Epidemiology, ecology and gene pool of influenza A virus in Egypt: will Egypt be the epicentre of the next influenza pandemic?

Abstract

Outside Asia, Egypt is considered to be an influenza H5N1 epicentre and presents a far greater pandemic risk than other countries. The long-term endemicity of H5N1 and the recent emergence of H9N2 in poultry call attention to the need for unravelling the epidemiology, ecology and highly diverse gene pool of influenza A virus (IAV) in Egypt which is the aim of this review. Isolation of a considerable number of IAV subtypes from several avian and mammalian hosts was described. Co-infections of poultry with H5N1 and H9N2 and subclinical infections of pigs and humans with H1N1 and H5N1 may raise the potential for the reassortment of these viruses. Moreover, the adjustment of IAV genomes, particularly H5N1, to optimize their evolution toward efficient transmission in human is progressing in Egypt. Understanding the present situation of influenza viruses in Egypt will help in the control of the disease and can potentially prevent a possible pandemic.

Keywords: ELISA, Enzyme linked immunosorbent assay; Egypt; H5N1; H9N2; HA, hemagglutinin; HI, hemagglutination inhibition test; HPAIV, highly pathogenic avian influenza viruses; IAV, influenza A viruses; LBM, live bird markets; LPAIV, low pathogenic avian influenza viruses; M, matrix; NA, neuraminidase; NAMRU-3, Naval Medical Research Unit–3; NLQP, National Laboratory for Veterinary Quality Control on Poultry Production; NS, non-structural; PA, acidic polymerase; PB, basic polymerase; WHO, World Health Organization; epidemiology; influenza; pandemic; reassortment; virulence.

Figure 1.

Sites of interfaces of H5N1 virus of different hosts in Egypt. From the currently available data, backyard birds are an important source for the infection of birds in the commercial sector and LBM as well as for humans. Over 90% of infected humans probably acquired the infection through direct contact with backyard birds, whereas only 2 and 3 human-infections occurred due to contact with birds in the LBM or commercial sector, respectively. The confirmed transmission routes between different sectors and species are shown as straight lines while possible, but not yet confirmed-sources of infection are shown as dashed arrows. The virus was isolated from donkeys, feral and wild birds and the viral RNA was detected in fish. Only anti-H5 antibodies were detected in pigs, cats and dogs but no virus isolation or detection trials were reported.

Figure 2.

Scenarios for the potential reassortment of influenza A virus in animals and humans in Egypt. There are many hosts to be considered as “mixing vessels” for the potential reassortment of IAV in Egypt. The arrows refer to the possible co-infection of susceptible host(s) with different IAV subtypes in Egypt. Waterfowls, vaccinated chickens and quails are frequently infected without showing clinical signs where H5N1, H9N2 and/or H7Nx viruses may reassort. Infected donkeys and horses with H5N1 and equine H3N8 or pigs co-infected with human IAV subtypes, H5N1 and/or H9N2 viruses are possible sources for reassortment of IAV in Egypt. Reassortants can also emerge after infection with human (H1N1, H3N2 or H1N2) and avian (H5N1 and/or H9N2) IAV's subtypes in humans.