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. 2019 Feb 27;9:2872. doi: 10.1038/s41598-019-39854-3

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© The Author(s) 2019

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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A schematic representation of PLP design strategy: (A). Multiple sequence alignment (MSA) of 335 NDV L-gene sequences using Geneious version 6.1.8, where the disagreements to the consensus sequences are highlighted in different colors; (B). Construction of unrooted phylogenetic tree using Neighbour-Joining method, showing the two groups A and B and the respective haplotypes; (C). Location of chosen target sites for PLP design, along the length of L-gene; (D). Extracted regions of L-gene sequences from the alignment view, representing the scoring for mismatches in the individual sequences relative to the consensus; seen below is the design of mutation-tolerant PLPs; seen on the right is the list of generated PLPs showing the inclusion of Wobbles.