Infokiri
| Dokumendiregister | Terviseamet |
| Viit | 13.2-7/24/1288-1 |
| Registreeritud | 01.02.2024 |
| Sünkroonitud | 27.03.2024 |
| Liik | Sissetulev dokument |
| Funktsioon | 13.2 Nakkushaiguste labor |
| Sari | 13.2-7 NHL kirjavahetus |
| Toimik | 13.2-7/2024 |
| Juurdepääsupiirang | Avalik |
| Juurdepääsupiirang | |
| Adressaat | European Centre for Disease Prevention and Control |
| Saabumis/saatmisviis | European Centre for Disease Prevention and Control |
| Vastutaja | Irina Odintsova (TA, Peadirektori asetäitja (2) vastutusvaldkond, Rahvatervise labor, Nakkushaiguste labor) |
| Originaal | Ava uues aknas |
Failid
From: Johanna Kristina Tamm
Sent: Thu, 01 Feb 2024 11:29:47 +0000
To: Regina Russanova <[email protected]>
Cc: Karita Helde <[email protected]>; Janne Pullat <[email protected]>; Irina Odintsova <[email protected]>; Marliin Koolmeister <[email protected]>
Subject: Ed: To OCPs FOR ACTION: Register for the EurIrina Odintsova <[email protected]>opean SARS-CoV-2 and influenza Bioinformatics External Quality Assessment (ESIB-EQA)
Tere
Registeerisin meid SARS-CoV-2 ja Influenza bioinformaatika välisvõrdluskatsele.
Heade soovidega
Johanna Kristina Tamm
laborispetsialist
nakkushaiguste labor
+372 794 3637 | +372 5561 0493
| Terviseamet +372 794 3500 [email protected] Paldiski mnt 81, 10614 Tallinn |
Käesolev kiri on konfidentsiaalne ning mõeldud kasutamiseks kirja päises nimetatud isikule/asutusele. Käesoleva kirja mistahes viisil kasutamine või kopeerimine isiku poolt, kes ei ole märgitud selle adressaadiks, on keelatud. Kui te olete saanud käesoleva kirja ekslikult, palume sellest koheselt teavitada kirja saatjat ning kustutada saadud kiri koos kõikide lisadega.
Saatja: ECDC respiratory viruses <[email protected]>
Saatmisaeg: kolmapäev, 31. jaanuar 2024 16:39
Koopia: ECDC Info <[email protected]>
Teema: To OCPs FOR ACTION: Register for the European SARS-CoV-2 and influenza Bioinformatics External Quality Assessment (ESIB-EQA)
Tähelepanu! Tegemist on väljastpoolt asutust saabunud kirjaga. Tundmatu saatja korral palume linke ja faile mitte avada. |
To: Operational Contact Points for COVID-19 and Influenza (Microbiology)
Dear colleagues,
We would like to inform you about the forthcoming European SARS-CoV-2 and influenza Bioinformatics External Quality Assessment (ESIB-EQA) planned for the beginning of March 2024.
This year, the ESIB-EQA will focus specifically on influenza viruses of zoonotic origin. The SARS-CoV-2 part on the other hand will focus as before on mainly currently circulating viruses.
The ESIB-EQA is facilitated by RIVM and Institut Pasteur.
Please find the invitation letter attached for more details and registration and note that Laboratories must confirm their participation by 14 February 2024.
This invitation has also been sent out to the Operational Contact Points for COVID-19 and Influenza and the National Focal Points for Viral Respiratory Diseases. If applicable, please coordinate with these colleagues to ensure optimal participation of staff involved in the bioinformatic processing and analysis of Influenza and/or SARS-CoV-2 sequences.
With thanks and best wishes,
The ECDC COVID-19 and Influenza Laboratory and Surveillance Teams
|
Confidentiality Notice
If you are not the intended recipient of this message, you are hereby kindly requested, to, consecutively, refrain from disclosing its content to any third party, delete it and inform its sender of the erroneous transmittal.
