The genesis and source of the H7N9 influenza viruses causing human infections in China

Abstract

A novel H7N9 influenza A virus first detected in March 2013 has since caused more than 130 human infections in China, resulting in 40 deaths. Preliminary analyses suggest that the virus is a reassortant of H7, N9 and H9N2 avian influenza viruses, and carries some amino acids associated with mammalian receptor binding, raising concerns of a new pandemic. However, neither the source populations of the H7N9 outbreak lineage nor the conditions for its genesis are fully known. Using a combination of active surveillance, screening of virus archives, and evolutionary analyses, here we show that H7 viruses probably transferred from domestic duck to chicken populations in China on at least two independent occasions. We show that the H7 viruses subsequently reassorted with enzootic H9N2 viruses to generate the H7N9 outbreak lineage, and a related previously unrecognized H7N7 lineage. The H7N9 outbreak lineage has spread over a large geographic region and is prevalent in chickens at live poultry markets, which are thought to be the immediate source of human infections. Whether the H7N9 outbreak lineage has, or will, become enzootic in China and neighbouring regions requires further investigation. The discovery here of a related H7N7 influenza virus in chickens that has the ability to infect mammals experimentally, suggests that H7 viruses may pose threats beyond the current outbreak. The continuing prevalence of H7 viruses in poultry could lead to the generation of highly pathogenic variants and further sporadic human infections, with a continued risk of the virus acquiring human-to-human transmissibility.

Figure 1. Phylogenies of haemagglutinin, neuraminidase and PB2 genes

Phylogenies of a, H7 haemagglutinin (n=46); b, N9 neuraminidase (n=34); c, N7 neuraminidase (n=25); d, PB2 (n=93) genes. Sequences reported in this study have their taxa names shown in bold. Genotypes of the influenza viruses are shown on the right (a, b, c) as eight coloured blocks representing each gene segment (from left to right: PB2, PB1, PA, HA, NP, NA, M, and NS; absent if the sequence is unavailable) with the colour indicating the subtype (for HA, NA) or lineage (internal genes; indicated by the solid vertical line in panel d) of that segment. Bootstrap support values (%) from 1,000 pseudo-replicates are shown for selected lineages. Support values for lineages ‘a’ – ‘d’ were all 100%. The scale bar to the left of each tree represents 0.01 substitutions/site. The ‘*’ in panel b denotes N9 sub-lineages linking the viruses of domestic ducks and wild birds. Host species are: Ck (chicken), SCk (silkie chicken), Dk (duck), SbD (spot-billed duck), Md (mallard), Gs (goose), Nsh (Northern shoveler), Wb (wild bird), Wwf (wild waterfowl), Te (common teal), Pg (pigeon), Pt (pintail). Geographic locations: SD (Shandong), ZJ (Zhejiang), JX (Jiangxi), GZ (Guizhou), GD (Guangdong), FJ (Fujian), HK (Hong Kong), WZ (Wenzhou), RZ (Rizhao) and SH (Shanghai). Viruses from different hosts are indicated by: humans, circles; chickens, blue names; domestic ducks or geese, green names.

Figure 2. Evolutionary pathways of the H7N9 and H7N7 viruses

Virus particles are represented by coloured ovals containing horizontal bars that represent the eight gene segments (from top to bottom: PB2, PB1, PA, HA, NP, NA, M, and NS). Segments in descendent viruses are coloured according to their corresponding source viruses (top row) to illustrate gene ancestry through reassortment events. Source viruses for a reassortment are adjacent to arrow tails; arrowheads point to the resulting reassortants. Bars coloured cyan indicate gene segments of the ZJ-5 sub-lineage of wild bird viruses. A broken bar in segment 6 (NA) indicates a stalk region deletion. The virus indicated by a broken oval represents a hypothetical reassortant.