APHL 2022 POSTER ABSTRACTS
COVID-19 kit in MiSeq platform ( Illumina ). Air samplers were decontaminated prior to cartridge replacement if SARS-CoV-2 RNA was detected to ensure there was no carryover contamination and deployed back in the field .
Results : Air sample substrates repeatedly tested positive for SARS- CoV-2 , especially during the initial deployments , which coincided with the emergence of the Omicron variant . Samples with low CT values were sequenced and resulted in the confirmation of the Omicron BA . 1 lineage . Positive results led to risk mitigation actions , such as increased rapid antigen testing and activating isolation protocols .
Conclusion : Air sampling surveillance of respiratory pathogens via air sampling is a promising technology to help develop risk mitigation strategies and strengthen the core concepts of emergency preparedness and response . This technology would be applicable in congregate spaces such as K – 12 schools , childcares , shelters and high-traffic areas , such as airports and other public transportation hubs . While this pilot study focused on the detection of SARS-CoV-2 , the method can be expanded to study other respiratory pathogens , such as the influenza and respiratory syncytial viruses . Lastly , air sampling is a promising low-cost approach to detecting airborne diseases in lieu of testing individuals in large groups .
Presenter : Lucas Beversdorf , City of Milwaukee Health Department , lbeversd @ milwaukee . gov
Validation and Implementation of Clear Lab Dx Platform in Public Health Laboratory for SARS-CoV-2 Genomic Surveillance
M Khubbar , A Bauer , K Akinyemi , A Skillman , J Lentz , S Scott , J Weiner , N Balakrishnan and S Bhattacharyya , City of Milwaukee Health Department
Introduction : On September 23 , 2020 , FDA issued emergency use authorization for Clear Labs Dx in vitro diagnostic system for COVID-19 sequencing . The Clear Dx™ SARS-CoV-2 Test is intended for use by qualified clinical laboratory personnel trained in the real-time PCR and Whole Genome Sequencing ( WGS ) and in vitro diagnostic procedures . City of Milwaukee Health Department Laboratory ( MHDL ) validated its use in SARS-CoV-2 genomic surveillance in October 2021 for real-time screening and detection of variants .
Methods : To evaluate the performance of the Clear Dx™ WGS SARS-CoV-2 Test , total nucleic acid was extracted on the Thermo Fisher Scientific KingFisher Flex Purification System and the bioMérieux NucliSENS ® EMAG ®. The purified nucleic acid is reverse transcribed , barcoded , pooled , purified and then sequenced using pre-packaged library prep and sequencing reagents and a MinION flow cell . Thirty SARS-CoV-2 positive specimens with published viral genomes in GISAID were chosen from the MHDL specimen repository . Additionally , eight negative specimens and 14 non-SARS- CoV-2 respiratory pathogen positive specimens were analyzed for validation of this assay . Sequencing run data was analyzed via the Nextclade and Pangolin web applications to get genomic characteristics ( lineage / clade etc .) for each specimen . Acceptance criteria was 90 % genomic coverage and ≥100 depth .
Results : The overall accuracy was 93.3 % ( 28 / 30 ). Sensitivity was 93 % and specificity was 95 %. With a panel of 14 specimens , 100 % repeatability and reproducibility were documented . Since October 2021 , MHDL has performed whole genome sequencing on 842 clinical specimens that tested positive for SARS-CoV-2 using the Clear Dx™ SARS-CoV-2 Test . Results are uploaded with de-identified patient information on to the national public database ( Global Initiative on Sharing Avian Influenza Data ( GISAID )) and reported to relevant public health authorities for the actionable outcome . The turnaround time has significantly decreased to an average of 3 – 6 days compared to other platforms where it takes a minimum of two weeks from the date of specimen collection .
Conclusion : Clear Labs Dx is a fully automated , next-generation sequencing platform and used at the MHD public health laboratories to characterize SARS-CoV-2 and its variants . The instrument plays a crucial role in near real-time genomic surveillance within our jurisdiction . The results are accurate , reliable and efficiently reported for epidemiological investigations to help prevent SARS-CoV-2 transmission .
Presenter : Manjeet Khubbar , City of Milwaukee Health Department , mkhubb @ milwaukee . gov
Children Infected With SARS-CoV-2 While the Delta Variant was Dominant in Colorado Had Higher Viral Loads Than in Previous Time Periods
L Bankers 1 , D Ir 1 , D Tapay 1 , E Ho , S O ’ Brien 1 , S Dominguez 2 , A Burakoff 1 , S Matzinger 1 ; 1 Colorado Department of Public Health and Environment , 2 Children ’ s Hospital Colorado
After the SARS-CoV-2 Delta variant emerged in Colorado , it rapidly became dominant in June 2021 . Adults infected by Delta exhibit higher viral loads and potentially increased disease severity than those infected by other variants . However , little is known about viral kinetics and severity in children infected with Delta compared to other variants . We evaluated relationships between the presence and severity of symptoms , viral load and SARS-CoV-2 lineage among hospitalized and non-hospitalized pediatric SARS-CoV-2 cases in Colorado to determine if children infected with Delta have different symptom severity or viral load compared to those infected by other variants . Viral lineage was determined by whole genome sequencing . To include samples for which we had Ct and symptom data but could not sequence , we performed analyses over two timeframes : pre-Delta ( Jan . 1 , 2021 – May 1 , 2021 ; prior to prevalence of Delta reaching 80 % in Colorado ) and Delta ( June 15 , 2021 – Sept . 29 , 2021 ; Delta prevalence ≥ 80 %). We used Ct values as a correlate of viral load and symptomatology was determined by chart review ( 196 inpatients ) or questionnaires ( 583 outpatients ). Finally , we performed phylogenetic analyses of sequenced samples . Children hospitalized due to COVID-19 had lower Ct values ( suggesting higher viral load ) than those diagnosed with COVID-19 but hospitalized for other reasons ( asymptomatic infections , Mann-Whitney U test , p = 0.002 ). During days -3 to 30 of symptom onset , Ct values were significantly lower overall for the Delta compared to the pre-Delta timeframe ( p = 0.02 , Mann- Whitney U test ). When separated into two age bins ( 0 – 4 years , 5 – 19 years ), children aged 0 – 4 years had lower Ct values in the Delta than the pre-Delta timeframe ( p = 0.005 ), while the difference was not significant for 5 – 19-year-olds ( one-way ANOVA , Ad Hoc Tukey HSD ). Of children hospitalized due to COVID-19 , a larger proportion were in the PICU during the Delta (~ 35 %) than the pre- Delta timeframe (~ 18 %). A larger proportion of inpatients were