Origins and evolutionary genomics of the novel 2013 avian-origin H7N9 influenza A virus in China: Early findings

In March and early April 2013, a new Avian-Origin Influenza A (H7N9) Virus (A-OIV) emerged in the eastern China. This virus has caused global concern as a potential pandemic threat. Here we use evolutionary analysis to reconstruct the origins and early development of the A-OIV viruses. We found that A-OIV was derived from a reassortment of three avian flu virus strains, and substantial mutations have been detected. Our results highlight the need for systematic surveillance of influenza in avian, and provide evidence that the mixing of new genetic elements in avian can result in the emergence of viruses with pandemic potential in humans. On April 1, 2013, the World Health Organization (WHO) first reported 3 human infections with the A-OIV in China. As of April 9, 2013, 24 laboratory confirmed infection cases have been reported in the eastern China. Most reported cases have severe respiratory illness and seven died since March[1]. No person-to-person transmission of the A-OIV has been found at this time, and the reported cases are not linked to each other. However, there are uncertainties about all aspects of the novel virus, including the transmissibility, virulence and origins, therefore, results in uncertainty in determining the pandemic potential of the virus, and to what extent pubic health organization should react, such as whether recommendations to stay at home or close school are need. Here we report our preliminary findings of the origins and genomic evolution of this virus. This study could aid policy decisions and developing proper treatment. We achieved 6 newly sequenced 2013 A-OIV genomes which have been deposited to the database GISAID (www.gisaid.org). Among them, 4 isolates are A-OIV in human and 2 isolates are A-OIV in avian. Using comprehensive phylogenetic analyses [2-4], we have estimated a reconstruction of the complex reassortment history of the novel virus, summarized in Fig. 1. The A-OIV virus contains eight genes. The haemagglutinin gene (HA) comes from H7 family virus, the neuraminidase gene (NA) comes from N9 family virus, and the six internal genes (PA, NS, PB2, PB1, NP, M) come from H9N2. The HA gene segment of A-OIV is in the H7 family avian influenza lineage (Fig. 2). The HA gene segment most closely related to the A-OIV is from a H7N3 strain (A/duck/Zhejiang/11/2011). The NA gene segment of A-OIV is in the clade of N9 family avian influenza. The two strains that are closely related to NA gene segment A-OIV are A/mallard/Czech Republic/13438-29K/2010(H11N9) and a H7N9 strain found in Korea wild duck. We found that the six internal gene segments are highly conserved with the H9N2 (Figs. S6-S14). Phylogenetic analyses indicate that the six internal gene segments of A-OIV are derived from H9N2 Avian influenza with sequence identity >98%, in particular, the A/chicken/Zhejiang/Q1D4/2011(H9N2) strain, which was found in Zhejiang province of China, the same location as A-OIV infection cases in human. The H9N2 flu strains have been circulating in the East Asia for many years. We also observed that the sequence of HA and NA protein of A-OIV in human are nearly identical to that of A-OIV in avian, which suggests that the same A-OIV may have the ability to infect both human and avian. Classical H7N9 viruses have been reported as early as 1999. We found that A-OIV and classic H7N9 share less similarity compared to other strains such as H7N3 and H7N1. Therefore, the A-OIV is not likely mutated from the classical H7N9. Together, our results show that the A-OIV is a new virus that stems from a reassortment of three avian influenza virus strains and the reassortment events likely happened in the eastern China. Although the A-OIV has been reported in just one week, we already observed mutations in their genome. Within the 6 newly sequenced genomes, the HA protein of A/Shanghai/1/2013 strains have 8 amino acid differences compared to 5 other strains. This indicates that the A-OIV has significant sequence diversity, which increases our concern that genetic mutation may lead to the change of transmissibility and virulence. There has been persisting concern that avian flu may become the next pandemic among international community. H5N1 is one such avian flu that has been extensively studied and monitored for many years. Most of the A-OIV infection cases experienced close contact with poultries before infection, and the cases appeared geographically widely in three provinces of the eastern China at the same time. The virus seems not to cause diseases in poultries and could be spreading out in poultry undetected — and thus could create a reservoir of infection that would lead to frequent sporadic human infections without warning. Yet despite widespread influenza surveillance in humans, the lack of systematic avian surveillance allowed for the undetected persistence and evolution of this potentially pandemic strain for many years. Our results highlight the need for systematic surveillance of influenza in avian, and provide evidence that the mixing of new genetic elements in avian can result in the emergence of viruses with pandemic potential in humans.