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CSTE National ELR Workgroup

Welcome to the CSTE National ELR Workgroup Basecamp! We hope you will utilize the space to share resources with colleagues, start discussion threads, and identify topics for the workgroup to tackle on future calls. All workgroup members will have the opportunity to join. Please note that you may edit your notification preferences to suit your needs (and your email inbox). If you are not already on the ELR distribution list and would like to receive call communications, please enroll using this subscription form (copy and paste in browser): https://app.smartsheet.com/b/form/5a91a4579952496682084796b82112e6
Becky Lampkins, Manager, Surveillance/Informatics Program at CSTEMegan Toe, CSTEScott Troppy, Surveillance Epidemiologist at MA DPHMeredith Lichtenstein, CSTEAmy Drake, NMJohn RobertsNancy Barrett, Epi 4/PH Informatics SpecialistErin Holt, TDHRita Altamore, EpidemiologistDavid DiCesareJason HallWalter Kemper, ELR Coordinator, NC DHHS Div of Public HealthJulie LuepkeCarmen Pugh, Labcorp Manager State Reporting at LabCorpTom Safranek +399 others
Posted by Annie Fine ·

Forwarding of pos SARS-CoV-2 specimens from commercial labs for WGS

Hi everyone, and happy holidays!  For those of you who are working, we just had an issue come up where a commercial lab (ARUP) raised the issue of being required to forward all positive SARS-CoV-2 specimens to some state health departments, and within a short timeframe. CDC informed us that ARUP said 16 jurisdictions are requiring submissions for purposes of WGS. I wondered if you could let us know 

1) if your jurisdiction does require submissions - 
2) from which labs
3) all vs a sample or based on certain criteria?
4) within what timeframe

I know there is existing APHL guidance (https://www.aphl.org/programs/preparedness/Crisis-Management/Documents/SCoV-2-genetic-seq-rec.pdf) that does recommend that jurisdictions conduct local WGS and also recommends 300 samples a week, and doing sequencing within 7 days of specimen collection, which does imply rapid turnaround at commercial labs. The guidance was written a while ago and may need to be updated.

Labs may have a difficult time complying given the current volume I guess.

Thank you!!

Comments & Events

Robb Byres Robb Byres
Good morning

Idaho does not require labs to send samples for WGS but does request that they do. Idaho has a preferred criteria for PCR positives with a Ct <= 30 but does not restrict to that criteria.

Thank You

Robb
Notified 300 people
Karla Norsworthy Karla Norsworthy
NC encourages labs to send samples for sequencing - but does not require it.  
Notified 300 people
Danny Power Danny Power
Montana is also not requiring labs to send samples for WGS, we accept them from labs/providers that want sequencing performed, but do not require every sample to be sequenced.
Notified 300 people
Tamara Hennessy Burt Tamara Hennessy Burt
California is not requiring commercial labs to send samples for WGS.
Notified 301 people
Deb Loniewski Deb Loniewski
Michigan does not require commercial labs to submit samples for sequencing.

Best regards,
Deb Loniewski
Michigan Dept. Health and Human Services
Notified 301 people
John Satre, Informatician at Iowa Department of Public Health John Satre, Informatician
Iowa does not require labs to submit samples for sequencing, but Iowa's public health lab does receive a certain number of samples provided by voluntary sentinel surveillance participants on a regular basis.

John Satre
Iowa Department of Health and Human Services
Notified 301 people
Cody McNeese Cody McNeese
Oregon does not require the forwarding of all SARS-CoV-2 specimens that are positive for WGS. 

Happy Holidays, 

Cody McNeese
Oregon Health Authority
Notified 301 people
Peter Schmit Peter Schmit
In Minnesota, our current guidance is that all laboratories (regardless of size): Submit up to 10 specimens per week with a Ct ≤ 30. 

In addition, we request labs send ALL positive specimens with a Ct value of ≤30 from:
  • hospitalized SARS-CoV-2 positive patients and
  • patients with failures of monoclonal antibody treatment.
If their testing platform does not generate a Ct value, we ask that they submit any positive specimens following the current guidance above.
Notified 301 people
Abhilasha Saxena, ELR Coordinator/Epidemiologist Abhilasha Saxena, ELR Coordinator/Epidemiologist
Tennessee does not require labs to forward positive SARS-CoV-2 specimens for WGS.  
- 
Abhi
ELR Coordinator
Tennessee Department of Health
Notified 301 people
Lori Walker Lori Walker
Oklahoma does require submissions of samples for sequencing. 

1) if your jurisdiction does require submissions – Yes, under OAC 310:517, Novel Coronavirus Regulations. 
 2) from which labs – Required from all hospitals/laboratories in Oklahoma; strongly encouraged for external laboratories when testing Oklahoma residents
 3) all vs a sample or based on certain criteria? – Minimum 10% of positive specimens collected in a media suitable for sequencing
 4) within what timeframe - Weekly
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Annie Fine, CSTE Annie Fine
You all are amazing. Thank you so much for taking the time to respond!  Have a wonderful holiday.

Annie
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Meagan Burns, Surveillance Epidemiologist at MA DPH Meagan Burns, Surveillance Epidemiologist
Massachusetts does not currently require anything to be submitted. We have in the past requested samples from commercial and clinical labs be sent to our SPHL based on selection criteria (vaccine breakthrough cases, CT value, S gene target failure) if they weren't being sequenced elsewhere.
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Charlotte Picard Charlotte Picard
Illinois does not require submissions for sequencing, submission is voluntary. We receive samples on a weekly basis and maintain communication with submitters regarding how many samples are needed to meet our target each week. The number varies depending on testing volumes, positivity rate, and CT values.
Notified 301 people