JN.1 variants circulating in Italy from October 2023 to April 2024: genetic diversity and immune recognition

Abstract

Background: The continuous emergence of SARS-CoV-2 variants and subvariants poses significant public health challenges. The latest designated subvariant JN.1, with all its descendants, shows more than 30 mutations in the spike gene. JN.1 has raised concerns due to its genomic diversity and its potential to enhance transmissibility and immune evasion. This study aims to analyse the molecular characteristics of JN.1-related lineages (JN.1*) identified in Italy from October 2023 to April 2024 and to evaluate the neutralization activity against JN.1 of a subsample of sera from individuals vaccinated with XBB.1.5 mRNA.

Methods: The genomic diversity of the spike gene of 794 JN.1* strain was evaluated and phylogenetic analysis was conducted to compare the distance to XBB.1.5. Moreover, serum neutralization assays were performed on a subsample of 19 healthcare workers (HCWs) vaccinated with the monovalent XBB.1.5 mRNA booster to assess neutralizing capacity against JN.1.

Results: Sequence analysis displayed high spike variability between JN.1* and phylogenetic investigation confirmed a substantial differentiation between JN.1* and XBB.1.5 spike regions with 29 shared mutations, of which 17 were located within the RBD region. Pre-booster neutralization activity against JN.1 was observed in 42% of HCWs sera, increasing significantly post-booster, with all HCWs showing neutralization capacity three months after vaccination. A significant correlation was found between anti-trimeric Spike IgG levels and neutralizing titers against JN.1.

Conclusions: The study highlights the variability of JN.1* in Italy. Results on a subsample of sera from HCWs vaccinated with XBB.1.5 mRNA booster vaccine suggested enhanced neutralization activity against JN.1.

Keywords: Genomic surveillance; JN.1; Neutralizing antibodies; Phylogenetic analysis; SARS-CoV-2.

Fig. 1

The lineage composition of the cleaned dataset and the trend of the total Italian SARS-CoV-2 vs JN.1* sequences, as present in GISAID. The lower part of the graph shows the JN.1* lineage assigned to the dataset of Italian sequences with spike coverage > 90%. The upper part of the graph includes the total number of JN.1* (blue) and SARS-CoV-2 (orange) sequences uploaded from Italy between October 2023 to April 2024

Fig. 2

Spike gene mutations distribution over time. The mutations are represented by sampling week. A The grey area shows the total number of mutations found in the sequences in each week. The three bars indicate the mutation found in the N-Terminal (blue bar), RBD (green bar) and C-Terminal (orange bar) regions, respectively. B Heatmap of non-synonymous substitutions of unique sites among Italian JN.1*

Fig. 3

JN.1* and XBB.1.5 phylogenetic tree. Phylogenetic analysis of the spike gene of the Italian JN.1* (red) vs XBB.1.5 (blue) using a maximum likelihood approach with 1,000 replications. Only the principal nodes with bootstrap > 90% are indicated with green points

Fig. 4

Serum neutralization results. A MN titers of sera of 19 HCWs at T0 and T1. Sera are used to neutralize JN.1 of BA.2.86 strains. Individual MNT50 are reported together with median values. Non-neutralizing sera (MNT < 8) are placed below the dotted line; statistical differences between two groups are calculated by the Kruskall-Wallis test (p < 0.05 are significant). Grey dots represent MNT50 values of sera from anti-N seroconverted subjects. B MN titers of sera of 19 HCWs (same sera in panel A) plotted according to the number of vaccine doses received. Non-neutralizing sera (MNT < 8) are placed below the dotted line. The median of values is represented by a continuous line. C Linear regression correlating the levels of anti-trimeric spike IgG titers with serum neutralization activity against JN.1 (r and P value are shown)