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Phylogenetic analysis of a swine influenza A(H3N2) virus isolated in Korea in 2012.

Kim JI, Lee I, Park S, Lee S, Hwang MW, Bae JY, Heo J, Kim D, Jang SI, Kim K, Park MS - PLoS ONE (2014)

Bottom Line: The genome nature of IAVs may contribute to viral adaptation in different animal hosts, resulting in gene reassortment and the reproduction of variants with optimal fitness.Herein, we report the isolation and phylogenetic study of a swine IAV, A/swine/Korea/PL01/2012 (swPL01, H3N2 subtype).These data suggest the possibility that various swine H3N2 viruses may co-circulate in Korea, which underlines the importance of a sustained surveillance system against swine IAVs.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Gangwon-do, Republic of Korea ; Center for Medical Science Research, College of Medicine, Hallym University, Chuncheon, Gangwon-do, Republic of Korea.

ABSTRACT
Influenza A virus (IAV) can infect avian and mammalian species, including humans. The genome nature of IAVs may contribute to viral adaptation in different animal hosts, resulting in gene reassortment and the reproduction of variants with optimal fitness. As seen again in the 2009 swine-origin influenza A H1N1 pandemic, pigs are known to be susceptible to swine, avian, and human IAVs and can serve as a 'mixing vessel' for the generation of novel IAV variants. To this end, the emergence of swine influenza viruses must be kept under close surveillance. Herein, we report the isolation and phylogenetic study of a swine IAV, A/swine/Korea/PL01/2012 (swPL01, H3N2 subtype). After screening nasopharyngeal samples from pigs in the Gyeongsangnam-do region of Korea from December 2011 to May 2012, we isolated the swPL01 virus and sequenced its all of 8 genome segments (polymerase basic 2, PB2; polymerase basic 1, PB1; polymerase acidic, PA; hemagglutinin, HA; nucleocapsid protein, NP; neuraminidase, NA; matrix protein, M; and nonstructural protein, NS). The phylogenetic study, analyzed with reference strains registered in the National Center for Biotechnology Information (NCBI) database, indicated that the swPL01 virus was similar to the North American triple-reassortant swine strains and that the HA gene of the swPL01 virus was categorized into swine H3 cluster IV. The swPL01 virus had the M gene of the triple-reassortant swine H3N2 viruses, whereas that of other contemporary strains in Korea was transferred from the 2009 pandemic H1N1 virus. These data suggest the possibility that various swine H3N2 viruses may co-circulate in Korea, which underlines the importance of a sustained surveillance system against swine IAVs.

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The phylogenetic relationships of surface glycoprotein segments.The evolutionary phases of the HA (A) and NA (B) segments of the swPL01 virus were inferred using the method described above (see the legend in Figure 1). The sequences with more than 60% bootstrap scores among the evolution branches of the swTx/98 virus and those of reference were used for the final ML tree evaluation. The HA phylogenetic groups were indicated as cluster I, II, III, and IV. The NAs were indicated as TRIG H3N2, human H1N2 (huH1N2), human H3N2 (huH3N2), and clade IV. The colors represent the following viruses: pink, A/swine/Texas/4199-2/1998 (swTx/98); green, Korean swine H3N2; and red, A/swine/Korea/PL01/2012 (swPL01).
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pone-0088782-g002: The phylogenetic relationships of surface glycoprotein segments.The evolutionary phases of the HA (A) and NA (B) segments of the swPL01 virus were inferred using the method described above (see the legend in Figure 1). The sequences with more than 60% bootstrap scores among the evolution branches of the swTx/98 virus and those of reference were used for the final ML tree evaluation. The HA phylogenetic groups were indicated as cluster I, II, III, and IV. The NAs were indicated as TRIG H3N2, human H1N2 (huH1N2), human H3N2 (huH3N2), and clade IV. The colors represent the following viruses: pink, A/swine/Texas/4199-2/1998 (swTx/98); green, Korean swine H3N2; and red, A/swine/Korea/PL01/2012 (swPL01).

