Monday, August 24, 2015

EID Journal: H7N9’s Evolution During China’s Third Wave – Guangdong Province


3 waves of H7N9  -  Credit WHO




We are only a few months away from China’s expected return of H7N9, an avian influenza virus that first appeared during the winter and spring of 2013, and has returned each winter since.  While of low pathogenicity to birds, this virus can cause significant illness and even death in humans, and has been responsible for more than 600 human infections during its first couple of years.


The actual number of human infections is unknown, but believed much higher, as only those sick enough to end up hospitalized are usually tested and identified. 


Increasingly erratic surveillance and reporting – particularly during the most recent third wave (see H7N9: No News Is . . . . Curious) – has also complicated our reading of the impact of the virus.  Despite these gaps in surveillance, one bright spot has been the number and quality of papers published by local researchers on the evolution and epidemiology of the virus.

The constant in these studies has been the continual evolution, and increasing diversity, of the H7N9 viruses circulating across China.


While we talk about H7N9 as if it were a single virus – in truth, that designation represents a growing collection of viruses of the same subtype (the same HA and NA genes) which are constantly evolving and reassorting with other viruses.


Last March, in Nature: Dissemination, Divergence & Establishment of H7N9 In China, we saw a study that found that the family of  H7N9 viruses continues to expand and by the summer of 2014 included at least 48 genotypes, spread across three major clades.


Not only do these viruses evolve naturally on their own (antigenic drift, host adaptations, etc.), they also continue to reassort with other viruses, a process which can give rise to new subtypes of influenza. As the number of potential reassortment partners increase  (H7N9, H5N1, H5N6, H5N8, H10N8, etc.), so do the opportunity for new viruses to emerge.

Recent examples include the emergence of novel North American H5N1 and H5N2 viruses last winter – both the product of reassortment – and just two months ago we learned of a new H5N9 reassortant discovered in China (see J. Virol: Emergence Of AN HPAI H5N9 Virus In China).

Since the virulence or behavior of a given subtype can vary between variants or clades (see Differences In Virulence Between Closely Related H5N1 Strains), it is important to closely follow the evolution of these viruses. 


To that end we’ve an EID Journal Dispatch that looks at a small geographic subset (Guangdong Province) of H7N9 viruses collected during the third wave of H7N9 in China, and confirms the ongoing evolution of the H7N9 subtype.


Volume 21, Number 9—September 2015

Third Wave of Influenza A(H7N9) Virus from Poultry, Guangdong Province, China, 2014–2015

Shumin Xie1, Weixin Jia1, Yicun Lin, Kaixiang Xing, Xingxing Ren, Wenbao Qi, and Ming LiaoComments to Author

Author affiliations: South China Agricultural University, Guangzhou, China



Fourteen influenza A(H7N9) viruses were isolated from poultry or the environment in live poultry markets in Guangdong Province, China during 2014−2015. Phylogenetic analysis showed that all viruses were descended from viruses of the second wave of influenza A(H7N9) virus infections during 2013. These viruses can be divided into 2 branches.


A new influenza A(H7/N9) virus was detected in China on February 19, 2013, and has caused worldwide concern (1). Since 2013, the outbreak of this virus in humans has occurred in 3 waves. The third wave began when 2 additional laboratory-confirmed cases of human infection with this virus were detected in Xinjiang Province, China, on September 2, 2014. This wave has continued with increasing numbers of human cases during 2015, including infections in Fujian, Hong Kong, Guizhou, Jiangsu, and Guangdong Provinces. The largest number of human cases has been reported in southern China; >50 infected patients were detected in Guangdong Province January and February (2).

The virus has been identified as a novel triple reassortant of avian influenza A(H7N3), A(H7N9), and A(H9N2) viruses and has low pathogenicity in poultry (35). Influenza A(H7N9) virus is now endemic to China, and its continuing reassortment in poultry makes it probable that humans will continue to be infected sporadically.

Because influenza A(H7N9) virus−contaminated live poultry markets (LPMs) are regarded as major sources of human infections with this virus (68), we implemented LPM sampling programs in Guangdong Province and analyzed the evolution of the virus during the third wave. In this study, we also collected samples from chicken farms and integrated epidemiologic and sequence data to infer the genetic diversity and evolution of influenza A(H7N9) viruses found in poultry in Guangdong Province, China.



Fourteen influenza A(H7N9) viruses were isolated from poultry or environment in LPMs in Guangdong Province, China, during 2014−2015. Phylogenetic analyses of HA and NA genes confirmed that all third-wave influenza A(H7N9) viruses in Guangdong Province were descended from viruses of the second wave. Two H7N9 lineages from poultry co-circulated in Guangdong Province during the third wave, and both are closely related to H7N9 strains isolated from humans in local or adjacent regions. These data suggest that the dominant H7N9 strains have a dynamic evolutionary process for adapting to the local environment. Their internal genes show more regional characteristics, which might be related to transportation of live birds across provinces or to migratory birds.

The results of our study are limited by the number of samples obtained and locations of sampling. However, our findings serve as a warning to public health officials to be aware of the risk of poultry farms being infected with influenza A(H7N9) virus.

Ms. Xie is a research assistant at South China Agricultural University, Guangzhou, China. Her research interest is the epidemiology of avian influenza.


Although H7N9 has been thus far confined  to China, it expanded its range considerably during its third wave, showing up last fall in the far western province of Xinjiang.  As with H5N1 and H5N8 before it, there is a pretty good chance that H7N9 will eventually show up outside of the Chinese mainland.

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