High-throughput, single-copy sequencing reveals SARS-CoV-2 spike variants coincident with mounting humoral immunity during acute COVID-19

Abstract

Tracking evolution of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) within infected individuals will help elucidate coronavirus disease 2019 (COVID-19) pathogenesis and inform use of antiviral interventions. In this study, we developed an approach for sequencing the region encoding the SARS-CoV-2 virion surface proteins from large numbers of individual virus RNA genomes per sample. We applied this approach to the WA-1 reference clinical isolate of SARS-CoV-2 passaged in vitro and to upper respiratory samples from 7 study participants with COVID-19. SARS-CoV-2 genomes from cell culture were diverse, including 18 haplotypes with non-synonymous mutations clustered in the spike NH2-terminal domain (NTD) and furin cleavage site regions. By contrast, cross-sectional analysis of samples from participants with COVID-19 showed fewer virus variants, without structural clustering of mutations. However, longitudinal analysis in one individual revealed 4 virus haplotypes bearing 3 independent mutations in a spike NTD epitope targeted by autologous antibodies. These mutations arose coincident with a 6.2-fold rise in serum binding to spike and a transient increase in virus burden. We conclude that SARS-CoV-2 exhibits a capacity for rapid genetic adaptation that becomes detectable in vivo with the onset of humoral immunity, with the potential to contribute to delayed virologic clearance in the acute setting.

The ongoing evolution of variants of concern and interest of SARS-CoV-2 in Brazil revealed by convergent indels in the amino (N)-terminal domain of the spike protein

“…2021 ). Finally, a recent study revealed the emergence of virus haplotypes bearing NTD deletions ∆144 and ∆141-144 following the development of autologous anti-NTD-specific antibodies during acute infection in one immunocompetent individual ( Ko et al. 2021 : 1).…”

Natural isolate and recombinant SARS-CoV-2 rapidly evolve in vitro to higher infectivity through more efficient binding to heparan sulfate and reduced S1/S2 cleavage

“…In prior studies, the FCS could be inactivated by either its deletion or accumulation of point mutations eliminating the arginines essential for furin cleavage (29). Viral mutants with deleted FCS, and R682L, S686G and H655L mutations have been detected in the stock of WA1/2020 isolate from CDC (31). The effect of the FCS deletion was experimentally evaluated in the context of pseudovirions or recombinant SARS-CoV-2 (32, 33).…”

“…Analysis of sequences submitted to GISAR revealed that accumulation of mutations that increase the positive charge of NTD upon passaging in Vero cells, is quite common: N74K was detected in EPI_ISL_1039208, EPI_ISL_1190402, EPI_ISL_1718321, EPI_ISL_1707039, EPI_ISL_1785073, EPI_ISL_1785076, and I68R/K was found in EPI_ISL_493139, EPI_ISL_2226226. The WA1/2020 from CDC was reported to contain 9 low frequency R/K substitutions in NTD including a 4-aa-long insertion after D215 (31). The indicated I68R and N74K mutations, which additionally increase the positive charge of the NTD surface (Fig.…”

Viral Load and Patterns of SARS-CoV-2 Dissemination to the Lungs, Mediastinal Lymph Nodes, and Spleen of Patients with COVID-19 Associated Lymphopenia

“…We exclude PCR cross-contamination, as this is the only case of the c.23191T variant detected in our laboratory. This case can be explained by the fact that the SARS-CoV-2 coronavirus is characterized by a high frequency of mutations with the formation of quasispecies (subpopulations) in the body of the host [ 39 , 40 , 41 ].…”