Recombinomics Commentary 19:00
March 5, 2012

Detection of three new human infections with the deadly H5NI strain of bird flu in a week has set alarm bells ringing as scientists have found evidence of the virus in the live-bird market in crowded Dhaka.

The above comments describe three confirmed H5N1 cases in wet market workers in Dhaka, Bangladesh.  The first case has been WHO confirmed and has recovered, but the three 2012 cases has doubled the number of H5N1 confirmed cases in Bangladesh.  This significant up tick is almost certainly due to clade 2.3.2.1 which has now expanded its geographic spread and was confirmed in crows in India earlier this season.  New sub-clade migrate into India and Bangladesh each season, which are closely related to each other.

The first human clade 2.3.2 was described in media reports in the spring of 2008 when a culler (soldier) developed symptoms and was H5 PCR confirmed.  However, South Korea denied the culler was infected with clade 2.3.2 because prior human infections in China were clade 2.3.4.  Moreover, South Korea used the failure to isolate the H5 virus as an excuse for not filing a report.  However, the sequence had V223I and M230I, which were in the Gharbya cluster and fatal clade 2.3.2.1 cases were subsequently reported in China, including the recent case from Shenzhen who had no reported poultry contact (but had wild bird exposure).

The appearance of clade 2.3.2 in south Asia raised concerns of additional human cases, and the three confirmed cases in Bangladesh are likely confirmation of the realization of such concerns.

Click map to enlarge
We have had 5 deaths.
An additional death (part of a family cluster) on December 31st.

In Indonesia, we have a cluster of 6 Family members, 3 alive (last we knew); 3 dead. 14 in ICU No information as to their diagnosis.

In Indonesia, we have another confirmed by the Director of the Hospital, but not yet by the Health Minister.

Source:

Thanks to Commonground

http://pandemicinformationnews.blogspot.com/2012/01/summary-map-of-2012-confirmed-human.html#links

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 2.3.2.1 while the H5N1 strain that was reported in the country in 2006 belonged to Clade 2.2."

The above comments confirm that clade 2.3.2.1 has migrated into south Asia, as expected.  In the past, clade 2.3.2.1 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 2.3.2.1 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.