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Qinghai H5N1 Bird Flu In India

Recombinomics Commentary

June 7, 2006

A study of the gene sequences (HA1 and HA2) of the virus, isolated from the Navapur and Jalgaon outbreaks, concluded that the viruses originated from Qinghai (central China) and Jiangxi (south China).
HHSADL joint director in charge HK Pradhan says the findings shatter a common belief: that the outbreaks at Navapur and Jalgaon (140 km apart) in Maharashtra were related.

He says the genetic analysis revealed that the viruses from Navapur and Jalgaon were not identical (they showed 3.5 per cent divergence). This points to the fact that the two outbreaks were independent of each other and were caused by different sources.

Study is on to identify the other country, says Pradhan.

Another interesting finding. Jalgaon was the first to be hit and not Navapur -- as widely believed.

Though the outbreak at Jalgaon was reported 12 days after Navapur (February 18), its virus had evolved earlier, says Pradhan. Since the Jalgaon outbreak was in backyard poultry (involving scattered deaths), it was reported later than the Navapur outbreak in which a large number of birds in organised poultry farms died.

That was also the reason why it took more time in Jalgaon to control the disease, as it had spread far and wide.

Pradhan says probably the Navapur virus was responsible for the outbreak in Uchhal in Gujarat, and the Jalgaon virus for the Burhanpur outbreak in Madhya Pradesh

The above comments on H5N1 in India point towards a migratory bird origin, which is not a surprise.  The Qinghai strain of H5N1 was first identified in May, 2005 in bar-headed geese at Qinghai Lake.  Since these birds winter in northern India, and Indian origin could not be excluded.  Although India had denied that H5N1 had been present, serum collected in 2002 from poultry workers had H5N1 antibodies.
Many of the bar-headed geese that survived the H5N1 in May 2005 would have returned to India in the winter of 2006.  They would have returned to central China, and China has reported H5N1 in bar headed geese in Tibet and Qinghai province, again pointing toward in Indian origin.

However, India still has not acknowledged H5N1 in wild birds,  However, they have detected H5N1 in poultry outbreaks described above, and the sequencing of the H5N1 points toward additional evolution via recombination.

Sequences from six Jiangxi isolates, listed below, are publicly available.  The first 3 sequences are identical to each other and are closely related to poultry isolates from adjacent Fujian and Guangzho isolates.  The other three Jiangxi isolates are closely related to each other as well as the Qinghai strain.  However, the Jiangxi sequences are distinguished from the Qinghai strained because of the PB2 polymorphisms E627K.

Prior to Qinghai Lake this polymorphism was not found in any H5N1 isolate from birds. However, it was in all 17 Qinghai isolates from 2005.  The change became fixed and all reported PB2 sequences from the Qinghai strain had E627K including multiple isolates from multiple locations in Russia (Kurgan, Novosibirsk, Astrakhan), Mongolia in 2005, and 2006 isolates from Denmark, Italy, and Nigeria.

The description of sequences in India indicate H5N1 there is linked to wild bird origins in both Qinghai Province as well as Jiangxi Province.  However, the 2005 isolates from China differ from each other by 4-5%, while the Indian isolates differ by 3.5% suggesting there has been some recombination leading to isolates that are more closely related to each other.

The polymorphism at position PB2 627 would also be of interest since none of the 2005 sequences from Jiangxi had E627K.  Moreover, the full sequences from both location would help determine how the Qinghai H5N1 in evolving in South Asia.

  DQ320850  A/migratory duck/Jiangxi/1653/2005   2005  H5N1   
  DQ320851  A/migratory duck/Jiangxi/1657/2005   2005  H5N1   
  DQ320852  A/migratory duck/Jiangxi/1701/2005   2005  H5N1   
  DQ320853  A/migratory duck/Jiangxi/2136/2005   2005  H5N1  
  DQ320854  A/migratory duck/Jiangxi/2295/2005   2005  H5N1   
  DQ320855  A/migratory duck/Jiangxi/2300/2005   2005  H5N1 

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