Host shifts and molecular evolution of H7 avian influenza virus hemagglutinin

Table 1 Molecular evolution of the HA gene for the main genetic lineages and sub-lineages of H7 IA viruses

Geographic origin	Host	N¹	Time period²	Mean nucleotide substitution rate³	Virulence	Mean d_N/d_S [95% CI]	Positive selection⁴			Amino acid position
							SLAC	FEL	REL
Eurasia-Africa-Australia	W	30	25	4.32 [2.24-6.47]	LP	0.09 [0.08-0.11]	0	0	0
Sweden - Netherlands	W	15	4	11.21 [0.23-21.14]	LP	0.18 [0.13-0.25]	0	0	0
Eurasia-Africa-Australia	D	151	144	2.25 [1.59-2.86]	LP-HP	0.13 [0.12-0.14]	2	1⁵	NA	143, 341
Italy	D	52	4	2.99 [1.26-4.90]	LP-HP	0.44 [0.34-0.55]	0	1⁵	1	143
Italy	D	27	6	5.59 [3.99-7.33]	LP	0.27 [0.21-0.35]	0	0	0
Pakistan	D	18	11	0.37 [0.06-0.69]	HP	0.73 [0.53-0.99]	0	1⁵	4	46, 139, 143, 152
Australia	D	10	29	4.62 [2.78-6.28]	HP	0.11 [0.09-0.15]	0	2⁵	2	150, 284
North America	W	37	32	6.59 [4.93-8.28]	LP	0.09 [0.07-0.11]	0	0	0
North America	W	28	9	11.74 [6.55-17.88]	LP	0.10 [0.07-0.12]	0	0	0
North and South America	D	195	59	3.87 [2.82-4.79]	LP-HP	0.16 [0.15-0.17]	1	1 + 1⁵	NA	150, 340
USA	D	175	13	4.32 [3.66-5.01]	LP	0.24 [0.21-0.26]	1⁵	3	NA	143, 148, 276

¹ number of sequences; ² number of years of circulation between the time of the most recent common ancestor of the genetic lineage and the last time of virus collection; ³ per 10^-3 substitution/site/year, with [95% HPD]; ⁴ number of sites under positive selection, with p <0.05, according to the single likelihood ancestor counting (SLAC), fixed-effects likelihood (FEL) and random effects likelihood (REL) methods; ⁵ evidence of positive selection for the same site(s), as found with another method, but with 0.1 <p <0.05. D: domestic bird; W: wild bird; LP: low pathogenic; HP: highly pathogenic; CI: confidence interval; NA: not available because of computational limitations.

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