A Unique SARS-CoV-2 Spike Protein P681H Variant Detected in Israel

Abstract

The routine detection, surveillance, and reporting of novel SARS-CoV-2 variants is crucial, as these threaten to hinder global vaccination efforts. Herein we report a novel local variant with a non-synonymous mutation in the spike (S) protein P681H. This local Israeli variant was not associated with a higher infection rate or higher prevalence. Furthermore, the local variant was successfully neutralized by sera from fully vaccinated individuals at a comparable level to the B.1.1.7 variant and an Israel wild-type strain. While it is not a variant of concern, routine monitoring by sequencing is still required.

Keywords: Covid-19; SARS-CoV-2; sequencing; variant of concern; virus neutralization.

Figure 1

Characterization of the B.1.1.50 + P681H variant. Phylogenetic trees highlighting the genotype at site 681 in the S protein, with the wild-type proline (P) in green and the mutations histidine (H) and arginine (R) in yellow and blue, respectively. (A) SARS-CoV-2 genomes sequenced in Israel from March 2020 to January 2021 (n = 2482). The main clusters harboring the P681H mutation (in yellow) are the B.1.1.7 (20I/501Y.V1) and the B.1.1.50 + P681H variant. (B) SARS-CoV-2 genomes from of the B.1.1.50 lineage only (n = 489). The B.1.1.50 + P681H cluster is composed of local (Israel) viruses only, with the exception of 2 sequences from isolates identified in the Palestinian authorities, and includes a sub-cluster with an additional S protein non-synonymous mutation, A27S. Additional mutations are listed by each branch. Phylogenetic trees were created with Nextstrain Augur pipeline and visualized with Auspice [3]. Non-Israeli B.1.1.50 lineage sequences were downloaded from GISAID and identified with Pangolin classification [4].

Figure 2

Identification of the P681H mutation in sewers across Israel. Frequency of P681H mutation in SARS-CoV-2 genomes sequenced from nine sewage samples of wastewater treatment plants across Israel each month in August 2020–January 2021. The frequency of the P681H mutation in each region was estimated by measuring the fraction of the mutation from the total number of nucleotides mapped at this position (i.e., depth of sequencing).

Figure 3

Neutralization of the B.1.1.50 + P681H variant. Neutralization assays were carried out with VERO-E6 cells infected with the B.1.1.50 + P681H variant, B.1.1.7 variant and an Israel WT strain from Israel, using sera from fully vaccinated individuals. On day 6, plates were colorized overnight with Gentian violet +4% formaldehyde solution for virus neutralization. Titers were calculated by qualitative measurements of the cytopathic effect for each patient. Bars represent the geometric mean titer (GMT) and 95% confidence intervals.