Genomic Epidemiology of SARS-CoV-2 in Metropolitan Detroit

Document Type

Conference Proceeding

Publication Date

11-27-2023

Publication Title

Open Forum Infect Dis

Abstract

Background. The COVID-19 pandemic, resulting from the rapidly evolving SARS-CoV-2 virus, has drastically impacted health systems and economies worldwide. Genomic sequencing is critical for the surveillance of SARS-CoV-2 to monitor the rapidly evolving virus and identify new strains. Methods. 583 isolates from Henry Ford Health were retrospectively profiled across 3 years (117 isolates in 2020; 39 in 2021; 427 in 2022). DNA was extracted using Kingfisher viral isolation kit; RT-PCR screening was used to identify isolates with cycle threshold < 32 for whole genome sequencing (WGS). Libraries were generated using QIAseq DIRECT SARS-CoV-2 Kit, followed by Illumina sequencing (MiSeq or NovaSeq 6000; 300 cycles). Lineage analysis of the SARS-CoV-2 consensus genome sequences generated from samtools variant analysis pipeline was determined using Nextclade and Pangolin software. Results. Sequences were classified into 11 unique clades across 108 lineages by Nextclade and Pangolin, respectively. Almost three-fourths of the sequenced isolates were from 2022. 117 (20%) genomes were from the early pandemic (2020) and were clustered into 8 clades: 19A, 19B, 20A, 20B, 20C, 21 J (Delta) and 21L (Omicron). Most of the 2022 genomes (72%) were in clade 20C from lineage B.1, identified during the outbreak in Europe. 15 (13%) genomes had clade 19A (lineage B) and 1 had 19B (lineage A.3), identified early in the pandemic in Wuhan, China. Of the 39 (7%) genomes from 2021, the majority (82%) clustered into clade Delta 21J that originated in India. Only 2 (5%) of the genomes from 2021 had Alpha variant of concern (21I) from the lineage B1.1.7, which were suspected to be more transmissible. Of the 427 (73%) genomes from 2022, 393 (92%) had variants within Omicron variant of concern (21L), with 79 different lineages; 1 was Omicron variant 21K from the lineage BA1.1. Other clades observed in the 2022 batch were 19A (6%), 20A (0.2%), 20B (0.2%), 20C (0.2%) and 21M (1%). Conclusion. Our genomic surveillance data suggest that SARS-CoV-2 infections at the local level mirrored global outbreaks. This underscores the importance of robust genomic surveillance efforts to inform public health planning and practice.

Volume

10

First Page

S979

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