Variant Reporting
Hello All,
For discussion. My understanding is that CDC has reached and agreement with some national laboratories around the genetic sequencing of a proportion (I assume) of the SAR CoV-2 isolates they confirm. Great idea, I'll add, in that it is part of a multipronged (with PH labs and academia) to identify the introduction of variant virus which can impact on our public health response.
We've been chasing some of the B.1.1.7 variant here in Michigan and I know that the P.1 was identified by Minnesota's PH lab in a returning Brazillian traveller a few days back. Now, we're seeing the B.1.351 variant that was originally identified in South Aftrica, has been identified in South Carolina. I'm not sure if that detection was through a PH lab or commercial.
A couple of nights ago, Michigan got our first couple variant notices of B.1.1.7 variant in the State from a commericial laboratory (Helix Labs in CA). And that got me thinking about something that I'd like this group to consider.
While we are asked to provide ID numbers for the variant cases so that they can be matched to our NEDSS submissions around COVID cases, there is a number that would be of interest to me. The denominator. It seems that if CDC is compensating these commercial labs for this enhanced testing, it would add to our perspective to have a list of how many samples are being analyzed in our jurisdiction, where in our jurisdiction, how they are selected. That type of thing. I do appreciate getting this information, for sure, but I think that context would likely add value.
Could this group help define that context?
Am I off on this?
Trust you guys to tell me the whole what for.
Jim
For discussion. My understanding is that CDC has reached and agreement with some national laboratories around the genetic sequencing of a proportion (I assume) of the SAR CoV-2 isolates they confirm. Great idea, I'll add, in that it is part of a multipronged (with PH labs and academia) to identify the introduction of variant virus which can impact on our public health response.
We've been chasing some of the B.1.1.7 variant here in Michigan and I know that the P.1 was identified by Minnesota's PH lab in a returning Brazillian traveller a few days back. Now, we're seeing the B.1.351 variant that was originally identified in South Aftrica, has been identified in South Carolina. I'm not sure if that detection was through a PH lab or commercial.
A couple of nights ago, Michigan got our first couple variant notices of B.1.1.7 variant in the State from a commericial laboratory (Helix Labs in CA). And that got me thinking about something that I'd like this group to consider.
While we are asked to provide ID numbers for the variant cases so that they can be matched to our NEDSS submissions around COVID cases, there is a number that would be of interest to me. The denominator. It seems that if CDC is compensating these commercial labs for this enhanced testing, it would add to our perspective to have a list of how many samples are being analyzed in our jurisdiction, where in our jurisdiction, how they are selected. That type of thing. I do appreciate getting this information, for sure, but I think that context would likely add value.
Could this group help define that context?
Am I off on this?
Trust you guys to tell me the whole what for.
Jim
We work under the assumption that all of the sequenced records have been reported as confirmed cases already.
Are these records being entered into the international database of sequences?
Who is uploading the sequence information Commercial Lab/CDC?
What information is included in this upload?
Can we get the sequence database ID for the uploads to marry to the existing records in our systems? (just trying to prompt some discussion here, pretty sure there is no existing "home" for this data in any current databases or message guides.)
Your questions are provocative and need to go to Greg Armstrong at CDC who heads the AMD office. I did hear him say that the goals of the NS3 are national, and that state and local objectives of sequence surveillance will be different (e.g. need to take a PH action based on a sequence result).
CSTE is working on regular updates from Greg on NS3, probably on a Tues or Wed regular call. Stay tuned.
Jeff