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

Abstract

The JN.1 variant (BA.2.86.1.1), arising from BA.2.86.1 with the S:L455S substitution, showed increased fitness and outcompeted the previous dominant XBB lineage by the beginning 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 an additional substitution in the non-S protein compared with JN.1 (appendix p 15). We estimated the relative effective reproduction number (R_e) of KP.2 based on the genome surveillance data from the USA, UK, and Canada, where more than 30 sequences of KP.2 have been reported, using a Bayesian multinomial logistic model (appendix pp 8–13, 15).

 The R_e of KP.2 is 1·22-times, 1·32-times, and 1·26-times higher than that of JN.1 in the USA, UK, and Canada, respectively (appendix p 15). 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 the UK (appendix p 15).

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DOI

http://dx.doi.org/10.1016/S1473-3099(24)00298-6

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https://eprints.gla.ac.uk/327690/