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Brazil finds new strain of H1N1 virus - NOT

Re: Brazil finds new strain of H1N1 virus - NOT

Interesting. Maybe this is just about economics and politics after all.

Nothing different at the active site of the HA gene segment that are recognized by antibodies of the host, but we need a different vaccine from the one being produced for the Northern Hemisphere.

OK.
 
Re: Brazil finds new strain of H1N1 virus - NOT

tropicalgirl said:
Just found this, buried in yesterday news... modified at 7pm it sounds to me that the "new strain stuff" was a reporter stuff, not from the researcher... anyways... here it goes...
Click to expand...

Thanks for this background information tropicalgirl !

Reporters seem to hyperventilate when they see the word "mutation" .
 
Re: Brazil finds new strain of H1N1 virus - NOT

Mamabird said:
Interesting. Maybe this is just about economics and politics after all. .........
Click to expand...

The above makes sense.

Also your earlier post with ....

the Swine Flu virus emerged in at least five main variants. The Sao Paulo virus is an identical match (at least as to the two segments provided) with one of those variants.
Click to expand...

..........explains a lot.

.
 
Re: Brazil finds new strain of H1N1 virus - NOT

Mamabird said:
Interesting. Maybe this is just about economics and politics after all.

Nothing different at the active site of the HA gene segment that are recognized by antibodies of the host, but we need a different vaccine from the one being produced for the Northern Hemisphere.

OK.
Click to expand...
Actually, I was just going to put up a "positive spin" post, which is that the researcher didn't mislead the media, but the media mislead the public. The sequence in Brazil is the consensus sequence, so it is NOT a new sequence.

However, the CDC selected a sequence from California as the vaccine target, which has a few differences when compared to the consensus. Thus, when the researcher, who was focused on a vaccine target, compared the Brazilian sequence to the current vaccine target, he saw a few differences, and argued that the Brazilian sequence should be the new target because it is slightly different than the target selected by the CDC.
 
Re: Brazil finds new strain of H1N1 virus - NOT

several other sequences from Brazil are being uploaded.
So far only segment 7.
They all have A815C,C816T,T823C
 
Re: Brazil finds new strain of H1N1 virus - NOT

niman said:
....... The sequence in Brazil is the consensus sequence, so it is NOT a new sequence.

However, the CDC selected a sequence from California as the vaccine target, which has a few differences when compared to the consensus. Thus, when the researcher, who was focused on a vaccine target, compared the Brazilian sequence to the current vaccine target, he saw a few differences, and argued that the Brazilian sequence should be the new target because it is slightly different than the target selected by the CDC.
Click to expand...

Why wouldn't CDC select the consensus sequence?

.
 
Re: Brazil finds new strain of H1N1 virus - NOT

More politics:

- google translated -

Health Minister Jose Gomes Temporão said today that the complete sequencing of two genes of the virus A (H1N1) was an important step in the development of a national vaccine against swine flu. He said he did not believe that the multinational laboratories, such as Novartis and Baxter, can finish the test and market the vaccine before the start of winter in the Northern Hemisphere, in September.

"The Butanta Institute has all the technological and industrial capacity to produce the vaccine before the start of the next Brazilian winter, and the sequencing of the Institute Adolfo Lutz strengtheneth that."

Yesterday, the Institute Adolfo Lutz, Department of Health of São Paulo, announced the isolation of an H1N1 subtype of a major step forward for the Brazilian production of vaccine against swine flu. The isolation of the virus made possible the genetic sequencing of the Brazilian strain of the virus, which was called A / Paulo/1454/H1N1 .

To the minister, although the number of cases of swine influenza in Brazil will increase, the fact still no evidence of virus circulation in domestic sanitary barriers shows that adopted in the ports and airports are working. Today, the ministry confirmed 17 more new cases of the disease, which occurred through the transmission of two people who had contact with patients within the country, the so-called autochthonous cases. In all, the number of confirmed cases of swine flu in the country reached 96.

http://ultimosegundo.ig.com.br/bras...amento+de+virus+a+h1n1+no+brasil+6791947.html
 
Re: Brazil finds new strain of H1N1 virus - NOT

Source: http://www.cidrap.umn.edu/cidrap/content/influenza/swineflu/news/jun1709flustrain.html


CDC rejects report of mutant H1N1 strain in Brazil

Robert Roos * News Editor

Jun 17, 2009 (CIDRAP News) ? The Centers for Disease Control and Prevention (CDC) and other experts have rejected a report that a new strain of the novel H1N1 influenza virus has been identified in a Brazilian patient.

Scientists at Adolfo Lutz Bacteriological Institute in Sao Paolo said they found the new strain in a local patient who has recovered, according to a Medical News Today (MNT) report, which was based on information from the institute and Agence France-Presse.

The story said the scientists found "a number of discrete alterations in nucleotide and amino acid sequences" in the isolate's hemagglutinin (HA) gene. They also analyzed the matrix-protein (MP) gene and found no changes.

But CDC spokesman Joe Quimby in Atlanta discounted the report that the isolate is a new strain. "Our scientists have no knowledge of a new strain of novel A H1N1 influenza," he said.

"It's the same strain, it's not a new strain," Quimby added.

The Brazilian researchers labeled the isolate A/Sao/Paolo/1454/H1N1. They deposited the nucleotide sequences for the HA and MP genes in GenBank under accession numbers GQ247724 and GQ250156, the MNT report said.

Vincent Racaniello, PhD, a Columbia University virologist who writes Virology Blog, also dismissed the claim of a new strain.

"Comparison of the amino acid sequence of the HA protein of A/Sao Paulo/1454/H1N1 with those of other isolates of the current pandemic strain reveals no alterations in the HA protein which would allow the virus to infect new hosts," Racaniello wrote in his blog. "The HA protein of this virus and many other 2009 H1N1 isolates are identical. The few amino acid differences with other 2009 H1N1 isolates are in areas that would not be expected to influence antigenicity or host range."

The MNT report said the virus came from a 26-year-old Sao Paolo man who fell ill shortly after returning from a trip to Mexico. He was hospitalized on Apr 24 and later recovered.
 
Re: Brazil finds new strain of H1N1 virus - NOT

A word of caution when using BLAST. The algorithm will search for the highest scored nucleotide matches. However, when there is no difference in the score, especially amongst closely related hits (>95%) the BLAST results will be ordered by date of submission. Hence, the top hit can be misleading.

This is a common mistake that continues to show up in publications. For example, the NEJM papers and the SCIENCE paper from CDC and Cambridge highlight the top blast hit. However, this is not the closest phylogenetically related sequence. A BLAST search does not replace a phylogenetic analysis.
 
Re: Brazil finds new strain of H1N1 virus - NOT

AlaskaDenise said:
Why wouldn't CDC select the consensus sequence?

.
Click to expand...

It's not a matter of selecting a consensus sequence or not. That approach would require recreating the virus. The easiest thing to do would be select a whole virus that has similar antigenic properties. This would have been selected based on antigenic cartography from the Garten et al paper in Science.
 
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