1
Contribution ID: b51258ec-7a65-4e91-aba4-fdefd08a96dc Date: 01/02/2024 12:22:08
European SARS-CoV-2 and Influenza Bioinformatics EQA
2024
Fields marked with * are mandatory.
European SARS-CoV-2 and Influenza virus Bioinformatics EQA 2024
Participation Registration Form
Please complete this online registration form to before 12 February 2024
register your laboratory's participation in the ESIB-EQA 2024.
Contact Information
Name contact person
Johanna Kristina Tamm
Institute
*
*
2
Health Board
Street and number
Paldiski mnt 81
City
Tallinn
Postal code
10614
Country
Estonia
Email address
Telephone number
+37255610493
Which SARS-CoV-2 EQA components will your laboratory participate in?
SARS1 (Nanopore reads, 20 fastq files): Yes No
SARS2 (Illumina reads, around 20 fastq files): Yes No
SARS3 (clustering and classification, around 20 genomes): Yes No
SARS4 (mutation detection, around 10 genomes): Yes
*
*
*
*
*
*
*
*
*
*
3
No
Which influenza virus EQA components will your laboratory participate in?
INFL1/3/4 (Nanopore reads for 10 samples generated as part of wetlab EQA; clustering and classification; resistance prediction):
Yes No
INFL2/3/4 (Illumina reads for 10 samples generated as part of wetlab EQA; clustering and classification; resistance prediction):
Yes No
Additional Comments
In case you have particular points for us to keep in mind about your participation, please add them here.
Thank you for completing this participation registration form!
Contact Contact Form
*
*
4
January 2024
European SARS-CoV-2 and influenza virus Bioinformatics External
Quality Assessment (ESIB-EQA 2024)
Dear colleagues,
Herewith you can find all the necessary information about the forthcoming European SARS-CoV-2 and influenza virus Bioinformatics External Quality Assessment (ESIB-EQA) planned for the beginning of March 2024.
Rationale
It is essential that the reliability and robustness of technologies for SARS-CoV-2 and influenza virus sequencing data analysis are assessed through effective Quality Control (QC) within all National Influenza Centers and national reference laboratories for SARS-CoV-2. An integral part of QC is external quality assessment (EQA). Regular participation in EQA programmes will provide confidence in the techniques performed at a national level and therefore in the results reported. This ESIB-EQA, now in its second iteration, is dedicated to sequence analyses primarily conducted through bioinformatic workflows. The influenza virus part of the EQA is held together with the regular European External Influenza virus Quality Assessment Programme (EEIQAP). This year, the EEIQAP and ESIB-EQA will focus specifically on influenza viruses of zoonotic origin. The SARS-CoV-2 part on the other hand will focus as before on mainly currently circulating viruses.
As data from NICs/national reference laboratories are reported to The European Surveillance System (TESSy) and analysed and published weekly at a European level, this EQA also helps ensure the quality and validity of the results. Furthermore, EQA studies provide useful information for targeting capacity building measures to participating laboratories, Member States, and ECDC but also to other stakeholders including the European Commission and the World Health Organization (WHO). Over time, results from this EQA can be used to monitor the impact of training and support and determine priorities for future training and support for the network. Therefore, participation in this EQA is strongly recommended.
The major objective of the ESIB-EQA 2024 is to examine the ability of laboratories to generate full-length consensus genome sequences from raw sequence reads, perform clustering and classification of full-length genomes as well as mutational analysis for both SARS-CoV-2 and influenza viruses. In the case of influenza, it also includes prediction of the antiviral susceptibility profile, as well as host adaptation mutations.
Objectives
The ESIB-EQA 2024 will consist of eight different components, described in Table 1. Laboratories can choose which EQA components they want to participate in. The four components for SARS-CoV-2 will be organised by RIVM in the Netherlands, and the four components for influenza by Institut Pasteur in France.
Each EQA component assesses a different type of analysis and, in the case of SARS-CoV-2, is designed to be entirely independent from any of the other components, so that specifically the performance on the type of analysis in question can be assessed. A separate dataset will consequently be made available for each component for SARS-CoV-2, and the date that this is made available will be used as the start time for measuring processing time as an additional performance metric.
