Lisa SchnirringStaff Writer

Apr 12, 2013 (CIDRAP News) A new analysis of H7N9 genetic sequences from the first Chinese patients infected with the virus and from poultry markets found more signals that the virus can attach and replicate efficiently in the airways of humans and other mammals, raising concerns about the virus's pandemic potential.

The new findings, published late yesterday in Eurosurveillance, are the first detailed comparison of both the human and market sequences. Results are similar to the genetic details of samples from the first three cases reported by Chinese scientists yesterday in the New England Journal of Medicine.

The new results also affirm early observations from some experts that the novel virus has adapted to infect mammals, yielding more information that health officials need to gauge the pandemic threat from the new virus.

The research team from Japan includes Yoshihiro Kawaoka, DVM, PhD, who heads a group at the University of Wisconsin that has done extensive genetic studies on the H5N1 virus, and Masato Tashiro, MD, PhD, director of the World Health Organization Collaborating Center for Reference and Research on Influenza at Japan's National Institute of Infectious Diseases in Tokyo.

Their look at sequences from influenza databases included human samples from the first two patients from Shanghai, as well as from a woman from Anhui province and a man from Hangzhou province. All of the patients died.

Samples from a market in Shanghai include isolates from a pigeon, a chicken, and an environmental sample.

Phylogenetic analysis of the four human samples suggest they have a common ancestor, with the hemagglutinin (HA) gene part of the Eurasian avian influenza lineage and closely resembling HA genes of low-pathogenic H7N3 viruses detected in 2011 in Zhejiang province, south of Shanghai. The group reported that the neuraminidase (NA) gene closely resembles a low-pathogenic H11N9 virus found in the Czech Republic in 2010.

Internal genes of the H7N9 virus were closely related to H9N2 avian flu viruses that recently circulated in poultry in Shanghai, as well as Zhejiang and Jiangsu provinces, according to the report. Researchers said the findings strongly suggest that the new viruses are reassortants that got their HA and NA genes (the H7 and N9) from avian influenza viruses and the rest of their genes from recent H9N2 poultry viruses.

When they compared the nucleotides from the four human specimens, they found that one of the Shanghai samples and the ones from Anhui and Hangzhou were 99% similar, despite the fact that they came from cities that were several hundred kilometers apart. They found differences between the two Shanghai samples and noted other patterns with the human and market samples that suggest five of the viruses came from a closely related infection source, while one of the Shanghai samples and the one from the pigeon came from different sources.

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H7N9 genetic analysis raises concern over pandemic potential

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