APHL 2022 POSTER ABSTRACTS
COVID-19
The Impact of COVID-19 on Laboratory Operations and Mitigation Strategies at the Utah Public Health Laboratory
K Christensen , A Atkinson , J Harbour , A Rohrwasser and A Rossi , Utah Public Health Laboratory
Introductions of SARS-CoV-2 infections in workplaces performing essential functions , such as public health laboratories , represent a formidable challenge to their continuity of operations . Here we describe the impact of COVID-19 on the Utah Public Health Lab ( UPHL ) workforce between September 2020 and January 2022 , as well as the mitigation measures that were implemented over time . UPHL is an institution currently employing approximately 140 individuals . COVID-19 illnesses were first detected at UPHL in September 2020 and continued sporadically until January 2021 . During this period , coinciding with the first big wave of cases in Utah , 10 lab members were infected . Vaccination with the Moderna mRNA vaccine was provided to the whole staff in January-February 2021 and additional cases were not observed until July 2021 . During the period between July and November 2021 , coinciding with the surge of the Delta variant , 8 cases were detected . The highly infectious Omicron variant was first detected in Utah on December 3rd 2021 and began an explosive ascent around December 20th , quickly becoming the prevalent circulating strain . Between December 29 , 2021 and January 19 , 2022 , 16 employees were infected , most likely with Omicron . No severe COVID-19 outcomes have been seen among UPHL workforce , probably reflecting the high percentage of employee vaccination ( now 86 % for 2 mRNA vaccine doses ). Secondary transmission within UPHL has been rare , with only four instances of likely or probable “ employee to employee ” transmission . Only five employees have experienced reinfections with SARS-CoV-2 over the course of the pandemic . UPHL ’ s leadership has strived to ensure a safe workplace environment and protect the integrity of the lab`s operations . Mandatory masking was the first measure introduced in June 2020 . Mandatory vaccination was introduced early in 2021 . Voluntary employee saliva testing via RT-PCR was made available in January 2021 . The arrival of Omicron in the US has lead to the implementation of more stringent mitigation measures and contingency measures to maintain critical functions . 3rd Booster doses , introduced to contrast waning immunity against Delta , were made available to UPHL employees in November 2021 and are now part of the SARS- CoV-2 vaccination requirement . Higher quality masks such as KN95 have been provided and cloth masks have been entirely banned . Daily NAT testing of critical staff has been recommended . The CDC ’ s isolation / quarantine updated guidance for healthcare workers issued in December 2021 was applied to UPHL critical teams with some modifications , such as a shortened isolation contingent on a negative antigen test . While the increase of Omicron cases at the lab has been striking and expected , emphasis on mitigation and workforce engagement have so far allowed UPHL to continue operating at normal capacity .
Presenter : Kim Christensen , Utah Public Health Laboratory , kchriste @ utah . gov
Data Lake in the Cloud : Centralizing Public Health Data in Response to the SARS-CoV-2 Pandemic
C Jossart and K Florek , Wisconsin State Laboratory of Hygiene
The SARS-CoV-2 pandemic has demonstrated the value of genomic epidemiology and the need to build capacity to manage and process the growth of data . In order to meet the demand for variant surveillance , laboratories have expanded sequencing efforts and focused their efforts on reporting in near real-time . At the Wisconsin State Laboratory of Hygiene ( WSLH ) and the Wisconsin Department of Health Services , the existing data infrastructure was inadequate to meet the needs of integrating genomic and epidemiological data to inform public health partners . To support the integration of numerous data sources , the WSLH has developed a cloud-based centralized data repository for raw and disparate data , known as a data lake . A data lake consists of multiple layers for data storage and processing , which include an ingestion layer for raw data , a curated layer for processed and transformed data , and an application or production layer , which serves cleansed data to end-users . This unbiased approach to data collection allows joining genomic , clinical and epidemiological data from a multitude of sources providing a framework for a highly adaptable data repository . Leveraging a data lake infrastructure to contextualize genomic data will support valuable SARS-CoV-2 analytics including , identifying associations between vaccine breakthroughs and changes in health outcomes . Additionally , a cloud-based approach offers a scalable and cost-efficient platform that will allow the WSLH to immediately expand capacity to meet data expansion needs while only paying for the resources and services used . The scalability and affordability of this platform increase access to pre-built cloudbased tools and computationally intensive analytical methods , such as machine learning , allowing the WSLH to operationalize advanced analytical methods to inform public health partners . Cloud-based platforms also ensure data security through durable data infrastructure and data redundancy to prevent data loss and provide the WSLH with total control of the data lake governance to manage data usability and accessibility for users and services . This cloud-based data lake will prepare the state of Wisconsin for future outbreaks of disease , increase the data and analytical capacity , and more effectively apply genomic data to public health disease surveillance .
Presenter : Christopher Jossart , Wisconsin State Laboratory of Hygiene , cjjossart @ gmail . com