APHL 2021 Poster Abstracts
Comparative Performance of Assays for SARS-CoV-2 Sequencing at a Public Health Laboratory
K . George , J . Tobias , S . Lunn , A . Young , T . Fields , R . Zinner , R . Lucas , M . Johnson and V . Arora , Kentucky State Public Health Laboratory , Frankfort , KY
Whole genome sequencing of SARS-CoV-2 is becoming increasing critical to detect the transmission , prevalence , and dominant strains circulating within communities . Several different commercial assays are currently available which provide whole genome coverage of SARS-CoV-2 . In this study , we compare two amplicon based assays , the Swift Normalase Amplicon Panels ( SNAP ) as well as a modified version of the Qiaseq in combination with the ARTIC which includes the Illumina DNA Library PREP ( formerly Flex kit ). All libraries were sequenced using Next-Generation Sequencing Technology Illumina Miseq ( model number ). Raw sequencing data was generated into consensus genomes and mapped to the Wuhan-1 reference strain using the Staph-B Toolkit Monroe bioinformatics pipeline PE _ assembly . Quality metrics include comparison of viral loads , CT values , genome coverage , assay time , and cost . The poster will present the comparative findings of this study , and comparative performance of the two assays .
Presenter : Karim George , Kentucky State Public Health Laboratory , karim . george @ ky . gov
The Use of Whole Genome Sequencing ( WGS ) to Investigate the Spread of COVID-19 in Fire Camps During the Cameron Peak Fires ( August 2020 ) in Larimer County , Colorado
M . Hetherington-Rauth1 , S . Matzinger1 , M . Brauer2 , A . Metz1 , C . Epperly1 , S . E . Totten1 , E . Tavanty1 ; 1Colorado Department of Public Health and Environment , Denver , CO , 2Larimer County Department of Public Health and Environment , Fort Collins , CO
The COVID-19 pandemic presented challenges for the 2020 wildfire season . Wildland firefighters are often deployed from multiple locations and share close living quarters . Without mitigation strategies , fire camps provide ideal opportunities for transmission of SARS-CoV-2 . The Cameron Peak Fires started mid-August in Larimer County , CO and lasted for five months . Fire crews were deployed from multiple states every two weeks . Crews were tested prior to arrival , isolated as modular units and encouraged to practice social distancing . Both surveillance and symptom based testing was performed on site . In total 78 firefighters tested positive for COVID-19 . To investigate the role of mitigation strategies at controlling the spread of COVID-19 and identify potential sources of introduction we performed whole genome sequencing on 42 of the 72 positive cases and obtained high quality data for 21 cases . Phylogenetic analysis identified five sequence types suggesting at least five independent introductions . Additionally , the sequences did not cluster by fire crew , suggesting that there was spread among crews . To identify potential sources of introduction , a phylogeny was constructed with contextual sequences collected from the states the firefighters were deployed from using the public repository GISAID . Sequence similarity among one firefighter with sequences from their state of deployment , suggesting that they were positive for COVID-19 prior to deployment . In conclusion , our analysis indicates that transmission of COVID-19 in the fire camps was the result of a series of independent introduction events followed by transmission among fire crews . This suggests that both stricter guidelines regarding quarantine and testing prior to deployment and stronger social distancing guidelines between crews may better limit the introduction of SARS-CoV-2 into fire camps and the spread between crews . Our WGS analysis of the positive cases of COVID-19 that occurred during the Cameron Peak Fires in combination with epidemiological data provides insight into the role of mitigation strategies to contain the spread of COVID-19 at fire camps during the 2020 wildfire season .
Presenter : Shannon Matzinger , Colorado Department of Health and Environment , shannon . matzinger @ state . co . us
SARS-CoV-2 B . 1.1.7 Variant Detection and the Implementation of a Statewide Surveillance Initiative in Colorado
L . Bankers , M . Hetherington-Rauth , D . Ir , A . Rossheim , R . Johnson , S . Matzinger , S . E . Totten and E . Travanty , Colorado Department of Public Health and Environment , Denver , CO
Whole genome sequencing has played an integral role in public health throughout the SARS-CoV-2 pandemic . Analysis of SARS-CoV-2 genomes has bettered our understanding of the virus , has aided in monitoring the spread of the virus , and has helped with vaccine development . Surveillance-based sequencing programs have allowed the scientific community to identify novel mutations in the virus , monitor mutation spread at both local and global scales , and observe viral evolution in near-real time . Such programs have been especially important for identifying novel SARS-CoV-2 variants of concern ( VOCs ) and variants under investigation ( VUIs ). Colorado has implemented a state-wide surveillance sequencing program , which allowed us to quickly identify the appearance of VOCs in our state to effectively monitor their spread . Because of such sequencing efforts , CO identified the first confirmed US case of the B . 1.1.7 variant that is significantly more transmissible than previously identified variants . A deletion at amino acids 69 and 70 of the spike ( S ) proteins leads to the dropout of the S gene in ThermoFisher Taqpath PCR tests for SARS-CoV-2 . This VOC and signature were first identified and announced by the UK in mid-December 2020 . In order to swiftly identify and attempt to contain the spread of such a variant in CO , CDPHE prioritized the identification of S gene target failures ( SGTFs ) from the ThermoFisher assay used in house , as well as the bioinformatic analysis of such samples . After first identifying a probable candidate sample on December 27th , the sample was tested , sequenced , and analyzed in three days . Since this case was identified , CDPHE has continued to quickly identify additional B . 1.1.7s , but with the knowledge that a broader surveillance is needed to detect additional newly emerging VOCs and VUIs that may affect vaccine efficacy and transmission rates . Using our layered approach of sequencing samples with this S gene target failure signature as well as a less biased randomized sampling from different counties of the state , a subset of our internal positive samples , and samples sequenced by our commercial testing partners , through February 2021 we have identified an additional 71 cases of the B . 1.1.7 variant in CO as well as other variants of interest , such as 28 cases of B . 1.429 originally found in CA . The initial successes of our surveillance sequencing ignited the expansion of this program to dozens of locations statewide , totaling a possible maximum sampling of 375 samples per week . More broadly , surveillance based sequencing performed for the SARS-CoV-2 pandemic can inform our surveillance efforts for other pathogens of public health concern and can provide a model for response to future pandemics and emerging diseases .
Presenter : Shannon Matzinger , Colorado Department of Health and Environment , shannon . matzinger @ state . co . us
COVID-19
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Summer 2021 LAB MATTERS 43 |