Extended Data Table 1 Deep-sequence analysis of NA protein amino acid substitutions in virus-positive brain or lung tissue

From: Baloxavir improves disease outcomes in mice after intranasal or ocular infection with Influenza A virus H5N1-contaminated cow’s milk

Mouse ID	Tissue	Inoculation route	Treatment regimen	PA a.a change^{a, b} (% Frequency, read count/coverage)
76	Brain	Ocular	OSE 200 mg/kg	No Changes
99	Brain	Oral	OSE 200 mg/kg	No Changes
100	Brain	Oral	OSE 200 mg/kg	No Changes
109	Brain	Oral	OSE 20 mg/kg	No Changes
110	Brain	Oral	OSE 20 mg/kg	No Changes
111	Brain	Oral	OSE 20 mg/kg	No Changes
120	Brain	Intranasal	OSE 200 mg/kg	No Changes
121	Brain	Intranasal	OSE 200 mg/kg	No Changes^c
122	Brain	Intranasal	OSE 200 mg/kg	No Changes
134	Brain	Intranasal	OSE 20 mg/kg	No Changes^c
135	Brain	Intranasal	OSE 20 mg/kg	No Changes
136	Brain	Intranasal	OSE 20 mg/kg	No Changes
145	Brain	Ocular	Non-treated	K257T (6.6%, 307/4624)
146	Brain	Ocular	Non-treated	No Changes
147	Brain	Ocular	Non-treated	No Changes
156	Brain	Oral	Non-treated	No Changes
157	Brain	Oral	Non-treated	No Changes
158	Brain	Oral	Non-treated	No Changes
167	Brain	Intranasal	Non-treated	No Changes^c
168	Brain	Intranasal	Non-treated	No Changes
60	Brain	Intranasal	Non-treated	No Changes
76	Lung	Ocular	OSE 200 mg/kg	No Changes
89	Lung	Ocular	OSE 20 mg/kg	No Changes
99	Lung	Oral	OSE 200 mg/kg	No Changes
100	Lung	Oral	OSE 200 mg/kg	No Changes
109	Lung	Oral	OSE 20 mg/kg	No Changes
110	Lung	Oral	OSE 20 mg/kg	No Changes
111	Lung	Oral	OSE 20 mg/kg	No Changes
120	Lung	Intranasal	OSE 200 mg/kg	No Changes
121	Lung	Intranasal	OSE 200 mg/kg	No Changes^c
122	Lung	Intranasal	OSE 200 mg/kg	No Changes
134	Lung	Intranasal	OSE 20 mg/kg	No Changes
135	Lung	Intranasal	OSE 20 mg/kg	No Changes
136	Lung	Intranasal	OSE 20 mg/kg	No Changes
145	Lung	Ocular	Non-treated	K257T (6.5%, 277/4246)
146	Lung	Ocular	Non-treated	D284N (12.6%, 487/3861)
147	Lung	Ocular	Non-treated	No Changes
156	Lung	Oral	Non-treated	No Changes
157	Lung	Oral	Non-treated	No Changes
158	Lung	Oral	Non-treated	No Changes
167	Lung	Intranasal	Non-treated	No Changes^c
168	Lung	Intranasal	Non-treated	No Changes
60	Lung	Intranasal	Non-treated	No Changes

^aIdentified from Illumina sequencing of NA fragments comprising nucleotides 1-1413
^bAmino acid variant calling in CLC Genomics was performed with a variant frequency cutoff of 5% for ≥1000 reads at the target region
^cSample contained 1 synonymous change in the coding region
a.a. = amino acid.

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Extended Data Table 1 Deep-sequence analysis of NA protein amino acid substitutions in virus-positive brain or lung tissue

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