Genesis and Spread of Newly Emerged Highly Pathogenic H7N9 Avian Viruses in Mainland China

Abstract

The novel low-pathogenic avian influenza A H7N9 viruses (LPAI H7N9 viruses) have been a threat to public health since their emergence in 2013 because of the high rates of mortality and morbidity that they cause. Recently, highly pathogenic variants of these avian influenza A H7N9 viruses (HPAI H7N9 viruses) have emerged and caused human infections and outbreaks among poultry in mainland China. However, it is still unclear how the HPAI H7N9 virus was generated and how it evolved and spread in China. Here, we show that the ancestor virus of the HPAI H7N9 viruses originated in the Yangtze River Delta region and spread southward to the Pearl River Delta region, possibly through live poultry trade. After introduction into the Pearl River Delta region, the origin LPAI H7N9 virus acquired four amino acid insertions in the hemagglutinin (HA) protein cleavage site and mutated into the HPAI H7N9 virus in late May 2016. Afterward, the HPAI H7N9 viruses further reassorted with LPAI H7N9 or H9N2 viruses locally and generated multiple different genotypes. As of 14 July 2017, the HPAI H7N9 viruses had spread from Guangdong Province to at least 12 other provinces. The rapid geographical expansion and genetic evolution of the HPAI H7N9 viruses pose a great challenge not only to public health but also to poultry production. Effective control measures, including enhanced surveillance, are therefore urgently needed.IMPORTANCE The LPAI H7N9 virus has caused five outbreak waves in humans and was recently reported to have mutated into highly pathogenic variants. It is unknown how the HPAI H7N9 virus originated, evolved, and disseminated in China. In this study, we comprehensively analyzed the sequences of HPAI H7N9 viruses from 28 human and 21 environmental samples covering eight provinces in China that were taken from November 2016 to June 2017. The results show that the ancestor virus of the HPAI H7N9 viruses originated in the Yangtze River Delta region. However, the insertion of four amino acids into the HA protein cleavage site of an LPAI H7N9 virus occurred in late May 2016 in the Pearl River Delta region. The mutated HPAI H7N9 virus further reassorted with LPAI H7N9 or H9N2 viruses that were cocirculating in poultry. Considering the rapid geographical expansion of the HPAI H7N9 viruses, effective control measures are urgently needed.

Keywords: genesis; geographic dissemination; highly pathogenic H7N9 avian viruses; origins.

FIG 1

Geographic distribution and prevalence of HPAI H7N9 viruses. (A) Map showing the HPAI H7N9 virus-positive regions in China. Both orange and yellow indicate regions where HPAI H7N9 viruses were detected; provinces with available HPAI H7N9 sequences are highlighted in orange, while those with unavailable sequences are shown in yellow. Provinces marked with a human figure are the regions where human cases were reported. (B) Weekly virus numbers (indicated on the y axis) and geographic information for the HPAI H7N9 viruses isolated from humans. The different colors indicate the isolation locations. The designations on the x axis indicate the year and the week (W) of the year.

FIG 2

Genomic divergence and evolutionary analysis of H7N9 avian influenza A virus H7 gene sequences. (A) A Bayesian maximum clade credibility (MCC) phylogeny of HA genes of influenza A H7N9 viruses. The phylogenetic clades that include avian influenza A H7N9 viruses were obtained from the dated phylogeny of HA gene segments constructed by a molecular phylogenetic analysis and were further aligned onto the same time scale. The branches in black and red represent LPAI and HPAI H7N9 viruses, respectively. (B) Representative clades in the gray box in panel A. The branches in black and red represent LPAI and HPAI H7N9 viruses, respectively. All viruses, including the LPAI and HPAI H7N9 viruses, which were isolated in Guangdong Province are highlighted in blue. The blue bar shown in the tree indicates the 95% highest posterior density of tMRCA of HPAI H7N9 viruses. LPAI H7N9 virus strains A/Environment/Guangdong/15120/2016(H7N9) and A/Environment/Guangdong/15123/2016(H7N9), which were likely the ancestor of HPAI H7N9 viruses, are underlined. The viruses isolated and sequenced in this study are highlighted with a solid circle at the beginning of the virus name.

FIG 3

Nucleotide sequence similarity for each gene segment among all HPAI H7N9 virus sequences. The bottoms and tops of the boxes are the first and third quartiles, respectively, and the band inside the box is the median. The ends of the whiskers represent the minimum and maximum of all of the data.

FIG 4

Genotypes of HPAI H7N9 avian influenza viruses. The six internal gene segments are indicated at the top. The colors of the bars represent the groups in the trees in Fig. S2 in the supplemental material.

FIG 5

Geographic dissemination (A) and evolutionary pathways (B) of the HPAI H7N9 viruses. (A) The two outbreak sources of the Yangtze River Delta region and Pearl River Delta region are shown in dashed red triangles. The geographic spread of the viruses is indicated by arrows. The dashed arrow indicates the migrated H7N9 infection case. (B) The formation and dynamic reassortments of the HPAI H7N9 influenza viruses are illustrated with thin arrows in the gray rectangle. Dashed gray or red circles represent the LPAI or HPAI H7N9 viruses, respectively. The locations of human infections with HPAI H7N9 viruses are indicated with cartoon figures. Thick arrows point to the geographic spread of H7N9 viruses.