Table 1: EQA components that laboratories can participate in.
Id
Organism
Samples
Objective
SARS1
SARS-CoV-2
20
Consensus sequence generation from complete amplicons based on Nanopore reads.
SARS2
SARS-CoV-2
20
Consensus sequence generation from fragmented amplicons based on Illumina reads.
SARS3
SARS-CoV-2
20
Clustering and classification of full-length genomes.
SARS4
SARS-CoV-2
10
Detection of particular amino-acid substitutions.
INFL1, INFL3, INFL4 (linked)
Influenza (zoonotic, in human)
10
Consensus sequence generation from complete amplicons or metagenomic sequencing based on Nanopore reads (INFL1).
Clustering and classification of full-length genomes (INFL3).
Prediction of reduced susceptibility to antivirals and/or host adaptation mutations (major and minor variants) (INFL4).
INFL2, INFL3, INFL4
(linked)
Influenza (zoonotic, in human)
10
Consensus sequence generation from fragmented amplicons or metagenomic sequencing based on Illumina reads (INFL2).
Clustering and classification of full-length genomes (INFL3).
Prediction of reduced susceptibility to antivirals and/or host adaptation mutations (major and minor variants) (INFL4).
Further details regarding performing each EQA component will be provided upon confirmation of participation.
Distribution of the datasets
The dataset for each EQA component will be made available for download to each participant. The datasets will be encrypted, and each participating laboratory will be provided with the password the moment they indicate they are ready to start the EQA for that component.
Data collection
Data will be collected by means of a filled-in reporting template sent by email. The receipt of this email will count as the end time of the EQA component in question.
Timeline for EQA
• Laboratories must confirm their participation for selected EQA components by 14 February 2024.
• The EQA is expected to be open between 1 March and 1 April 2024.
• During this period, participants need to complete each EQA component that they chose to participate in.
Reports
Each participating laboratory will receive a report with the expected results after the last participant has completed submission of results including details on their own performance in the EQA. After completion of data analysis all participants will receive an overall EQA report that will also be published on the ECDC website including pseudonymized or aggregated data.
Certificate
Each laboratory will receive a certificate of participation for those EQA components that they completed data submission for.
Intellectual property
After completion of the study, the cleaned and analysed ESIB-EQA data reported to RIVM and Institut Pasteur will be transferred to ECDC. Ownership of these data is with ECDC.
RESPONSE REQUIRED FROM PARTICIPANT
Please complete all boxes of the ESIB-EQA 2024 Participation Registration Form to register your laboratories participation in the ESIB-EQA 2024 exercise before 14 February 2024.
Link: https://ec.europa.eu/eusurvey/runner/BioinformaticsEQA2024. In case of technical problems, please use the form on the next page and return the completed form to [email protected].
Yours sincerely,
Ivo van Walle and Etienne Simon-Loriere
Ivo van Walle, PhD
Senior researcher
Centre for Infection Research, Diagnostics and Laboratory Surveillance
Dutch National Institute for Public Health and the Environment (RIVM)
Bilthoven, The Netherlands
Phone: +31 6 31138351
[email protected]
Etienne Simon-Loriere, PhD
G5 Evolutionary Genomics of RNA Viruses
Virology Department
Institut Pasteur
Paris, France
[email protected]
ESIB-EQA 2024 Participation Registration Form
Contact person for this ESIB-EQA:
[Name contact person]
[Institute]
[Street & number]
[City]
[Post Code]
[Country]
[Email address]
[Telephone number]
Which EQA components will your laboratory participate in (strongly recommended to participate in all the components for which you perform the corresponding analyses in your laboratory):
SARS1 (Nanopore reads)
Yes / No
SARS2 (Illumina reads)
Yes / No
SARS3 (clustering, classification)
Yes / No
SARS4 (mutation detection)
Yes / No
INFL1+INFL3+INFL4 (Nanopore reads)
Yes / No
INFL2+INFL3+INFL4 (Illumina reads)
Yes / No
In case you have particular points for us to keep in mind about your participation, please add them here
Return by email before 14 February 2024 to: [email protected]
From: ECDC respiratory viruses <[email protected]>
Sent: Wed, 31 Jan 2024 14:33:18 +0000
Cc: ECDC Info <[email protected]>
Subject: To OCPs FOR ACTION: Register for the European SARS-CoV-2 and influenza Bioinformatics External Quality Assessment (ESIB-EQA)
|
Tähelepanu! Tegemist on väljastpoolt asutust saabunud kirjaga. Tundmatu saatja korral palume linke ja faile mitte avada. |
To: Operational Contact Points for COVID-19 and Influenza
Cc: National Focal Points for Viral Respiratory Diseases, National Coordinators
Dear colleagues,
We would like to inform you about the forthcoming European SARS-CoV-2 and influenza Bioinformatics External Quality Assessment (ESIB-EQA) planned for the beginning of March 2024.
