The SARS-CoV-2 JN.1 variant (BA.2.86.1.1), which emerged from BA.2.86.1 with the spike protein (S) substitution S:L455S, outcompeted previously dominant XBB lineages by early 2024. Subsequent subvariants, including KP.2 (JN.1.11.1.2) and KP.3 (JN.1.11.1.3), acquired additional S substitutions such as S:R346T, S:F456L, and S:Q493E. Further subvariants, like 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 carried a deletion of Serine at the 31st position in S (S:S31del), emerged and spread by June 2024. This study focuses on the virological properties of KP.3.1.1. Using a Bayesian multinomial logistic model, the relative effective reproduction number (Re) of KP.3.1.1 was estimated to be over 1.2-fold higher than JN.1 and other subvariants in Spain, with similar trends observed in other countries. Pseudovirus assays showed that KP.3.1.1 had significantly higher infectivity compared to KP.3. Neutralization assays using convalescent sera from breakthrough infections and vaccinated individuals revealed that KP.3.1.1 had significantly lower neutralization titers (NT50) compared to KP.3, particularly against XBB.1.5 vaccine sera. KP.3.1.1 also demonstrated stronger resistance to neutralization by convalescent sera infected with EG.5 and HK.3. These findings highlight the enhanced reproductive advantage and immune evasion capabilities of KP.3.1.1, emphasizing the evolutionary significance of the S:S31del mutation in the JN.1 lineages.The SARS-CoV-2 JN.1 variant (BA.2.86.1.1), which emerged from BA.2.86.1 with the spike protein (S) substitution S:L455S, outcompeted previously dominant XBB lineages by early 2024. Subsequent subvariants, including KP.2 (JN.1.11.1.2) and KP.3 (JN.1.11.1.3), acquired additional S substitutions such as S:R346T, S:F456L, and S:Q493E. Further subvariants, like 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 carried a deletion of Serine at the 31st position in S (S:S31del), emerged and spread by June 2024. This study focuses on the virological properties of KP.3.1.1. Using a Bayesian multinomial logistic model, the relative effective reproduction number (Re) of KP.3.1.1 was estimated to be over 1.2-fold higher than JN.1 and other subvariants in Spain, with similar trends observed in other countries. Pseudovirus assays showed that KP.3.1.1 had significantly higher infectivity compared to KP.3. Neutralization assays using convalescent sera from breakthrough infections and vaccinated individuals revealed that KP.3.1.1 had significantly lower neutralization titers (NT50) compared to KP.3, particularly against XBB.1.5 vaccine sera. KP.3.1.1 also demonstrated stronger resistance to neutralization by convalescent sera infected with EG.5 and HK.3. These findings highlight the enhanced reproductive advantage and immune evasion capabilities of KP.3.1.1, emphasizing the evolutionary significance of the S:S31del mutation in the JN.1 lineages.