Mentions: We then analyzed the phylogenetic characteristics of the swPL01 HA and NA genes. In the ML tree of the overall sequences, the HA of swPL01 (indicated as c in Figure S4) virus was distant from those of other contemporary Korean viruses (b, d in Figure S4). We confirmed this phylogenetic distance with the selected HA sequences. In the ML (Figure 2A), MP and NJ (Figure S4) trees, each cluster (clusters I, II, III, and IV) of swine H3 HAs diverged from that of the swTx/98 virus [25]–[27]. In these group denotations, three Korean HAs between 2005–2006 were classified into cluster I, with the parental swTx/98 HA. The HAs of the 2007 Korean isolates consisted of subsequent tertiary and quaternary branches from the HA of the swTx/98 virus whereas that of the A/swine/Korea/CY10/2007 virus that was classified into cluster III in the MP and NJ tree (Figure S4). Farther down in the tree, two Korean HAs in 2004 were categorized as clusters II (A/swine/Korea/CAS05/2004) and III (A/swine/Korea/JNS06/2004), respectively. Under the trunk of cluster III, various HAs were diverged into two large clades. These constituted cluster IV [28], and the HA of the swPL01 virus was included in the upper clade group with others from North America whereas Korean HAs isolated from 2011–2012 were in the lower clade (Figures 2A and S4). In a similar manner to that of the phylogenetic relations of polymerase genes unveiled in Figure 1, the swPL01 HA was located in one of the branches of the cluster IV phylogenetic trunk shared with the other contemporary Korean HAs, but it was categorized in a different group (Figures 2A and S4). These differences were also apparent in the ML tree using the full-length HA sequences of Asian avian, human, and swine H3N2 viruses and North American avian and swine H3N2 viruses (Figure S9). Similarly above, the HA of the swPL01 virus was included in the completely different clade from those of other Korean isolates in the same swine H3 HA trunk. Amino acid differences also explained these phylogenetic distances (Table S1). Compared with the HAs of other Korean isolates, we found 35 amino acid mutations (35/567, 6.17%) from that of the swPL01 virus. 27 mutations (27/345, 7.83%) were located in the HA1 region, and 8 (8/222, 3.6%) were in the HA 2. By concurrent E292N and N294S mutations, the HA of swPL01 virus gained one more potential N-linked glycosylation (NLG; N-Xaa-S/T, any amino acid for Xaa except proline) at HA residue 292 (Table S1). The HA of the A/swine/Ohio/11sw347/2011 virus exhibited the highest sequence similarity (96.6%) with that of the swPL01 virus (Table 1). On the other hand, maximum 94.8% similarity was found with the HAs of the Korean swine H3N2 viruses (Table 1).


Phylogenetic analysis of a swine influenza A(H3N2) virus isolated in Korea in 2012.

Kim JI, Lee I, Park S, Lee S, Hwang MW, Bae JY, Heo J, Kim D, Jang SI, Kim K, Park MS - PLoS ONE (2014)

The phylogenetic relationships of surface glycoprotein segments.The evolutionary phases of the HA (A) and NA (B) segments of the swPL01 virus were inferred using the method described above (see the legend in Figure 1). The sequences with more than 60% bootstrap scores among the evolution branches of the swTx/98 virus and those of reference were used for the final ML tree evaluation. The HA phylogenetic groups were indicated as cluster I, II, III, and IV. The NAs were indicated as TRIG H3N2, human H1N2 (huH1N2), human H3N2 (huH3N2), and clade IV. The colors represent the following viruses: pink, A/swine/Texas/4199-2/1998 (swTx/98); green, Korean swine H3N2; and red, A/swine/Korea/PL01/2012 (swPL01).
© Copyright Policy
Related In: Results  -  Collection

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Show All Figures
getmorefigures.php?uid=PMC3921248&req=5

