Novel reassortant of H1N1 swine influenza virus detected in pig population in Russia

Figures & data

Table 1. Antigenic analysis of A/Sw/2016 and A/Sw/2017 in HI test. Assay was started from first dilution 1/10. The “5” value indicates the absence of cross-reactivity between virus and antisera (below the first dilution).

	A/New Caledonia/22/99 (H1N1)	A/Novosibirsk/653/2009 (H1N1)	A/California/07/2009 (H1N1)pdm09	A/Sw/2016	A/Sw/2017
A/NewCaledonia/22/99 (H1N1)	320	160	5	5	5
A/Novosibirsk/653/2009 (H1N1)	40	640	5	5	5
A/California/07/2009 (H1N1)pdm09	5	5	1280	5	5
A/Sw/2016	5	5	5	320	160
A/Sw/2017	5	5	5	160	640

Figure 1. Experimental infection of Balb/c mice by A/Sw/2016 influenza virus.

Table 2. Nucleotide identity of near homologs in GISAID to the influenza A(H1N1) strains A/Sw2016 and A/Sw2017.

	A/Sw/2016		A/Sw/2017		A/Sw/2016 - A/Sw/2017
Segment	Name	% of identity	Name	% of identity	% of identity
PB2	A/St._Petersburg/204/2010	98,21	A/California/VRDL102/2009	97,46	98,90
	A/Arkhangelsk/CRIE-GNY/2009
	A/Oslo/INS110/2009
PB1	A/Australia/26/2009	98,20	A/Australia/26/2009	97,85	99,38
PA	A/Singapore/DMS913/2009	98,22	A/Wisconsin/629-S0254/2009	98,05	99,39
	A/Wisconsin/629-S0254/2009
HA	A/Memphis/7/1980	90,48	A/Memphis/7/1980	89,79	98,77
NP	A/Florida/01/2010	98,26	A/Florida/01/2010	98,20	99,27
NA	A/Memphis/49/1983	90,54	A/Memphis/49/1983	90,30	99,28
	A/Baylor/11515/1982		A/Baylor/11515/1982
MP	A/Russia/165/2009	99,08	A/Russia/165/2009	98,78	99,69
NS	A/Qingdao/F966/2010	98,57	A/Qingdao/F966/2010	98,33	99,28
	A/Russia/12/2009		A/Russia/12/2009

Figure 2. Phylogenetic analysis of HA-gene of A/Sw2016 and A/Sw2017 (rhombuses). Circles – other Russian swine H1N1 viruses. Triangles – H1N1pdm09 virus vaccine strains. Each sequence is classified according to a Phylogeny-Based Global Nomenclature System and Automated Annotation Tool for H1 Hemagglutinin Genes from Swine Influenza A Viruses.

Figure 3. Phylogenetic analysis of NA-gene of A/Sw2016 and A/Sw2017 (rhombuses). Circles – other Russian swine H1N1 viruses. Triangles – H1N1pdm09 virus vaccine strains.

Table 3. Comparative analysis of the amino acid sequences of internal proteins between A/Sw2016 and A/Sw2017.

Protein	a.a. position	A/California/07/2009	A/Sw2016	A/Sw2017
PB2	54	R	K	K
	65	D	N
	107	S	N	N
	194	Q	H	H
	225	G		S
	300	Q		H
	340	K	N	N
	511	V	I	I
PB1	182	T	I	I
	257	T	A	A
	386	K	R	R
	628	L	Q	Q
PB1-F2	5	L	P	P
	32	E	G	G
PA	19	K		R
	158	K	Q	Q
	212	R	L	L
	216	D	N	N
	224	P	S	S
	354	I		V
	369	A	V	V
	387	V	I	I
	535	H		Y
PA-X	19	K		R
	158	K	Q	Q
	207	L	S	S
	212	A	S	S
	225	A	V	V
	228	T	I	I
NP	34	G	D
	38	R		K
	53	D	E	E
	100	V	I	I
	190	A	V	V
	313	V		I
	444	V	I	I
M2	24	D	N	N
	82	S		N
NS1	44	K	R	R
	98	M	L	L
	102	W		C
	123	I	V	V
	171	Y	Y
	196	E		K
	197	N		D
NS2	14	M		V