Recombinomics: Wisconsin H1N1v Links U.S. H3N2v, China H5N1 & Swiss H1N1v

Recombinomics Commentary 21:15
January 8, 2012 The recent increase in novel influenza in the United States has led to a CDC request for all 50 states to increase surveillance.

In addition to 12 H3N2v (trH3N2 and H3N2pdm11) cases, there has also been a H1N2v (trH1N2) case as well as an H1N1v (trH1N1) case.

All 14 cases in 2011 as well as the 6 H3N2v cases in 2010 have a PB1 with E618D, which is in H1N1pdm09, or a H1N1pdm09 M gene signaling adaptation to human.

The most recent H3N2v (Iowa and West Virginia confirmed cluster) and H1N2v (A/Minnesota/19/2011 suspect cluster) cases have not had any reported swine exposure.

The H1N1v case (55M), A/Wisconsin/28/2011, had an occupational swine exposure, but many of the newly acquired polymorphisms of the internal genes are also present in the US H3N2v and H1N2v cases.

However, newly acquired internal gene polymorphisms are also found in H5N1 cases in China (A/Guangdong-Shenzhen/1/2011, A/Hubei/1/2010, A/Guangxi/1/2009) and Cambodia, as well as three H1N1v cases in Switzerland (A/Switzerland/9356/2009, A/Switzerland/5165/2010, A/Switzerland/4607377/2011) –see list here.

The acquisitions are via recombination and linked to wild bird sequences which raises concerns of rapid evolution in these novel influenza genomes.

Animal-Related Diseases Concern Scientists #h5n1 #birdflu

uary 04, 2012

Animal-Related Diseases Concern ScientistsHealth researchers and wildlife biologists say the number of infectious diseases that have jumped the boundary from animals to humans and between animal species is on the rise. Scientists believe the increase may be a result of more frequent contact between humans and wild animals, as well as the growing trade in wild animals, both legal and illegal.


Towards the end of the 1990s, several Asian countries lived one of their worst health nightmares. A new, highly pathogenic, strain of Avian Influenza known as H5N1 killed hundreds of people. Over the next years, more than 9-million chickens were destroyed in an effort to stem the epidemic. Scientists believe the H5N1 virus was transmitted from wild birds to domestic poultry and pigs, which then passed it to humans. H5N1 is just the latest of various influenza strains that have killed up to 100 million people over the last century.

Now scientists are concerned about the appearance of new illnesses. Jonathan Sleeman is the director of the National Wildlife Health Center at the U.S. Geological Survey.

"Human health, wildlife health and domestic animal health are all interconnect within the context of the environment," said Sleeman. "And environmental changes and changes in environmental quality will have negative impacts in all 3 groups."

Experts say there are many causes: the increasingly rapid ..  http://www.voanews.com/english/news/health/Animal-Related-Diseases-Raise-Concern-with-Scientists-136677768.html

Indonesia Denies H5N1 Lab Confirmatory Cluster in Sulawesi

Indonesia Denies H5N1 Lab Confirmatory Cluster in Sulawesi
Recombinomics Commentary 16:15
November 20, 2008

The sample inspection of blood by using Polymerase Chain Reaction (PCR) was carried out in the Hasanuddin University laboratory (Unhas) and was sent to the Department of Health

Initial tests of the first seven patients indicated the presence of the H5N1 avian virus.

The hospital was now awaiting confirmation of the results from blood tests done by the Micro Laboratory of the Hasanuddin University Medical School, he said.

The 17 were hospitalised this month after falling sick shortly after a rash of unexplained chicken deaths in the area.

"The result of the tests is negative," said Lily Sulistyowati, spokeswoman of the ministry, without giving details.

The above translations describe a large PCR confirmed H5N1 cluster in Sulawesi, Indonesia. The above wire service quotes do not include confirmation that the poultry deaths were due to H5N1 and provide yet another denial of lab confirmed H5N1cases reported by local media.

Although Indonesian denials have been met with skepticism previously, the latest case in Semarang, as well as the current cluster in Sulawesi, appears to signal a new level of denials. Previous cases were highly suspect, but lacked lab confirmation. The latest cases however, were lab confirmed, based on local media reports or wire service quotes from the lead physician, but were still denied by the Ministry of Health.

In the latest cluster, the circumstantial evidence strongly supports the local reports of H5N1 PCR confirmation. The local poultry was H5N1 positive and at least four local slaughterhouses were closed permanently. Fourteen of the patients were placed in isolation (which had a capacity of 14) with guards stationed at the isolation wing. Three other hospitals were readied to receive additional bird flu patients. Two more patients were recently admitted, including a sibling of one of the hospitalized patients. The patients recovered after being treated with Tamiflu, but remained hospitalized until today.

