Bird Flu (H5N1) Genetics

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Avian flu or bird flu first emerged as a deadly strain that killed two chicken flocks in Scotland. This strain, which is called A/chicken/Scotland/59 has since undergone several genetic mutations to become the highly pathogenic H5N1 influenza virus known today. With each mutation, the virus has become increasingly dominant and pathogenic, causing more severe disease and an increasing number of deaths.

The dominant H5N1 strain from 2004 evolved between 1999 and 2002 to become the Z genotype and is also referred to as Asian lineage HPAI A(H5N1). This strain can be further divided into two clades. Clade 1 is made up of H5N1 human and bird isolates that come from Cambodia, Vietnam and Thailand as well as bird isolates from Malaysia and Laos. The clade 2 viruses are those that were found in isolates from bird populations in Japan, China, Indonesia and South Korea, which then spread to Europe, the Middle East and Africa.

The H5N1 infections that occurred in 2005 and 2006 in humans were generally caused by clade 2 viruses. Within clade 2 are six subclades that have been identified using genetic analysis. Three of these have a distinct geographic distribution and cause human infections. Subclade 1 is found in Indonesia, while subclade 2 is found in the Europe, the Middle East and Africa and subclade 3 is found in China.

Only five other genomes from Europe between 2004 and 2006 are contained in Genbank, none of which are genomes form the Middle East or northern Africa. One study into subclade 2 carried out in 2007 showed 36 new isolates, which has extended the sequence data available for H5N1.


How the different isolates are identified can be described using the A/chicken/Nakorn-Patom/Thailand/CU-K2/04(H5N1) strain as an example.

This can be broken down into the following:

  • A refers to the species of influenza (could be A, B or C)
  • Chicken is the animal the isolate is found in
  • Nakorn-Patom/Thailand is the place where the virus is isolated
  • CU-K2 is the laboratory number used to distinguish the strain from other influenza isolated in the same place and year.
  • 04 represents the year of isolation (2004)
  • H5 refers to the fifth of several known types of hemaglutinin
  • N1 comes from the first of several known types of neuraminidase



Further Reading

Last Updated: Jun 19, 2023

Dr. Ananya Mandal

Written by

Dr. Ananya Mandal

Dr. Ananya Mandal is a doctor by profession, lecturer by vocation and a medical writer by passion. She specialized in Clinical Pharmacology after her bachelor's (MBBS). For her, health communication is not just writing complicated reviews for professionals but making medical knowledge understandable and available to the general public as well.


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