Molecular Epidemiology and Evolutionary Analysis of Avian Influenza A(H5) Viruses Circulating in Egypt, 2019–2021

Abstract

The highly pathogenic avian influenza (HPAI) H5N8 virus was first detected in Egypt in late 2016. Since then, the virus has spread rapidly among different poultry sectors, becoming the dominant HPAI H5 subtype reported in Egypt. Different genotypes of the HPAI H5N8 virus were reported in Egypt; however, the geographic patterns and molecular evolution of the Egyptian HPAI H5N8 viruses are still unclear. Here, extensive epidemiological surveillance was conducted, including more than half a million samples collected from different poultry sectors (farms/backyards/live bird markets) from all governorates in Egypt during 2019–2021. In addition, genetic characterization and evolutionary analyses were performed using 47 selected positive H5N8 isolates obtained during the same period. The result of the conducted surveillance showed that HPAI H5N8 viruses of clade 2.3.4.4b continue to circulate in different locations in Egypt, with an obvious seasonal pattern, and no further detection of the HPAI H5N1 virus of clade 2.2.1.2 was observed in the poultry population during 2019–2021. In addition, phylogenetic and Bayesian analyses revealed that two major genotypes (G5 and G6) of HPAI H5N8 viruses were continually expanding among the poultry sectors in Egypt. Notably, molecular dating analysis suggested that the Egyptian HPAI H5N8 virus is the potential ancestral viruses of the European H5N8 viruses of 2020–2021. In summary, the data of this study highlight the current epidemiology, diversity, and evolution of HPAI H5N8 viruses in Egypt and call for continuous monitoring of the genetic features of the avian influenza viruses in Egypt.

Prevalence of Two Distinct Genotypes of Highly Pathogenic Avian Influenza A/H5n8 Viruses in Backyard Waterfowls in Upper Egypt During 2018

“…In the current study, we surveyed live backyard ducks and geese either apparent healthy or showed severe AIV suspected clinical signs reared in different regions in Assiut governorate. The prevalence rate of AIVs (20.4%) was detected among collected samples , which is higher than previously reported by (Ahmed et al, 2019;Hagag et al, 2022;Mady et al, 2019).…”

State and situation of avian influenza in the Eastern Mediterranean Region

“… 8 Clade 2.2.1.2 viruses established themselves in Egyptian poultry until they were eventually replaced by the wider circulation of H9N2 viruses and the sporadic introduction of clade 2.3.4.4 H5 viruses. 9 In 2016, a HPAI H5N8 virus of clade 2.3.4.4 was first isolated from the common coot from Egypt and was closely related to H5N8 viruses from Europe suggesting its introduction into Africa through migratory birds. 10 Since then, several cases of H5N8 have been recorded among domestic poultry in Egypt.…”

“…Since its introduction, the virus became endemic in poultry and diversified into clade 2.2.1 and sub‐clades 2.2.1.1a and 2.2.1.2 8 . Clade 2.2.1.2 viruses established themselves in Egyptian poultry until they were eventually replaced by the wider circulation of H9N2 viruses and the sporadic introduction of clade 2.3.4.4 H5 viruses 9 . In 2016, a HPAI H5N8 virus of clade 2.3.4.4 was first isolated from the common coot from Egypt and was closely related to H5N8 viruses from Europe suggesting its introduction into Africa through migratory birds 10 .…”