Lab Matters Fall 2023 | Page 110

APHL 2023 POSTER ABSTRACTS

blood . The selected mosquitoes were pooled based on county and placed into sample racks . Each sample rack may contain up to 92 pools of 1-50 mosquitoes . The filled racks were then sent to the virology laboratory to be tested . Samples were homogenized with the QIAGEN Tissue Lyser II and BA-1 diluent ( QIAGEN ), centrifuged at 6,000 x g for 13 minutes at 4 º, and prepared for RNA extraction using the RNeasy 96 QIAcube HT kit ( QIAGEN ). Extractions took place on the QIAGEN QIAcube HT robotic workstation which allows for 3-4 runs ( around 300 mosquito pools ) per day . RT-PCR was performed on the ABI 7500 Fast Dx instrument using CDC primers and probes for WNV . Previously confirmed WNV positive RNA samples were used as the positive control and PCR grade H20 was used as the negative control . The final qualitative results were reported to respective counties . If there was an increase in expected WNV positive mosquitoes , spraying would be conducted in those areas to eliminate flying mosquitoes . From 2016-2022 ( excluding 2020 due to no testing from COVID-19 ) a strong positive correlation ( R = 0.9002 ) was observed between the number of clinical human cases of WNV and positivity rate in tested pools of mosquitoes in Ohio with a P-value of . 0372 <. 05 . This indicates that increased incidence levels of WNV in mosquitoes can lead to an anticipated increase in clinical cases . In conclusion , the QIAcube HT offers a high throughput method for WNV testing of around 300 mosquito pools per day over the manual method , leading to a more representative sample size . The data obtained in this study demonstrates that the use of efficient surveillance methods can help to improve mitigation strategies , resulting in an overall improvement to public health .

Presenter : Shelby Anders , shelby . anders @ odh . ohio . gov

WASTEWATER SURVEILLANCE OF INFECTIOUS DISEASES

Changes in the Correlation between Clinical Cases and Levels of SARS-CoV-2 RNA in Colorado Wastewater

M . Ghanbari 1 , J . Huang 1 , A . Luc 1 , J . Goldman 2 , M . Arabi 1 , R . Ferrell 2 , T . Fielder 2 , R . Byrne-Nash 4 , S . Kane 4 , S . De Long 1 , C . Wilusz 1 ;

1

Colorado State University , Fort Collins , 2 Metro Water Recovery , Denver , 3 Metropolitan State University , Denver , 4 GT Molecular

The utility and interpretation of wastewater signal as a predictor of community health can be confounded by factors that vary between locations and over time , such as wastewater system complexity , human behavior and viral evolution . We explored the relationship between SARS-CoV-2 concentration in wastewater and caseload for 23 locations in Colorado over a 22-month period , including multiple waves and the implementation of vaccines . Location-specific models showed strong correlations for all facilities , independent of normalization , with the best correlations seen for facilities with populations > 10,000 . Change point analysis identified events leading to decreases in numbers of clinical cases reported per SARS-CoV-2 genome copies detected in wastewater . The first change points occurred in several , but not all facilities , over a sixmonth period during which vaccination became widespread and the Alpha variant arose . Another more dramatic increase occurred synchronously within a narrow one-month period for all facilities and coincided with extensive distribution of at-home test kits and the rise of the Omicron variant . Models accounting for these shifts in pandemic phase showed significantly improved correlations , yet the original models likely provide a better estimate of actual caseload . In future pandemics , the effects of phase changes should be considered in modeling efforts .

Presenter : Carol Wilusz , cwilusz @ colostate . edu

Genomic Surveillance of SARS-CoV-2 : Comparing Data from Sequencing Clinical and Wastewater Specimens

C . Korban , K . English , R . Atwater , Mario Fiorillo , D . Yuce , R . A . Teran , M . Pacilli and I . Ghinai ; Chicago Department of Public Health

Genomic surveillance of COVID-19 has largely relied on whole genome sequencing of clinical respiratory specimens that test positive for SARS-CoV-2 by PCR . Many clinical specimens need to be sequenced to generate sufficient genomic data to approximate trends , and the availability of PCR-positive respiratory samples varies with epidemic conditions , between communities with differing healthcare access , and with changing testing behaviors . Sequencing wastewater might mitigate some limitations ; a single sample represents a large population and is agnostic to testing behaviors or access to care . However , the concordance between clinical and wastewater genomic data is not yet well characterized . We aimed to compare the date that new variants were detected and the growth rates between clinical and wastewater surveillance strategies to assess utility of a multi-prong genomic surveillance strategy . The Chicago Department of Public Health ( CDPH ) coordinates sequencing of clinical respiratory specimens and wastewater samples — approximately 15 clinical remnant specimens from patients testing positive for SARS-CoV-2 at 10 Chicago hospitals and four samples collected from three wastewater treatment plants processing wastewater from the Chicago area were submitted for sequencing each week between April 2022 and December 2022 . Lineage proportions were calculated : for clinical samples , this is a simple percentage . For wastewater , each sample was weighted according to the population served . We compared the date of first detection and the growth trajectories of two Omicron sublineages between clinical and wastewater samples ; BA . 5 ( which reached dominance during the study period ) and BQ . 1 ( which did not ). During April 2022 to December 2022 , 489 wastewater samples and 3,073 clinical respiratory specimens were sequenced . BA . 5 was detected two weeks earlier in wastewater than in clinical samples , while BQ . 1 was detected one week earlier in clinical samples than in wastewater . There was good concordance in growth trajectories across surveillance methods : in both clinical and wastewater samples , BA . 5 reached 50 % in the week ending July 2 , 2022 , and — as of December 3 , 2022 — was found at 44 % and 24 % in wastewater and clinical samples respectively . Analysis of other sublineages highlight lineage-specific differences in detection timing and growth characteristics . In Chicago , genomic sequence data from wastewater and clinical samples were largely concordant . Continued evolution of SARS-CoV-2 is inevitable , and genomic surveillance will remain critically important in the next phase of the pandemic , even as testing preferences continue to shift away from PCR testing in favor of antigen tests . Wastewater surveillance can be a useful supplement to genomic surveillance of respiratory specimens , and combining data sources may provide opportunities for earlier detection of emerging lineages .

Presenter : Colin Korban , colin . korban @ cityofchicago . org