Low-frequency variants in mildly symptomatic vaccine breakthrough infections presents a doubled-edged sword

Abstract

The emergence of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) variants of concern (VOC) has raised questions regarding vaccine protection against SARS-CoV-2 infection, transmission, and ongoing virus evolution. Twenty-three mildly symptomatic "vaccination breakthrough" infections were identified as early as January 2021 in Alachua County, Florida, among individuals fully vaccinated with either the BNT162b2 (Pfizer) or the Ad26 (Janssen/J&J) vaccines. SARS-CoV-2 genomes were successfully generated for 11 of the vaccine breakthroughs, and 878 individuals in the surrounding area and were included for reference-based phylogenetic investigation. These 11 individuals were characterized by infection with VOCs, but also low-frequency variants present within the surrounding population. Low-frequency mutations were observed, which have been more recently identified as mutations of interest owing to their location within targeted immune epitopes (P812L) and association with increased replicative capacity (L18F). We present these results to posit the nature of the efficacy of vaccines in reducing symptoms as both a blessing and a curse-as vaccination becomes more widespread and self-motivated testing reduced owing to the absence of severe symptoms, we face the challenge of early recognition of novel mutations of potential concern. This case study highlights the critical need for continued testing and monitoring of infection and transmission among individuals regardless of vaccination status.

Keywords: SARS coronavirus; epidemiology; genetic variation; genetics; virus classification.

Figure 1

Distribution of identified lineages. Lineage as identified using Pangolin² distribution over time for Alachua County, the surrounding Florida areas, and locations outside of Florida linked to Florida sequences via genetic similarity

Figure 2

Geographical origin of sampling over time and within the phylogenetic tree of SARS‐CoV‐2 data collected from Florida and relevant non‐Florida locations. (A) Distribution of both assigned lineages and geographic origin (as in Figure 1) across the maximum likelihood phylogenetic tree. Branches are scaled in genetic substitutions/site, and nodes with ≥90% support using bootstrap sampling are indicated by gray dots. Vaccinated individuals within well‐supported clades have been emphasized, and corresponding clades are represented as insets in panels (B–F). *Other lineages, defined as present within <1% of the total sample population. SARS‐CoV‐2, severe acute respiratory syndrome coronavirus 2

Figure 3

Mutations of interest and of concern in Spike found in the 11 vaccine‐breakthrough individuals and their frequencies across Alachua, remainder, and outside of Florida. Mutational profiles for vaccine‐breakthrough individuals (A) and comparison of (B) B.1.2 and (C) Alpha individuals with remaining sequence data. Mutations in red are present in vaccinated individual (VAC), but not fixed in the parental lineage. Spike protein architecture is displayed at the top of both panels, wherein CTD (1–3), C‐terminal domain; FP, fusion peptide; HR (1–2), heptad repeat; NTD, N‐terminal domain; PRRA, SARS‐CoV‐2 characteristic PRRA insertion at the S1/S2 cleavage site; RBD, receptor‐binding domain; S, spike subunit (1–2). Positions numbers are relative to the spike protein in the MN908947 reference sequence

Figure 4

Potential effect on trimer stabilization of Floridian Alpha variant mutation of interest from lysine (A) to phenylalanine (B) at position 18 of the Spike protein N‐terminal domain (NTD). Loops N1, N2, and N5 of the NTD are represented in green, pink, and blue, respectively. Modified interactions as a result of the mutation are represented as dotted lines, with original L18 oriented toward position F79 (cyan) of the N1 loop (A), and the variant F18 toward S252 of the N5 loop (B), potentially acting to stabilize. Dotted lines represent distances 3.8 (A) and 3.6 (B) Angstrom. Positions numbers are relative to the Spike protein in the MN908947 reference sequence

Figure 5

Cytopathic effects in Vero E6 cells inoculated with saliva sample FL‐STP‐VTM‐11. (A) Mock‐infected Vero E6 cells, 12 dpi. (B) Early SARS‐CoV‐2‐specific CPE, 12 dpi. Rounded cells, some in the process of detaching from the growth surface, are pointed out by yellow arrows. Original magnification at 400X. SARS‐CoV‐2, severe acute respiratory syndrome coronavirus 2