Dynamic of H5N1 virus in Cambodia and emergence of a novel endemic sub-clade.
In Cambodia, the first detection of HPAI H5N1 virus in birds occurred in January 2004 and since then there have been 33 outbreaks in poultry while 21 human cases were reported. The origin and dynamics of these epizootics in Cambodia remain unclear. In this work we used a range of bioinformatics methods to analyze the Cambodian virus sequences together with those from neighboring countries. Six HA lineages belonging to clades 1 and 1.1 were identified since 2004. Lineage 1 shares an ancestor with viruses from Thailand and disappeared after 2005, to be replaced by lineage 2 originating from Vietnam and then by lineage 3. The highly adapted lineage 4 was seen only in Cambodia. Lineage 5 is circulating both in Vietnam and Cambodia since 2008 and was probably introduced in Cambodia through unregistered transboundary poultry trade. Lineage 6 is endemic to Cambodia since 2010 and could be classified as a new clade according to WHO/OIE/FAO criteria for H5N1 virus nomenclature. We propose to name it clade 1.1A. There is a direct filiation of lineages 2 to 6 with a temporal evolution and geographic differentiation for lineages 4 and 6. By the end of 2011, two lineages, i.e. lineages 5 and 6, with different transmission paths cocirculate in Cambodia. The presence of lineage 6 only in Cambodia suggests the existence of a transmission specific to this country whereas the presence of lineage 5 in both Cambodia and Vietnam indicates a distinct way of circulation of infected poultry.
Virology Unit/National Influenza Centre, Institut Pasteur in Cambodia, 5 Monivong Blvd, PO Box 983, Phnom Penh, Cambodia.
San
S
Sorn
Touch
T
Sok
Sovann
S
Ly
Sareth
S
Rith
Nguyen
N
Tung
Alain
A
Viari
Laurent
L
Gavotte
Davun
D
Holl
Heng
H
Seng
Nima
N
Asgari
Beat
B
Richner
Denis
D
Laurent
Nora
N
Chea
Veasna
V
Duong
Tetsuya
T
Toyoda
Chadwick Y
CY
Yasuda
Paul
P
Kitsutani
Paul
P
Zhou
Sun
S
Bing
Vincent
V
Deubel
Ruben
R
Donis
Roger
R
Frutos
Philippe
P
Buchy
D000818:Animals; D002160:Cambodia / Q000453:epidemiology; D002460:Cell Line; D002642:Chick Embryo; D004196:Disease Outbreaks; D019143:Evolution, Molecular; D005814:Genes, Viral; D019267:Hemagglutinin Glycoproteins, Influenza Virus / Q000235:genetics; D053124:Influenza A Virus, H5N1 Subtype / Q000145:classification* / Q000235:genetics; D005585:Influenza in Birds / Q000453:epidemiology*; D008969:Molecular Sequence Data; D009154:Mutation; D010802:Phylogeny; D011110:Polymorphism, Genetic; D011200:Poultry / Q000821:virology; D012641:Selection, Genetic; D017386:Sequence Homology, Amino Acid
D019267:Hemagglutinin Glycoproteins, Influenza Virus