Lab Matters Fall 2023 | Page 53

APHL 2023 POSTER ABSTRACTS

South Carolina , including our state Public Health laboratory , submit COVID-19 WGS results to SCION . Results with specimen collection dates between March 27 , 2020 , and December 19 , 2022 , were obtained using unique identifiers from SCION . LOINCs , indicating WGS variant results , were selected for analysis . Lineages and sublineages of all variants were identified and classified by the main variant classification using outbreak . info , while Omicron sublineages were further classified using CDC ’ s Variant Proportions within the COVID-19 Data Tracker . Invalid and duplicate results were removed from analysis . Microsoft Access / Excel and SAS were used for descriptive analysis . Results : A total of 31,154 unique individuals ( 1.7 % of total confirmed and probable cases reported to public health in SCION ) yielded 31,694 WGS results . Of those , 508 ( 1.6 %) individuals had multiple WGS results . A majority of WGS results identified Delta ( 42.8 %) and Omicron ( 52.7 %) variants . Among the 508 individuals with multiple WGS results , the average time between specimen collection dates was 33 days , with most ( 95.1 %) individuals having 2 WGS results and the remainder having up to 5 results . Multiple infections with different variants or differing Omicron sublineages were reported among 86 ( 16.9 %) individuals ( total of 87 infections due to some individuals having more than 2 infection events ), with an average time between specimen collection dates of 168 days . Among these , 54 ( 62.1 %) had different variant infections and 33 ( 37.9 %) had differing Omicron sublineage infections . Conclusion : This analysis assessed the current state of variant dynamics among South Carolina COVID-19 cases with WGS results . A small percentage ( 1.7 %) of confirmed and probable cases had WGS results and may not be representative of the population . The large proportion of Delta / Omicron discordant pairs is likely due to the Omicron surge and its greater infectivity and transmissibility . Within-host diversity may have contributed to the short time duration between many of the differing Omicron sublineage infections . These findings prompt advanced investigation into variant dynamics . This analysis is ongoing , and updated results will be available for the May APHL Conference .

Presenter : Sunanda Sarkar , sarkars @ dhec . sc . gov

Developing Resources to Facilitate Expanded Application of Non-Targeted Analysis Methods

J . McCord 1 , S . Nason 2 , Y . Feng 3 , J . Sobus 1 , C . Fisher 4 , R . Marfil-Vega 5 , A . Phillips 1 , J . Sloop 6 , S . Bayen 7 , G . Johnson 8 ; 1 US Environmental Protection Agency , 2 Connecticut Agricultural Experiment Station ,

3

Health Canada , 4 US Food and Drug Administration , 5 Shimadzu ,

6

Oak Ridge Institute for Science and Education , 7 McGill University ,

8

University of North Carolina - Chapel Hill

Non-targeted analysis ( NTA ) using gas or liquid chromatography coupled with high resolution mass spectrometry is a powerful analytical technique that is increasingly used to study organic contaminants in situations where it is impossible or impractical to have analytical standards for all analytes . Common applications include environmental monitoring , food safety evaluation , human exposure and biomonitoring , forensic science , epidemiology , and chemical threat detection , and there is enormous potential for increased use in many analytical contexts . However , methods for ensuring quality control , accuracy , and reproducibility of NTA results are still in development for this emerging technique . The Benchmarking and Publications for Non-Targeted Analysis working group ( BP4NTA ) is focused on increasing use of and improving the quality of NTA . We have recently published several products that contribute to this goal including the NTA Study Reporting Tool ( SRT ), a manuscript that proposes performance metrics for NTA , and a website that includes substantial NTA reference content . As additional BP4NTA efforts develop and progress , the Stakeholders Subcommittee is working to engage with data producers and users from various fields through a series of meetings and surveys with a main goal of learning about drivers and barriers of NTA adoption and data use . Results from this effort will be used to inform and prioritize future BP4NTA activities , ensuring that BP4NTA-generated resources will be of value to the broader scientific community . To date , we have hosted three separate stakeholder meetings , with representatives from food and agriculture laboratories , medical devices regulators , and rapid responders . Future stakeholder meetings will include employees of commercial environmental laboratories , regulatory risk assessors , epidemiologists , students / trainees and others . Preliminary stakeholder survey results indicate high interest in the use of current BP4NTA resources such as our website and proposed performance metrics , demand for data processing tools such as databases and libraries , and enthusiasm for additional strategies to demonstrate data quality and study reproducibility . Continued feedback from NTA-adjacent stakeholders , including those in the Association of Public Health Laboratories ( APHL ) community will help us to further refine our efforts towards the most useful tools and resources for broadening NTA implementation and use .

Presenter : James McCord , jmccord314 @ gmail . com

How to Make Informed Decisions to Build Healthcare Resilience for the Future : The Criticality of Data Synchronization Between the Frontlines and Supply Chain Operations

T . Coleman , J . Franck ; Deloitte Consulting LLP

Numerous supply chain articles discuss the potential for technology such as blockchain and artificial intelligence ( AI ), to turbocharge supply chain resilience . They delve into how technology will transform an organization ’ s supply chain to become more agile and resilient . However , in practice , many technology projects do not achieve their promised return on investment and target resilience outcomes . Deloitte recently analyzed 55 survey responses and interviewed over 50 supply chain leaders in the private and public sector across a range of industries , including life sciences , government , health care providers , academic institutions , humanitarian non-governmental organizations ( NGOs ), retail and technology to better understand key determinants for resilient health care supply chains . Our recently published research indicated that organizations , i . e ., health care entities , are not achieving supply chain resilience by leading with technology . Instead , they are increasing resilience through organizational commitment from leadership and staff , and conscious spending by identifying and addressing root causes of health care supply chain issues . We discovered that technology proves far less effective in crisis when the members in the same supply chain ecosystem do not have standardized definitions , communication methods and roles , with the lack of clarity slowing response and hindering operations . Standardizing the basics , like data sharing , authorities and role of the entities involved , is key to maintaining a healthy supply chain ecosystem . Our latest round of research examined how private and public sector frontline workers overcame recurring obstacles to maintain efficient operations and promote supply chain resilience .