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Genome Sequences Unravel Bird Flu Reemergence Routes in China

NEW YORK (GenomeWeb) – A team from China, the US, and Australia used genome sequencing to understand the re-emergence of human infections with avian influenza A virus H7N9 in China from the fall of 2013 to the following summer.

As they reported online today in Nature, the researchers did genome sequencing on hundreds of viruses detected in live poultry markets between October 2013 and July 2014, along with related influenza viruses found in poultry and 19 H7N9 isolates from infected humans at hospitals in Shenzhen.

Based on phylogenetic relationships between the influenza viruses, the group concluded that the so-called "second wave" of H7N9 involved viruses related to those in the first wave, which moved from eastern China to southern parts of the country multiple times — most likely via poultry — to produce reassorted viruses that vary by region.

"Repeated introductions of viruses from Zhejiang to other provinces and the presence of H7N9 viruses at live poultry markets have fuelled the recurrence of human infections," senior authors Yi Guan and Huachen Zhu, both affiliated with the State Key Laboratory of Emerging Infectious Diseases, Shantou University Medical College, and the University of Hong Kong, and their colleagues wrote.

The first wave of human infections with H7N9 was documented in the spring of 2013, the team noted, and was localized mainly in the eastern part of China.

In a 2013 study published in Science, researchers from the Chinese Academy of Agricultural Science and Gansu Agricultural University relied on genome sequences to investigate the transmissibility of H7N9 viruses circulating in wild birds and poultry markets during that first round of human infections.

Though the initial outbreak was staunched within a few months, a new round of infections starting in October 2013 claimed more than 100 lives and infected at least 318 individuals — many of them in parts of southern China that were largely spared during the first infection wave.

As part of their influenza surveillance at live poultry markets in more than a dozen Chinese cities in five provinces, the researchers tested fecal samples, orophoaryngeal swabs, and cloacal swabs from seemingly healthy birds.

Ducks from the markets did not test positive for the virus, the team noted, and H7N9 turned up only rarely in the chicken cloacal swabs. But the virus did show up in nearly 500 oropharyngeal swabs from chickens, including birds from markets in cities where human H7N9 infection cases were detected.

The researchers then used the Roche 454 GS Junior platform to do genome sequencing on 438 H7N9 poultry isolates and 263 other influenza viruses found in poultry, generating enough sequence data to cover each flu virus genome at an average depth of around 150-fold. They also sequenced H7N9 isolates from 19 human cases treated at hospitals in Shenzhen.

By comparing the resulting genomes to one another and to existing influenza A sequences in GenBank and the Global Initiative on Sharing Influenza Data (GISAID) databases, the team found that H7N9 isolates in the second wave of human infections were descended from the virus behind the first human H7N9 infections.

But the re-emerged viruses showed divergence in H7 hemagglutinin gene sequences, producing three clades with differing distributions that were used to retrace H7N9 spread — starting near the city of Zhejiang or the Yangtse River delta and taking on new rearrangements as it moved to other parts of China.