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. 2023 May 16;14:2800. doi: 10.1038/s41467-023-38435-3

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© The Author(s) 2023

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 1 — a Muximum likelihood tree of representative sequences from PANGO lineages of interest: BA.1, BA.2, BA.4, BA.5, BA.2.75, BJ.1 and BM.1.1.1, rooted on a B.1.1 outgroup (not shown). The recombinant parents of XBB are annotated on the tree as cartoon clades. b Amino acid differences in the S proteins of Omicron lineages. c Nucleotide differences between the consensus sequences of the BJ.1, BM.1 (including BM.1.1/BM.1.1.1) lineages and the XBB (including XBB.1) lineage, visualized with snipit (https://github.com/aineniamh/snipit). d Maximum clade credibility time-calibrated phylogeny of the 5ʹ non-recombinant segment (1–22,920) of the XBB variant (left) and non-calibrated maximum likelihood phylogeny of the 3ʹ non-recombinant segment (22,920–29,903) (right). The right hand-side tree is rooted on a BA.2 outgroup (not shown). e Relative effective reproduction number (R_e) values for viral lineages in India, assuming a fixed generation time of 2.1 days. The R_e of BA.2 is set at 1. Dot color indicates the posterior mean of the R_e, and an arrow indicate phylogenetic relationship. See also Supplementary Fig. 1b. f Difference in the circulated regions between BQ.1 and XBB lineages. Estimated lineage frequency as of November 15^th, 2022 in each country is shown. Countries with ≥50% and ≥20% frequencies are annotated for the BQ.1 and XBB lineages, respectively. g Relative R_e values for viral lineages, assuming a fixed generation time of 2.1 days. The R_e value of BA.5 is set at 1. The posterior (violin), posterior mean (dot), and 95% Bayesian confidential interval (CI; line) are shown. The global average values estimated by a hierarchical Bayesian model²⁷ are shown. See also Supplementary Fig. 1c. h Estimated lineage dynamics in each country where BQ.1 and XBB lineages cocirculated. Posterior mean, line; 95% CI, ribbon. Source data are provided with this paper.