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.