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. 2018 Feb 1;13(2):e0192081. doi: 10.1371/journal.pone.0192081

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© 2018 Yebra et al

This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.

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Fig 3 — Panel A) Recombination pattern (according to jpHMM) of the URF_A1D (accession number MF109466) discovered in the ICONIC dataset and the GenBank full-length A1/D sequence KT022394, which presented high similarity in the PR+RT pol region. B) Maximum-likelihood tree of the PR+RT pol region (1,000bp) of the A1/D cluster of sequences with high similarity to the ICONIC URF_A1D. Tips corresponding to the UKHRD are in orange. Tip names show, for the GenBank sequences: subtype, sampling country, accession number and sampling year; for UKHDRD sequences: country of birth, ID and sampling year. Branches corresponding to the A1/D cluster are shown in blue. The ICONIC URF_A1D and the GenBank sequence KT022394 are highlighted with arrows. The tree is rooted to a subtype B sequence. The diagram at the right shows the recombination pattern shown by the sequences in the cluster, according to jpHMM.