APHL 2022 POSTER ABSTRACTS that it could only be used with a multi-channel pipette , resulting in limited functionality for tasks requiring single tube access ( e . g ., small volume reagent prep , hit-picking , normalizations ). The release of the D-ONE single channel pipetting module provides this capability . This evaluation showed that the D-ONE on the ASSIST PLUS provides reliable , robust pipetting capability for automated preparation and plating of master mix . Used in conjunction with the MINI 96 , a 96-channel portable electronic pipette to deliver extracted nucleic acid in one pipetting step , the system reduces the opportunity for manual pipetting errors , while freeing up technicians to perform other tasks .
Presenter : Jessica Alexander , New Hampshire Public Health Laboratory , jessica . l . alexander @ dhhs . nh . gov
Significance of High-Containment Biological Laboratories Performing Work During the COVID-19 Pandemic : Biosafety Level-3 and -4 Labs
K Yeh 1 , K Tabynov 2 , F Parekh 3 , I Mombo 4 , K Parker 1 , K Tabynov 5 , S Bradick 1 , A Tseng 6 , J-R Yong 7 , L Gardiner 1 , G Olinger 1 , B Setser 8 ;
1
MRIGlobal , 2 NSCEDI , 3 EpiPointe , 4 International Center for Medical Research of Franceville ( CIRMF ), 5 International Center for Vaccinology , 6 University of Washington School of Public Health , Seattle , 7 Taiwan Centers for Disease Control , 8 JRAD
High containment biological laboratories ( HCBL ) are required for work on Risk Group 3 and 4 agents across the spectrum of basic , applied and translational research . These laboratories include biosafety level ( BSL ) -3, BSL-4 , animal BSL ( ABSL ) -3, BSL-3-Ag ( agriculture livestock ) and ABSL-4 laboratories . While SARS-CoV-2 is classified as a Risk Group 3 biological agent , routine diagnostic can be handled at BSL-2 . Scenarios involving virus culture , potential exposure to aerosols , divergent high transmissible variants and zoonosis from laboratory animals require higher BSL-3 measures . Establishing HCBLs , especially those at BSL-4 , is costly and needs continual investments of resources and funding to sustain labor , equipment , infrastructure , certifications and operational needs . There are now over 50 BSL-4 laboratories and numerous BSL-3 laboratories worldwide . Besides technical and funding challenges , there are biosecurity and dual-use risks , and local community issues to contend with in order to sustain operations . Here , we describe case histories for distinct HCBLs : representative national centers for diagnostic and reference , nonprofit organizations . Case histories describe capabilities and assess activities during COVID-19 and include capacities , gaps , successes and summary of lessons learned for future practice .
Presenter : Kyle Parker , MRIGlobal , kparker @ mriglobal . org
Fast Surveillance of Major SARS-CoV-2 Variants Without Sequencing : One Year ’ s Experience From Advanced Diagnostics Labs in National Jewish Health
J Crumby 1 , E Decurtis 1 , I Machado 1 , Z Stewart 2 , M Jackson 1 , S Groshong 1 , K Reeti 1 , Y Wang 1 ; 1 Advanced Diagnostics Labs , National Jewish Health , 2 Genetics , National Jewish Health
Background : To promptly monitor the prevalence of SARS-CoV-2 variants and facilitate contact tracing , positive samples from COVID testing labs were subject to variant analysis by SARS- CoV-2 Variant Assay ( Poster # 89 . APHL 2021 ) since early 2021 .
Continued updates for the SARS-CoV-2 Variant assay enables us to continuously survey emergence , spread and disappearance of major variants in a one-year period . The current version is able to detect 19 mutations to identify eight major variants : Alpha , Gamma , Beta , Epsilon , Kappa , Delta , Lambda and Omicron with one multiplexed reaction .
Methods : The assay is based on reverse transcription PCR with end-point analysis on matrix-assisted laser desorption ionization time-of-flight mass spectrometry ( MALDI-TOF MS ). This combined platform eliminates the need for fluorescence-based detection and harnesses high sensitivities from both PCR and MALDI-TOF MS technologies ( Poster # 89 . APHL 2021 ). New PCR and extension primers targeting mutations from new variants were quickly supplemented into the assay primer pools and optimized when Delta and Omicron first reported in June and November 2021 . Specificities and sensitivities of new primers were optimized and verified through synthetic variants and Sanger sequencing .
Results : Of 2,028 positive samples analyzed since February 2021 through mid-January 2022 , we identified 199 of Alpha ( 9.8 %), 130 of Epsilon ( 6.4 %); five of Gamma ( 0.2 %); 1,008 of Delta ( 49.7 %) and 261 of Omicron ( 12.9 %). We were able to detect the very early emergence of new variants in Colorado , including Delta and Omicron , and observed phasing-out of variants like Alpha , Epsilon and Delta as well . In October 2021 , we detected an unusual Delta variant with an additional Q677H mutation and 20 Delta variant samples carrying Q677H mutation were subsequently identified that came from the same facility . This provided valuable information for contact tracing of the virus origin within that facility .
Conclusion : From this one-year ’ s experience of running the variant assay weekly , we demonstrated a major variant prevalence landscape since February 2021 . The assay has a much faster turnaround time ( eight hours in wet-lab ) and much lower cost compared with other variant identification methods , such as SARS-CoV-2 NGS sequencing used by most public health labs for virus surveillance . Its flexibility with rapid expansion to include emerging variants makes this assay an ideal tool for ongoing detection of major SARS- CoV-2 variants of concern .
Presenter : Reeti Khare , National Jewish Health , kharer @ njhealth . org
Routine Viral Load Assessment of SARS-CoV-2 in Northern Nevada Wastewater
L Massic , B Elam , A Gorzalski and M Pandori , Nevada State Public Health Laboratory
Monitoring the public infection rate of SARS-CoV-2 during the Coronavirus disease 2019 ( COVID-19 ) pandemic has been crucial for public health decision making . Examining SARS-CoV-2 positivity rate through patient specimens is currently being utilized but has its limitations such as laboratory testing capacity and will of communal population to get tested . Studies with other viruses such as polio have demonstrated that monitoring wastewater is an effective and sensitive means to monitor pathogen presence within the area . Since SARS-CoV-2 infects gastrointestinal glandular epithelial cells and is excreted through feces into wastewater in both symptomatic and asymptomatic persons , wastewater surveillance for SARS-CoV-2 is a valuable tool to combat the limitations of patient diagnostic testing . Detection of SARS-CoV-2 RNA through wastewater provides a rapid , non-intrusive tool for monitoring new COVID infection rates
COVID-19