Chinese Team Finds Rearranged H1N1 Flu in Hong Kong Pigs

NEW YORK (GenomeWeb News) – Viral rearrangement in pigs is producing new influenza A viruses containing bits and pieces of the H1N1 strain involved in last year's pandemic, according to a new paper appearing online today in Science.

A Chinese research team used phylogenetic analyses to assess nearly three dozen H1N1 and H1N2 flu strains isolated from pigs at a Hong Kong slaughterhouse over almost a year, focusing largely on the 10 H1N1 2009 pandemic strains that have turned up there since last fall. The researchers found that while all of the H1N1/2009 isolates shared genes from the same lineage, those collected earlier were not genetically identical to those found more recently.

"[V]iruses from different sampling dates were genetically distinct from each other and also from H1N1/2009-like swine viruses isolated in other countries," Yi Guan, a microbiology and infectious disease researcher affiliated with the University of Hong Kong and Shantou University Medical College, and co-authors wrote, "indicating multiple independent introductions of these viruses from humans to swine."

The team also found that one of the isolates collected this year contained a gene from H1N1/2009 in combination with genes from other H1N1 and H1N2 viruses.

Consequently, they are urging increased surveillance of pig populations for tracking the viral reassortment, which they say could potentially spawn new forms of human flu.

"The 2009 pandemic, although mild and apparently contained at present, could undergo further reassortment in swine and gain virulence," the researchers wrote. "It is therefore important that surveillance in swine is greatly heightened and that all eight gene segments are genetically characterized so that such reassortment events are rapidly identified."

Past analyses of the 2009 pandemic H1N1 flu virus suggests it originated from the combination of flu strains from swine, bird, and human flu viruses — and likely circulated in pigs for several months before the first human infections were reported.

For the current study, researchers focused on 32 influenza strains isolated from pigs at a Hong Kong slaughterhouse. These included 10 H1N1/2009 strains, five European avian-like H1N1 strains, a single triple-reassorted H1N2 virus, and 16 other reassorted viruses.

Consistent with H1N1/2009 emergence outside of China, the team did not find any pandemic H1N1 flu in the pigs until they looked at samples collected last October — roughly four months after the World Health Organization declared an H1N1 pandemic.

But their phylogenetic analyses did turn up at least one reassorted virus containing a combination of H1N1/2009 genes not identified in the past.

When they investigated this isolate further, looking at the source of all eight genes, the researchers found that the virus contained one gene from H1N1/2009, one from a European avian-like H1N1 strain, and six more genes resembling those in triple-reassorted H1N2 strains.

Based on these findings, those involved in the study say additional research is needed to understand the genetic underpinnings of existing flu strains. And, they added, the presence of the reassorted strain in Chinese pigs — combined with past reports of bird and mammalian flu strains circulating in China — should spur increased flu surveillance efforts.