APHL 2022 POSTER ABSTRACTS implementation data showed an increase to 98.4 % and 99.0 % for Phases 1 and 2 , respectively . The average specimen-received to result-released TAT decreased from 99 mins ( pre-implementation , n = 144,796 ) to 71 mins ( post-implementation , n = 50,554 ).
Conclusions : LIS automated solutions were successfully implemented resulting in streamlined post-analytical processes by reducing manual processes for COVID testing . This also reduced TAT by 28 minutes and staff involvement with > 98 % of post-analytical processes being automated . Automation Rate and TAT metrics proved to be important quality indicators for monitoring the success of LIS automated algorithms .
Presenter : Mauricio Mariscal , New York City Public Health Laboratory , mdelgadomariscal @ health . nyc . gov symptomatic and 39 asymptomatic ) and 203 specimens negative for SARS-CoV-2 had saliva specimens submitted to RU for DRUL testing .
Conclusions : This study demonstrates how important partnerships between public health and academic labs are in addressing the challenges of the COVID-19 pandemic . Key takeaways from this study included buy-in from all parties , clear and consistent communication among investigators , facilitators and clinic / lab staff , and having well-defined study goals . This collaboration resulted in exceeding study goals , facilitating the validation process of a new saliva assay and establishing a framework for future collaborations .
Presenter : Sharifah Suleiman , New York City Public Health Laboratory , ssuleiman @ health . nyc . gov
A Perfect Marriage : An Academic Lab and a Local Public Health Lab Work Together to Validate a New SARS-CoV-2 Test for Self-collected Saliva Specimens
S Suleiman 1 , R Fowler 2 , M Frank 3 , R Darnell 3 , T Searles 3 , S Hughes 1 ;
1
New York City Department of Health and Mental Hygiene , 2 New York City Public Health Laboratory , 3 The Rockefeller University
Introduction : The COVID-19 pandemic has strengthened partnerships between public health and academic labs . With surges in new COVID-19 cases , there is a significant need to provide simple , reliable and scalable SARS-CoV-2 tests to local communities . The Rockefeller University ( RU ) developed a real-time RT-PCR assay ( DRUL test ) that detects SARS-CoV-2 in self-collected saliva to address this issue . RU partnered with the NYC Public Health Lab ( PHL ) and 8 off-site PHL COVID labs to validate the DRUL test for submission for FDA EUA approval . This study describes the process developed to validate a new SARS-CoV-2 at an academic center and understand key takeaways and lessons learned for future collaborations .
Methods : NYC PHL and RU developed and submitted an application , protocols and personnel trainings for Institutional Review Board ( IRB ) review . Following IRB approvals , staff were provided inperson group trainings on patient enrollment , specimen collection and specimen / data workflows . Consenting patients had a nasopharyngeal ( NP ) swab collected by a collection specialist and were given a collection kit to self-collect a saliva specimen . NP and saliva were submitted to the NYC DOHMH Lab but only the NP was tested by the Xpert Xpress SARS-CoV-2 test and reported to the patient . Saliva specimens were shipped to RU for DRUL testing , with no results provided to the patient . Data collected included symptoms , test results and Ct values . Data requirements included collecting up to 50 SARS-CoV-2 positive NP specimens ( 25 symptomatic and 25 asymptomatic ) with Ct values ≤40 and up to 100 SARS-CoV-2 negative NP specimens .
Results : Study goals were achieved quickly by focusing on only enrolling patients at 3 / 8 PHL COVID off-site labs which had the highest SARS-CoV-2 positivity rate ( average < 2 %) at the time . Due to staff turnover and inexperience , we faced slow enrollment and exclusion of specimens due to incomplete consent forms . To mitigate these challenges , refresher trainings and guided recruitment were provided to clinic and lab staff and the IRB was amended to expand patient enrollment at all 8 PHL COVID off-site labs . This increased enrollment and reduced the study timeline by 30 days . In total , 71 specimens positive for SARS-CoV-2 ( 32
Lessons Learned from “ Pop-up ” Testing Following the First SARS-CoV-2 Pandemic Wave in New York City
M Leelawong , J Sunshine , R Fowler and S Hughes , New York City Public Health Laboratory
A key component of pandemic response is the rapid mobilization of testing to identify infected individuals . This is particularly important in New York City , where population density is high and there is a large volume of international travelers . In the summer of 2020 , the city ’ s Department of Health and Mental Hygiene opened two community SARS-CoV-2 testing sites to provide increased access to testing . The temporary pop-up sites were quickly organized to provide rapid , point-of-care testing in neighborhoods with high positivity rates but low testing rates . We detail the decision making during a time when limited data was available . Although a rapid nucleic acid amplification test was deployed , a reflex testing workflow was also implemented . Our rationale for the initial workflow and why it was modified is discussed . The main advantage of the point-of-care testing is its turnaround time , which enabled immediate , on-site resource navigation for individuals who tested positive . However , this must be weighed against the potential disadvantages of rapid testing such as modified biosafety practices and higher cost compared to laboratory-based testing . We retrospectively review our approach to the challenges and share the lessons learned with the optimism that they may help to inform the early response to future pandemics . With thoughtful planning , popup testing can provide more timely resources where they are needed most .
Presenter : Mindy Leelawong , New York City Public Health Laboratory , mleelawong @ health . nyc . gov
SARS-CoV-2 Pangolin Lineage Calling : Comparing pangoLEARN and UShER
M Su , J Amin , J Wang and S Hughes , New York City Department of Health and Mental Hygiene
Pangolin lineage calling has been indispensable for tracking the evolution of SARS-CoV-2 and monitoring the rise and fall of variant caseloads . Due to the fast-moving nature of the pandemic , pangolin designations , which determine the defining traits of lineages , have been constantly updated and refined as more cases were sequenced , in turn requiring model updates to the pangoLEARN decision tree . As such , NYC DOHMH adopted the practice of rerunning historical data with any pangolin software
COVID-19