and [https://drive.google.com/file/d/1C6MxYRJEE3w7GJvJwHqevOMWM-C734HL/view?usp=sharing Spanish] are available too, already!
-Here is our latest [[:File:SimplerOnePager Accurate Inexpensive Covid 19 Testing for Low Resource Settings.pdf|simple one page summary]] to seek more partners to help get this out where it is needed most!
+With our Colombian colleagues we also discussed the method virtually also, as the 2nd of a 3-part series of talks (Oct2020).
 [[File:MinilogoB.jpg |200px|thumb|]]

← Older revision		Revision as of 10:15, 6 October 2021
Line 11:		Line 11:

	The latest [http://wiki.hackuarium.ch/w/File:CoronaDetective_simpleUSERprotocol.pdf 'simple' protocol is available here], and your input is welcome.<br>		The latest [http://wiki.hackuarium.ch/w/File:CoronaDetective_simpleUSERprotocol.pdf 'simple' protocol is available here], and your input is welcome.<br>
−	Versions in [https://drive.google.com/file/d/1dh8CtQ7T2gQDi0DfiUOVVBhu_V2wJViS/view?usp=sharing French] and [https://drive.google.com/file/d/1C6MxYRJEE3w7GJvJwHqevOMWM-C734HL/view?usp=sharing Spanish] are available too, already!	+	Versions in [https://drive.google.com/file/d/1dh8CtQ7T2gQDi0DfiUOVVBhu_V2wJViS/view?usp=sharing French] and [https://drive.google.com/file/d/1C6MxYRJEE3w7GJvJwHqevOMWM-C734HL/view?usp=sharing Spanish] are available too, already!
		+
		+	Here is our latest [[:File:SimplerOnePager Accurate Inexpensive Covid 19 Testing for Low Resource Settings.pdf\|simple one page summary]] to seek more partners to help get this out where it is needed most!
		+