Variant Reporting
Hi all,
I'm not sure what shape all of your jurisdiction are in relative to the prevalence of variant COVID-19, but we're certainly up there for B.1.1.7
Attached, you'll see a list of what we get from our CDC liaison. From that list, we copy out the specimen numbers and send them to the identified laboratory contact. Then we wait. (the labs, we've gotten messages from three so far), return the identified information, or access to the identified information on their secure site. Each lab has their own mechanism. Every lab provides different levels of information as well.
Once we get the identified information, we have to take that an pair it to existing records in our surveillance system because the lab should have already reported these as a confirmed case, but .... on some rare occasions they haven't, and on others the new information doesn't match to the existing information as well as it could. To do the match, we take this new information and add it to a variant line list, we then add the investigation ID's from our surveillance system to the line list as we find them during our match. Then we open all of the records and add a variant name (to date. mostly b.1.1.7).
In the meantime, we are getting much the same from our own public health laboratory. Next we take that list of ID's and forward it to the appropriate local health jurisdictions for follow up (we've been asking that they re-visit the cases, confirm the isolation status, re-elicit contact information and place all quarantined contacts on a full 14 day quarantine)
How many to date, over 990 (vast majority B.1.1.7).
We don't need to have the sequence transmitted, we need an electronic message that is rich enough to automatically pair to a record in our surveillance system without deduplication and contains a standard variant identifier. If CDC wants to throw in the GSAID number later, that's swell, we'll need it by the same mechanism though. We should also get some guidance on when a variant is no longer a variant if you know what I mean.
This system, while well intention as an effort to identify variant infections, was not well thought out in terms of information sharing and I really don't see any hallmarks of jurisdictional participation in the process to date. The partnership is failing here and the results are disheartening.
My Morning Take on this,
Jim
From this information
I'm not sure what shape all of your jurisdiction are in relative to the prevalence of variant COVID-19, but we're certainly up there for B.1.1.7
Attached, you'll see a list of what we get from our CDC liaison. From that list, we copy out the specimen numbers and send them to the identified laboratory contact. Then we wait. (the labs, we've gotten messages from three so far), return the identified information, or access to the identified information on their secure site. Each lab has their own mechanism. Every lab provides different levels of information as well.
Once we get the identified information, we have to take that an pair it to existing records in our surveillance system because the lab should have already reported these as a confirmed case, but .... on some rare occasions they haven't, and on others the new information doesn't match to the existing information as well as it could. To do the match, we take this new information and add it to a variant line list, we then add the investigation ID's from our surveillance system to the line list as we find them during our match. Then we open all of the records and add a variant name (to date. mostly b.1.1.7).
In the meantime, we are getting much the same from our own public health laboratory. Next we take that list of ID's and forward it to the appropriate local health jurisdictions for follow up (we've been asking that they re-visit the cases, confirm the isolation status, re-elicit contact information and place all quarantined contacts on a full 14 day quarantine)
How many to date, over 990 (vast majority B.1.1.7).
We don't need to have the sequence transmitted, we need an electronic message that is rich enough to automatically pair to a record in our surveillance system without deduplication and contains a standard variant identifier. If CDC wants to throw in the GSAID number later, that's swell, we'll need it by the same mechanism though. We should also get some guidance on when a variant is no longer a variant if you know what I mean.
This system, while well intention as an effort to identify variant infections, was not well thought out in terms of information sharing and I really don't see any hallmarks of jurisdictional participation in the process to date. The partnership is failing here and the results are disheartening.
My Morning Take on this,
Jim
From this information
Comments & Events
Kathy Turner,
Deputy State Epidemiologist
Jim – your process is extremely similar to Idaho’s. Nearly completely manual processes, multiple email processes, etc.