APHL 2022 POSTER ABSTRACTS
COVID-19 screen 10 – 20 specimens per hour , using nucleic acid amplification technology . Positive results were immediately reported , allowing the facility to isolate those individuals within one hour of specimen collection and contacts could be quarantined within 24 hours . According to the instructions for use ( IFU ), the Abbott ID NOW™ has a performance sensitivity of ≥ 95 % and specificity of 98.4 %. While there was concern regarding this lower sensitivity and specificity when compared to PCR testing , the advantage of receiving a rapid result considerably outweighed that concern . The MTU was deployed to 16 different facilities performing a total of 1,483 tests , with a median turnaround time ( TAT ) of 21.5 minutes ( range : 11 – 48 min ). The CDC estimates the SARS-CoV-2 reproduction number is 2.5 , when case contacts are identified in five days ; however , using the MTU , case contacts are quarantined within 24 hours such that the R0 could be reduced to less than 1 and stop the outbreak at the healthcare facility . This is clearly demonstrated at Facility A , which was dealing with an outbreak , where the dispatched MTU identified two additional cases . Immediately following rapid testing , Facility A experienced an 83.3 % decrease in cases . During a second MTU deployment to Facility A , six cases were identified by MTU testing and a subsequent 87.5 % decrease in cases immediately following testing . The timeliness that contacts are identified and quarantined is an important factor in reducing the spread of disease , such that testing can only be effective if contacts are identified before symptoms develop . The MTU rapid , on-site testing allowed facilities to identify contacts 48 – 72 hours sooner than private laboratory testing . In conclusion , the use of the MTU demonstrates how rapid field testing can aid in mitigating the spread of COVID-19 to residents of long-term care facilities by quarantining contacts within 24 hours after identifying a case .
Presenter : Channyn Williams , DC Department of Forensic Sciences , channyn . williams @ dc . gov
Quantitating SARS-CoV-2 Nasopharyngeal Viral Load using Real-time PCR and Digital Droplet PCR in Acute COVID-19 Patients
K Gavina 1 , 2 , 3 , D Bulir 1 , 2 , S Chong 2 , J Gilchrist 2 , R Relich 3 , M Smieja 1 ;
1
McMaster University , 2 St . Joseph ’ s Healthcare , 3 Indiana University School of Medicine
Background : Quantitation of SARS-CoV-2 viral load plays an integral role in diagnosis , infection prevention and control , and assessing COVID-19 infections . The aim of this study was to evaluate digitaldroplet PCR ( ddPCR ) and reverse-transcriptase qPCR ( RT-qPCR ) for measuring SARS-CoV-2 viral loads in a clinical lab setting .
Methods : We evaluated quantitation using ddPCR compared to RTqPCR in a point-prevalence cohort of 86 COVID-19 patients . Further , we followed and assessed SARS-CoV-2 viral loads after acute infection in a cohort of 21 COVID-19 patients .
Results : We observed high agreement between ddPCR and RT-qPCR for viral quantitation of SARS-CoV-2 targeting nucleocapsid genes ( N1 and N2 ). In 21 patients with acute infection , SARS-CoV-2 viral loads were significantly lower at follow-up compared to enrolment by both RT-qPCR ( N1 , p < 0.0001 ; N2 , p = 0.001 ) and ddPCR ( N1 , p < 0.0001 ; N2 , p < 0.0001 ).
Conclusions : ddPCR is effective at quantitating SARS-CoV-2 at low copy numbers , but given method agreement with RT-qPCR , increased cost and turn-around-time , RT-qPCR remains a more practical method for quantitating SARS-CoV-2 within clinical settings . While an important quantitative metric , clinicians should use viral load in conjunction with a symptoms-based approach for guiding patient care and assessing COVID-19 infections .
Presenter : Kenneth Gavina , Indiana University School of Medicine , gavinak @ iu . edu
Evaluation of the INTEGRA Biosciences D-ONE Single Channel Pipetting Module on the Assist Plus Robot , Paired with the MINI 96 Portable Electronic Pipette for Semi- Automated Set-Up of the CDC Influenza / SARS CoV-2 RT- PCR Assay
C Loring 1 , J Alexander 2 , P Tirado Velez 2 , D Deloge 2 ; 1 Integra Biosciences , 2 New Hampshire Public Health Laboratories
Background : INTEGRA Biosciences released the D-ONE single channel pipetting module for use on the ASSIST PLUS automated pipetting platform in February 2022 . Used in conjunction with the INTEGRA Biosciences MINI 96 , a 96-channel portable electronic pipette , the D-ONE on the ASSIST PLUS allows for automated master mix preparation , automated PCR plate setup followed by single step addition of 96 specimens / controls to a PCR reaction plate . This functionality was evaluated for use with the Centers for Disease Control and Prevention ( CDC ) Influenza / SARS CoV-2 rRT-PCR Assay .
Method : Serial dilutions of five previously tested SARS CoV-2 positive specimens were prepared , extracted and pooled . Ct values were evaluated and displayed linearity from 19 – 34 . Programming of the ASSIST PLUS was accomplished using VIALAB Software ( INTEGRA Biosciences ). Master mix was prepared and plated using the D-ONE on the ASSIST PLUS . Samples were added using the MINI 96 . Five replicates of each sample were tested over five days for a total of 125 tests per method . Test results were compared to results obtained from manual master mix preparation , plating and sample addition . Results were evaluated for accuracy , precision and analyst hands-on time .
Results : When compared to manual plate preparation , automated PCR plate set-up by the D-ONE / ASSIST PLUS and MINI 96 demonstrated 100 % accuracy . Precision was evaluated by calculating the coefficient of variation ( CV ) of Ct values of all samples tested . Automated PCR plate preparation displayed a CV of 0.39 %, while manual plate preparation displayed a CV of 0.52 %. Ct values from the automated plate preparation averaged 0.431 higher compared to manual plate preparation . Initial data indicates that PCR plate preparation by the D-ONE / ASSIST PLUS and MINI 96 reduced hands-on technician time by 27 %.
Discussion : Ongoing surges in SARS CoV-2 testing and high staff turnover has posed challenges to public health laboratories across the country . One strategy to address these challenges is to use more automation in the laboratory . The ASSIST PLUS is a lowcost , open platform pipetting robot in use in many public health laboratories . Until recently , a limitation of the ASSIST PLUS was