This year, the ESIB-EQA will focus specifically on influenza viruses of zoonotic origin. The SARS-CoV-2 part on the other hand will focus as before on mainly currently circulating viruses.
The ESIB-EQA is facilitated by RIVM and Institut Pasteur.
Please find the invitation letter attached for more details and registration, and note that Laboratories must confirm their participation by 14 February 2024.
With thanks and best wishes,
The ECDC COVID-19 and Influenza Laboratory and Surveillance Teams
|
Confidentiality Notice
If you are not the intended recipient of this message, you are hereby kindly requested, to, consecutively, refrain from disclosing its content to any third party, delete it and inform its sender of the erroneous transmittal.
January 2024
European SARS-CoV-2 and influenza virus Bioinformatics External
Quality Assessment (ESIB-EQA 2024)
Dear colleagues,
Herewith you can find all the necessary information about the forthcoming European SARS-CoV-2 and influenza virus Bioinformatics External Quality Assessment (ESIB-EQA) planned for the beginning of March 2024.
Rationale
It is essential that the reliability and robustness of technologies for SARS-CoV-2 and influenza virus sequencing data analysis are assessed through effective Quality Control (QC) within all National Influenza Centers and national reference laboratories for SARS-CoV-2. An integral part of QC is external quality assessment (EQA). Regular participation in EQA programmes will provide confidence in the techniques performed at a national level and therefore in the results reported. This ESIB-EQA, now in its second iteration, is dedicated to sequence analyses primarily conducted through bioinformatic workflows. The influenza virus part of the EQA is held together with the regular European External Influenza virus Quality Assessment Programme (EEIQAP). This year, the EEIQAP and ESIB-EQA will focus specifically on influenza viruses of zoonotic origin. The SARS-CoV-2 part on the other hand will focus as before on mainly currently circulating viruses.
As data from NICs/national reference laboratories are reported to The European Surveillance System (TESSy) and analysed and published weekly at a European level, this EQA also helps ensure the quality and validity of the results. Furthermore, EQA studies provide useful information for targeting capacity building measures to participating laboratories, Member States, and ECDC but also to other stakeholders including the European Commission and the World Health Organization (WHO). Over time, results from this EQA can be used to monitor the impact of training and support and determine priorities for future training and support for the network. Therefore, participation in this EQA is strongly recommended.
The major objective of the ESIB-EQA 2024 is to examine the ability of laboratories to generate full-length consensus genome sequences from raw sequence reads, perform clustering and classification of full-length genomes as well as mutational analysis for both SARS-CoV-2 and influenza viruses. In the case of influenza, it also includes prediction of the antiviral susceptibility profile, as well as host adaptation mutations.
Objectives
The ESIB-EQA 2024 will consist of eight different components, described in Table 1. Laboratories can choose which EQA components they want to participate in. The four components for SARS-CoV-2 will be organised by RIVM in the Netherlands, and the four components for influenza by Institut Pasteur in France.
Each EQA component assesses a different type of analysis and, in the case of SARS-CoV-2, is designed to be entirely independent from any of the other components, so that specifically the performance on the type of analysis in question can be assessed. A separate dataset will consequently be made available for each component for SARS-CoV-2, and the date that this is made available will be used as the start time for measuring processing time as an additional performance metric.
