New Ordering Method for SARS-CoV-2 Next Generation Sequencing Test

New Ordering Method for SARS-CoV-2 Next Generation Sequencing Test
August 10, 2021 -- All facilities that wish to submit PCR positive SARS-CoV-2 samples for next generation sequencing are strongly encouraged to use the COVID-19 Electronic Test Request Form that is part of the OpenELIS Web Portal.

This is the same electronic form that is used to order the 2019 Novel Coronavirus Real-Time PCR and SARS-CoV-2 IgG Antibody tests from the State Hygienic Laboratory. Multiple tests can be ordered at the same time on a sample through this electronic form, such as both the PCR and Sequencing tests. Using this electronic test request form instead of a paper form helps to improve the testing turnaround time and reduces possible transcription errors which cause costly time to be spent by both our clients’ and SHL staff on corrections. Questions regarding the OpenELIS Web Portal can be directed to or to 319/335-4358.

There are three important things to keep in mind when determining if the SARS-CoV-2 Next Generation Sequencing test should be ordered.

  1. SHL and IDPH are currently prioritizing sequencing for hospitalized and congregate living facility residents.
  2. Results of the sequencing test are only reported back to IDPH for surveillance purposes. Your facility will not receive these results or be notified of their status.
  3. Sequencing is most successful on samples with Ct values under 28. If you know that the Ct values are 28 or higher, please do not send the sample for sequencing.

Three of the questions on the form are now required to be answered, as they provide information that is valuable to our COVID testing. Please answer the following questions for every sample.

  1. Hospitalized at time of COVID test? Yes/No/Unknown
  2. Resident in a congregate care setting Yes/No/Unknown
  3. Vaccinated for COVID-19 Yes/No/Unknown

Three additional questions are required to be answered if the sequencing test is ordered as these questions provide valuable information to our testing staff as to whether the PCR test needs to be performed first.

  1. PCR performed? Yes/No
  2. PCR platform/manufacturer
  3. Viral Ct values

Together, we will continue to assure a rapid and thorough public health response to the COVID-19 pandemic.

Thank you for all of your work and dedication.