Table 1.

Minority variant analysis of genetically closely related low pathogenic avian influenza (LPAI) viruses isolated from potential between‐farm transmission cases

Potential case	Virus alignment	No. of nucleotide differences	No. of shared minority variants	No. of minority variants at consensus‐level variant sites
H1N5‐2007	1–2	4	0	4
H10N7‐2009	1–2	10	1	2
H6N1‐2010	1–2	14	0	4
H7N7‐2011	2–3	12	0	12
H10N9‐2012	1–2	25	0	4
	1–3	25	0	12
	2–3	8	1	6
H5N3‐2013	1–2	24	0	2
H6N2‐2014	1–2	9	0	4
	1–3	11	0	4
	2–3	6	0	0

The number of nucleotide differences, the number of shared minority variants (i.e. minority variants that are present in both viruses) and the number of minority variants at consensus‐level variant sites (i.e. minority variants at sites that varied between viruses at consensus level) are shown. Minority variants were detected using a minimum frequency of 2.0% and a minimum coverage of 1,000 reads. All samples were collected as part of the national avian influenza (AI) surveillance program in the Netherlands between January 2006 and September 2016. Detailed information on the virus sequences is provided in Table S1.