Genetic and evolutionary analysis of emerging H3N2 canine influenza virus

Figures & data

Fig. 1 Phylogenetic tree of the complete coding sequences of H3N2 CIVs based on BEAST 1.8.0.

Origin, China, and Korea/USA clades are represented in green, red, and orange, respectively

Fig. 2 ENC values in H3N2 CIV segments.

The H3N2 CIV strains are clustered into three genotypic groups, namely, Origin, China, and Korea/USA, represented in green, red, and orange, respectively

RSCU of H3N2 CIVs, genotypes, and potential hosts

		H3N2 CIVs				Potential host
AA	Codon	All	Original	China	Korea	Homo sapiens	Canis familiaris	Felis catus	Gallus gallus
Phe	UUU(F)	0.84	0.81	0.84	0.84	0.93	0.82	0.77	0.91
	UUC(F)	1.16	1.19	1.16	1.16	1.07	1.18	1.13	1.09
Leu	UUA(L)	0.65	0.61	0.63	0.68	0.46	0.35	0.35	0.45
	UUG(L)	1.07	1.14	1.1	1.04	0.77	0.71	0.76	0.81
	CUU(L)	1.21	1.19	1.22	1.19	0.79	0.70	0.67	0.80
	CUC(L)	0.9	0.91	0.89	0.91	1.17	1.30	1.29	1.08
	CUA(L)	1	0.91	0.96	1.06	0.43	0.39	0.36	0.38
	CUG(L)	1.16	1.24	1.2	1.12	2.37	2.56	2.57	2.48
Ile	AUU(I)	1.15	1.12	1.14	1.16	1.08	0.96	0.95	1.06
	AUC(I)	0.8	0.82	0.81	0.79	1.41	1.60	1.58	1.39
	AUA(I)	1.05	1.06	1.05	1.05	0.51	0.45	0.47	0.55
Val	GUU(V)	0.99	0.97	0.98	0.99	0.73	0.58	0.62	0.84
	GUC(V)	0.76	0.78	0.76	0.76	0.95	1.07	1.13	0.87
	GUA(V)	0.9	0.86	0.93	0.88	0.47	0.41	0.38	0.50
	GUG(V)	1.35	1.38	1.33	1.37	1.85	1.94	1.87	1.80
Ser	UCU(S)	0.98	0.99	0.97	0.98	1.13	1.08	1.12	1.09
	UCC(S)	0.93	0.92	0.92	0.94	1.31	1.45	1.48	1.21
	UCA(S)	1.39	1.35	1.39	1.39	0.90	0.77	0.74	0.89
	UCG(S)	0.37	0.37	0.38	0.36	0.33	0.36	0.38	0.40
	AGU(S)	1.08	1.09	1.07	1.1	0.90	0.85	0.80	0.86
	AGC(S)	1.25	1.28	1.28	1.23	1.44	1.49	1.47	1.55
Pro	CCU(P)	1.16	1.16	1.17	1.15	1.15	1.08	1.03	1.10
	CCC(P)	0.74	0.73	0.74	0.74	1.29	1.42	1.51	1.22
	CCA(P)	1.62	1.57	1.58	1.67	1.11	1.01	0.97	1.13
	CCG(P)	0.48	0.54	0.51	0.44	0.45	0.48	0.50	0.56
Thr	ACU(T)	1.01	1.02	1.02	1.01	0.99	0.89	0.84	0.99
	ACC(T)	0.98	0.99	0.97	0.99	1.42	1.55	1.59	1.23
	ACA(T)	1.82	1.8	1.82	1.82	1.14	1.03	0.94	1.20
	ACG(T)	0.19	0.19	0.2	0.18	0.46	0.52	0.63	0.57
Ala	GCU(A)	1.05	1.05	1.05	1.05	1.06	1.00	0.96	1.16
	GCC(A)	0.78	0.79	0.79	0.77	1.60	1.75	1.79	1.27
	GCA(A)	1.89	1.87	1.87	1.91	0.91	0.79	0.76	1.06
	GCG(A)	0.28	0.29	0.29	0.26	0.42	0.46	0.50	0.51
Tyr	UAU(Y)	1	0.97	0.99	1.01	0.89	0.79	0.78	0.80
	UAC(Y)	1	1.03	1.01	0.99	1.11	1.21	1.22	1.20
His	CAU(H)	1.22	1.27	1.26	1.19	0.84	0.78	0.74	0.80
	CAC(H)	0.78	0.73	0.74	0.81	1.16	1.22	1.26	1.20
Gln	CAA(Q)	1.11	1.04	1.11	1.12	0.53	0.50	0.56	0.54
	CAG(Q)	0.89	0.96	0.89	0.88	1.47	1.50	1.44	1.46
Asn	AAU(N)	1.11	1.1	1.13	1.11	1.08	0.96	0.82	0.86
	AAC(N)	0.89	0.9	0.87	0.89	1.41	1.60	1.18	1.14
Lys	AAA(K)	1.25	1.21	1.25	1.25	0.87	0.79	0.86	0.89
	AAG(K)	0.75	0.79	0.75	0.75	1.13	1.21	1.14	1.11
Asp	GAU(D)	1.1	1.12	1.11	1.1	0.93	0.86	0.84	1.01
	GAC(D)	0.9	0.88	0.89	0.9	1.07	1.14	1.16	0.99
Glu	GAA(E)	1.14	1.09	1.14	1.15	0.84	0.79	0.86	0.86
	GAG(E)	0.86	0.91	0.86	0.85	1.16	1.21	1.14	1.14
Cys	UGU(C)	0.92	0.9	0.93	0.92	0.91	0.85	0.87	0.80
	UGC(C)	1.08	1.1	1.07	1.08	1.09	1.15	1.13	1.20
Arg	CGU(R)	0.23	0.23	0.22	0.25	0.48	0.44	0.41	0.59
	CGC(R)	0.33	0.34	0.35	0.32	1.10	1.21	1.09	1.14
	CGA(R)	0.59	0.56	0.58	0.6	0.65	0.64	0.55	0.58
	CGG(R)	0.59	0.62	0.6	0.58	1.21	1.25	1.19	1.07
	AGA(R)	2.66	2.61	2.66	2.68	1.29	1.19	1.33	1.34
	AGG(R)	1.6	1.64	1.6	1.58	1.27	1.27	1.41	1.29
Gly	GGU(G)	0.56	0.58	0.55	0.56	0.65	0.65	0.58	0.70
	GGC(G)	0.59	0.61	0.61	0.58	1.35	1.39	1.42	1.22
	GGA(G)	1.82	1.77	1.8	1.84	1.00	0.97	1.01	1.09
	GGG(G)	1.03	1.04	1.04	1.02	1.00	1.00	0.99	0.99

