Tuesday, March 22, 2016

Virology Journal: Evolution of H5N1 Clade 2.2.1 In Egypt


Almost a year ago, in Eurosurveillance: Emergence Of A Novel Cluster of H5N1 Clade we looked at troubling evidence that suggested the H5N1 avian flu virus in Egypt had acquired several mutations thought to increase its ability to infect humans.

The study's Abstract read:

A distinct cluster of highly pathogenic avian influenza viruses of subtype A(H5N1) has been found to emerge within clade in poultry in Egypt since summer 2014 and appears to have quickly become predominant. Viruses of this cluster may be associated with increased incidence of human influenza A(H5N1) infections in Egypt over the last months.

Getting avian flu information out of Egypt has become increasingly difficult over the past few years, as their MOH rarely acknowledges human infections, their MOA is mired in scandal, and press freedoms continue to erode. 

This month, we have seen 4 human infections reported by the FAO, but as we saw last January in EID Journal: H5N1 In Egypt, reported cases are likely a significant under count of the true number of avian flu infections.

An (admittedly small) seroprevalence study cited in this paper found antibodies for H5 in roughly 2% of the people tested, suggesting thousands of cases have gone uncounted in Egypt.

Remarkably, the seroprevalence for H9N2 ranged from 5.6% to 7.5%, even though it has only rarely been reported in humans.

The rapid evolution of H5N1 viruses in Egypt appears to be the result of poorly matched and inconsistently applied poultry vaccines (see  A Paltry Poultry Vaccine), along with the co-circulation of H9N2 in Egyptian poultry. 

From January's EID Journal study:

The genetic dissimilarity and poor reactivity between commercial vaccines and currently circulating viruses indicate that the vaccines are not efficacious in the field. These vaccines confer partial protection and thus might lead to vaccine-induced escape mutants, thereby complicating, rather than solving, the problem of H5N1 virus circulation in Egypt. 

The problem of poorly-matched vaccines driving avian flu evolution is something we've looked at a number of times in the past (see The HPAI Poultry Vaccine Dilemma and EID Journal: Subclinical HPAI In Vaccinated Poultry – China).

All of which brings us to a new study, published today in the Virology Journal, that similarly finds H5N1 in Egypt is acquiring (in their words `alarming') changes, and suggests that `the rapid evolution of H5N1 viruses in Egypt was possibly linked to vaccination pressure due to sub-optimal use of vaccines.'

 The full study may be read at the link below:

Abdelsatar Arafa ,Ihab El-Masry, Shereen Kholosy, Mohammed K. Hassan, Gwenaelle Dauphin, Juan Lubroth and Yilma J. Makonnen

Virology Journal201613:49
DOI: 10.1186/s12985-016-0477-7

Published: 22 March 2016



Highly pathogenic avian influenza (HPAI) viruses of the H5N1 subtype are widely distributed within poultry populations in Egypt and have caused multiple human infections. Linking the epidemiological and sequence data is important to understand the transmission, persistence and evolution of the virus. This work describes the phylogenetic dynamics of H5N1 based on molecular characterization of the hemagglutinin (HA) gene of isolates collected from February 2006 to May 2014.


Continuous evolution of H5N1 HPAI viruses in Egypt has been observed in all poultry farming and production systems in almost all regions of the country. The wide circulation of the clade carrying triple mutations (120, 129∆, I151T) associated with increased binding affinity to human receptors is an alarming finding of public health importance.