Lab Matters Summer 2018 | Page 64

APHL 2018 Annual Meeting Poster Abstracts

Infectious Disease the conditions of this study . Qualification of additional RNA extraction procedures expands the options for domestic PHLs to use equipment already in place to perform testing for influenza . The data generated in this study supported FDA clearance of these two automated extraction platforms for influenza diagnostic testing using the CDC rRT-PCR Flu Panel .

Presenter : LaSondra Berman , PhD , Centers for Disease Control and Prevention , Atlanta , GA , Phone : 404.639.1686 , Email : zhj5 @ cdc . gov

Incorporation of Non-Influenza Respiratory Virus Detections from the Public Health Laboratory Interoperability Project into the National Respiratory and Enteric Virus Surveillance System

R . Dahl , A . Haynes , M . Prill and S . Gerber , US Centers for Disease Control and Prevention , Atlanta , GA

National surveillance of non-influenza respiratory viruses ( NIRVs ) is essential to identify temporal and geographical trends for these pathogens in the US along with detecting re-emerging and novel viruses . Two national-level laboratory-based surveillance systems currently collect information on NIRVs . The CDC ’ s National Respiratory and Enteric Virus Surveillance System ( NREVSS ) monitors the circulation of respiratory viruses including adenoviruses , coronaviruses , enteroviruses , metapneumovirus , parainfluenza viruses , respiratory syncytial virus and rhinoviruses through voluntary reporting of antigen , culture and PCR diagnostic test data primarily from university , hospital and commercial laboratories . NREVSS collects weekly aggregate counts of tests , typically via manual entry , which does not allow for more detailed analyses of respiratory virus activity due to a lack of specimen-level epidemiologic data . The Public Health Laboratory Interoperability Project ( PHLIP ) and Public Health Lab Information System replacement ( PHLIS2 ) are two mechanisms by which state and local health laboratories ( PHLs ), plus several other non-commercial laboratories , can report to CDC for the purposes of conducting influenza surveillance . It also routinely receives specimen-level NIRV testing results . Specimen-level test results along with descriptive patient information are reported automatically to CDC and these data allow for detection of co-infections and more refined epidemiologic characterization than is possible with NREVSS . In an effort to streamline CDC ’ s data sources , reduce PHLs ’ reporting burden and enhance epidemiologic capacity , the Division of Viral Diseases ( DVD ) and Influenza Division ( ID ) are collaborating to increase reporting of specimen-level NIRV data via PHLIP or PHLIS2 and to incorporate these data into NREVSS . First , to determine if PHLIP data were appropriate for inclusion in NREVSS , data from four PHLs that reported to both systems were assessed for comparability . Next , an 11 additional PHLs reporting to PHLIP or PHLIS2 with robust NIRV test results not currently reporting to NREVSS were asked to share their data with DVD and to provide a secondary source of data to validate the messages . To date , DVD has validated data from these 15 labs and all are now reporting their specimenlevel data to NREVSS exclusively through PHLIP or PHLIS2 . Several more labs are currently undergoing validation checks and / or upgrading their messaging systems to include NIRV test results in their PHLIP or PHLIS2 transmissions to CDC . Collaborations that make reporting methods more efficient strengthens the relationship between CDC and participating laboratories , in particular state and local public health departments ; helps maintain a robust surveillance system ; and ultimately contributes to a better understanding of viral respiratory disease trends in the US .

Presenter : Rebecca Dahl , US Centers for Disease Control and Prevention , Atlanta , GA , Email : itm6 @ cdc . gov

Development of a Targeted Resequencing Approach to Identify and Characterize Pathogens in Respiratory Specimens from Unexplained Respiratory Disease Outbreak Responses

M . Diaz 1 , A . Benitez 1 , B . J . Wolff 1 , S . S . Morison 1 , T . Fink 2 , G . Gallagher 2 , G . Liu 3 , D . Boxrud 3 , S . Smole , J . Winchell 1 ; 1 US Centers for Disease Control and Prevention , Atlanta , GA , 2 Massachusetts Department of Public Health , Boston , MA , 3 Minnesota Department of Health , St . Paul , MN

Rapid identification of etiology is critical during respiratory outbreaks when early targeted interventions may be effective for halting disease transmission . The Unexplained Respiratory Disease Outbreak ( URDO ) working group at the US Centers for Disease Control and Prevention ( CDC ) provides laboratory and epidemiologic support to public health laboratories during respiratory disease outbreak investigations . Since 2009 , routine implementation of the TaqMan Array Card ( TAC ), a microfluidic real-time PCR array for multi-pathogen detection , has improved time to results and increased the proportion of outbreaks in which a probable etiology is identified to over 50 %. Still , an etiology remains elusive in many outbreak investigations and immediate results are limited to pathogen detection . Further testing is required in order to identify features that may direct vaccination recommendations , prescribing practices or source attribution . To expand upon existing laboratory testing capacity , CDC , along with Minnesota and Massachusetts state public health laboratories ( PHL ), have developed a targeted resequencing approach that enables simultaneous pathogen detection and characterization , such as antibiotic and antiviral resistance determinants or strain types . Custom oligonucleotides are used to generate sequence-ready amplicon libraries for nextgeneration sequencing ( MiSeq ) analysis . Each state has contributed to the panel of assays through oligonucleotide design , performance assessment and cross-evaluation of assays designed by the other sites . Together we have developed 41 total assays for identification ( 24 ), strain typing ( 14 ), or antimicrobial resistance determination ( 3 ). For all assays , the lower limit of detection was equivalent or superior to the corresponding real-time PCR assay performed on TAC . Following comprehensive performance evaluation in 96- well plate format , assays were evaluated for performance on a nanofluidic chip system ( Wafergen SmartChip , Takara Bio Inc .). Testing of a panel of 6 mock specimens in 96-well plate at CDC , MA PHL and MN PHL , as well as on the Smartchip at the manufacturer ’ s facility yielded similar results . All pathogens spiked into each sample were detected by each site in both formats ; in each case the expected amplicon comprised = 90 % of recovered cleaned sequence reads . Multiple data analysis strategies , including both whole read and kmer based methods , were compared to maximize accuracy of read identification , minimize computing time and capture naturally-occurring variants . Engagement of state laboratories has helped to increase genomic and informatics capacity at highly functional PHLs that may serve as regional centers for future URDO investigations . Comprehensive regional laboratory testing may improve determination of etiology by reducing the time from sample collection to testing .