Abstract
The pandemic of SARS-CoV-2 is characterized by the emergence of new variants of concern (VOCs) that supplant previous waves of infection. Here, we describe our investigation of the lineages and host-specific mutations identified in a particularly vulnerable population of predominantly older and immunosuppressed SARS-CoV-2-infected patients seen at our medical center in Chicago during the transition from the Delta to Omicron wave. We compare two primer schemes, ArticV4.1 and VarSkip2, used for short read amplicon sequencing, and describe our strategy for bioinformatics analysis that facilitates identifying lineage-associated mutations and host-specific mutations that arise during infection. This study illustrates the ongoing evolution of SARS-CoV-2 VOCs in our community and documents novel constellations of mutations that arise in individual patients. The ongoing evaluation of the evolution of SARS-CoV-2 during this pandemic is important for informing our public health strategies.
Keywords: Artic primer scheme; Delta variant; Omicron variant; SARS-CoV-2; variants of concern; vulnerable population.
【저자키워드】 SARS-CoV-2, variants of concern, delta variant, Omicron variant, Artic primer scheme, vulnerable population., 【초록키워드】 public health, pandemic, Mutation, VoC, variant, Infection, Delta, omicron, delta variant, variants, VOCs, Lineage, Evolution of SARS-CoV-2, Community, Omicron variant, Chicago, Bioinformatics analysis, lineages, patients, Amplicon sequencing, Immunosuppressed, vulnerable population, Older, transition, primer, facilitate, characterized, SARS-CoV-2-infected patient, 【제목키워드】 Delta, omicron, clinical, Wave, time, Sample, Evaluating,