Lab Matters Fall 2023 | Page 68

APHL 2023 POSTER ABSTRACTS

Gotta Catch ‘ Em All : Defining Cost-Effective Variant Surveillance Through Retrospective Analysis of SARS-CoV-2 Whole Genome Sequencing

R . Cox , A . Smith , J . Freeman , G . Godfrey , G . Goodwin , C . Aroh , O . Adair , N . Epie ; South Carolina Department of Health & Environmental Control

New SARS-CoV-2 ( SC2 ) variants are continually arising that modify viral infectivity , vaccine efficacy , and the public health response . The goal of variant surveillance is the detection of viral diversity in a community , allowing for the rapid identification of new variants of concern and enabling the implementation of new pharmacological or non-pharmacological interventions . Establishing a surveillance program that captures the broadest array of variants in a sustainable and cost-effective manner remains an ongoing priority given heightened public interest during epidemics . Here we perform control-matched retrospective analysis of data from PCR testing and sequencing workflows to determine the impact of selective sequencing of samples on the breadth of variants detected , both from the laboratory data and statewide sequencing data . Specifically , we define the impact on variant capture and reagent cost of establishing a cycle threshold limit for sequencing PCR positive samples , modifying sequencing workflow with an Agilent TapeStation quality control reflexed from Qubit QC , and correcting loading concentration to achieve optimal Illumina MiniSeq run metrics . It is hoped that the lessons learned from this pandemic will enable data-driven decisions for establishing an adequately broad variant surveillance program for the next epidemic .

Presenter : Greg Goodwin , goodwigr @ dhec . sc . gov

Maximizing Lessons Learned from Past Outbreaks to Develop a Sustainable Laboratory Cross-training Program

C . Williams , D . Payne , Jocelyn Hauser ; District of Columbia Department of Forensic Sciences Public Health Laboratory Division ,

Although public health laboratories range in complexity and size , all face the unexpected in the form of outbreaks and other public health emergencies . Laboratories must be able to manage the unexpected without disrupting day-to-day operations or reducing the laboratory ’ s efficiency . We performed a retrospective analysis of how our laboratory adapted to accommodate the increased testing demands during both the COVID-19 pandemic and the mpox outbreak of 2022 to develop a sustainable cross-training plan to ensure our laboratory is better prepared for future outbreaks . Here , we describe steps taken to strategically plan a laboratory-wide cross-training program at the District of Columbia Public Health Laboratory ( DC PHL ). DC PHL ’ s cross-training model is centered around coordinating preemptive cross-training in all units to ensure proper coverage for future emergencies . In reviewing our mpox response , it was evident that training staff during the outbreak resulted in substantial lag time and caused added strain for our testing team , as they had to train and test suspected samples . As part of a strategic cross-training plan , we developed a plan that included proactive cross-training which would allow our lab to increase testing capabilities and efficiency while reducing the strain on staff , further improving overall preparedness . Our cross-training plan includes a new hire bootcamp to review basic concepts , such as pipetting , quality control , accessioning and LIMS . Training ensured a baseline competency and reduced the amount of time required for individuals to cross-train in other units , allowing us to maximize the number of cross-trained staff . Having staff available to assist a unit for an unexpected outbreak or emergency will maximize our laboratory ’ s emergency preparedness exponentially , creating a resilient laboratory system our nation ’ s capital can count on .

Presenter : Channyn Williams , channyn . williams @ dc . gov

NEWBORN SCREENING AND GENETICS

Impact of Birthweight on TREC-Based SCID Screening

C . Weaver , South Carolina Department of Health & Environmental Control Public Health Laboratory

Newborn screening for Severe Combined Immunodeficiency ( SCID ) improves clinical outcomes by identifying high-risk individuals prior to symptom onset . These patients may then receive confirmatory diagnostic testing and early therapeutic interventions which have been proven to dramatically improve clinical outcomes . The genetic causes of SCID are complex so newborn screening is based on the quantification of T-cell Receptor ( TCR ) Excision Circles ( TRECs ). TRECs are a byproduct of T cell maturation wherein TCR gene rearrangement leads to the formation of T cell receptor antigenic diversity . During this process , some regions of the genome are excised and circularized into TRECs . Since SCID is characterized by the absence or severe depletion of T cells , patients also exhibit low TREC counts . Although TREC-based SCID newborn screening is effective , decreased TREC counts are also found in preterm neonates whose T-cells have not fully matured . This complicates the interpretation of TREC results and characterization of highrisk groups . The South Carolina Public Health Laboratory ( SCPHL ) recently validated the PerkinElmer NeoMDx assay for SCID newborn screening . The impact of birthweight on results interpretation of the TREC-based test method was evaluated using data from the initial three months of testing . Regression analysis revealed very weak linear correlation between TREC copy number and birthweight . The correlation was not markedly improved when birthweights were binned into broad classes . Despite lack of direct correlation , qualitative screen results were affected by birthweight . Very low (< 2500 grams ) and low ( 1500-2499 grams ) birthweight neonates were found to comprise only 15 % of the population but 87 % of abnormal screens . Compared to the population at large , very low birthweight babies were over 20-fold more likely to screen abnormal . In contrast , normal birthweight neonates ( ≥2500 grams ) were tenfold less likely to screen abnormal . The effect of birthweight on screen results is likely a shift in the TREC frequency distribution as median TREC copy numbers were lowest among very low birthweight neonates . Finally , retesting of abnormal specimens yielded normal screen results in just 36 % of very low birthweight individuals compared to 60 % from those of normal birthweight . Taken together , these results support the hypothesis that performance of TREC-based SCID screening is impacted by birthweight . Findings presented here suggest that neonates whose abnormal screens are not attributable to low birthweight may represent a high-risk group for SCID . Future studies will incorporate specimen recollection data and clinical follow-up to provide a more comprehensive risk profile for this group .

Presenter : Cory Weaver , weavercj @ dhec . sc . gov