Virological characteristics of the SARS-CoV-2 KP.2 variant

Kaku, Y.; Uriu, K.; Kosugi, Y.; Okumura, K.; Yamasoba, D.; Uwamino, Y.; Kuramochi, J.; Sadamasu, K.; Yoshimura, K.; Nagashima, M.; Asakura, H.; The Genotype to Phenotype Japan (G2P-Japan) Consortium,; Ito, J.; Sato, K.

doi:10.1101/2024.04.24.590786

bioRxiv · 10.1101/2024.04.24.590786

Virological characteristics of the SARS-CoV-2 KP.2 variant

Kaku, Y.·Uriu, K.·Kosugi, Y.·Okumura, K.·Yamasoba, D.·Uwamino, Y.·Kuramochi, J.·Sadamasu, K.·Yoshimura, K.·Nagashima, M.·Asakura, H.·The Genotype to Phenotype Japan (G2P-Japan) Consortium,·Ito, J.·Sato, K.

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Abstract

The JN.1 variant (BA.2.86.1.1), arising from BA.2.86(.1) with the S:L455S substitution, exhibited increased fitness and outcompeted the previous dominant XBB lineage by the biggening of 2024. JN.1 subsequently diversified, leading to the emergence of descendants with spike (S) protein substitutions such as S:R346T and S:F456L. Particularly, the KP.2 (JN.1.11.1.2) variant, a descendant of JN.1 bearing both S:R346T and S:F456L, is rapidly spreading in multiple regions as of April 2024. Here, we investigated the virological properties of KP.2. KP.2 has three substitutions in the S protein including the two above and additional one substitution in non-S protein compared with JN.1. We estimated the relative effective reproduction number (Re) of KP.2 based on the genome surveillance data from the USA, United Kingdom, and Canada where >30 sequences of KP.2 has been reported, using a Bayesian multinomial logistic model. The Re of KP.2 is 1.22-, 1.32-, and 1.26-times higher than that of JN.1 in USA, United Kingdom, and Canada, respectively. These results suggest that KP.2 has higher viral fitness and potentially becomes the predominant lineage worldwide. Indeed, as of the beginning of April 2024, the estimated variant frequency of KP.2 has already reached 20% in United Kingdom. The pseudovirus assay showed that the infectivity of KP.2 is significantly (10.5-fold) lower than that of JN.1. We then performed a neutralization assay using monovalent XBB.1.5 vaccine sera and breakthrough infection (BTI) sera with XBB.1.5, EG.5, HK.3 and JN.1 infections. In all cases, the 50% neutralization titer (NT50) against KP.2 was significantly lower than that against JN.1. Particularly, KP.2 shows the most significant resistance to the sera of monovalent XBB.1.5 vaccinee without infection (3.1-fold) as well as those who with infection (1.8-fold). Altogether, these results suggest that the increased immune resistance ability of KP.2 partially contributes to the higher Re more than previous variants including JN.1.

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Kaku, Y., Uriu, K., Kosugi, Y., Okumura, K., Yamasoba, D., Uwamino, Y., Kuramochi, J., Sadamasu, K., Yoshimura, K., Nagashima, M., Asakura, H., The Genotype to Phenotype Japan (G2P-Japan) Consortium,, Ito, J., Sato, K.. 2024-04-26. Virological characteristics of the SARS-CoV-2 KP.2 variant. https://doi.org/10.1101/2024.04.24.590786

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