APHL 2022 POSTER ABSTRACTS
COVID-19 updates . Following the emergence of Delta ( B . 1.617.2 ) and its associated sublineages ( AY ), it was reported that these lineages may have increased transmissibility , infectivity , or virulence , and it became imperative to try to validate these claims using NYC data . However , it became apparent that pangoLEARN lineage calls were not always monophyletic , making any associations of lineages to vaccine breakthrough or hospitalization potentially spurious . Thus , we sought to determine the extent of the miscalling in Delta and validate Ultrafast Sample placement on Existing tRees ( UShER ) as a potential alternative method to determine pangolin lineages . A phylogenetic tree containing 7229 Delta sequences from NYC , created by aligning consensus SARS-CoV-2 genomes using MAFFT and inputting it to IQ-TREE , was used to determine the phylogenetic relationship between sequences determined to be the same pangolin lineage . This analysis was conducted seven times between September 22 , 2021 and November 4 , 2021 and span the following versions of pangolin and its software dependencies : Pango designation v . 1.2.76-91 , pangolin v . 3.1.11-16 , pangoLEARN 2021-09-17 to 2021-10-18 . The multiple comparisons also allowed us to compare stability of pangolin lineage calls over time as new sublineages emerged and were defined ( e . g ., AY . 4 ). Overall , both methods were able to correctly assign lineages to monophyletic clades in most cases . However , pangoLEARN was more prone to outliers and most importantly had difficulty correctly calling newly defined lineages . This difficulty in first identifying emerging lineages negatively affected pangoLEARN ’ s stability through the study period as lineage calls were likely to be discordant with subsequent lineage calls . UShER results , on the other hand , were remarkably stable except in the case of reassignment of lineages as new sublineages were defined . As a result , NYC DOHMH has switched to UShER pangolin lineage calling .
Presenter : Michelle Su , New York City Public Health Laboratory , msu4 @ health . nyc . gov
Detection of SARS-CoV-2 in Wastewater Samples in Ohio
J Saxena , J Stiverson , J Scott and E Leasure , Ohio Department of Health Laboratory
Wastewater-based epidemiology is potentially effective for an early detection of SARS-CoV-2 in wastewater before the outbreak is clinically detected . Four wastewater treatment plant sites in Ohio ( Jackson Pike , Newark , Lancaster and Zanesville ) were selected for SARS-CoV-2 surveillance based on the presence of SARS-CoV-2 , population size , COVID-19 vaccination percent and proximity to Ohio Department of Health Laboratory . Wastewater samples ( 1 L ) were collected twice per week for 7 weeks ( mid-October to early December 2021 ) and stored at 4 º C until processing . The samples were processed within 2-3 days of sample collection . Each sample was processed , extracted and analyzed in duplicate . The GT- Molecular method from GT-Digital Wastewater Surveillance Guide was employed for virus filtration , concentration , RNA extraction and SARS-CoV-2 quantification . Bovine Coronavirus ( BCoV ) was used as a matrix recovery control to normalize changes in viral recovery caused by the variable and complex nature of wastewater . The virus from wastewater samples were concentrated using the Innovaprep Concentrating Pipette Select . RNA was extracted from the viral concentrate using QIAGEN AllPrep PowerViral DNA / RNA Kit . The N2 region of the SARS-CoV-2 nucleocapsid gene was quantified to monitor SARS-CoV-2 in wastewater via digital PCR ( dPCR ) using GT- Digital SARS-CoV-2 Wastewater Surveillance Assay Kit and QIAcuity
One-Step Viral RT-PCR Kit . The initial BCoV percent recovery ( BCR ) amongst four sites was low ranging from 0.07 to 4.29 % ( average 1.37 ± 0.099 %) when 20 µ l template volume was used . The initial BCR did not differ ( P = 0.96 ) among the sites ( 0.95 , 1.56 , 1.67 and 1.22 % for Jackson Pike , Lancaster , Newark and Zanesville , respectively ). Low BCR was probably due to the presence of some inhibitory materials in wastewater extract and were present in all sites . However , this BCR improved significantly ( P < 0.001 ), which ranged from 1.13 to 13.5 ( average 6.28 ± 2.96 ) on reducing the template volume to 10 µ l from 20 µ l . The recovery rate was similar ( P = 0.77 ) among the sites ( 6.70 , 5.11 , 6.96 and 6.34 % for Jackson Pike , Lancaster , Newark , and Zanesville , respectively ). In this study period , [ N2 ] gene abundances ( copies / L ) increased from 1813 to 15355 in Jackson Pike , 8766 to 39538 in Lancaster , 7442 to 63050 in Newark , and 6772 to 23038 in Zanesville wastewater site , probably due to an increased incidence of COVID-19 in Ohio . Overall , gene abundance did not differ significantly ( P = 0.87 ) among wastewater sites during this time period . In conclusion , this study reveals that the use of 10 µ l template volume increases BCoV recovery rate and the surveillance of the N2 gene abundance of SARS-CoV-2 in wastewater may be useful to early detect COVID-19 cases in the community .
Presenter : Jyotisna Saxena , Ohio Department of Health Laboratory , jyotisna . saxena @ odh . ohio . gov
Performance of the VITROS ® Immunodiagnostic Products Anti-SARS-CoV-2 IgG Quantitative Assay * Calibrated to the WHO 1st International Antibody Standard
B Hirsch , A Gardner , C Mcclendon and P Contestable , Ortho Clinical Diagnostics
Background : This study was designed to assess the performance of the VITROS Immunodiagnostic Products Anti-SARS-CoV-2 IgG Quantitative assay ( VITROS IgG Quant ). The assay is for the fully quantitative detection of SARS-CoV-2 IgG antibodies with calibration traceable to the First WHO International Standard for Anti-SARS- CoV-2 antibody . Results are reported in both qualitative ( reactive / non-reactive ) and quantitative values ( Binding Antibody Units / mL ( BAU / mL )).
Methods : Reference calibrators ( RC ) were assigned values through a traceability study with the WHO 1st International Standard ( NIBSC 20 / 136 ). A titration panel of the standard was used to assign values to an average calibration curve generated through 10 measurements of RC run on two VITROS systems . These RCs are then used to value assign sets of three Customer Calibrators on a reagent lot-to-lot basis for customer lab use . The assay reportable range was determined by calculation of the assay LoD / LoQ and demonstration of linearity . Clinical specificity was assessed using 533 samples collected prior to the start of the COVID-19 pandemic . Sensitivity ( Percent Positive Agreement ( PPA )) was evaluated using samples from 264 RT-PCR positive individuals collected ≥15 days since reported symptom onset . Reproducibility was evaluated consistent with CLSI EP05 . Quantitative results of 45 vaccinated individuals were assessed prior to vaccine , after the first dose and after the second dose to demonstrate vaccine induced antibody response . An additional 74 fully vaccinated individuals were assessed months after vaccination to look for evidence of antibody waning post vaccination .