Table 1: EQA components that laboratories can participate in.
Id
Organism
Samples
Objective
SARS1
SARS-CoV-2
20
Consensus sequence generation from complete amplicons based on Nanopore reads.
SARS2
SARS-CoV-2
20
Consensus sequence generation from fragmented amplicons based on Illumina reads.
SARS3
SARS-CoV-2
20
Clustering and classification of full-length genomes.
SARS4
SARS-CoV-2
10
Detection of particular amino-acid substitutions.
INFL1, INFL3, INFL4 (linked)
Influenza (zoonotic, in human)
10
Consensus sequence generation from complete amplicons or metagenomic sequencing based on Nanopore reads (INFL1).
Clustering and classification of full-length genomes (INFL3).
Prediction of reduced susceptibility to antivirals and/or host adaptation mutations (major and minor variants) (INFL4).
INFL2, INFL3, INFL4
(linked)
Influenza (zoonotic, in human)
10
Consensus sequence generation from fragmented amplicons or metagenomic sequencing based on Illumina reads (INFL2).
Clustering and classification of full-length genomes (INFL3).
Prediction of reduced susceptibility to antivirals and/or host adaptation mutations (major and minor variants) (INFL4).
Further details regarding performing each EQA component will be provided upon confirmation of participation.
Distribution of the datasets
The dataset for each EQA component will be made available for download to each participant. The datasets will be encrypted, and each participating laboratory will be provided with the password the moment they indicate they are ready to start the EQA for that component.
Data collection
Data will be collected by means of a filled-in reporting template sent by email. The receipt of this email will count as the end time of the EQA component in question.
Timeline for EQA
• Laboratories must confirm their participation for selected EQA components by 14 February 2024.
• The EQA is expected to be open between 1 March and 1 April 2024.
• During this period, participants need to complete each EQA component that they chose to participate in.
Reports
Each participating laboratory will receive a report with the expected results after the last participant has completed submission of results including details on their own performance in the EQA. After completion of data analysis all participants will receive an overall EQA report that will also be published on the ECDC website including pseudonymized or aggregated data.
Certificate
Each laboratory will receive a certificate of participation for those EQA components that they completed data submission for.
Intellectual property
After completion of the study, the cleaned and analysed ESIB-EQA data reported to RIVM and Institut Pasteur will be transferred to ECDC. Ownership of these data is with ECDC.
RESPONSE REQUIRED FROM PARTICIPANT
Please complete all boxes of the ESIB-EQA 2024 Participation Registration Form to register your laboratories participation in the ESIB-EQA 2024 exercise before 14 February 2024.
Link: https://ec.europa.eu/eusurvey/runner/BioinformaticsEQA2024. In case of technical problems, please use the form on the next page and return the completed form to [email protected].
Yours sincerely,
Ivo van Walle and Etienne Simon-Loriere
Ivo van Walle, PhD
Senior researcher
Centre for Infection Research, Diagnostics and Laboratory Surveillance
Dutch National Institute for Public Health and the Environment (RIVM)
Bilthoven, The Netherlands
Phone: +31 6 31138351
[email protected]
Etienne Simon-Loriere, PhD
G5 Evolutionary Genomics of RNA Viruses
Virology Department
Institut Pasteur
Paris, France
[email protected]
ESIB-EQA 2024 Participation Registration Form
Contact person for this ESIB-EQA:
[Name contact person]
[Institute]
[Street & number]
[City]
[Post Code]
[Country]
[Email address]
[Telephone number]
Which EQA components will your laboratory participate in (strongly recommended to participate in all the components for which you perform the corresponding analyses in your laboratory):
SARS1 (Nanopore reads)
Yes / No
SARS2 (Illumina reads)
Yes / No
SARS3 (clustering, classification)
Yes / No
SARS4 (mutation detection)
Yes / No
INFL1+INFL3+INFL4 (Nanopore reads)
Yes / No
INFL2+INFL3+INFL4 (Illumina reads)
Yes / No
In case you have particular points for us to keep in mind about your participation, please add them here
Return by email before 14 February 2024 to: [email protected]
