TABLE 2.

Amino acid/nonsynonymous mutations associated with at least one chain of respiratory droplet transmission

				Nucleotide frequencyd
					Trio 1			Trio 2			Trio 3			Trio 4			Trio 5			Trio 6
Virus straina	Protein	Nucleotide changeb	Amino acid change relative to inoculumc	Virus inoculum	DI	RC1	RC2	DI	RC1	RC2	DI	RC1	RC2	DI	RC1	RC2	DI	RC1	RC2	DI	RC1	RC2
A/California/07/2009 (H1N1)	PB2	C251A	A84D												66	83
	PB2	G550A	A184T														7	21	33
	PB2	A1684T	I562F															24	39
	HA	A716G	D239 [222] (225)G		86			91	99	96	91	94	95	93	97	97	93	97	99	94	98	98
	HA	G719A	R240 [223] (226)Q		93			95	100	100	94	100	100	97	100	100	97	100	100	98	100	100
	NP	G302A	G101D	29	7			13	40		27	51	63	13			20			25
	NP	G1123A	D375N	6					36		13	48	57				5			12
A/Anhui/1/2013 (H7N9)	PB2	A2132G	N711S														15	100	99
	PB2	G2141A	S714N														13	99	98
	PB1	C413T	P138L												91	100
	PA	A1226G	N409S		8			7			8			10	100	100	12			8
	HA	A421G	N141 [123] (133)D	47	43			52			55			42	98	99	50	100	100	47	5
	HA	G499A	D167 [149] (158)N	32	37			41			29			38			28			30	95
	HA	T704A	L235 [217] (226)Q		21			32			26			27	99	99	24	100	99	10
	NA	C29T	T10I												99	100
	NA	A1379G	K460R															99	100
A/Texas/50/2012 (H3N2)e	HA	T725A	I242 (226)N	38	53			36	99								9			n/p	n/p	n/p
	NS	A796C	S266R		6	92	100	8			6						12			n/p	n/p	n/p
A/harbor seal/New Hampshire/179629/2011 (H3N8)	HA	G433A	G145 (129)R												100	100
	HA	G460A	A154 (138)T						99	77											53
	HA	G668A	R223 (207)K	29	15			13			9			4	98	98	11	99		11
	NA	C352T	P118S	38	37			32	83		35	100	99	47			34			29	86	99
	NA	G1180A	V394I	35	41			47	16	94	40			42	100	100	33	100		47	10

^aEach group consists of 1 directly inoculated (DI) ferret and 1 or 2 respiratory contact (RC) ferrets if onward transmission occurred. The first respiratory contact is RC1. If this animal became infected, it was housed with a second respiratory contact designated RC2.

^bNucleotide numbering is from the start codon of each gene.

^cFor HA, amino acid numbering in square brackets is numbering with signal peptide removed (i.e., H1 numbering or H7 numbering); parentheses indicate H3 numbering without signal peptide.

^dGray shading indicates that transmission did not occur, and underlining indicates that the mutation was associated with transmission in one or more trios of ferrets.

^eFor A/Texas/50/2012 (H3N2), trio 6 was removed (see Results, discussion of Fig. 4); thus, a deep-sequencing analysis was not performed (n/p).