APHL 2022 POSTER ABSTRACTS symptomatic due to COVID-19 during the Delta (~ 78 %) than the pre-Delta timeframe (~ 67 %); however , overall Ct values did not differ among symptomatic inpatients between timeframes . We found that children infected during the Delta timeframe exhibited higher viral loads ( lower Ct ) and a larger proportion were hospitalized in the PICU than children infected earlier in the pandemic or with other variants , suggesting Delta may result in more severe disease in children .
Presenter : Laura Bankers , Colorado Department of Public Health and Environment , laura . bankers @ state . co . us
Introduction and Dispersal Dynamics of SARS-CoV-2 Lineages within a State Corrections Center and a County Detention Facility in Colorado
D Ir 1 , M Hetherington-Rauth 1 , L Bankers 1 , L Warren 2 , B Albanese 2 , R Jervis 1 , A Rossheim 1 , T Mappe 1 , S Matzinger 1 , E Travanty 1 ; 1 Colorado Department of Public Health and Environment , 2 TriCounty Health Department
SARS-CoV-2 outbreaks in correctional and detention facilities are difficult to prevent and contain because of the populationdense housing , limited space , resources for medical isolation and quarantine , and potential introductions by new people who are detained or incarcerated ( PDI ), staff members and visitors . However , little is known about the circulation patterns of SARS-CoV-2 within these facilities . PDI at state correctional facilities on average have longer incarceration stay periods whereas PDI at county detention facilities are typically temporarily detained and have shorter stay periods . These differences may affect both the prevalence and transmission dynamics of SARS-CoV-2 within these facilities . To better understand SARS-CoV-2 prevalence and transmission dynamics in correctional and detention settings , we analyzed 579 SARS-CoV-2 whole genome sequences from a state correctional facility and 1,079 SARS-CoV-2 sequences from a county detention facility in Colorado . Sampling was performed between the period of April 01 , 2020 – November 30 , 2021 , coinciding with outbreak investigations . We generated SARS-CoV-2 whole genome consensus sequences and constructed maximum likelihood phylogenetic trees . We found that in the county detention facility , the outbreak was characterized by a larger range of SARS-CoV-2 lineages ( 27 different lineage calls ) compared to the correctional facility ( 10 ) suggesting that , based on the genetic divergence of sequences , there were likely more overall introductions to the detention center during this time period . Our sequencing data show higher diversity in the detention facility than the correctional facility suggesting that the rate of PDI turnover was likely an important determinant in SARS-CoV-2 transmission in the two facility types . However , pairing sequencing data with epidemiological data , such as detailed contact tracing , is an important next step in confirming these results . Our results improve our understanding of SARS-CoV-2 transmission dynamics in population-dense housing scenarios and inform methods for surveillance tracking of pathogens of public health concern in correction and detention facilities .
Presenter : Diana Ir , Colorado Department of Public Health and Environment , diana . ir @ state . co . us
Whole Genome Sequencing of SARS-CoV-2 : Assessment of Multiplatform cDNA Preparation
A Rossheim , G Hareland , Jr ., J Bello , S Baird , A Alford , V Nguyen , L Chaudhry , D Mallal , N Pysnack , L Bankers , M Hetherington- Rauth and S Matzinger , Colorado Department of Public Health and Environment
Streamlined , high throughput whole-genome sequencing ( WGS ) of the Severe Acute Respiratory Syndrome Coronavirus 2 ( SARS- CoV-2 ) genome to track mutations and identify emerging variants is critical in supporting the public health response during the ongoing pandemic . Efficient and consistent WGS surveillance through volume surges and supply chain challenges is dependent on an adaptable and robust workflow that capitalizes on the strengths of the different available sequencing platforms . However , a limitation to this approach is that each platform has their own recommended cDNA preparation , which hampers the flexibility to redirect sequencing runs beyond early preparatory steps . Although the ARTIC cDNA preparation protocol can be used with both the Illumina and Oxford Nanopore Technologies ( ONT ) platforms , it is unclear if the Illumina specific COVIDSeq cDNA preparation protocol would yield comparable results when library prepped and sequenced on the ONT GridION . To assess the interchangeability of Illumina COVIDSeq cDNA preparation and the ARTIC cDNA preparation for use on the ONT GridION Platform , cDNA preparation was performed using either the Illumina COVIDSeq cDNA or the ARTIC cDNA protocol on four clinical samples with Ct values 20 % and depth of coverage increased by an average of > 1,500 for the ONT cDNA preparation relative to the COVIDSeq preparation . Therefore , a greater number of high-quality reads were successfully aligned to the reference genome and because of these increases , we were able to more reliably determine lineage information with the ONT cDNA preparation . These results suggest that the Illumina COVIDSeq cDNA preparation is best reserved for the Illumina workflow and not directly interchangeable with the ARTIC SARS-CoV-2 ONT GridION workflow . More broadly , our comparison provides valuable information for those developing , optimizing and streamlining whole genome sequencing protocols on multiple platforms .
Presenter : Alexandria Rossheim , Colorado Dept . of Public Health and Environment , alexandria . rossheim @ state . co . us
Reducing the Curve : How Mobile Testing Can Mitigate the Spread of COVID-19 in a Congregate Setting
C Williams , K Tran and M McCarroll , DC Public Health Laboratory
Continuous testing for SARS-CoV-2 amongst the congregate setting was critical in identifying outbreaks . Polymerase chain reaction ( PCR ) tests are the gold standard for performing this testing ; however , due to the surge of community testing , an increase in the length of time to get a report from a laboratory was observed . In the District of Columbia ( DC ), private laboratories were providing reports 3 – 7 days after the date of collection . Studies have shown that the COVID-19 latent period is between 4 – 5 days ; therefore , residents of long-term care facilities could be exposed to positive cases before they were notified and isolated . This failing of the laboratory system led the DC Public Health Laboratory ( PHL ) to optimize testing efforts by providing rapid field screening . The DC PHL used a mobile laboratory truck , on loan from the CDC NHANES division , to provide on-site SARS-CoV-2 testing . Equipped with five Abbott ID NOW™ instruments , the mobile testing unit ( MTU ) had the capacity to
COVID-19