Next-Generation Sequencing COVID-19 Sample Submission
Sending positive samples to the Infectious Disease Laboratory
March 2023 Update:
The Minnesota Public Health Lab’s Infectious Disease Lab (IDL) has been requesting that a proportion of specimens positive for SARS-CoV-2 be submitted for next generation sequencing (NGS) to better understand the emergence and trends of variants circulating in the community.
Due to the changing dynamics of COVID-19 in Minnesota, we are now requesting an increase in submission of positive SARS-CoV-2 specimens for sequencing to maintain adequate surveillance for detecting new variants.
All laboratories (regardless of size): submit up to 40 positive specimens per week with a Ct ≤ 30.
If your testing platform does not generate a Ct value, please submit any positive specimens following the current guidance above.
Note: MDH-PHL is no longer asking specifically for specimens from vaccine breakthrough cases or suspected re-infection. Those specimens can be submitted as part of the weekly submission for surveillance.
The Minnesota Department of Health (MDH) CloudDrive application is a secure file drop location for standard batch submission spreadsheets. It was designed to make large submissions of 25 or more specimens less time-consuming.
Once your facility is approved, MDH will send you directions for logging into your account and the spreadsheet template for data submission. Files dropped into the CloudDrive will be accessible for 90 days.
CloudDrive login and upload directions (PDF)
If you are interested in using the CloudDrive to submit spreadsheets of 25 specimens or more for sequencing submission, please fill out the CloudDrive Submission Interest Form.
Patient test reports will not be generated for sequencing tests. Minnesota-focused subsampling data correlated by the CDC is available at Nextstrain.
Variant tracking and results reporting: While the Minnesota Department of Health is working internally to provide regular variant updates to the general public, the high-level Minnesota variant report will be shared with submitters via MLS on a bi-weekly basis.
Please Contact the Infectious Disease Laboratory with any questions.