Dissemination, divergence and establishment of H7N9 influenza viruses in China

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Abstract

Since 2013 the occurrence of human infections by a novel avian H7N9 influenza virus in China has demonstrated the continuing threat posed by zoonotic pathogens1,2. Although the first outbreak wave that was centred on eastern China was seemingly averted, human infections recurred in October 2013 (refs 3, 4, 5, 6, 7). It is unclear how the H7N9 virus re-emerged and how it will develop further; potentially it may become a long-term threat to public health. Here we show that H7N9 viruses have spread from eastern to southern China and become persistent in chickens, which has led to the establishment of multiple regionally distinct lineages with different reassortant genotypes. 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. This rapid expansion of the geographical distribution and genetic diversity of the H7N9 viruses poses a direct challenge to current disease control systems. Our results also suggest that H7N9 viruses have become enzootic in China and may spread beyond the region, following the pattern previously observed with H5N1 and H9N2 influenza viruses8,9.

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Figure 1: Map showing the sampling sites in China and H7N9 isolation rates in market chickens.
Figure 2: Evolution of H7N9 influenza viruses from wave 1 to wave 2.

Accession codes

Primary accessions

GenBank/EMBL/DDBJ

Data deposits

All sequences generated by this study have been deposited in GenBank/EMBL/DDBJ under accession numbers KP413163KP418563. Detailed phylogenetic inferences are available from http://dx.doi.org/10.5061/dryad.5q7kf.

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Acknowledgements

We thank C. L. Cheung, H. Y. Liang and G. C. Yu for their assistance in data processing; Z. H. Ou, Z. Y. Jin, T. Y. Leung, K. K. Chan, Y. R. Qiu, J. Z. Xie, N. Qi, J. Zhou, P. Y. Huang and all staff members at the Joint Influenza Research Centre (SUMC/HKU) for technical support, the four collaborative hospitals in Shenzhen for human sample collection, and P. Lemey for his advice on phylogeographic analysis. This study was supported by the Shenzhen Peacock Plan High-End Talents Program (KQTD201203), the Health and Medical Research Fund of the Hong Kong Government (RRG-10 and RRG-14), the University Grants Committee of Hong Kong (Area of Excellence Scheme grant AoE/M-12/06), the National Institute of Allergy and Infectious Diseases (contract HHSN272201400006C), and the Li Ka Shing Foundation. E.C.H. is supported by an NHMRC Australia Fellowship (AF30).

Author information

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Authors

Contributions

Y.G., H.Z. and T.T.-Y.L. conceived the study; B.Z., J.W., Y.S., X.C., W.H., L.D., P.C., J.J. conducted surveillance; Y.C., C.M., Yu Z., L.L. performed sequencing; H.Z, T.T.-Y.L., E.C.H., D.K.S., Y.G. performed the analysis and wrote the manuscript; Y.C., Ya.Z., L.L.M.P., R.J.W., G.M.L., J.S.M.P. participated in the discussion and interpretation of findings. T.T.-Y.L., B.Z., J.W., Y.C., Y.S., X.C. contributed equally to this work.

Corresponding authors

Correspondence to Yi Guan or Huachen Zhu.

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The authors declare no competing financial interests.

Extended data figures and tables

Extended Data Figure 1 Condensed phylogenies for the internal genes.

a, PB2 (n = 1681), b, PB1 (n = 1620), c, PA (n = 1682), d, NP (n = 1733), e, M (n = 1696) and f, NS (n = 1707) genes. The H9N2 ZJ-HJ/07 lineage from the large phylogenies (available from http://dx.doi.org/10.5061/dryad.5q7kf) is annotated and shown. Red branches indicate the H7N9 viruses, with the remaining branches representing H9N2 (the majority) or other viruses. Mutations leading to changes in amino acid usage from wave 1 to wave 2 (Extended Data Table 4) are shown in blue. Dashed brackets indicate the major clades 1–3, and vertical lines indicate their sub-clades. The background shading indicates the provinces from which the viruses were isolated (see inset map). Human samples are indicated as grey circles.

Extended Data Figure 2 Prevalence of H7N9 reassortant variants.

a, Time-line of reassortant variants of H7N9 viruses (n = 505) and human infections. Clade 1.1 was the predominant sub-clade in the first wave (see Fig. 2 and Extended Data Fig. 1). Symbols represent H7N9 viruses and their time of isolation, and the number of non-clade 1.1 internal gene segments (that is, those falling outside clade1.1 as defined in the phylogenies; Extended Data Fig. 1) in the virus (y-axis). The colours indicate the provinces of isolation of the viruses. Viruses from HA clades W1, W2-A, W2-B and W2-C are indicated by triangles, circles, squares and diamonds, respectively. Solid and empty symbols represent avian and human viruses. The underlying blocks give the number of human infection cases per week (WHO data7, as of July 2014). b, The percentage of wave 1 and wave 2 viruses having different numbers of non-clade 1.1 internal genes (y-axis) in their genomes.

Extended Data Table 1 Surveillance in apparently healthy chickens at live poultry markets
Extended Data Table 2 Surveillance in apparently healthy ducks at live poultry markets
Extended Data Table 3 Genotypes of H7N9 viruses in this study
Extended Data Table 4 Amino acid changes from the first to second waves
Extended Data Table 5 Amino acid changes from avian to human H7N9 viruses

Supplementary information

Supplementary Information

This file contains a Supplementary Discussion with additional references and Supplementary Data (see separate excel file for data in table format). (PDF 77 kb)

Supplementary Data

This file shows the haemagglutinin inhibition (HI) assays of H7N9 viruses in table format. (XLS 44 kb)

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Lam, T., Zhou, B., Wang, J. et al. Dissemination, divergence and establishment of H7N9 influenza viruses in China. Nature 522, 102–105 (2015). https://doi.org/10.1038/nature14348

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