APHL 2022 POSTER ABSTRACTS
COVID-19 of entire communities sooner than patient diagnostic testing . This tool can also be used to mitigate SARS-CoV-2 disease outbreak and influence public health decision making . The Nevada State Public Health Laboratory has established a mainly automated same day workflow for routine viral load detection and quantification of SARS-CoV-2 in wastewater . This workflow consists of an automated 40-fold concentration of wastewater specimen using Ceres Magnetic Nanotrap Beads , automated viral RNA extraction using Thermofisher MagMax beads , and SARS-CoV-2 detection and quantification through Promega ’ s RT-qPCR Kit for SARS-CoV-2 detection in wastewater . Weekly , wastewater RNA extracts are sequenced using Illumina technology . Sequence reads undergo bioinformatic analysis to calculate concentration of SARS-CoV-2 variants in the wastewater . Utilizing this workflow , the Nevada State Public Health Laboratory has organized a wastewater surveillance system for northern Nevada that is composed of four sites over the past year . In this poster , SARS-CoV-2 detection , quantification and variant data of these four sites would be presented . These sites are three wastewater treatment plants in three different northern Nevada counties and four separate sites on the University of Nevada Reno ’ s campus ( three dormitories and one student union ). The next steps for this project include optimizing digital droplet PCR for direct quantification , analyzing wastewater metagenomics , and expanding this workflow to be able to identify other pathogens ( mainly bacteria ) than SC2 such as Neisseria gonorrheae and Chlamydia trachomatis .
Presenter : Lauryn Massic , Nevada State Public Health Laboratory , lmassic @ nevada . unr . edu
Establishment of Wastewater Sequencing Methods Allow for Surveillance of SARS-CoV-2 in the State of New Jersey
N Palmateer , E Acheampong , S Verma , B Jeong , L Schlitt , R Siderits and T Kirn , New Jersey Public Health and Environmental Laboratories
Throughout the COVID-19 pandemic , a leading indicator of the presence and level of SARS-CoV-2 infection within a community has been the presence of viral RNA in wastewater . Fecal shedding of the virus by infected individuals can occur prior to the presentation of symptoms . This surveillance capability is an important tool for public health , indicating the presence of the virus in a community prior to individual testing , as well as the severity of infection and proportion of each variant strain that is present . Wastewater surveillance can also inform public policy decisions regarding the allocation of testing and treatment resources , in preparation for a potential outbreak within a community . As a pilot project , intended to develop methods for effective testing for the presence of SARS-CoV-2 , two wastewater facilities in southern New Jersey were selected to provide samples to the New Jersey Public Health and Environmental Laboratories on a weekly basis . This study represents the first implementation of whole genome sequencing surveillance in wastewater by the New Jersey Department of Health . This project was undertaken as part of the FDA Center for Food Safety and Applied Nutrition ’ s LFFM special wastewater project , with data being shared through the FDA ’ s GenomeTrakr network . Virus concentration was performed using a polyethylene glycol precipitation , in combination with ultracentrifugation . Following extraction of viral RNA , RT-qPCR was used to detect the presence of SARS-CoV-2 in the wastewater samples . Prior to sequencing , the NEBNext ARCTIC SARS-CoV-2 kit , including the VarSkip Short primers to improve performance with variants , was used for library preparation . Samples testing positive for SARS-CoV-2 were then sequenced using the Illumina MiSeq sequencing platform . Quality assessments of raw reads were performed using the wastewater quality control workflow in GalaxyTrakr . Data passing quality control standards were submitted into NCBI public database and assigned accession numbers . Twice weekly testing allowed for regular surveillance of the presence of SARS-Cov-2 and population structure of SARS-CoV-2 strains circulating within the selected communities , along with a comparison of the level of RNA copies in wastewater with community nasal swab testing results . This project allowed for validation of methods that can be implemented on a larger scale throughout the state of New Jersey . The establishment of this testing infrastructure with wastewater treatment plants throughout the state of New Jersey will allow for surveillance of a broader array of pathogens of concern , under a One Health approach . This project has laid the groundwork for testing for organisms in wastewater that not only impact public health , but with the collaboration of other state agencies , those that impact plant and animal health , as well as the environment .
Presenter : Nicholas Palmateer , New Jersey Department of Health , nicholas . palmateer @ doh . nj . gov
Improving Post-analytic Processes for COVID-19 Testing Through Automated Laboratory Information System ( LIS ) Solutions
M Mariscal , S Suleiman , S Hughes and R Fowler , New York City Public Health Laboratory
Introduction : Routine post-analytic lab processes can include several layers of manual result entry and checks both on paper and electronically to ensure accurate reporting of test results . Although these processes are functional , they are redundant and consume critical staffing resources . Increasing test volumes due to COVID-19 surges has highlighted the need to address these lab inefficiencies . LIS applications can be used to design custom algorithms to improve post-analytic processes . This study aims to develop , validate , implement and monitor LIS solutions that automate post-analytic processes for COVID-19 testing at NYC Department of Health operated labs .
Methods : LIS solutions were developed based on regulatory reporting requirements and the need for system flexibility to facilitate an automated electronic-based lab workflow . Automated LIS algorithms were developed with a result-based criterion to account for all possible test results . A thorough end-to-end validation process was used to ensure algorithms functioned as intended . Implementation was done in two phases : 1 ) automated release of only negative results and 2 ) automated release of negative and positive results . Automation Rate , which measures how many analyte results are directly reported by the system without user involvement , and turnaround time ( TAT ) from specimen receipt to release of results were monitored pre- and post-implementation .
Results : Automated LIS algorithms were developed and validation testing showed that all algorithms functioned as intended , but revealed end-user involvement would be required when a specimen needed retesting . Automation Rate and TAT were monitored to determine post-analytical process improvement . Pre-implementation data showed the Automation Rate was 0 %, whereas post-