Influenza A (H5N1) viruses from pigs, Indonesia

Abstract

Pigs have long been considered potential intermediate hosts in which avian influenza viruses can adapt to humans. To determine whether this potential exists for pigs in Indonesia, we conducted surveillance during 2005-2009. We found that 52 pigs in 4 provinces were infected during 2005-2007 but not 2008-2009. Phylogenetic analysis showed that the viruses had been introduced into the pig population in Indonesia on at least 3 occasions. One isolate had acquired the ability to recognize a human-type receptor. No infected pig had influenza-like symptoms, indicating that influenza A (H5N1) viruses can replicate undetected for prolonged periods, facilitating avian virus adaptation to mammalian hosts. Our data suggest that pigs are at risk for infection during outbreaks of influenza virus A (H5N1) and can serve as intermediate hosts in which this avian virus can adapt to mammals.

Figure 1

Provinces in Indonesia (gray shading) where surveillance for influenza A (H5N1) virus in pigs was conducted during 2005–2009.

Figure 2

Phylogenetic relationships among the A) hemagglutinin (HA) and B) neuraminidase (NA) genes of influenza A (H5N1) viruses isolated in Indonesia. The numbers below or above the branch nodes indicate neighbor-joining bootstrap values. Analysis was based on nucleotides 281–1675 of the HA gene and 43–1037 of the NA gene. The HA and NA gene trees were rooted to A/goose/Guangdong/1/96 and A/duck/Guangxi/50/2001, respectively. Colors indicate swine viruses (blue) and chicken viruses (red) most closely related to swine viruses. Scale bars indicate 0.01 nt substitutions per site. Ck, chicken; Dk, duck; Fl, feline; Gd, Guangdong; Gs, goose; Gx, Guangxi; HK, Hong Kong; IDN, Indonesia; ST, Shantou; Sw, swine; Tk, turkey; Qa, quail.

Figure 3

Receptor-binding activity of influenza A (H5N1) viruses. Direct binding of viruses to sialylglycopolymers containing either α2,3-linked (blue) or α2,6-linked (red) sialic acids was measured. A) Human isolate A/Kawasaki/173/2001; B) avian isolate A/chicken/Central Java/UT3091/2005; C) swine isolate A/swine/Banten/UT3081/2005; D) swine isolate A/swine/Banten/UT3062/2005 clone 6; E) swine isolate A/swine/Banten/UT3063/2005 clone 1; F) swine isolate A/swine/East Java/UT6012/2007; G) swine isolate A/swine/Banten/UT6001/2006. Results represent means ± SDs of triplicate experiments.

Figure A1

Phylogenetic relationships of the polymerase basic protein (PB) 2 (A) and PB1 (B) genes of influenza A (H5N1) viruses in Indonesia. All trees were generated by neighbor-joining in ClustalW (www.clustal.org). Numbers above or below branches indicate neighbor-joining bootstrap values. Analyses were based on nucleotides 1062–1923 (862 bp) and 94–1485 (1392 bp) of the PB2 and PB1 genes, respectively. Each tree was rooted to A/duck/Guangxi/50/2001. Colors indicate swine isolates (blue) and chicken isolates (red) most closely related to swine viruses. Scale bar indicates 0.01 nt substitutions per site. Ck, chicken; Dk, duck; Fl, feline; Gx, Guangxi; HK, Hong Kong; IDN, Indonesia; Qa, quail; ST, Shantou; Sw, swine.

Figure A2

Phylogenetic relationships of the polymerase acidic protein (PA) (A) and nucleocapsid protein (NP) (B) genes of influenza A (H5N1) viruses in Indonesia. All trees were generated by neighbor-joining in ClustalW (www.clustal.org). Numbers above or below branches indicate neighbor-joining bootstrap values. Analyses were based on nucleotides 1426–2172 (747 bp) and 46–913 (868 bp) of the PA and NP genes, respectively. Each tree was rooted to A/duck/Guangxi/50/2001. Colors indicate swine isolates (blue) and chicken isolates (red) most closely related to swine viruses. Scale bar indicates 0.01 nt substitutions per site. Ck, chicken; Dk, duck; Fl, feline; Gx, Guangxi; HK, Hong Kong; IDN, Indonesia; Qa, quail; ST, Shantou; Sw, swine.

Figure A3

Phylogenetic relationships of the M (A) and NS (B) genes of H5N1 influenza viruses in Indonesia. All trees were generated by the neighbor-joining method in ClustalW (www.clustal.org). Numbers above or below branches indicate neighbor-joining bootstrap values. Analyses were based on nucleotides 77-955 (879 bp) and 64-789 (726 bp) of the M and NS genes, respectively. Each tree was rooted to A/duck/Shantou/4003/03 for M and NS. Colors indicate swine isolates (blue) and chicken isolates (red) most closely related to swine viruses. Scale bar indicates 0.01 nt substitutions per site. Ck, chicken; Dk, duck; Fl, feline; Gx, Guangxi; HK, Hong Kong; IDN, Indonesia; Qa, quail; ST, Shantou; Sw, swine.