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. Author manuscript; available in PMC: 2020 Nov 1.

Published in final edited form as: Virology. 2019 Aug 22;537:172–185. doi: 10.1016/j.virol.2019.08.020

Figure 4. — Viral genomes sequenced from infected chickens have a higher number of nucleotide changes compared to those from mallards, relative to the inoculum. Consensus sequences were obtained from whole genome sequencing of the TD16 inoculum and experimental samples from birds directly inoculated with the high dose (6 log₁₀ EID₅₀). Nucleotide changes relative to the inoculum were annotated and counted for each sample. (A) Total number of changes observed across the genome from mallards and chickens as classified by sample type where OP = oropharyngeal swab, CL = cloacal swab. Total number of changes in swab (B) and tissue (C) samples from chickens or mallards, as classified by genome segment. (D) Mean frequency of SNVs within each swab sample in chickens and mallards. Mean frequencies are expressed as proportions where 0.5 is equivalent to 50%. *p<0.05 using the Kruskal-Wallis (A) or Mann-Whitney test (B-D). For (A), the lowercase letters above indicate statistical pairwise comparisons between groups. In this case, a significant difference between two groups was observed if the two groups do not share a letter. Statistical comparisons for (B-C) were made with the same gene between the two groups.

Figure 4. — Viral genomes sequenced from infected chickens have a higher number of nucleotide changes compared to those from mallards, relative to the inoculum. Consensus sequences were obtained from whole genome sequencing of the TD16 inoculum and experimental samples from birds directly inoculated with the high dose (6 log₁₀ EID₅₀). Nucleotide changes relative to the inoculum were annotated and counted for each sample. (A) Total number of changes observed across the genome from mallards and chickens as classified by sample type where OP = oropharyngeal swab, CL = cloacal swab. Total number of changes in swab (B) and tissue (C) samples from chickens or mallards, as classified by genome segment. (D) Mean frequency of SNVs within each swab sample in chickens and mallards. Mean frequencies are expressed as proportions where 0.5 is equivalent to 50%. *p<0.05 using the Kruskal-Wallis (A) or Mann-Whitney test (B-D). For (A), the lowercase letters above indicate statistical pairwise comparisons between groups. In this case, a significant difference between two groups was observed if the two groups do not share a letter. Statistical comparisons for (B-C) were made with the same gene between the two groups.