APHL 2021 Poster Abstracts
COVID-19
SARS-CoV-2 Detection in Wastewater : A Long-term Application
J . Kettlewell and E . Desmond , Hawaii State Laboratories Division , Pearl City , HI
SARS-CoV-2 presence in sewage precedes the appearance of clinical cases by 4-10 days and gastrointestinal viral shedding occurs even with a lack of symptoms . Sampling of wastewater from treatment facilities is primarily used for surveillance and requires viral concentration steps of liquid-phase waste that results in a laboratory turn-around-time of 48 hours or more . Data suggest viral particles may be more likely to be absorbed to the particulate matter of solid-phase waste and testing of solid-phase waste removes the need for viral concentration steps , potentially reducing turn-around-time . By identifying SARS-CoV-2 in solid-phase waste from congregate settings prior to known clinical cases , intervention through routine clinical testing and isolation of cases could prevent large-scale outbreaks and deaths . Hawaii State Laboratories Division ( SLD ) is collaborating with Hawaii ’ s Wastewater Branch and epidemiologists within Hawaii ’ s Disease Outbreak Control Division within the Hawaii Department of Health to optimize the collection and testing of solid-phase waste from congregate facilities . The collection and testing procedures optimized by Hawaii SLD will continue to be relevant in the atmosphere of viral variance and to monitor for potential vaccine breakthrough . Beyond the SARS- CoV-2 pandemic , the Hawaii Department of Health and Hawaii SLD can cross-utilize sewage collection procedures to monitor for the emergence of antimicrobial resistance and new or existing viral pathogens which threaten public health .
Presenter : Joanne Kettlewell , Hawaii State Laboratories Division , joanne . kettlewell @ doh . hawaii . gov
SARS-CoV-2 N Gene Mutations Impact Detection by Clinical Molecular Diagnostics
M . Leelawong , J . Wang , E . Gonzalez , R . Fowler , S . Hughes and J . Rakeman , New York City Public Health Laboratory , New York City , NY
Nucleic acid amplification tests ( NAATs ) have been instrumental for the detection of SARS-CoV-2 during the ongoing pandemic . Although the primers and probes used in the NAATS are designed to detect conserved sequences within the SARS-CoV-2 genome , singlenucleotide polymorphisms ( SNPs ) will still arise within these regions . The New York City Public Health Laboratory identified 2814 SARS- CoV-2-positive nasopharyngeal specimens from August 2020 to mid- January 2021 with the Cepheid Xpert ® Xpress SARS-CoV-2 ( Xpert ) test . Twelve of these specimens representing 10 unique patients tested as presumptive positive , wherein the E target was detected but the N2 target was not detected . Based on their low to moderate E-target Ct values ( < 33 ), six presumptive positive specimens from six unique patients were subjected to secondary testing by the New York SARS-CoV-2 Real-Time RT-PCR Diagnostic Panel . Both the N1 and N2 targets were detected in all six specimens with Ct values within two cycles of each other . Whole genome sequencing was performed to identify SNPs in the N2 target region as defined by the CDC 2019-nCoV Real-time rRT-PCR Panel primer / probe sequences . Two SNPs in the N2 region were identified : C29200T and C29197T . Given the presence of two distinct SNPs within the same region and their detection in different viral genetic backgrounds , it appears that these SNPs arose independently multiple times .
Although the C29200T and C29197T SNPs interfered with N2 detection in the Xpert SARS-CoV-2 test , they should have limited effect on the newer Cepheid SARS-CoV-2 / Flu / RSV test , which features the same two SARS-CoV-2 targets but does not differentiate between them . Nevertheless , as other SNPs continue to arise , laboratories must maintain vigilance to ensure that test sensitivity is not negatively impacted .
Presenter : Mindy Leelawong , New York City Public Health Laboratory , mleelawong @ health . nyc . gov
Minnesota Molecular Surveillance of SARS-CoV-2
A . Lorentz1 , D . Gohl2 , J . Yao3 , M . Binnicker3 , A . Nelson4 , S . Yohe4 , P . Ferrieri4 , S . Vetter1 , X . Wang1 ; 1Minnesota Department of Health , St . Paul , MN , 2University of Minnesota Genomics Center , Minneapolis , MN , 3Mayo Clinic , Rochester , MN , 4University of Minnesota Medical School , Twin Cities , MN
The Minnesota Molecular Surveillance of SARS-CoV-2 ( MN-SOS ) initiative is a state surveillance system built by the state public health laboratory , academic institutions and clinical laboratories , for WGS of SARS-CoV-2 . The goal of MN-SOS initiative is to track variants of concern ( VOCs ), identify emerging mutations , and to understand the baseline of viral diversity in the state . Minnesota Department of Health Public Health Laboratory ( MDH-PHL ) utilized WGS for outbreak investigations focused on congregate settings such as correctional and long-term care facilities ; this provided an understanding of COVID-19 outbreaks and aided epidemiologists with investigations , but did not provide an understanding of viral diversity in MN as a whole . With the emergence of SARS-CoV-2 variants , there was also an urgent need to expand community WGS for detection of VOCs due to potential increased transmissibility and virulence ; variants may also reduce vaccine efficacy and natural antibody response . Beginning in December of 2020 , MDH-PHL began receiving 50 specimens per week from each of its clinical partners . In addition , one clinical partner has also been submitting S gene target failures ( SGTFs ) to identify B . 1.1.7 variant cases . As of February 23 , 2021 there have been 558 samples successfully sequenced . Two key VOC investigations were possible through the MN-SOS surveillance system , including the first case with the P . 1 variant identified in the United States . The identification of the P . 1 variant through WGS initiated an epidemiological investigation that found the case had travel to Brazil within 14 days of illness . A second case was also identified in a travel partner / household contact . The partnership with COVID-19 clinical testing laboratories also allowed for the investigation of the introduction of the B . 1.1.7 variant to the state . WGS for surveillance for SARS-CoV-2 is a critical public health tool to detect and monitor the spread of VOCs and other significant mutations . The collaboration between the public health laboratory , epidemiology and clinical testing partners is key for this successful Minnesota SARS-CoV-2 genomic surveillance program .
Presenter : Alexandra Lorentz , Minnesota Public Health Laboratory , Alexandra . lorentz @ state . mn . us
42 |
LAB MATTERS Summer 2021 |
|
|
|