pone-0088782-g002: The phylogenetic relationships of surface glycoprotein segments.The evolutionary phases of the HA (A) and NA (B) segments of the swPL01 virus were inferred using the method described above (see the legend in Figure 1). The sequences with more than 60% bootstrap scores among the evolution branches of the swTx/98 virus and those of reference were used for the final ML tree evaluation. The HA phylogenetic groups were indicated as cluster I, II, III, and IV. The NAs were indicated as TRIG H3N2, human H1N2 (huH1N2), human H3N2 (huH3N2), and clade IV. The colors represent the following viruses: pink, A/swine/Texas/4199-2/1998 (swTx/98); green, Korean swine H3N2; and red, A/swine/Korea/PL01/2012 (swPL01).
Mentions: We then analyzed the phylogenetic characteristics of the swPL01 HA and NA genes. In the ML tree of the overall sequences, the HA of swPL01 (indicated as c in Figure S4) virus was distant from those of other contemporary Korean viruses (b, d in Figure S4). We confirmed this phylogenetic distance with the selected HA sequences. In the ML (Figure 2A), MP and NJ (Figure S4) trees, each cluster (clusters I, II, III, and IV) of swine H3 HAs diverged from that of the swTx/98 virus [25]–[27]. In these group denotations, three Korean HAs between 2005–2006 were classified into cluster I, with the parental swTx/98 HA. The HAs of the 2007 Korean isolates consisted of subsequent tertiary and quaternary branches from the HA of the swTx/98 virus whereas that of the A/swine/Korea/CY10/2007 virus that was classified into cluster III in the MP and NJ tree (Figure S4). Farther down in the tree, two Korean HAs in 2004 were categorized as clusters II (A/swine/Korea/CAS05/2004) and III (A/swine/Korea/JNS06/2004), respectively. Under the trunk of cluster III, various HAs were diverged into two large clades. These constituted cluster IV [28], and the HA of the swPL01 virus was included in the upper clade group with others from North America whereas Korean HAs isolated from 2011–2012 were in the lower clade (Figures 2A and S4). In a similar manner to that of the phylogenetic relations of polymerase genes unveiled in Figure 1, the swPL01 HA was located in one of the branches of the cluster IV phylogenetic trunk shared with the other contemporary Korean HAs, but it was categorized in a different group (Figures 2A and S4). These differences were also apparent in the ML tree using the full-length HA sequences of Asian avian, human, and swine H3N2 viruses and North American avian and swine H3N2 viruses (Figure S9). Similarly above, the HA of the swPL01 virus was included in the completely different clade from those of other Korean isolates in the same swine H3 HA trunk. Amino acid differences also explained these phylogenetic distances (Table S1). Compared with the HAs of other Korean isolates, we found 35 amino acid mutations (35/567, 6.17%) from that of the swPL01 virus. 27 mutations (27/345, 7.83%) were located in the HA1 region, and 8 (8/222, 3.6%) were in the HA 2. By concurrent E292N and N294S mutations, the HA of swPL01 virus gained one more potential N-linked glycosylation (NLG; N-Xaa-S/T, any amino acid for Xaa except proline) at HA residue 292 (Table S1). The HA of the A/swine/Ohio/11sw347/2011 virus exhibited the highest sequence similarity (96.6%) with that of the swPL01 virus (Table 1). On the other hand, maximum 94.8% similarity was found with the HAs of the Korean swine H3N2 viruses (Table 1).

Bottom Line: The genome nature of IAVs may contribute to viral adaptation in different animal hosts, resulting in gene reassortment and the reproduction of variants with optimal fitness.Herein, we report the isolation and phylogenetic study of a swine IAV, A/swine/Korea/PL01/2012 (swPL01, H3N2 subtype).These data suggest the possibility that various swine H3N2 viruses may co-circulate in Korea, which underlines the importance of a sustained surveillance system against swine IAVs.

View Article: PubMed Central - PubMed

Affiliation: Department of Microbiology, College of Medicine, Hallym University, Chuncheon, Gangwon-do, Republic of Korea ; Center for Medical Science Research, College of Medicine, Hallym University, Chuncheon, Gangwon-do, Republic of Korea.

ABSTRACT
Influenza A virus (IAV) can infect avian and mammalian species, including humans. The genome nature of IAVs may contribute to viral adaptation in different animal hosts, resulting in gene reassortment and the reproduction of variants with optimal fitness. As seen again in the 2009 swine-origin influenza A H1N1 pandemic, pigs are known to be susceptible to swine, avian, and human IAVs and can serve as a 'mixing vessel' for the generation of novel IAV variants. To this end, the emergence of swine influenza viruses must be kept under close surveillance. Herein, we report the isolation and phylogenetic study of a swine IAV, A/swine/Korea/PL01/2012 (swPL01, H3N2 subtype). After screening nasopharyngeal samples from pigs in the Gyeongsangnam-do region of Korea from December 2011 to May 2012, we isolated the swPL01 virus and sequenced its all of 8 genome segments (polymerase basic 2, PB2; polymerase basic 1, PB1; polymerase acidic, PA; hemagglutinin, HA; nucleocapsid protein, NP; neuraminidase, NA; matrix protein, M; and nonstructural protein, NS). The phylogenetic study, analyzed with reference strains registered in the National Center for Biotechnology Information (NCBI) database, indicated that the swPL01 virus was similar to the North American triple-reassortant swine strains and that the HA gene of the swPL01 virus was categorized into swine H3 cluster IV. The swPL01 virus had the M gene of the triple-reassortant swine H3N2 viruses, whereas that of other contemporary strains in Korea was transferred from the 2009 pandemic H1N1 virus. These data suggest the possibility that various swine H3N2 viruses may co-circulate in Korea, which underlines the importance of a sustained surveillance system against swine IAVs.

Show MeSH
Related in: MedlinePlus