Virus persistence in pig herds led to successive reassortment events between swine and human influenza A viruses, resulting in the emergence of a novel triple-reassortant swine influenza virus

Table 2 Amino acid differences in HA protein sequences of the H1 _av N2 viruses described in this study as compared to HA residues in reference strain A/Sw/Cotes d’Armor/0388/09 (CA/388/09)

CA/388/09^a	A-11	A-12	B-14	A-16	Reported effect^c
V14	A^b	A^b	A^b	A^b	–
V22	I	I	I	I	–
S53	N	N	N	N	Antigenic drift/escape mutant
Q68	H	H	H	H	–
V74	–	–	I	I	–
L86	S	S	P	P	–
L88	–	–	–	P	Antigenic drift/escape mutant
S154	P	P	P	P	Antigenic drift/escape mutant
S156	–	–	L	L	Antigenic drift/escape mutant
G172	–	–	–	R	Antigenic drift/escape mutant and other
L178	–	–	–	I	–
K186	–	–	R	R	–
G187	–	–	–	E	–
I192	V^b	V^b	V^b	V^b	–
D202	–	–	V	V	–
T249	I	I	I	I	–
H270	–	–	–	Y	–
G277	S	S	S	S	Creates a new potential N-glycosylation site at position 275
V282	I^b	I^b	I^b	I^b	–
D286	N	N	N	N	–
H288	–	N	N	N	–
Y300	H^b	H^b	H^b	H^b	–
K304	–	–	N	N	–
S305	G	G	G	–	–
N306	S	S	S	S	–
E319	–	K	–	–	–
G391	R	R	R	R	Virulence
S393	N	N	N	N	–
I444	–	–	V	V	–
K460	R	R	R	R	–
E516	–	–	–	K	–

Swine H1_avN2 reassortants were abbreviated A-11 for A/Sw/France/37-110543/2011 [Farm A], A-12 for A/Sw/France/37-120345/2012 [Farm A], B-14 for A/Sw/France/61-140350/2014 [Farm B] and A-16 for A/Sw/France/37-160178/2016 [Farm A].
^aCA/388/09 is a reference strain representative of European swine avian-like H1_avNy viruses belonging to the HA clade 1C.2.1 (after Anderson et al. [10]).
^bResidue fixed in French swIAV strains of avian-like H1 (H1_av) lineage since 2000’.
^cAccording to the BII FluSurver.

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