APHL 2021 Poster Abstracts
COVID-19
Comparison of the Logix Smart TM Coronavirus Disease RT-PCR Kit with the CDC 2019 nCoV RT PCR Assay for the Detection of SARS-CoV-2 in Nasopharyngeal Specimens
B . Abdalhamid , P . Iwen and E . Mitchell , Nebraska Public Health Laboratory , Omaha , NE
Background : Many FDA Emergency Use Authorization RT-PCR assays for the detection of SARS-CoV-2 ( SC2 ) are available that show a wide range of accuracy when used under clinical conditions . The aim of this study was to compare the Logix Smart TM Coronavirus Disease 2019 kit ( Logix CoDiagnostics , Inc , Salt Lake , UT ) with the CDC 2019 nCoV RT-PCR assay ( CDC2019 , Atlanta , GA ) for the detection of SC2 in nasopharyngeal ( NP ) specimens .
Methods A total of 67 NP specimens ( 57 COVID-19 positive specimens and 10 COVID-19 negative specimens ) were used for this comparison study . Positive specimens were selected based on a range of cycle threshold ( Ct ) values with 19 specimens representing Cts < 30 and 38 specimens with Cts > 30 ( 19 specimens with Cts =( 30-35 ), and 19 specimens with Cts > 35 . The KingFisher Flex platform was used to extract RNA from all samples . Extracted RNA was run on each kit following the manufacturer ’ s instructions . Discrepancy results were re-tested by the Xpert ® Xpress SARS-CoV-2 test ( Xpert , Cepheid , Sunnyvale , CA ).
Results : Results correlated between CDC2019 and Logix RT-PCR for all negative specimens and 47 of the positive specimens with Cts < 34 . However , 10 positive specimens with Cts ≥ 34 that were positive by CDC2019 were negative by the Logix assay . The Xpert assay correlated 100 % with the CDC2019 results when re-testing these discrepant specimens . Using the consensus results from testing with discrepancy analysis , the sensitivity and specificity of Logix were 85 % and 100 %, respectively .
Conclusions These results show that the Logix Smart COVID-19 test kit did not detect NP specimens that contained a lower viral load . The significance of the lower viral load however needs to be studied further to determine what effects this finding has on the transmissibility of the SC2 as pertaining to control of the COVID-19 pandemic . Additional studies are also needed to evaluate further the utilization of the Logix assay for use when testing specimens such as a nasal swab or saliva where lower viral loads are present .
Presenter : Bala Abdalhamid , Nebraska Public Health Laboratory , babdalhamid @ umnc . edu
Outbreak of SARS-CoV-2 Lineage B . 1.1.29 in a Correctional Facility
M . Grose , P . Griffin , B . Olson and P . Adam , Kansas Department of Health and Environment , Topeka , KS
COVID-19 poses unique infection control challenges in correctional facility settings . SARS-CoV-2 ( SCV2 ) B . 1.1.29 was identified as the etiologic agent of an outbreak at a correctional facility via WGS of specimens that tested positive via RT-PCR for SCV2 . Lineage B . 1.1.29 had not been described in the United Stated prior to this finding by the Kansas WGS team .
Spike protein mutations , H207R , D614G , and A1078T , were observed after performing analysis utilizing Nextstrain and all sequences with this combination of mutations were assigned to Clade 20B . A1078T had been previously observed in the US ; however , H207R had not been observed in the US as of early February 2021 , though it had been described in the United Kingdom in June . Interestingly , the Kansas WGS team identified B . 1.1.29 in a specimen collected in March 2020 from a county near the correctional facility in question . H207R is in the N-terminal domain of the protein and is considered a conservative mutation due to preservation of the residue ’ s charge . A1078T is located within the S2 subunit of the spike protein and appears to be within a connector domain between secondary structural elements . The impact of these mutations on spike protein function is not apparent , but they do not appear to be deleterious .
The correctional facility in question experienced two consecutive weeks with no new cases until several large groups of offenders suddenly developed symptoms consistent with COVID-19 . At this point , the Bureau of Disease Control and Prevention and the Department of Corrections implemented a mass testing and cohorting campaign to quell the spread of the virus within the offender population . A total of 3,088 specimens ( 800 unique patients ) were tested via RT PCR during January and February and , of those , 237 were positive for SCV2 . Of these SCV2 specimens , 126 were analyzed via WGS and revealed that linage B . 1.1.29 was predominate . 24 specimens collected in January or February 2021 from the county and a neighboring county were analyzed via WGS and this particular lineage was not found in any of the specimens . At the time of submission , it was not known how this lineage was introduced to the correctional facility , but it is suspected that B . 1.1.29 was circulating in the community at a low enough level as to have not been identified by WGS routine surveillance . This study examines the epidemiological and genetic characteristics of this outbreak .
Presenter : Michael Grose , Kansas Department of Health and Environment , michael . grose @ ks . gov
Mini-Meta-Study : Collection and Sample Concentration for Rapid SARS-CoV-2 Detection in Wastewater and Wastewater Aerosols
D . Alburty , D . Goad and A . Packingham , InnovaPrep LLC , Drexel , MO
COVID-19 and other emerging threats outbreak investigations will be an important and ongoing role of public health officials and first responders long after the rollout of COVID-19 vaccines for ensuring that hotspots are found quickly to reduce additional incidences of harm to the public . The same is true with emerging threats that lack vaccines , both for humans and animals , such as African Swine Fever . The combination of aerosol sampling and wastewater sampling , supplemented by rapid sample concentration , provide powerful tools for public health . Fast and efficient workflow is a must and may include using rapid molecular analysis methods rather than traditional culture methods , pooling samples ( and removing an aliquot for follow-up analysis if needed ) and using alternative sample preparation approaches .
This poster summarizes and ties together the power of these approaches for public health as demonstrated by three studies from Bolivia , the US , and Spain . Wastewater was collected and concentrated for rapid detection through qPCR and ddPCR . Aerosol samples were collected near wastewater canals and detected
COVID-19
|
|
|
Summer 2021 LAB MATTERS 35 |