APHL 2021 Poster Abstracts estimated ; however , transmission risk seems reduced within three months due to low viral titers and transient colonization of the nasopharynx . Partnerships between Public Health Laboratories with next generation sequencing capacity and local hospitals with routine SARS-CoV-2 PCR screening can identify otherwise undetected cases of sub-clinical re-infections or vaccine break through variants to quickly inform public health policies and guidelines .
Presenter : Emika Aroh , Dallas County Health and Human Services , Emika . aroh @ dallascounty . org
Emergence and Transmission Dynamics of SARS-CoV-2 During Early Stages of COVID-19 Pandemic in Wisconsin
M . Khubbar 1 , G . Moreno 2 , K . Braun 2 , J . Weiner 1 , T . Friedrich 2 , D . O ’ Connor 2 , S . Bhattachayya 1 ; 1 City of Milwaukee Health Department , Milwaukee , WI , 2 University of Wisconsin – Madison , Madison , WI
Introduction : COVID-19 was declared a pandemic by WHO on March 11 , 2020 followed by the US declaring a national emergency on March 13 , 2020 , the same day first confirmed SARS-CoV-2 case was reported in Milwaukee , WI . Milwaukee Health Department Laboratory ( MHDL ) played a pivotal role by detecting COVID-19 cases within 24 hours of specimen collection from the city and surrounding communities . Active genomic surveillance and collection of associated epidemiological metadata was prioritized to understanding transmission patterns and minimize spread of SARS-CoV-2 clusters .
Methods : A subset of SARS-CoV-2 positive specimens were received in March- April , 2020 from Milwaukee ( 97 total cases ) and other neighboring cities ( 66 total cases ) were sequenced . Selection was based on isolate from hot spots ( used zip Codes ), long term care facilities , jails , travel associations , households and outbreaks . RNA extracts from positive cases were used to sequence at the University of Wisconsin AIDS Vaccine Research Laboratory ( AVRL ) per modified ARTIC protocol using MinION ( Oxford Nanopore ). Consensus sequences were derived by using a modified ARTIC protocol and were shared on Global Initiative on Sharing All Influenza Data ( GISAID ). A time-resolved phylogenetic tree was built and clades assigned using Nextstrain tools and nomenclature .
Results : Local transmission in Milwaukee County found to begin early March leading to a large number of the COVID-19 cases . In late March and early April , there were multiple introductions of SARS- CoV-2 detected into Milwaukee County , likely lineages from Asianorigin , resulting in large local epidemic with widespread community transmission . The most common clades included 19A ( n = 75 ; 60.0 %) followed by 20A clade ( n = 31 ; 24.8 %), 20C , 19B and 20B . In Milwaukee , the SARS-CoV-2 mostly found to be clustered closely , consistent with fewer introductions and subsequent community transmission in comparison to Madison Dane County , Wisconsin .
Conclusion : The preliminary results indicated that expanded detection capabilities and whole genome sequencing efforts at local level will aid to not only isolate and contain SARS-CoV-2 cases but limit the establishment of new transmission clusters . Near realtime sequencing and data analysis will also enable public health jurisdictions to identify emerging variants of SARS-CoV-2 for further characterization by scientific community or researchers . Partnership with academic centers , industry , non-governmental organizations , and public health agencies is needed to accomplish this task of real-time genomic surveillance to prevent emergence and spread of highly transmissible and infectious variants in future .
Presenter : Manjeet Khubbar , City of Milwaukee Health Department , mkhubb @ milwaukee . gov
To All the Other Diseases : P . S . We Still Test for You ( A Local PHL Response to COVID-19 )
S . Scott , J . Hilleshiem , B . Pfotenhauer , J . Lentz , A . Bauer , S . Mardanu-Budiono , Z . Amezquita-Montes , J . Weiner , N . Leigh , M . Khubbar , K . Schieble and Sanjib Bhattacharyya , City of Milwaukee Health Department , Milwaukee , WI
Introduction : Public health laboratories working at the federal , state and local level have played a vital role in the response to the COVID-19 pandemic . The City of Milwaukee Health Department Laboratory ( MHDL ) is one of two public health laboratories in Wisconsin , and not only was early in onboarding SARS-CoV-2 PCR testing but also adjusted quickly throughout the pandemic . MHDL was able to respond to the demands of SARS-CoV-2 testing almost immediately . The lab began adapting by cross-training current staff , bringing on new staff , quickly implementing novel tests and new equipment , upgrading inventory systems , and flexing to work around supply chain issues and a rapidly increasing workload .
Methods : Supply shortages and an increasing demand for testing during the COVID-19 pandemic has forced laboratories to pivot to new tests and new testing platforms at an alarming rate . MHDL rapidly brought on multiple nucleic acid extraction systems and 8 tests for SARS-CoV-2 comprising of seven molecular tests and an antibody test for prior infections . As early as March 2020 , MHDL began cross-training current staff to accommodate the increasing workload of the pandemic . Between March and June 2020 , three additional staff were hired , and in January 2021 , two COVID-19 Laboratory Associates were sponsored through APHL and CDC .
Results : In a typical year , MHDL receives around 45,000 to 50,000 clinical specimens for infectious disease diagnostics . Prior to the COVID-19 pandemic , MHDL ’ s infectious disease sample volume was primarily comprised of sexually transmitted infection ( STI ) specimens with respiratory specimens only making up 1.4 % of specimens . At the height of Wisconsin ’ s peak , in the fall of 2020 , MHDL was receiving around 1,000 specimens weekly just for SARS- CoV-2 . In 2020 , the lab tested 26,714 specimens for SARS-CoV-2 , which is more than 40 times the normal respiratory specimen volume in a typical year . Increasing trained and competent staff greatly improved MHDL ’ s ability to respond to the pandemic .
Conclusion : Balancing the ever-changing availability of reagents and ancillary supplies kept laboratory staff on their toes and ready to switch tests at a moment ’ s notice . One practice that greatly helped was the implementation of a new inventory management system to track which supplies were in and out of stock . With the changes that a pandemic brings to a local PH laboratory , a modular approach to staff training , new instrument implementation , and diagnostic test verification is key . This approach allows for quicker ramp up and a smoother transition into high throughput diagnostic testing as well as de-escalation when volumes and testing decrease .
Presenter : Samantha Scott , City of Milwaukee Health Department , sascott @ milwaukee . gov
Summer 2021 LAB MATTERS 37
COVID-19