Reassortment events among swine influenza A viruses in China: implications for the origin of the 2009 influenza pandemic

Abstract

That pigs may play a pivotal role in the emergence of pandemic influenza was indicated by the recent H1N1/2009 human pandemic, likely caused by a reassortant between viruses of the American triple-reassortant (TR) and Eurasian avian-like (EA) swine influenza lineages. As China has the largest human and pig populations in the world and is the only place where both TR and EA viruses have been reported to cocirculate, it is potentially the source of the H1N1/2009 pandemic virus. To examine this, the genome sequences of 405 swine influenza viruses from China were analyzed. Thirty-six TR and EA reassortant viruses were identified before and after the occurrence of the pandemic. Several of these TR-EA reassortant viruses had genotypes with most segments having the same lineage origin as the segments of the H1N1/2009 pandemic virus. However, these viruses were generated from independent reassortment events throughout our survey period and were not associated with the current pandemic. One TR-EA reassortant, which is least similar to the pandemic virus, has persisted since 2007, while all the other variants appear to be transient. Despite frequent reassortment events between TR and EA lineage viruses in China, evidence for the genesis of the 2009 pandemic virus in pigs in this region is still absent.

Fig. 1.

TR and EA phylogenies of the M gene of the influenza A virus. Shown is the ML phylogeny of the M gene, with numbers showing bootstrap support (left) and posterior probability (right) for selected nodes. The genotypes of these swine influenza viruses are shown on the right as an array of eight blocks representing each gene segment (numbers 1 to 8 indicate PB2, PB1, PA, HA, NP, NA, M, and NS, respectively), and the color of a block indicates the lineage in which that segment is located in the gene phylogeny (orange, TR; green, EA; blue, CS; purple, HuH3N2). The names of the TR-EA reassortant viruses are highlighted in red, and those of representative viruses for the sublineages are in blue. Only reference viruses relevant to the TR-EA reassortant viruses are included. The phylogenies of the complete data sets are shown in Fig. S1 to S3 in the supplemental material.

Fig. 2.

TR and EA phylogenies of the PB2 gene of the influenza A virus. See the legend to Fig. 1 for details. The names of the TR-EA reassortant viruses are highlighted in red, and those of representative viruses for the sublineages are in blue.

Fig. 3.

Genotypes and reassortment of TR-EA swine viruses. Each horizontal bar represents a gene segment (from top to bottom, PB2, PB1, PA, HA, NP, NA, M, and NS), and its color indicates the lineage from which it originated (see the legend). The arrows indicate the recombination sources (arrow tails) and the resulting reassortant (arrowheads). The numbers at the arrow tails indicate the segments that were contributed to the reassortant virus. Only genotypes relevant to the TR-EA reassortant viruses are shown. HuIV, AvIV, and SwIV are human, avian, and swine influenza viruses, respectively. Divergence time estimates (tDIV) are shown for each segment (PB2 to NS, left to right) of each reassortant virus. The sublineages of the parent viruses are H3N2 HuIV (closest to NY/336/99), EA-Hu3 (HK5200/99-like sublineage), TR SwIV (HK623/02-like sublineage and North American isolates), EA SwIV (HK8512/01-like sublineage and European isolates), and EA-TR SwIV (HK72/07-like subgroup).