Lab Matters Fall 2023 | Page 83

APHL 2023 POSTER ABSTRACTS

Molecular Detection of Respiratory Pathogens from Congregate Spaces Using Aerosol Samplers for Public Health Actions

S . Siomko , J . Zimmer , N . Tomaro , H . Kraussel , L . Schmidt and L . Beversdorf ; City of Milwaukee Health Department Laboratory

The COVID-19 pandemic has increased concerns regarding transmission of infectious respiratory pathogens , particularly in congregate spaces such as schools , transportation hubs , restaurants and shelters where these pathogens can spread rapidly . Monitoring for respiratory pathogens in the community can inform public health officials on how to best protect the public from disease outbreaks . Aerosol samplers actively filter air , collect respiratory pathogens that would otherwise be released in the space , allow for the detection of respiratory pathogens without the presence of symptoms or need for clinical sampling , and can be deployed for as little as two hours or up to several days . The City of Milwaukee Health Department Laboratory ( MHDL ), in conjunction with the MHD Emergency Preparedness Team , deployed four Thermo AerosolSense Samplers in a warming house in Milwaukee County , Wisconsin to monitor for the presence of SARS-CoV-2 , influenza A / B and respiratory syncytial viruses ( RSV ). To detect pathogen presence , MHDL validated a commercially-available TaqMan realtime PCR assay that employs probe-based detection of SARS-CoV-2 ( S and N genes ), influenza A / B , and RSV . Commercially available kits such as these require individual laboratory validation , and here we describe a method to efficiently validate an assay optimized for a local public health laboratory . Using this method , we evaluated the limit of detection of the three targets , defined cut-off criteria for positive results , assured assay precision and assessed the effects of matrix inhibition . We compared the results of this assay with three other molecular assays used by MHDL to detect the presence of respiratory pathogens in clinical samples and during previous air sampling seasons . Air surveillance is an effective and low-cost strategy for pathogen surveillance in lieu of testing individuals , and this method can increase the speed at which outbreak mitigation can be initiated .

Presenter : Samantha Siomko , siomsa01 @ gmail . com

Overcoming Variant Mutation-related Impacts on Viral Sequencing and Detection Methodologies

Y . Bei , K . Pinet , K . Vrtis , J . Borgaro , E . Alpaslan , M . Campbell , L . Sun , L . Apone , G . Patton , B . Langhorst , N . Nichols ; New England Biolabs

In the last three years , we have experienced how disruptive a pandemic has been in every aspect of our lives . Prompt and accurate pathogen identification , by diagnostics and sequencing , has proven to be an effective tool for tracking and potentially curbing pathogen spread . Targeted detection and amplification of viral genomes depends on annealing oligonucleotides complementary to genomic DNA or cDNA . However , genomic mutations that occur during viral evolution may perturb annealing , which can result in incomplete sequence coverage of the genome and / or false negative diagnostic test results . Using SARS-CoV-2 as an example , we demonstrate how to assess , test , and optimize sequencing and detection methodologies to attenuate the negative impact of mutations on genome targeting efficiency . We developed a monitoring tool ( primer-monitor . neb . com ) to identify variant mutations that align with registered primer / probe sets . The effects of the variant mutations on sequencing and diagnostics were evaluated using in vitro-transcribed ( IVT ) RNA as well as RNA extracted from clinical SARS-CoV-2 variant samples , including the heavily mutated Omicron variant . These results demonstrate how to maintain reliable targeted pathogen sequencing and how to evaluate detection methodologies as new variants emerge .

Presenter : Yanxia Bei , beiy @ neb . com

Pacific Rim Consortium Quality Project

K . Bolin 1 , H . Kozar 2 ; 1 International Responder Systems , 2 California Department of Public Health

The Enhanced Laboratory Emergency Network for Operations and Response ( ELENOR ) is a crisis communications tool that provides situational awareness on a common operating platform . ELENOR is a secure , web-based software designed to be used not only during an emergency , but also to enhance day-to-day communications , streamline collaboration , and improve overall situational awareness throughout the state of California . As ELENOR grows , it will interconnect the 28 county Public Health Laboratories with the California Department of Public Health ( CDPH ), California Office of Emergency Services , and other emergency preparedness organizations and services . The system is managed by a combination of user accounts , positions , and group assignments that allow each specific permissions . Its development has been driven by the users and through community collaboration . CDPH intends to build more daily processes , such as grant management and invoicing within the platform . ELENOR users can provide updates to their laboratory ’ s staffing levels , equipment , testing capacity and capabilities , contact information , and more . Laboratories can utilize the continuity of operations planning ( COOP ) checklists for both emergency preparation and COOP activation and can notify other laboratories of significant events such as weatherrelated incidents or natural disasters . Specific positions can request resources , extra staff , and overflow testing from other laboratories . The ELENOR platform was adapted for the APHL Pacific Rim Consortium member laboratories for a quality improvement project . The intent of adapting ELENOR to the Pacific Rim Consortium laboratories is to create efficiency and improve information sharing . Efficiency will be tested through a tabletop exercise and roundtable , followed by an after-action review . The target date for this is March 2023 . Evaluation of the data and efficiencies will be completed by May 2023 .

Presenters : Katie Bolin ( katiebolin @ internationalrespondersystems . com ); Holli Dowless Kozar , ( holli . dowlesskozar @ cdph . gov )

Preparing for the Next Surge : Building Resilient Inventory Management at New Jersey Public Health and Environmental Laboratories

S . Patel 1 , N . Hampton 2 , H . Cheung 1 , J . Mulligan 1 , A . Oyelade 1 , L . Heidenberg 3 , S . Penumatcha 4 , S . Ritchie 4 , J . Ochal 1 , P . Ma 1 ; M . Schachter 1 , S . Mikorski 1 , R . Finney 1 , R . Siderits 1 , T . Kirn 1 ; 1 New Jersey Department of Health Public Health and Environmental Laboratories , 2 Montclair State University , 3 New Jersey Department of Health - Office of Disaster Resilience , 4 New Jersey Department of Health - Office of Health Information Technology ,

Effective inventory management practices include leveraging inventory management technologies , conducting regular inventory checks , setting periodic automatic replacement ( PAR ) levels , and