Swine influenza viruses in Northern Vietnam in 2013–2014

Figures & data

Fig. 1 Genotypes of the viruses isolated in Hanoi in 2013–2014.

Genotype numbers were defined by Takemae et al.²⁸ Lineages: red: H1N1 Pandemic 2009; yellow: Triple-reassortant; blue: human-like

Fig. 2 Phylogenetic tree for the full-length hemagglutinin of H1N1pdm09 viruses isolated in a slaughterhouse in Vietnam in 2013–2014.

The trees were constructed with PhyML. Branch support aLRT statistics were shown at major nodes with values larger or equal to 0.8. GenBank accession numbers of retrieved sequences are indicated. Red: sequences from our study; blue: sequences from Takemae et al.²⁸; green: viruses from Vietnam from other studies including H1N1pdm09 from NIHE; black: other sequences from GenBank

Fig. 3 Phylogenetic tree for the full-length neuraminidase of H1N1pdm09 viruses isolated in a slaughterhouse in Vietnam in 2013–2014.

The trees were constructed with PhyML. Branch support aLRT statistics were shown at major nodes with values larger or equal to 0.8. GenBank accession numbers of retrieved sequences are indicated. Red: sequences from our study; blue: sequences from Takemae et al.²⁸; green: viruses from Vietnam from other studies including H1N1pdm09 from NIHE; black: other sequences from GenBank

Fig. 4 Phylogenetic tree for the full-length neuraminidase of H1N2 and H3N2 viruses isolated in a slaughterhouse in Vietnam in 2013–2014.

The trees were constructed with PhyML. Branch support aLRT statistics were shown at major nodes with values larger or equal to 0.8. GenBank accession numbers of retrieved sequences are indicated. Red: sequences from our study; blue: sequences from Takemae et al.²⁸; green: viruses from Vietnam from other studies including H1N1pdm09 from NIHE; black: other sequences from GenBank

Fig. 5 Phylogenetic tree for the full-length hemagglutinin of H3N2 viruses isolated in a slaughterhouse in Vietnam in 2013–2014.

The trees were constructed with PhyML. Branch support aLRT statistics were shown at major nodes with values larger or equal to 0.8. GenBank accession numbers of retrieved sequences are indicated. Red: sequences from our study; blue: sequences from Takemae et al.²⁸; green: viruses from Vietnam from other studies including H1N1pdm09 from NIHE; black: other sequences from GenBank

Hemagglutination inhibition seroprevalence for the different strains of influenza A across locations

HI strains	HI seroprevalence % (number of sera)
	Collective slaughterhouse (N = 964)	Local slaughterhouses (N = 677)	Market (N = 609)	Overall (N = 2250)
H3N2/415	3.4 (33)	1.5 (10)	0 (0)	1.9 (43)
H3N2/601	10.1 (97)	23.6 (160)	1.1 (7)	11.7 (264)
H1N1/pdm	14.2 (137)	23.2 (157)	1.6 (10)	13.5 (304)
H1N2/826	10.9 (105)	13.1 (89)	0 (0)	8.6 (194)
H1N1/EA	2.8 (27)	1.6 (11)	0 (0)	1.7 (38)
Total HI positive	29.1 (281)	48.7 (330)	2.8 (17)	27.9 (628)

All HI test results were included regardless of titer differences between strains of same subtype

Fig. 6 Serological and virological distributions of different influenza A strains across time in slaughterhouses.

Undet. undetermined strain, i.e., HI titer positive to several H1 or H3 strains with a titer difference < 4-fold. Viruses were isolated at the collective slaughterhouse

Logistic regression results for the different influenza A strains

Variables	β	SE	OR	95% CI		p-value
				Lower	Upper
H3N2/415 (AIC: 338.07)
(Intercept)	−4.315	0.387	0.013	0.006	0.027	0.000	***
Familial farm
Company farm	1.269	0.573	3.558	1.195	11.331	0.027	*
Unknown farm	1.134	0.645	3.107	0.842	10.698	0.079
Hung Yen
Hanoi	0.964	0.608	2.621	0.817	8.837	0.113
Other	0.074	0.599	1.077	0.317	3.394	0.902
Unknown	−0.378	0.693	0.685	0.178	2.740	0.585
No concurrent isolation
Concurrent isolation	0.690	0.325	1.993	1.046	3.773	0.034	*
H3N2/601 (AIC: 1078.8)
(Intercept)	−0.465	0.110	0.628	0.505	0.779	0.000	***
Hung Yen
Hanoi	−1.918	0.307	0.147	0.077	0.259	0.000	***
Other	−0.191	0.198	0.826	0.558	1.212	0.334
Unknown	−0.456	0.197	0.634	0.428	0.928	0.021	*
Before 1st isolation
After 1st isolation	−0.632	0.170	0.532	0.379	0.738	0.000	***
H1N2/826 (AIC: 946.59)
(Intercept)	−1.920	0.173	0.147	0.103	0.204	0.000	***
Familial farm
Company farm	−0.543	0.285	0.581	0.329	1.009	0.057
Unknown farm	−0.121	0.307	0.886	0.478	1.598	0.694
Hung Yen
Hanoi	−0.224	0.353	0.799	0.393	1.578	0.526
Other	0.332	0.229	1.394	0.886	2.178	0.147
Unknown	0.572	0.327	1.771	0.937	3.392	0.081
Before 1st isolation
After 1st isolation	0.914	0.180	2.493	1.759	3.572	0.000	***
H1N1/pdm (AIC: 1179.9)
(Intercept)	−0.636	0.112	0.530	0.425	0.658	0.000	***
Familial farm
Company farm	−0.601	0.168	0.549	0.393	0.759	0.000	***
Unknown farm	−0.846	0.206	0.429	0.284	0.637	0.000	***
No concurrent isolation
Concurrent isolation	0.278	0.142	1.321	0.999	1.744	0.050
H1N1/EA (AIC: 276.55)
(Intercept)	−6.275	0.769	0.002	0.000	0.007	0.000	***
Hung Yen
Hanoi	1.221	0.474	3.391	1.310	8.593	0.010	**
Other	1.173	0.437	3.232	1.366	7.726	0.007	**
Unknown	0.549	0.525	1.731	0.579	4.712	0.296
Not positive to other H1
Positive to other H1	3.245	0.733	25.650	7.713	159.067	0.000	***

Only sera from slaughterhouses were included *p-value ≤0.05; **p-value ≤0.01; ***p-value ≤0.001

Takemae, N. et al. Influenza A viruses of swine (IAV-S) in Vietnam from 2010 to 2015: multiple Introductions of A(H1N1)pdm09 viruses into the pig population and diversifying genetic constellations of enzootic IAV-S. J. Virol.91, e01490-16 (2017).

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