APHL 2021 Poster Abstracts
COVID-19
Surveillance of SARS-CoV-2 in Washington , DC by Next Generation Sequencing
S . Nguyen , E . Zelaya , S . Scott , J . Doss , M . McCarroll , J . Hauser , DC Department of Forensic Sciences , Washington , DC
University campuses have been a focal point for SARS-CoV-2 outbreaks and subsequent epidemiological investigations . 1-4 The majority of higher education campuses within the District of Columbia are offering virtual courses , however despite preventative measures , there have been outbreaks within student populations . A super spreading event was suspected , involving as many as 120 students on off-campus housing in the span of one week . SARS- CoV-2 isolated from a subset of positive respiratory samples from the outbreak were analyzed using next generation sequencing . Sequencing data revealed high genetic diversity of SARS-CoV-2 within the sample set demonstrated by the detection of four different SARS-CoV2 lineages including two isolates of B . 1.1.7 , the variant of concern first reported in the United Kingdom . Additionally , the two isolates of B . 1.1.7 each contained mutations independent of one another , suggesting that the students obtained the variants during two independent transmission events and not from one another . Of the samples analyzed only a small cluster of students appeared linked by a single transmission event . This data demonstrates how next generation sequencing can be utilized to assist epidemiological investigations and determining the complex circumstances leading to outbreaks associated with student populations .
References :
1 . Fung , I ., Cheung , C ., & Handel , A . ( 2020 ). SARS-CoV-2 Viral and Serological Testing When College Campuses Reopen : Some Practical Considerations . Disaster Medicine and Public Health Preparedness , 1-5 . doi : 10.1017 / dmp . 2020.266 &
2 . Richmond C . S ., Sabin , A . P ., Jobe , D . A ., Lovrich , S . D ., Kenny , P . A . ( 2020 ). SARS-CoV-2 sequencing reveals rapid transmission from college student clusters resulting in morbidity and deaths in vulnerable populations . medRxiv . doi : 10.1101 / 2020.10.12.20210294
3 . 3Bhoyar R . C ., Jain A ., Sehgal P ., Divakar M . K ., Sharma D ., Imran M ., et al . ( 2021 ). High throughput detection and genetic epidemiology of SARS-CoV-2 using COVIDSeq next-generation sequencing . PLoS ONE 16 ( 2 ): e0247115 . https :// doi . org / 10.1371 / journal . pone . 0247115
4 . 4Denny , T . N ., Andrews , L ., Bonsignori , M ., Cavanaugh , K ., Datto , M . B ., Deckard , A ., et al . ( 2020 ). Implementation of a Pooled Surveillance Testing Program for Asymptomatic SARS-CoV-2 Infections on a College Campus - Duke University , Durham , North Carolina , August 2-October 11 , 2020 . MMWR . Morbidity and mortality weekly report , 69 ( 46 ), 1743 – 1747 . https :// doi . org / 10.15585 / mmwr . mm6946e1
Presenter : Scott Nguyen , Washington , DC Department of Forensic Sciences , scott . nguyen @ dc . gov
Correlation Between the QIAGEN QIAprep & Viral RNA UM Kit and Three Other SARS-CoV-2 PCR Assays Used in the Public Health Laboratory Setting
H . Guevara , C-Y . Pan , C . Wright , L . Moua , D . Wadford and C . Morales , California Department of Public Health , Richmond , CA
Introduction : During the initial response to COVID-19 , public health laboratories faced supply chain issues and long turnaround times in testing for SARS-CoV-2 ( SC2 ). QIAGEN ’ s QIAPrep & amp ( QIAp & a ) kit was developed to perform PCR without the need of nucleic acid ( NA ) extraction , using a two-minute liquid-based sample preparation directly in the PCR vessel . We compared this assay with three Emergency Use Authorization ( EUA ) PCR tests : the CDC 2019-Novel Coronavirus ( nCoV ), the CDC Influenza SARS-CoV-2 ( Flu SC2 ), and the Thermofisher ’ s TaqPath COVID-19 Combo kit to evaluate their workflow and their performances .
Methods : The QIAp & a kit uses a proprietary sample treatment buffer , whereas the CDC assays ( nCoV and FluSC2 ) use the bioMerieux easyMAG and the TaqPath uses the Kingfisher Flex for NA extraction . The specimen input is 8 µ L , 100 µ L / 100 µ L , and 200 µ L for the QIAp & a kit , CDC 2019 nCoV / Flu SC2 assays , and TaqPath kit , respectively . All PCRs were performed using the ABI 7500 Fast Dx platform . To determine the limit of detection ( LOD ), a pool of nasopharyngeal ( NP ) specimens with a known number of SC2 viral copies ( cp ) was tenfold serially diluted from one million viral cp /µ L to 0.1 viral cp /µ L . Each dilution was tested in triplicate by the four assays on the same day . For accuracy , 83 SC2 (+) samples with crossing thresholds ( CT ) ranging from 15 to 35 and 15 SC2 negative samples were divided in two sets (~ 40 ) and each set was tested by all four methods at the same time to avoid extra freeze-thawing . The time to test 40 samples in each assay was also assessed .
Results : The QIAp & a kit uses less consumables and time compared to the other assays . The LOD for the QIAp & a was estimated to be similar compared with the other methods that use purified and concentrated NA , around 1 cp /µ L . Input PCR sample volume varies by method ( QIAp & a 8 µ L of treated specimen / reaction , CDC nCoV and FluSC2 5 µ L and TaqPath 10 µ L of purified NA / reaction ). Among all samples with SC2 detected , the QIAp & a had similar median distribution CT values compared with the other tests . There was also a linear CT correlation between the QIAp & a ’ s values and those from the three other tests with a Pearson coefficient ( r ) ranging from 0.9588-0.9742 . Of all samples detected by the FluSC2 assay ( 83 ), three were negative by the QIAp & a and inconclusive on the other two methods .
Discussion : Our data found the research-use-only ( RUO ) QIAp & a assay has comparable LODs to the widely used EUA kits in the PHLs . There was a strong performance correlation between the three assays and the QIAp & a assay without the need of an NA extraction step . The significantly less amount of sample needed , the reduction in plasticwares and reliance on supplies , the removal of an expensive extraction step , and a faster turnaround time could potentially alleviate many problems encountered in surge testing which demands a high throughput surveillance screening assay for SARS-CoV-2 virus .
Presenter : Hugo Guevara , California Department of Public Health , hugo . guevara @ cdph . ca . gov
46 |
LAB MATTERS Summer 2021 |
|
|
|