APHL 2022 POSTER ABSTRACTS sequencing ( WGS ) was performed on the Clear Labs ( Clear DxTM WGS SARS-CoV-2 ) platform , as well as utilizing the ARTIC network workflow on MinION ( Oxford Nanopore Technologies ) and / or MiSeq ( Illumina ). Specimens that were successfully sequenced in accordance with in-house QC metrics were uploaded to GISAID , the open-source global repository for the SARS-CoV-2 genome .
Results : From September 2020 to December 2021 , SARS-CoV-2 genomic surveillance was conducted on a total of 2,141 specimens at the Milwaukee Health Department Laboratory ( MHDL ). Of 2,098 specimens submitted to GISAID , 322 ( 15.3 %) were from the two university campuses located within the MHDL jurisdiction and the remaining 1,827 ( 84.7 %) were from the broader community . Of 322 specimens sequenced from universities , 53.7 % were the Delta variant , 8.4 % Alpha , 3.4 % Epsilon , 2.2 % Omicron and 32.3 % were other lineages , including Zeta , Eta , Iota and Mu . Omicron was detected in community sequencing 12 days prior to first university detection , indicating that spread was potentially from community to university rather than the other way around .
Conclusions : Due to existing partnerships with the two local universities , MHDL was able to quickly implement genomic surveillance for SARS-CoV-2 . University policies of weekly COVID-19 testing for unvaccinated students and staff members ensured adequate surveillance samples for WGS . MHDL surveillance efforts assisted in the identification of outbreak clusters on campus and helped the universities monitor and track suspected cases . Sequencing specimens from these university populations improved our understanding of the transmission patterns of SARS- CoV-2 variants circulating on a local community level , the level of transmissibility amongst high-risk populations and provided timely actionable data for contact tracing .
Presenter : Amy Bauer , City of Milwaukee Health Department , ambauer @ milwaukee . gov
Application of Rapid Whole Genome Sequencing to Identify a SARS-CoV-2 Omicron Variant Outbreak Among Highly Vaccinated Wedding Attendees
DA Wadford 1 , L Page 2 , K Mosack 2 , A Bauer 3 , M Khubbar 3 , N Balakrishnan 3 , J Elder 1 , N Moss 4 , A Goeldner 5 , I Pray 5 , M Lambert 5 , 6 , Y Cruz 1 , S Gibbons-Burgener 5 , S Bhattacharyya 3 , K Johnson 2 , R Westergaard 5 , 6 ; 1 California Department of Public Health , 2 City of Milwaukee Health Department , 3 City of Milwaukee Public Health Laboratory , 4 Alameda County Public Health , 5 Wisconsin Department of Health Services and 6 University of Wisconsin Madison
Background : The SARS-CoV-2 Omicron variant was first described on Nov . 24 , 2021 , with the first detection in the US on Dec . 1 , 2021 . On Dec . 2 , the California Department of Public Health ( CDPH ) detected SARS-CoV-2 with RT-qPCR spike gene target failures ( a proxy for Omicron ) from six vaccinated residents returning from a late- November wedding in Wisconsin . Rapid whole genome sequencing ( WGS ) subsequently confirmed these as Omicron on Dec . 3 .
Methods : WGS analysis of available outbreak specimens was performed at the CDPH Laboratory and Milwaukee Health Department Laboratory ( MHDL ) using modified ARTIC-sequencing protocols , with Nanopore ( ONT ) technology on Clear Lab ( Clear DxTM ) or MiSeq ( Illumina ) platforms . WGS data were processed using the ARTIC bioinformatics pipeline with modifications to generate consensus sequences , variant calls and perform phylogenetic analysis .
Results : Of 169 wedding attendees , 73 were tested for SARS-CoV-2 and 39 ( 53 %) tested positive . Thirty-five ( 90 %) cases had completed their primary immunization series and 10 had received a booster dose . WGS from 18 of the 35 PCR-confirmed cases found that 17 were Omicron ( BA . 1 sub-lineage ) and one was Delta lineage . Phylogenetic analysis revealed that 13 cases shared identical BA . 1 genomes , including the presumed index case who had recently returned from international travel .
Conclusions : The application of rapid WGS to one of the earliest Omicron outbreaks in the US allowed for rapid follow up across state jurisdictions for additional case findings , rapid confirmation and epidemiologic characterization . This multi-jurisdictional collaboration highlights the effectiveness of strong laboratory and epidemiology partnerships to investigate interstate outbreaks .
The findings and conclusions in this article are those of the author ( s ) and do not necessarily represent the views or opinions of the California Department of Public Health or the California Health and Human Services Agency , City of Milwaukee Health Department / Laboratory , or Wisconsin Department of Health Services and University of Wisconsin Madison
Presenter : Debra Wadford , California Department of Public Health , debra . wadford @ cdph . ca . gov
Piloting Air Samplers to Assess SARS-CoV-2 Exposure and Improve Risk Mitigation in Congregate Settings for Public Health Actions
K Beversdorf 1 , J Zimmer 1 , M Khubbar 1 , N Tomaro 1 , L Schmidt 1 , H Kraussel 1 , E Durkes 1 , M Ramuta 2 , C Newman 2 , S Brakefield 2 , D O ’ Connor 2 , S O ’ Connor 2 , S Bhattacharyya 1 ; 1 City of Milwaukee Health Department , 2 University of Wisconsin-Madison
Introduction : The COVID-19 pandemic has exacerbated concerns regarding the transmission of airborne illnesses , testing for respiratory pathogens and subsequent contact tracing , and employing enhanced genomic surveillance to support public health emergency preparedness and response . As such , there is great interest in developing new technologies and approaches to improve risk mitigation and public health actions . Clinical genomic sequencing and wastewater-based epidemiology have improved SARS-CoV-2 variant tracking and increased the understanding of dynamic community transmission . However , there is still a need for congregate surveillance ( e . g ., schools , transportation hubs and restaurants ) and supporting data related to community spread and outbreak investigations . In collaboration with local and regional partners , the Milwaukee Health Department Laboratory ( MHDL ) placed aerosol samplers in select congregate spaces with the goal of monitoring SARS-CoV-2 , thereby validating an air sampling method as an effective strategy for improving surveillance , assessing exposure and risk mitigation .
Method : Starting in December 2021 , Thermo AerosolSense™ Samplers were deployed in several congregate settings in Milwaukee County to monitor for SARS-CoV-2 on a daily to weekly basis . Total genomic RNA from air sample substrates were extracted and tested using the Thermo TaqPath™ COVID-19 Combo Kit , which targets SARS-CoV-2 ORF1a / b , N gene and S gene . Samples with low cycle thresholds ( CT < 30 ) were sequenced at MHDL using Nextera
COVID-19