APHL 2021 Poster Abstracts
COVID-19
Disclaimer : The findings and conclusions in this report are those of the author ( s ) and do not necessarily represent the official position of the US Centers for Disease Control and Prevention ( CDC )
Presenter : Megan Hahn , New York City Public Health Laboratory , mhahn @ health . nyc . gov
Review of the BinaxNOW Point of Care Ag Test
C . Hayes1 , M . Leelawong1 , S . Suleiman1 , T . Searles1 , A . DeVito1 , B . Limbago2 , W . Kuhnert-Tallman2 , J . Rakeman1 ; 1New York City Public Health Laboratory , New York City , NY , 2US Centers for Disease Control and Prevention , Atlanta , GA
In August 2020 , the US Department of Health and Human Services announced that 150 million Abbott BinaxNOW COVID-19 Ag Card Point of Care SARS-CoV-2 ( Binax ) diagnostic tests would be available for deployment to schools and other settings as part of the effort to increase access to testing . However , the emergency use authorization ( EUA ) from the US Food and Drug Administration ( FDA ) only indicated use within the first seven days of the onset of symptoms . The New York City Department of Health and Mental Hygiene ( NYC DOHMH ) Public Health Laboratory in collaboration with the US Centers for Disease Control and Prevention designed and conducted a study at two COVID-19 testing sites operated by NYC DOHMH to compare the accuracy of the Binax test against the current standard of care diagnostic test , the Cepheid Xpert Xpress SARS-CoV-2 diagnostic real-time RT-PCR ( XpertXpress ) test .
Participants of at least 18 years of age with previously scheduled COVID-19 testing appointments were recruited from 11 / 30 / 20- 12 / 11 / 20 and 12 / 22 / 20-12 / 31 / 20 . Collected data include date of birth , sex , symptom status , Binax test result , and XpertXpress test result with Ct values when applicable . The Binax tests were conducted by laboratory staff from 11 / 30 / 20-12 / 11 / 20 and conducted by clinical staff from 12 / 22 / 20-12 / 31 / 20 to better represent point of care-based use of the test .
The analysis included data from 1,487 participants . During the study , combined overall daily positivity rates for the testing sites ( based on study- and non-study-population XpertXpress testing ) ranged from 3.52 % to 11.03 % with a mean of 7.00 % and a median of 7.05 %. A total of 71 participants tested positive for SARS-CoV- 2 ( including both concordant positive results and discordant results ). The overall performance of the Binax study assay as compared with XpertXpress diagnostic test was as follows : sensitivity ( Se ): 42.9 %, specificity ( Sp ): 99.9 %, positive predictive value ( PPV ): 96.8 %, negative predictive value ( NPV ): 97.3 %. The sensitivity of the test was lowest among asymptomatic participants ( 34.8 %), followed by those reporting symptoms of any duration ( 58.3 %), with the highest sensitivity identified among those reporting symptoms of a duration of seven days or less ( 87.5 %). Additionally , among XpertXpress (+)/ Binax (+) participants Ct values for PCR targets N2 and E were lower on average than the in XpertXpress (+)/ Binax ( - ) participants . The observed results support the product guidelines and FDA EUA intended use by those in the first seven days of the onset of symptoms . The increased sensitivity among those with symptoms for less than a week suggests that limiting testing to this group would reduce the number of false negatives resulting from the Binax test . Patients who are asymptomatic or who have had symptoms for longer than a week could continue to receive the XpertXpress test .
Presenter : Craig Hayes , New York City Public Health Laboratory , chayes @ health . nyc . gov
Surveillance and Genomic Epidemiology of SARS-CoV-2 in Michigan Communities Using NextStrain Analysis
K . Jacob , B . Mabvakure , G . LaLonde , H . Blankenship , M . Soehnlen Michigan Department of Health and Human Services , Lansing , MI
Background : SARS-CoV-2 is an upper respiratory virus originating out of Wuhan , China that quickly spread into a pandemic over the past year . The first sequenced genome of SARS-CoV-2 was published in January 2020 , since then , over 128,000 sequences have been generated in the US . Throughout the pandemic , the implementation of WGS and data analytics have allowed public health labs to support SARS-CoV-2 response through monitoring for important mutations that impact clinical or diagnostic outcomes , examining transmission dynamics , and supporting contact tracing of cluster outbreaks .
Methods : Since March 2020 , Michigan Department of Health and Human Services ( MDHHS ) has performed WGS on over 8000 SARS- CoV-2 samples . Bioinformatic analyses were developed in house to obtain consensus sequences and QC data for each sample . Genome diversity is examined through clade assignments using both NextClade and Pangolin databases . Routine disease surveillance is performed and communicated through real-time tracking of transmission trends and emergence of important phylogenetic clusters in NextStrain . Interactive visualizations and communication with NextStrain provide mechanisms of data communication among the laboratory and state epidemiologists .
Results : Phylogeographic analysis of samples in Michigan identified hypothetical transmission dynamics among the two peninsulas in Michigan . Clade identification was predominated by two clades : 20C ( 68.5 %) and 20G ( 31.6 %). Analysis of cluster outbreaks explored introductions into the facility and community relatedness to support contact tracing . 18 samples from a single facility were sequenced due to a known cluster outbreak occurring . Two different clades , 20A and 20C , were identified that formed phylogenetically distinct clusters . The outbreak associated clusters also reflected those detected within the connected counties and association of the infections was established with either worksite or community spread .
Discussion : The use of WGS and bioinformatic analysis for SARS- CoV-2 surveillance has been crucial for providing assistance to the pandemic response . Sequencing and analysis of cluster outbreaks and community samples has provided insight into baseline levels of the virus and information for pandemic response . Communication and visualization of the data through NextStrain has provided a platform for sharing data with epidemiological partners for public health response .
Presenter : Kristin Jacob , Michigan Department of Health and Human Services , jacobk1 @ michigan . gov
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LAB MATTERS Summer 2021 |
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