The SARS-CoV-2 JN.1 variant (BA.2.86.1.1), which arose from BA.2.86.1 with a spike protein (S) substitution S:L455S, outcompeted the previously dominant XBB lineage by early 2024. Subsequently, JN.1 subvariants, including KP.2 (JN.1.11.1.2) and KP.3 (JN.1.11.1.3), which acquired additional S substitutions, emerged. Later, JN.1 subvariants such as LB.1 (JN.1.9.2.1), KP.2.3 (JN.1.11.1.2.3), and KP.3.1.1 (JN.1.11.1.3.1.1), which also acquired a deletion of Serine at the 31st position in S (S:S31del), emerged and spread by June 2024. The virological features of KP.3.1.1 were investigated. Using a Bayesian multinomial logistic model, the relative effective reproduction number (Re) of KP.3.1.1 was estimated based on genome surveillance data from Spain, the USA, France, Canada, and the UK. In Spain, the Re of KP.3.1.1 was over 1.2-fold higher than that of JN.1 and even higher than those of KP.2, KP.3, LB.1, and KP.2.3. However, there is a possibility of overestimation due to limited sequence numbers. These results suggest that KP.3.1.1 will spread globally along with other JN.1 sublineages. Using pseudoviruses, KP.3.1.1 showed significantly higher infectivity than KP.3. Neutralization assays showed that KP.3.1.1 had significantly lower neutralization titers than KP.3 in all tested groups. KP.3.1.1 also showed lower neutralization titers against XBB.1.5 vaccine sera than KP.3 and stronger resistance to convalescent sera infected with EG.5 and HK.3 than KP.2.3. Altogether, KP.3.1.1 exhibited higher Re, higher pseudovirus infectivity, and higher neutralization evasion than KP.3. These results align with recent reports that JN.1 subvariants with S:S31del (e.g., KP.2.3 and LB.1) exhibited enhanced Re and immune evasion compared to other JN.1 subvariants without S:S31del (e.g., JN.1, KP.2, and KP.3), highlighting the evolutionary significance of S:S31del in theThe SARS-CoV-2 JN.1 variant (BA.2.86.1.1), which arose from BA.2.86.1 with a spike protein (S) substitution S:L455S, outcompeted the previously dominant XBB lineage by early 2024. Subsequently, JN.1 subvariants, including KP.2 (JN.1.11.1.2) and KP.3 (JN.1.11.1.3), which acquired additional S substitutions, emerged. Later, JN.1 subvariants such as LB.1 (JN.1.9.2.1), KP.2.3 (JN.1.11.1.2.3), and KP.3.1.1 (JN.1.11.1.3.1.1), which also acquired a deletion of Serine at the 31st position in S (S:S31del), emerged and spread by June 2024. The virological features of KP.3.1.1 were investigated. Using a Bayesian multinomial logistic model, the relative effective reproduction number (Re) of KP.3.1.1 was estimated based on genome surveillance data from Spain, the USA, France, Canada, and the UK. In Spain, the Re of KP.3.1.1 was over 1.2-fold higher than that of JN.1 and even higher than those of KP.2, KP.3, LB.1, and KP.2.3. However, there is a possibility of overestimation due to limited sequence numbers. These results suggest that KP.3.1.1 will spread globally along with other JN.1 sublineages. Using pseudoviruses, KP.3.1.1 showed significantly higher infectivity than KP.3. Neutralization assays showed that KP.3.1.1 had significantly lower neutralization titers than KP.3 in all tested groups. KP.3.1.1 also showed lower neutralization titers against XBB.1.5 vaccine sera than KP.3 and stronger resistance to convalescent sera infected with EG.5 and HK.3 than KP.2.3. Altogether, KP.3.1.1 exhibited higher Re, higher pseudovirus infectivity, and higher neutralization evasion than KP.3. These results align with recent reports that JN.1 subvariants with S:S31del (e.g., KP.2.3 and LB.1) exhibited enhanced Re and immune evasion compared to other JN.1 subvariants without S:S31del (e.g., JN.1, KP.2, and KP.3), highlighting the evolutionary significance of S:S31del in the