The denial of H5N1 confirmation of this large cluster also adds insight into the earlier statements by Ministry of Health head, Siti Fadilah Supari, who cited rapid treatment for the fall in H5N1 cases. Of course rapid treatment does not reduce H5N1 infections unless the patients are highly contagious. Early treatment would lead to recovery, which could also lower viral titers, leading to false negatives and failures to lab confirm. Therefore rapid treatment could lead to a lowering of confirmed cases, and an artificial elevation of case fatality rates, because milder recovered cases would not be counted. The case fatality rate in Indonesia s the highest in the world and has been around 80% since the first cluster was reported (including one confirmation) in 2005.

If confirmed, the 19 suspect cases in Sulawesi would be the largest H5N1 cluster reported to date, but today’s denial does not increase the confirmed cases or clusters in Indonesia, but significantly increases the level of concern.

H5N1 Spread to Xayabury Laos
Recombinomics Commentary 18:13
November 10, 2008

Donmai village, Xayabury, XAYABURY
Date of start of the outbreak 27/10/2008

Affected population backyard poultry (114 chickens and 41 ducks)

real-time PCR - 30/10/2008 – Positive

The above comments from today’s OIE report from Laos describe a confirmed H5N1 outbreak in Xayabury. This outbreak follows two earlier outbreaks in northern Laos, and is followed by a confirmed outbreak in northern Thailand, less than two hundred miles southwest of the above outbreak (see satellite map).

These outbreaks in northern Laos and northern Thailand are likely to be related to each other and outbreaks in northern Vietnam. Recent reports have described a number of clade 2.3.4 reassortants in northern Vietnam. These genes are related to 7 of the 8 gene segments in wild bird isolates in Japan (HA is clade 2.3.2), which are closely related to poultry isolates in South Korea and Primorie, which were reported earlier this year.

The recent outbreaks signal migration of wild birds into the region, which will likely lead to reported outbreaks in the regions described above.
http://www.recombinomics.com/News/11100801/H5N1_Xayabury.html

H1N1 in the United States RaisesTamiflu Resistance Concerns
Recombinomics Commentary 23:55
November 07, 2008

The latest CDC report on influenza in the United States this season indicates that 80/112 isolates have been influenza A and 16/25 of the sub-typed influenza A was H1. These initial data points indicate a significant portion of influenza infections in the upcoming weeks will be H1, raising concerns of Tamiflu resistance.

Although reports from the US have yet to comment on H274Y levels this season, the first characterized isolate in Canada had H274Y as did the first three reported H1 cases in the UK. The UK and Canadian data raise concerns that resistance will be at or near 100% for H1 isolates.

The isolates in Canada and England were characterized as Brisbane/59 although it remains unclear if the analysis will discriminate between Brisbane/59 (clade 2B) and Hong Kong/2562 (clade 2C). Last season all clade 2 isolate were characterized as Solomon Island-like (clade 2A), although there were no reported Solomon Island isolates. In the US all clade 2 isolates were Brisbane or Hong Kong and Tamiflu resistance was limited to Brisbane, and the vast majority of resistance cases were limited to a clade 2B sub-clade, which was also the case in Canada and Europe.

Eventually, isolates were called Brisbane/59-like, but the change in terminology did not provide any discrimination between clade 2B and clade 2C, which were easily distinguished phylogenetically. These sub-clades were also easily distinguished serologically, if the target isolates were grown in mammalian cells. The anti-sera used produced extensive cross-reactivity when the virus was grown in chicken eggs, but Brisbane anti-sera had a titer of 320 with Brisbane, which dropped to 40 for Hong Kong and was below the limits of detection with Solomon Island (and New Caledonia). This large differential led to changing the H1 immunogen from Solomon Island to Bisbane this season, but the utility of the new vaccine may be limited.

Isolates from South Africa had acquired a number of changes near the receptor binding domain, and recent isolates from Hong Kong were clade 2C and had H274Y. Moreover, one of the clade 2C isolates had a clade 2B NA (acquired through reassortment), while one of the changes near the clade 2B receptor binding domain was from clade 2C (acquired through recombination).

Therefore release of HA and NA sequences from new isolates in the northern hemisphere would be useful.
http://www.recombinomics.com/News/11070801/H1N1_US.html