Preferred H3N2 CIV codons, genotypes, and potential hosts are displayed in bold

Fig. 3 PCA based on the RSCU values of the 59 synonymous codons.

Genotype-specific PCA was structured for whole genomes and H3N2 (eight segments). Origin, China, and Korea/USA clades are represented in green, red, and orange, respectively

Fig. 4 Relationship between ENC and GC_3s of whole genomes and different H3N2 segments.

Solid curves represent the stranded ENC. Origin, China, and Korea/USA clades are represented as green, red, and orange diamonds, respectively

Correlation analysis among nucleotide composition, codon composition, ENC, Aroma, Gravy, Axis1, and Axis2

	A	C	G	U	U3s	C3s	A3s	G3s	GC	GC3s	ENC	Gravy	Aroma	Axis1	Axis2
A
C	−0.598**
G	−0.996**	0.568**
U	0.536**	−0.934**	−0.537**
U3s	0.628**	−0.841**	−0.629**	0.870**
C3s	−0.690**	0.905**	0.667**	−0.843**	−0.907**
A3s	0.992**	−0.570**	−0.986**	0.499**	0.576**	−0.673**
G3s	−0.986**	0.506**	0.987**	−0.454**	−0.557**	0.627**	−0.993**
GC	−0.986**	0.713**	0.982**	−0.670**	−0.725**	0.774**	−0.972**	0.957**
GC3s	−0.989**	0.650**	0.984**	−0.594**	−0.690**	0.763**	-0.988**	0.981**	0.988**
ENC	−0.903**	0.490**	0.902**	−0.438**	−0.489**	0.627**	−0.917**	0.911**	0.881**	0.903**
Gravy	−0.529**	−0.134	0.548**	0.157	−0.089	0.042	−0.502**	0.550**	0.435**	0.458**	0.570**
Aroma	−0.060	−0.178	0.025	0.349*	0.165	−0.071	−0.083	0.092	−0.017	0.051	−0.033	−0.059
Axis1	−0.892**	0.277	0.902	−0.245	−0.358*	0.432**	−0.906	0.933	0.832	0.871**	0.898**	0.745**	0.021
Axis2	−0.415**	0.827**	0.382*	−0.755**	−0.649**	0.710**	−0.405**	0.334*	0.516**	0.467**	0.229	−0.452**	0.106	0.000

*0.05 < p < 0.01; **p < 0.01, the individual number represents the correlation coefficient of the index

Fig. 5 Neutrality plot analysis (GC_3s against GC_12s) of the complete coding sequences of H3N2 CIVs and different clades

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Fig. 6 ML phylogenetic trees of the HA and NA(A) genes reconstructed with 597 sequences and phylogenetic tree of the HA(B) gene constructed with 43 H3N2 CIVs and 20 AIVs and the dN/dS(C) value of the influenza viruses (including avian, canine, and human) corresponding to the HA and NA genes (H3N2 AIVs are blue, CIVs are pink, and the human influenza virus is orange)