APHL 2023 POSTER ABSTRACTS public health responses with an eye toward equity and to guide clinical decision making . Wastewater monitoring for infectious disease targets is a passive method for disease monitoring in a community . Here we show that concentrations of viral nucleic acids from a diverse suite of human viruses in wastewater solids correlate well with customary clinical data streams on disease occurrence . We measured concentrations of mpox , SARS-CoV-2 variants , norovirus GII , influenza A and B , RSV A and B , parainfluenza ( 1-4 ), rhinovirus , seasonal coronaviruses , and metapneumovirus nucleicacids in wastewater solids between three and seven times per week for extended periods of time ( a year or more ). We measure viral nucleic acids in wastewater solids rather than wastewater influent because viruses partition to wastewater solids . Their concentrations are approximately 1,000 to 10,000 times higher in solids than in influent on an equivalent mass basis . We detected nucleic acids from all tested viruses in wastewater solids . We compared viral nucleic-acid concentrations to customary measures of disease occurrence including laboratory-confirmed disease incidence rates and test positivity rates . Virus concentrations correlated significantly and positively with occurrence of associated viral diseases . This work suggests that respiratory , gastrointestinal , and novel , emerging viral diseases can be tracked in communities using wastewater monitoring regardless of individual health seeking behavior . Wastewater monitoring represents a powerful tool for informing public health responses including clinical decision making , allocation of resources , timing and locations of vaccine campaigns , and implementation of non-pharmaceutical interventions . Based on these findings , we have scaled measurements of many of these viral targets nationally through our project WastewaterSCAN ; we currently provide measurements three times per week at over 130 wastewater treatment plants in twenty-five states . Data are available publicly within 48 hours of receiving a sample at the laboratory and displayed at : data . wastewaterscan . org .
Presenter : Alexandria Boehm , aboehm @ stanford . edu
Wastewater-based Techniques : Optimizing Bench Protocols from Sample Concentration to dPCR in a Local Public Health Laboratory
J . Zimmer , S . Siomko , L . Beversdorf ; City of Milwaukee Health Department
Wastewater analyses have been used for many years to surveil concentrations of chemicals , pharmaceuticals , biomarkers , and other substances that could reflect population behaviors . Wastewater-based epidemiology ( WBE ), however , is a more recent approach to using wastewater for public health . This approach has now been widely adopted , primarily in response to the SARS- CoV-2 pandemic , to surveil community disease burden , emerging pathogens , and leading indicators of community outbreaks . The CDC has provided guidance on wastewater method development through the National Wastewater Surveillance System . However , the onus to develop technical protocols has been left to individual laboratories , in part , because wastewater matrices are site specific . For public health laboratories at the local level , optimizing new techniques may be complicated by such restrictions as limited resources , constrained space , and fewer staff , when compared to larger-scale State , Federal , and commercial laboratories . Here , we describe how the City of Milwaukee Health Department Laboratory ( MHDL ), a local Wisconsin public health laboratory , approached these obstacles when it began wastewater surveillance of SARS-
CoV-2 in August 2021 . Wastewater samples provided to MHDL for analysis undergo the following steps : viral particle concentration , nucleic acid extraction , and digital PCR for the quantification of viral load . These three processing steps must not only be dependable , but also balance the restraints imposed on a local public health laboratory . Therefore , each step was evaluated using four criteria : 1 ) consistency and accuracy of viral particle recovery , 2 ) feasibility and practicality in the context of the laboratory layout , 3 ) longterm cost efficiency , and 4 ) turnaround time . Using these criteria , MHDL successfully compared several methods to determine the most reliable protocol that best optimized limited resources and available laboratory space , whilst creating a time-efficient process to allow meaningful WBE . Optimization of these steps for SARS-CoV-2 will allow MHDL to expand analyses to additional targets such as influenza , mpox , antimicrobial resistance , and more .
Presenter : Julia Zimmer , jzimmer @ milwaukee . gov
STRENGTHENING LABORATORY SYSTEMS AND STRATEGIC PLANNING
A Response Playbook for Early Detection and Population Surveillance of New SARS-CoV-2 Variants in a Regional Public Health Laboratory
H . Barbian 1 , K . English 2 , S . Bobrovska 1 , M . Fiorillo 2 , S . Green 1 , M . Hayden 1 , R . Teran 2 , I . Ghinai 2 ; 1 Rush University Medical Center ,
2
Chicago Department of Public Health
The Regional Innovative Public Health Laboratory ( RIPHL ) is a public-academic partnership between Chicago Department of Public Health ( CDPH ) and Rush University . It was established in March 2021 to serve as the molecular epidemiology laboratory for CDPH , providing flexible molecular detection , characterization , and genomic surveillance of pathogens of public health importance with the goal of timely and actionable data for public health response . Between April 3 , 2021 and December 31 , 2022 , RIPHL received 11,557 SARS-CoV-2-positive remnant clinical respiratory specimens from 15 acute care hospitals in Chicago for molecular characterization . Of these , 8,886 ( 77 %) specimens were successfully sequenced and yielded lineage assignments . Across the study period , RIPHL sequenced 3 % of all incident SARS-CoV-2 infections reported to CDPH , and accounted for 62 % of Chicago SARS-CoV-2 sequences in GISAID . Demographically , individuals who provided specimens for sequencing were broadly representative of all SARS-CoV-2 infections reported to CDPH in terms of sex , age , race / ethnicity , and ZIP code of residence . RIPHL has altered molecular methods in response to public health needs . When Omicron BA . 1 was rapidly emerging , RIPHL developed and implemented a genotyping PCR to provide lineage proportion estimates at much faster turnaround compared to whole genome sequencing ( WGS ). TaqMan SARS-CoV-2 Mutation Panel Assays ( ThermoFisher ) targeting mutations K417N and L452R were used to distinguish BA . 1 from the background of Delta variant . Genotyping PCR was able to call lineage in samples with low viral concentration more successfully than WGS , resulting in 1,657 ( 90.4 %) lineage calls from genotyping PCR compared to 1,560 ( 85.1 %) for WGS . Of 1,541 samples with both WGS and genoptying PCR data available , 1,539 ( 99.9 %) concordant . Since late 2021 , Chicago has experienced waves of successive Omicron sublineages . The relative speed with which sublineages
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Fall 2023 LAB MATTERS 91 |