Microevolution of Highly Pathogenic Avian Influenza A(H5N1) Viruses Isolated from Humans, Egypt, 2007–2011

Mary Younan¹, Mee Kian Poh¹, Emad Elassal¹, Todd Davis, Pierre Rivailler, Amanda L. Balish, Natosha Simpson, Joyce Jones, Varough Deyde, Rosette Loughlin, Ije Perry, Larisa Gubareva, Maha A. ElBadry, Shaun Truelove, Anne M. Gaynor, Emad Mohareb, Magdy Amin, Claire Cornelius, Guillermo Pimentel, Kenneth Earhart, Amel Naguib, Ahmed S. Abdelghani, Samir Refaey, Alexander I. Klimov, Ruben O. Donis

, and Amr Kandeel

Author affiliations: Author affiliations: US Naval Medical Research Unit No.3, Cairo, Egypt (M. Younan, E. Elassal, M.A. ElBadry, S. Truelove, A.M. Gaynor, E. Mohareb, C. Cornelius, G. Pimentel, K. Earhart); Centers for Disease Control and Prevention, Atlanta, Georgia, USA (M.K. Poh, T. Davis, P. Rivailler, A.L. Balish, N. Simpson, J. Jones, V. Deyde, R. Loughlin, I. Perry, L. Gubareva, A.I. Klimov, R.O. Donis); Cairo University, Cairo (M. Amin); Ministry of Health and Population, Cairo (A. Naguib, A.S. Abdelghani, S. Refaey, A. Kandeel)

Abstract

We analyzed highly pathogenic avian influenza A(H5N1) viruses isolated from humans infected in Egypt during 2007–2011. All analyzed viruses evolved from the lineage of subtype H5N1 viruses introduced into Egypt in 2006; we found minimal evidence of reassortment and no exotic introductions. The hemagglutinin genes of the viruses from 2011 formed a monophyletic group within clade 2.2.1 that also included human viruses from 2009 and 2010 and contemporary viruses from poultry; this finding is consistent with zoonotic transmission. Although molecular markers suggestive of decreased susceptibility to antiviral drugs were detected sporadically in the neuraminidase and matrix 2 proteins, functional neuraminidase inhibition assays did not identify resistant viruses. No other mutations suggesting a change in the threat to public health were detected in the viral proteomes. However, a comparison of representative subtype H5N1 viruses from 2011 with older subtype H5N1 viruses from Egypt revealed substantial antigenic drift.

Outbreaks of highly pathogenic avian influenza (HPAI) A(H5N1) virus infection among poultry in parts of Africa, the Middle East, and Asia have caused sporadic human infections with high case-fatality ratios and a few instances of possible human-to-human transmission (1). In Egypt, HPAI (H5N1) virus was first detected in poultry in February 2006, and in March 2006, the first human infection was detected (2). Surveillance in wild and domestic birds and phylogenetic analyses of viruses from the region indicated that subtype H5N1 virus was probably transported to Egypt by wild birds migrating from the Qinghai Lake region of the People’s Republic of China in the fall of 2005 (3). Analyses of the evolution of subtype H5N1 viruses in Egypt in the following years showed the exclusive circulation of clade 2.2 viruses in poultry, indicating no other subtype H5N1 viruses had been introduced (4). Subsequent genetic divergence of the clade 2.2 hemagglutinin (HA) genes in Egypt, however, resulted in a distinct phylogenetic group designated clade 2.2.1, which is enzootic in peridomestic poultry, and a more recently classified sister group known as clade 2.2.1.1, which is mostly found in commercial chicken flocks (4–6).
In 2011, a total of 39 human cases of subtype H5N1 infection and 15 related deaths were reported in Egypt; a total of 158 cases and 55 deaths were reported during 2006–2011, making Egypt the country with the second highest number of human cases after Indonesia (7). Increases in the annual number of human infections and accompanying decreases in case-fatality ratios in Egypt during 2009–2011, compared with those in 2006–2008, led to the hypothesis that the circulating viruses may have acquired distinct virologic properties (8). To address this issue, we studied the genetic and antigenic diversity of subtype H5N1 viruses isolated from humans in Egypt during 2007–2011. Analysis of 90 complete viral genomes was conducted to determine 1) the predominant genotype of subtype H5N1 viruses infecting humans and 2) other molecular changes that would suggest altered phenotypic properties, susceptibility to antiviral drugs, or the need for development of new candidate vaccine viruses.