Lab Matters Summer 2022 | Page 10

Photo : Minnesota Public Health Laboratory Division
The Minnesota Molecular Surveillance of SARS-CoV-2 ( MN- SOS ) system led to the discovery and investigation of the first identified case of the P . 1 variant in the US , from someone who had traveled to Brazil .
Conducting Whole Genome Sequencing
To better track and understand COVID-19 outbreaks in Minnesota , the state public health laboratory , in partnership with universities and clinical laboratories , created the Minnesota Molecular Surveillance of SARS-CoV-2 ( MN-SOS ) system to conduct whole genome sequencing to detect variants of concern .
Beginning in December 2020 , the public health laboratory began receiving 50 specimens a week from each of its clinical partners , according to the 2021 APHL poster abstract “ Minnesota Molecular Surveillance of SARS-CoV-2 .” This new system led to the discovery and investigation of the first identified case of the P . 1 variant in the US , from someone who had traveled to Brazil . ( A second P . 1 case was positive in that person ’ s travel partner or household contact .)
“ It was just by chance that we found that case ,” Kunas said . “ We received it as part of the 50 samples per week that we were getting from clinical labs . … The importance of the P . 1 case was to detect and identify cases quickly and to reduce potential spread . Our partners and epidemiologists did a lot of case investigation and contact tracing to identify close contacts .”
Other investigations focused on the first case of the B . 1.1.7 variant in Minnesota and the second Omicron case in the US , according to Kunas .
A more recent challenge that Kunas and her team problem-solved was the overwhelming number of samples they were receiving from clinical laboratories for sequencing during the Omicron surge . They requested 50 samples a week from laboratories but were sometimes getting up to 500 . Kunas admitted the backlog wasn ’ t truly addressed until the public health laboratory had around 11,000 samples in the queue . She pulled in staff from other areas and they worked through the samples over five weeks to eliminate the backlog .
That included identifying laboratories that were submitting too many samples , reducing how many samples were being sent from all laboratories and working with epidemiologist partners to truly prioritize their needs . This meant “ going through freezers to identify how many samples there were , what they were , where they were coming from , and then working with our epis to have a real sit-down like , ‘ We can ’ t do all of these , so let ’ s figure out what makes sense .’”
Next , a project manager created a dashboard to quickly visualize the samples that were arriving each day and to monitor capacity .
“ It ’ s helped everyone with tracking so that we could focus on testing and supporting the team through that challenge ,” Kunas said . “ The lesson learned there is when a team is struggling , they might not have the resources or the capacity to even ask for help until it ’ s a much bigger problem .”
Now , laboratory professionals know to check in and trust the newly-developed dashboard , and leadership knows to support staff differently when they ’ re getting overwhelmed , she said .
Recognition from Lawmakers
Another change at most public health laboratories since the pandemic started is how they are viewed by state and federal lawmakers .
8 LAB MATTERS Summer 2022
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