Lab Matters Fall 2023 | Page 90

APHL 2023 POSTER ABSTRACTS

evaluated patient demographics , lesion site frequency and assay performance by lesion site from specimens collected to characterize trends during the mpox response in NYC . Method : Swab specimens from suspected mpox lesions were submitted to NYC PHL May 19 – October 14 , 2022 for testing with the LRN NVO real-time PCR assay . Patient demographic characteristics ( age and zip code ), mpox lesion sites , and test result ( including real-time PCR threshold cycle [ Ct ] value ) were queried from the Laboratory Information System . Assay-defined cut offs were used to determine positive ( Ct < 37 ), equivocal ( Ct = 37 – 40 ), inconclusive ( no amplification of target or control ) and negative ( no signal within 40 cycles ) specimens . Specimens were analyzed by age , location and lesion site . Test results were used to evaluate assay performance among different lesion types . Results : NYC PHL tested 2,260 specimens using the LRN NVO real-time PCR assay during the mpox outbreak . Of those , 1,917 ( 84.8 %) were collected from NYC residents , and 1,643 ( 72.7 %) were from patients aged 25 – 44 years . Specimens collected from genital lesions were the most frequently submitted lesion site ( 19.4 %; 438 ). Overall , 1,349 ( 59.7 %) specimens tested positive , 749 ( 33.2 %) were negative , 141 ( 6.2 %) were inconclusive and 21 ( 0.9 %) were equivocal . Among 419 specimens tested from anal / rectal lesions 318 ( 75.9 %) were positive , whereas among 162 specimens tested from leg lesions only 57 ( 35.2 %) were positive . Specimens from hand lesions yielded inconclusive results in 31 ( 21.7 %) specimens , approximately 3.5-fold higher than the average specimen inconclusive rate . Conclusions : Our data revealed differences in NVO PCR assay performance based on specimen site that can be used to guide lesion site prioritization . As a result , these data can help public health officials provide lesion site collection guidance that maximizes NVO assay performance to more efficiently detect mpox lesions . This is especially important when prioritizing collection from patients presenting with lesions from multiple anatomical sites .

Presenter : Scott Hughes , shughes @ health . nyc . gov

Mpox Virus Lineage Assignments and Phylogeny in New York City , 2022

S . Akther , J . Wang , H . Amin , T . Clabby , N . De La Cruz , M . Chowdhury , V . Ruiz , R . Fowler , E . Omoregie , S . Hughes ; New York City Department of Health and Mental Hygiene Public Health Laboratory ,

Since May 2022 , mpox cases positive for sub-lineage mpox virus ( MPXV ) Clade IIb have emerged across several non-endemic countries . In New York City ( NYC ) alone , nearly 3,800 mpox cases have been reported as of December 2022 . With the emergence of MPXV , some genomic clusters may have specific genomic or phenotypic characteristics that could impact diagnostic testing , treatment , vaccine efficacy , disease severity , or transmission . Genomic sequencing and phylogenetic analysis have previously been used to cluster viral genomes that likely share genetic characteristics . Naming the clusters can aid in discussions of infectious disease surveillance and outbreak investigations . For example , Pangolin has aided in surveillance efforts by allowing researchers and public health officials to communicate across the globe with a common nomenclature for SARS-CoV-2 . Similarly , Nextclade is a tool that assigns viral lineages using the nearest neighbor from a reference tree . Here , we report on MPXV fullgenome phylogenetic analysis and Nextclade lineages identified during the NYC mpox outbreak in 2022 . Lesion specimens collected from patients in NYC and submitted to the NYC Public Health

Laboratory ( NYC PHL ) between May-December 2022 , were tested using the CDC LRN Non-Variola Orthopoxvirus assay . Positive specimens with a Ct < 30 were sequenced using Illumina technology and analyzed at the NYC PHL . Phylogenetic analysis was conducted using IQTree . Using ggtree , a bioconductor R package , the phylogeny was labelled with Nextclade lineage assignments to examine clusters with inconsistent lineages and determine the proportion of monophyletic designations . All 1,052 sequences sequenced by NYC PHL were MPXV Clade IIb , which Nextclade assigned correctly as B . 1 or its sublineages . Nextclade assigned 536 genomes as B . 1 , which were correctly placed as basal genomes of MPXV Clade IIb on the phylogenetic tree . The remaining 516 sequences were assigned predominantly as B . 1.2 , B . 1.3 , B . 1.7 , B . 1.8 and B . 1.12 sublineages and were clustered as distinct clades in the tree except for four genomes . Overall , genome phylogeny demonstrated that Nextclade lineage mis-assignment account for 0.4 % of NYC PHL mpox sequences . In conclusion , genomes sequenced at the NYC PHL from the 2022 mpox outbreak were all MPXV Clade IIb and were assigned as B . 1 or its sublineages . We find that Nextclade lineage assignment may serve as an appropriate tool for communicating genomic clusters for public health surveillance of mpox and will be critical to monitor the extent of its genome evolution in NYC .

Presenter : Saymon Akther , sakther @ health . nyc . gov

Multiplex RT-qPCR Assay of Detecting Influenza A Virus , Influenza B Virus , SARS-CoV-2 , & Human Respiratory Syncytial Virus

D . Ma , Promega Corporation

Respiratory viruses cause acute respiratory disease worldwide . Acute respiratory infections are the world ’ s third leading cause of death . Before the COVID-19 outbreak , there had been 4 million deaths each year caused by acute respiratory infections . Monitoring respiratory virus occurrence from the environment such as wastewater could provide surveillance of respiratory virus infection agents in communities . We developed a multiplex RTqPCR assay of detecting Influenza A , Influenza B , SARS-CoV-2 , & Human Respiratory Syncytial Virus ( RSV ). The assay also provides a possibility for a quick determination of respiratory virus from clinical samples .

Presenter : Dongping Ma , dongping . ma @ promega . com

Optimized Methods for Antimicrobial Resistance Testing

D . O ’ Neil , M . Fosbrink , R . Kellner , H . Block , T . Sperling , M . Sprenger- Haussels ; QIAGEN GmbH , Hilden , Germany

Introduction : Antimicrobial resistance ( AMR ) detection and surveillance has become a high priority in both healthcare and environmental settings for the safety of patients and the general public . Samples of interest for AMR , such as stool and wastewater , are challenging substrates for nucleic acid extraction , and choice of extraction method will determine the success of downstream analysis . Extraction methods must be able to address high levels of inhibitory substances and achieve extraordinary sensitivity to provide the best possible sensitivity of downstream assays . Downstream analysis must also be tuned to maximize information content derived from these samples . We investigated entire workflows for antimicrobial resistance . Methods : Fecal and