High-Throughput, Single-Copy Sequencing Reveals SARS-CoV-2 Spike Variants Coincident with Mounting Humoral Immunity during Acute COVID-19

• DOI: 10.1101/2021.02.21.432184
• Publication Date: 2021-02-23T03:10:51Z
• Authors: Sung Hee Ko; Elham Bayat Mokhtari; Prakriti Mudvari; Sydney Stein; Christopher D. St...; Danielle Wagner; Sabrina Ramelli; Marcos J. Ramos-B...; Jeffrey R. Strich; Richard T. Davey; Tongqing Zhou; John Misasi; Peter D. Kwong; Daniel S. Chertow; Nancy J. Sullivan; Eli A. Boritz
• Keywords: Furin; Coronavirus

Abstract Tracking evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within infected individuals will help elucidate disease 2019 (COVID-19) pathogenesis and inform use antiviral interventions. In this study, we developed an approach for sequencing region encoding SARS-CoV-2 virion surface proteins from large numbers individual virus RNA genomes per sample. We applied to WA-1 reference clinical isolate passaged in vitro upper samples 7 study participants with COVID-19. cell culture were diverse, including 18 haplotypes non-synonymous mutations clustered spike NH -terminal domain (NTD) furin cleavage site regions. By contrast, cross-sectional analysis COVID-19 showed fewer variants, without structural clustering mutations. However, longitudinal one revealed 4 bearing 3 independent a NTD epitope targeted by autologous antibodies. These arose coincident 6.2-fold rise serum binding transient increase burden. conclude that exhibits capacity rapid genetic adaptation becomes detectable vivo onset humoral immunity, potential contribute delayed virologic clearance setting. Author Summary Mutant sequences coronavirus-2 arising during any case could theoretically enable evade immune responses or therapies target predominant infecting sequence. commonly used technologies are not optimally designed detect variant each To address issue, novel technology genomic molecules across proteins. This extensive diversity cultured viruses SARS-CoV-2, but lower Importantly, concurrent paired selected relatively low levels antibody protein at time initial sequencing. With increased protein, detected multiple variants single epitope, as well findings suggest replication creates sufficient allow immune-mediated selection frame Large-scale studies variation specific define contributions intra-individual outcomes drug susceptibility.