2007 H5N1 HA and NA Sequences in Thailand Exactly Match 2004
Recombinomics Commentary
August 14, 2007
Today 2007 HA and NA sequences from a duck Thailand were released at Genbank (A/duck/Phitsanulok/NIAH6-5-0001/2007). The new H5N1 sequences from Thailand create another problem for explanations of influenza evolution via random mutations. In the swine sequences (described at Nature Precedings), the most dramatic examples of sequence conservation were in two internal genes, PB2 and PA. These genes encode proteins that are part of the polymerase complex, and would therefore have considerable selection pressure for high fidelity replication, although the sequence identities were at the nucleotide level, so even silent changes were absent.
HA and NA genes encode surface glycoproteins which change rapidly to escape from the immune response of the host. This “antigenic drift” is of interest, because most vaccines target these two surface proteins and the vaccines quickly become obsolete because of antigenic drift.
The recent sequences from Thailand are also of interest because Thailand now had two distinct H5N1 co-circulating. Clade 1 was first identified in 2003/2004 isolates from Vietnam and Thailand. Clade 1 was found in birds and humans. Recently, the Fujian strain (Clade 2.3), was reported in southeast Asia in multiple countries, including Thailand. New human cases in Thailand and Vietnam have refocused attention on H5N1 circulating there.
The sequences released today were both clade 1. However, the partial 2007 sequence (1101 BP) was an exact match of three 2004 sequences from Thailand (listed below). Similarly, the partial NA sequence (432 BP) also exactly matched the available sequences (up to 406 BP) from the same three isolates.
Thus, even the rapidly evolving surface genes were copied with absolute fidelity for three years, raising additional questions about the role of random mutations generated by an error prone polymerase in the evolution of influenza.
A/duck/Uthaithani-2-02/2004
A/chicken/Nakornsawan-2-06/2004
A/chicken/Thailand/Phitsanulok/01/2004
Media Sources
Recombinomics Presentations
Recombinomics Publications
Recombinomics' Paper at Nature Precedings