A brief summary of the epidemiology and genetic relatedness of avian influenza H9N2 virus in birds and mammals in the Middle East and North Africa

Abstract

H9N2 is the most widespread avian influenza virus subtype in poultry worldwide. It infects a broad spectrum of host species including birds and mammals. Infections in poultry and humans vary from silent to fatal. Importantly, all AIV, which are fatal in humans (e.g. H5N1, H7N9) acquired their 'internal' gene segments from H9N2 viruses. Although H9N2 is endemic in the Middle East (ME) and North Africa since the late 1990s, little is known about its epidemiology and genetics on a regional level. In this review, we summarised the epidemiological situation of H9N2 in poultry and mammals in Iran, Iraq, Kuwait, Qatar, United Arab Emirates, Oman, Bahrain, Yemen, Saudi Arabia, Jordan, Palestine, Israel, Syria, Lebanon, Turkey, Egypt, Sudan, Libya, Tunisia, Algeria and Morocco. The virus has been isolated from humans in Egypt and serosurveys indicated widespread infection particularly among poultry workers and pigs in some countries. Some isolates replicated well in experimentally inoculated dogs, mice, hamsters and ferrets. Insufficient protection of immunised poultry was frequently reported most likely due to concurrent viral or bacterial infections and antigenic drift of the field viruses from outdated vaccine strains. Genetic analysis indicated several distinct phylogroups including a panzootic genotype in the Asian and African parts of the ME, which may be useful for the development of vaccines. The extensive circulation of H9N2 for about 20 years in this region where the H5N1 virus is also endemic in some countries, poses a serious public health threat. Regional surveillance and control strategy are highly recommended.

Keywords: Avian influenza; H9N2; Middle East; North Africa; genetic analysis; poultry; vaccination.

Fig. 1.

Migratory flyways of wild birds in the Middle East and North Africa.

Fig. 2.

Phylogenetic relatedness of the HA gene sequences of H9N2 viruses in the Middle East from 1998 to 2016. HA gene sequences were collected from countries in the Middle East in addition to Pakistan. A total of 760 sequences were retrieved from the GenBank and GISAID and aligned using MAFFT and were further edited using Bio Edit. The phylogenetic tree was generated by IQTREE using the best fit model selection. The tree was further edited for publishing using FigTree and Inkscape. Two major lineages were observed, lineage A and lineage B. Lineage A contains viruses from Egypt (EG1, EG2 and EG3; red) in addition to viruses from Israel (IS1, IS2 and IS3; green), the Middle East group with viruses from Israel (green), KSA (magenta), UAE (cyan), Tunisia, Morocco and Libya (black), the Pakistani-Iranian groups (PA-IR1 and PA-IR2) with viruses from Iran (blue) and Pakistan (yellow) and, finally Gulf1 and Gulf2 representing viruses from UAE, Oman, Iraq, Iran and Pakistan. Lineage B contains three genetic groups IR1, IS4 and IS5. All viruses in lineages A and B belonged to the G1-like H9N2 lineage, except IR2 which was similar to the Korean-like lineage.