Lab Matters Summer 2021 | Page 43

APHL 2021 Poster Abstracts

Detection of the SARS-CoV-2 Beta * Variant ( B . 1.351 ) Strain at South Carolina Public Health Laboratory

H . Flores ¹ , M . Davis ¹ , C . Cole ² , H-Y . Kan ¹ , A . Diedhiou ³ , K . Eghtedary ⁴ , N . Epie ¹ ; South Carolina Public Health Laboratory , ² South Carolina DHEC Bureau of Population Health Data Analytics and Informatics ,

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South Carolina DHEC Bureau of Communicable Disease Prevention and Control , ⁴ South Carolina DHEC Bureau of Health Improvement & Equity , Columbia , SC

In February 2021 , two SARS-CoV -2 Beta * variant cases ( B . 1.351 ) were detected in South Carolina , including one sequenced at the Department of Health and Environmental Control ( DHEC ) Public Health Laboratory ( SC PHL ). These were the first cases of the B . 1.351 strain to be reported anywhere in the US and they were both reported to the DHEC ’ s Division of Acute Disease Epidemiology ( DADE ) and CDC for further investigation .

The SARS-CoV-2 , the causative agent of COVID-19 , is member of the Coronaviridae family which are recognized for its limited proofreading function of RNA-dependent RNA polymerase ( RdRP ). As more cases of COVID-19 are identified , the likelihood of detecting SARS-CoV-2 mutants became evident , such that tracking changes to the viral genome are now very instrumental for COVID-19 investigations . Some of these changes due to mutations could lead to an increase in transmissibility , disease severity , failure in vaccine and laboratory detection methods , or even a higher probability of re-infections . Implementation of SARS-CoV-2 WGS was therefore set as a high priority early on for SC PHL , because of the potential emergence of variants of the existing strain of the virus . In June 2020 , SC PHL implemented the ARTIC Network next-generation amplicon sequencing protocol of SARS-CoV-2 . To accomplish this , SC PHL randomly selected SARS-CoV-2 RNA extracts of PCR positive specimens for WGS . The samples were sequenced using MiSeq V2 Reagent Kit ( 500-cycles ) chemistry following Illumina Nextera XT DNA Library preparation . Raw sequence reads were assembled using the Illumina Basespace App , DRAGEN RNA Pathogen Detection . The assembled sequences were then analyzed by the DHEC Bureau of Population Health Data Analytics and Informatics ( PHDAI ) using the Phylogenetic Assignment of Named Global Outbreak LINeages ( PANGOLIN ) command-line tool . The sequence alignment was performed using a SARS-CoV-2 reference genome and single nucleotide polymorphisms ( SNP ) analyzed using MUSCLE and an in-house set of Python scripts .

After finding the Beta * variant , a strategic development team consisting of staff from the CDC , DADE , PHDAI , and SC PHL was established to investigate the local spread of B . 1.351 . Laboratory sequencing capacity , the total number of testing samples , selection of representative samples , data transfer , method validation , partnership with reference and academic laboratories , and reporting and notification processes were among the issues addressed . This collective effort was aimed at expediting variant strain detection in South Carolina and providing important information for COVID-19 investigations .

* In the original poster and abstract , this variant was identified with the country name . Per WHO naming conventions that were published at the end of May 2021 , these have been changed .

Presenter : Haley Flores , South Carolina Public Health Laboratory , floreshv @ dhec . sc . gov

Quality , Safety and Process Considerations for Emergency Response Surge Capacity Diagnostic Testing Workflows

M . S . Keckler , M . Martinez-Smith , S . McAllister , N . Reese , G . McAllister , A . Lyons , K . A . Perry-Dow , J . Daniels , L . Spicer , A . Shams , J . Noble-Wang , J . K . Rasheed , A . Laufer Halpin , C . Elkins , Centers for Disease Control and Prevention , Atlanta , GA

Challenge Addressed : The unprecedented COVID-19 pandemic strained the capacity of the United States public health system for diagnostic testing . The rapid spread of SARS-CoV-2 from both symptomatic and asymptomatic persons led to successive and exponential increases in testing demand . This necessitated a nationwide increase in testing capacity which was complicated by supply chain delays and shortages . Early in the CDC Emergency Response to SARS-CoV-2 , the Clinical and Environmental Microbiology Branch ( CEMB ) rapidly stood up a surge laboratory at CDC to help meet clinical diagnostic testing demands using the CDC 2019-Novel Coronavirus ( 2019-nCoV ) Real-Time RT-PCR Diagnostic Panel under a FDA Emergency Use Authorization ( EUA ).

Methods : We utilized existing diagnostic testing infrastructure established during previous emergency responses and collaborated closely with partners to rapidly implement this new diagnostic test . This report describes a planning toolkit developed from our efforts , which addresses quality and safety considerations required to maintain regulatory compliance , accuracy of testing results and safety of testing staff within the parameters of FDA and CLIA regulations and CDC policies .

Results : CEMB successfully expanded CLIA-compliant SARS-CoV-2 diagnostic testing within 17 days from support request to first tests reported despite multiple challenges . Our SARS-CoV-2 diagnostic testing capacity grew to 37 testing personnel and scientific staff , three different nucleic acid extraction platforms and five RT-PCR instruments . From this experience we created a standardized toolkit that contains process maps , checklists and lessons learned in the following areas : communications , continuity of operations planning , document control , equipment management , method verification / validation , personnel & training , process control from accessioning to reporting , procurement and safety .

Conclusions : This multistage process and detailed steps for establishing CLIA-compliant surge testing capacity using a new assay under an FDA EUA provides useful planning tools to inform future emergency responses . These tools may be adapted for establishing surge capacity for any assay or pathogen and are useful to support emergency response leadership , laboratory leadership , laboratory staff , quality managers and safety representatives of any group seeking to contribute to emergency responses requiring laboratory testing .

Impact : Provided emergency diagnostic testing support for patient management and research projects . Establishment of best practices for rapidly standing up diagnostic testing capacity during an emergency response .

Presenter : M . Shannon Keckler , Centers for Disease Control and Prevention , hbq0 @ cdc . gov

COVID-19