Avian Flu Diary: H5N1: An Increasingly Complex Family Tree

# 5921

My thanks to Crof at Crofsblog for picking up this morning on the publication by the World Health Organization of their:

Updated unified nomenclature system for the highly pathogenic H5N1 avian influenza viruses

While many of you will want to follow the above link to read the report in its entirety, this document basically identifies and updates the known clades of the H5N1 virus that have emerged since the detection of the A/goose/Guangdong/1996 H5N1 virus strain back in the mid 1990s.

`Clades’ are essentially branches on the virus’s family tree. Each new branch has a clearly identifiable lineage from its parental strain, but has mutated far enough away to become a new strain.

The criteria, from the report:

Based on criteria used to distinguish various groups of the H5 hemagglutinin (HA) gene, the system has formally identified 20 distinct clades of the virus since its inception in early 2008 [1-2]. These clades are defined as meeting the following three specific clade definition criteria developed by the WHO/OIE/FAO H5N1 Evolution Working Group:

sharing of a common (clade-defining) node in the phylogenetic tree;

monophyletic grouping with a bootstrap value of ≥60 at the clade-defining node (after 1000 neighbor-joining bootstrap replicates); and

average percentage pairwise nucleotide distances between and within clades of >1.5% and <1.5%, respectively.

All of which means we are not watching just one H5N1 virus strain with pandemic potential, we are watching at least 20 genetically separate clades of the virus, with many minor variants of each clade thrown in the mix.

And over time, it is expected that even more clades will emerge as the virus mutates and/or swaps genetic material with other viruses.

To give you an idea of just how much the virus has diversified over the past 15 years, I’ve reproduced one of the WHO charts from in this report below.

(click to load larger image)

In WHO Report : Antigenic & Genetic Characteristics of H5N1 & H9N2 Viruses from last month we looked at some of this viral evolution including the spread of the 2.3.2.1 clade of the virus – which was the subject of an FAO announcement (see FAO Warns On Bird Flu) at the start of September.

Scientists at the WHO must occasionally select candidate viruses for the production of human vaccines. Should a pandemic erupt, having a candidate vaccine already in hand could save weeks in the time it would take to produce and deploy an emergency vaccine.

This `new’ 2.3.2.1 clade differs antigenically from the poultry vaccines currently being used in many Asian countries, and the concern is that a new wave of bird flu may spread through poultry this winter.

While newer 2.3.2.1 clade samples reacted well against a couple of candidate vaccines already selected, the 2.3.4.2 clade out of Bangladesh does not.

Therefore, the development of a new clade 2.3.4.2 candidate vaccine virus is proposed.

For more on the ongoing evolution of avian influenza, you may wish to revisit: