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. 2022 Jan 6;23:31. doi: 10.1186/s12864-021-08272-z

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© The Author(s) 2022

Open AccessThis 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 licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence 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 licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data.

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Fig. 3 — Intra- and interpatient diversity of individual HCMV haplotype sequences determined by PacBio sequencing. Phylogenetic trees of 8 distinct F3 and 9 distinct F4 haplotype sequences, respectivley, were inferred by using the Maximum Likelihood method and Hasegawa-Kishino-Yano model (F3) or Kimura 2-parameter model (F4). F3 haplotype sequences cover a 7.7 kb region (from UL72 to UL76) and F4 haplotype sequences cover a 6.7 kb region (from UL146 to UL139) of the HCMV genome. Branches are labeled by the identified haplotypes of the respective sample and amplicon (e.g. BAL2_F3_hap1). Each font colour corresponds haplotypes that were identified in a single patient sample. Corresponding gN, gO and UL146 genotypes as determined by short amplicon sequencing are shown in bold italics in brackets next to the branch label. BAL, bronchoalveolar lavage; hap, haplotype