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Outbreak Sequencing -Temporarily Suspend

Posted Sep 2, 20211 min Read

Regulatory & Clinical

The Indiana Department of Health (IDOH) has decided to temporarily suspend the state’s participation in the CDC sequencing project due to the current delta surge and the need to prioritize resources and operations at the state level and within LTC facilities.


A total of 108 facilities were identified to have had 3 or more cases triggering the outbreak PCR sequencing process. Six of these were identified after we paused the project. Some facilities had performed PCR testing on their own, and some had cases that did not have any contact with the facility during the infectious process, so the PCR process was not initiated at these facilities.

Specimens were collected from 88 facilities as part of the outbreak PCR-sequencing process. A total of 7564 specimens were collected. 7032 had results so far, of which 302 were positive for PCR. Of the positive PCR specimens, 160 had a CT value under 28 which made them suitable for sequencing. The remaining positive PCR specimens did not have a high enough viral load to make sequencing possible.

Of the 160 specimens from 45 facilities that were sequenced, all were identified as delta variant. An additional 108 specimens still have pending results. All facilities with a sequencing result have been notified.

Prior to the project, we were able to collect specimens from five other facilities, one facility’s specimens had alpha variant, and specimens from the four other facilities were delta.

13 specimens were identified by PCR, that were not already known from POC results.