SARS-CoV-2 Variant Reporting
Hello,
On the weekly extended ELR call discussing variant reporting, getting GISAID IDs, info back from CDC, etc. I suggested we have a call about this. I think it would be good to include some of the epi staff who work with the info in our states (not all of us on those calls do both capture of info and the epi follow up in GISAID etc.)
Suggestions for when/where to have this call? I'm thinking an hour would be needed so we either 'take over' one of the weekly ELR calls, or set up a separate call or....
Agenda items welcome - from what I heard here are some topic ideas.
1. What labs are doing sequencing and how they report -- Vanessa Holley is setting up a spreadsheet for states to put that information and will share shortly (thanks CA and MA for giving lists to Vanessa as start). Are there any other things we need to know about how each of these reporters are sending this info? How do ensure the original positive PCR result was sent?
2. GISAID IDs - are we getting them? How to get from CDC? Lookups in GISAID to find an ID. What happens with discrepancies.
I'm sure there are other items - please add.
Let me know what you think and what would be helpful.
thanks all!
On the weekly extended ELR call discussing variant reporting, getting GISAID IDs, info back from CDC, etc. I suggested we have a call about this. I think it would be good to include some of the epi staff who work with the info in our states (not all of us on those calls do both capture of info and the epi follow up in GISAID etc.)
Suggestions for when/where to have this call? I'm thinking an hour would be needed so we either 'take over' one of the weekly ELR calls, or set up a separate call or....
Agenda items welcome - from what I heard here are some topic ideas.
1. What labs are doing sequencing and how they report -- Vanessa Holley is setting up a spreadsheet for states to put that information and will share shortly (thanks CA and MA for giving lists to Vanessa as start). Are there any other things we need to know about how each of these reporters are sending this info? How do ensure the original positive PCR result was sent?
2. GISAID IDs - are we getting them? How to get from CDC? Lookups in GISAID to find an ID. What happens with discrepancies.
I'm sure there are other items - please add.
Let me know what you think and what would be helpful.
thanks all!
Sincerely,
Chris Baumgartner
Senior Data Exchange Manager
Office of Public Health Outbreak Coordination, Informatics, and Surveillance (PHOCIS)
Division of Disease Control and Health Statistics
Washington State Department of Health
chris.baumgartner@doh.wa.gov<mailto:chris.baumgartner@doh.wa.gov>
206-418-5530 | www.doh.wa.gov<http://www.doh.wa.gov/>
[cid:image001.png@01D7CC99.301CDEE0]<https://www.doh.wa.gov/Newsroom/SocialMedia>
P.S. I sometimes work flexible hours, so while it suits me to email now, I don't expect a response or action outside of your own working hours.
"This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy the message."
Riki
Thanks,
Carmen Pugh
Labcorp State Reporting
Thank you!
Agenda - Update on Reporting of Variant Sequencing results
1. Overview -
a) Slide of variants in US - any changes in variants of concern?
2. Testing
a) CDC contracted labs
b) State contracted labs
3. Reporting
a) Main reporting issues in terms of the messages sent/received
4. GISAID and other IDs
a) Two main repositories -- GISAID and NCBI (?)
b) what do these IDs look like?
c) How do we get the ID if not provided by the lab?
d) What type of review should be done to reconcile differences in these IDs and results (WA state analysis).
Anything else?
Nancy
Thank you for continuing this discussion. Here's some suggested additions with a little background/details for each.
If any further information I can provide to assist please do not hesitate to contact me.
Under (3) Reporting, may want to consider adding:
1. Standardization of coding system and naming convention for Test results (OBX-5 value)
1. OBX 5.1
* Standard for PLR codes (or other coding system) that may be used in OBX 5.1.
i. Where is the centralized location that all other labs may use to access this code list?
ii. What is the mechanism for informing all other labs when updates occur to those codes?
1. OBX 5.2
* Standards for naming convention for test itself in OBX 5.2 would improve data consistency
i. Inconsistent naming conventions. Some examples below.
* SARS-CoV-2 B.1.526 lineage
* SARS-CoV-2-B.1.526 lineage
* SARS-CoV-2 variant B.1.526 lineage
Under (4) GISAID and other IDS, may want to consider adding:
1. Issues retrieving results from repository based on sequencing ID provided by lab in ELR
* NTE?
i. HL7 messages currently do not specify which repository was used. What is the recommended location for repository name to be specified?
* OBX 5
i. Lab assigned Sequence ID - LOINC 98062-3
* Does the HL7 result message include the lab assigned sequencing ID reported to the repository?
* Is that sequencing ID uniquely identified with the LOINC 98062-3 in an OBX including both the 98062-3 LOINC value and lab assigned ID value?
* Can CDC / data repositories provide consistent explanation of the relationship of the repository assigned sequence ID to the lab assigned sequence ID?
* For example, for some labs, the GISAID repository appears to add a set character string prior to the lab assigned sequencing ID
* What other transformations are performed by the repository to generate the repository sequence ID form the lab assigned sequence ID?
Thank you,
Kathleen Figetakis
Also - what effort at the state side would it take to capture these additional IDs and transform them?
One more thing to add to the agenda is whether facilities are really required to report the sequencing results. (We are requiring those that we fund to do sequencing to report them - but I'm not sure that there is a broad set of guidance requiring consistent reporting.)
Let me know what you think.
Thanks!
Nancy
Sincerely,
Chris Baumgartner
Senior Data Exchange Manager
Office of Public Health Outbreak Coordination, Informatics, and Surveillance (PHOCIS)
Division of Disease Control and Health Statistics
Washington State Department of Health
chris.baumgartner@doh.wa.gov<mailto:chris.baumgartner@doh.wa.gov>
206-418-5530 | www.doh.wa.gov<http://www.doh.wa.gov/>
[cid:image001.png@01D7DAE2.BF978000]<https://www.doh.wa.gov/Newsroom/SocialMedia>
P.S. I sometimes work flexible hours, so while it suits me to email now, I don't expect a response or action outside of your own working hours.
"This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential or privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy the message."