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Team Sequences Poultry Market Flu Virus Genomes in Effort to Understand Human H7N9 Outbreak

NEW YORK (GenomeWeb News) – A team from the Chinese Academy of Agricultural Sciences and Gansu Agricultural University used genome sequencing as part of its effort to understand the traits and transmissibility of influenza A H7N9 viruses that are behind a spate of human infections in China.

As they reported today in the early, online edition of Science, the researchers sequenced the genomes of more than three-dozen H7N9 isolates collected from birds and poultry market sites. By comparing those sequences with the genomes of five H7N9 viruses involved in human infections, they found hints about the small genetic changes needed to make the H7N9 more virulent and transmissible in mammals.

Together with results from infection studies on chicken, duck, mouse, and ferret models, the genetic profiles generated for the H7N9 viruses hint that fairly small genetic changes could potentially lead to a version of the virus capable of human-to-human transmission.

"Currently, implementation of compulsory control measures in H7N9 virus-positive live poultry markets is preventing further human infections," senior author Hualan Chen, a veterinary researcher affiliated with the Chinese Academy of Agricultural Sciences and Gansu Agricultural University, and her colleagues wrote. "[H]owever, the elimination of the H7N9 virus from nature is a huge and long-term challenge."

"Its non-pathogenic nature in poultry enables the avian H7N9 virus to replicate silently in avian species and to transmit to humans," they continued. "Its replication in humans will provide further opportunities for the virus to acquire more mutations and become more virulent and transmissible in the human population."

More than 130 individuals in China have come down with flu cases involving the avian influenza A virus H7N9 over the past few months, Chen and her co-authors noted, and the virus has been linked to 37 deaths in that country since mid-February.

That rash of flu infections has prompted closure of poultry-markets where the H7N9 virus was detected and spurred interest from several research groups keen to understand the strain's origins, pathogenicity, and transmissibility.

For their current analysis, Chinese researchers brought together more than 10,700 H7N9 samples from wild birds and poultry at farms, slaughterhouses, or markets, along with samples from related environments.

After inoculation in chicken eggs, they were left with a couple hundred flu virus isolates. Of those, 52 belonged to the H7N9 subtype and all but one stemmed from poultry market sources.

To get at the genetics behind the newly emerged flu virus subtype, the team sequenced all eight genes that make up the influenza A genome in 37 of the new H7N9 isolates.

When they compared the genomes to one another and to sequences from five human viruses — including an isolate called A/Anhui/1/2013 from the current outbreak in China — the researchers determined that much of the genome was similar across the isolates.

For instance, within hemagglutinin and neuraminidase genes coding for surface glycoproteins used to classify influenza A subtypes, they saw between 99 and 100 percent sequence homology in the set of isolates tested.

Other genes housed a bit more genetic diversity, the study's authors noted, and half a dozen genes showed signs of mixing with sequences from influenza A viruses in the H9N2 subtype.

Exposure to H7N9 viruses initially isolated from birds did not lead to discernible signs of disease in mice — nor did they produce symptoms in their typical avian hosts such as chickens and ducks. On the other hand, viruses involved in human H7N9 flu cases in China did appear capable of causing disease in mice: animals infected with those viruses dropped as much as 30 percent of their body weight.

Moreover, at least one of the human H7N9 isolates was readily passed from one ferret to another via respiratory droplets in the team's transmissibility experiments.

From their genome sequencing data, investigators speculated that the increased virulence and transmissibility of the human H7N9 isolates may stem from subtle genetic changes that alter one or two amino acids encoded by H7N9's basic polymerase 2 gene, for instance, and/or shift hemagglutinin interactions with host cell receptors.

"[I]t is difficult to conclude which amino acid substitution alone makes the virus highly transmissible," the study's authors concluded. But, they added, results from their analysis indicated that "only a few amino acid changes would be needed to make the avian H7N9 viruses highly transmissible in mammals."