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H5N1 Clade Migrates Into South Asia
Recombinomics Commentary 23:45
January 18, 2012

It is for the first time that it has been found in the country, Mishra said. “We have compared it to the strains from Vietnam, Indonesia and other places in Asia and found similarities with the Vietnam strain,” added Mishra.

The NIV had received samples that included four crows from among those that had died in several areas of Jharkhand, including Jamshedpur, Bokaro and Hazaribagh. The process of characterisation of the virus is underway and it is a different strain of the avian influenza virus, NIV scientists said.

The strain belongs to Clade while the H5N1 strain that was reported in the country in 2006 belonged to Clade 2.2.

The above comments confirm that clade has migrated into south Asia, as expected.  In the past, clade was largely confined to southern China and southeast Asia.  Hong Kong surveillance would identify the sub-clade in dead wild birds identified each year, generally between December and February.  However, in the spring of 2008 there was a major expansion of this sub-clade to wild birds in northern Japan as well as poultry in South Korea and poultry and wild birds in southeastern Russia.  These confirmed cases suggested that the Fujian clade 2.3.2 would be competing with Qinghai clade 2.2 due to infections in wild birds that share large flyways that overlap in Mongolia and Russia.

In 2008 one culler was infected and H5 PCR confirmed.  However, virus was not isolated and the human case was denied.  The denial included comments that human cases had involved the Fujian sub-clade 2.3.4 and not 2.3.2 even though the internal genes of the 2.3.2 were 2.3.4.  Fatal human cases involving 2.3.2 were subsequently confirmed in China and Hong Kong.  These cases were of concern because two receptor binding domain changes V223I and M230I were fixed in clade 2.3.2.  Many of the recent wild bird sequences had an additional receptor binding domain change S227R, and the recent fatal case in Shenzhen had the three changes above as well as Q196K raising concerns that many of the receptor binding domain changes use to create a more transmissible H5N1 in ferrets were recombining in wild birds and evolving in more transmissible H5N1 without the aid of scientists or terrorists.

It is likely that the recent H5N1 outbreaks in northeastern India as well as Bangladesh also involved clade containing two or more of the above changes, increasing the likelihood of human infections.  Recently released sequences from 2011 isolates from Japan and South Korea share polymorphisms with clade 2.2.1 isolates in Egypt, including sub-clade 2.2.1 G, (see list here and here) which has PB2 E627K as well as sequences from seasonal and pandemic H1N1 (H1N1pdm09).  Moreover, these sequences include identities with H3N2v sequences in United States cases.

Full sequences from the H5N1 in India and Bangladesh would be useful, in addition to full sequences from human cases in Egypt.

Similarly, release of the receptor binding domain changes described in the censored papers at nature and Science is overdue.  The withholding of this information by Nature and Science continues to be hazardous to the world’s health.

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