Brazil finds new strain of H1N1 virus - NOT

[HenryN]

Re: Brazil finds new strain of H1N1 virus - NOT

Right, but is there parts of it they didn't release maybe, or are they talking about the matrix and how it relates to HA. Something beyond the obvious that they posted at NCBI?

WRONG. The simply compared the HA sequence to the Califonia reference strain, saw differences, and held a press conference.

 

[HenryN]

Re: Brazil finds new strain of H1N1 virus - NOT

more understandable is the message for general people: Brazil has its own selected vaccine strain ready for tests and trials and then for production.

Brazil has a pharma industry well developed and in expansion toward less developed world.

The message is intended for big companies in the wealthy nations...

WRONG. The only message is that the researchers are clueless (or beyond).

 

[pflu]

Re: Brazil finds new strain of H1N1 virus - NOT

I posed the question about them possibly talking about the matrix earlier, and the new article states...

"They looked in particular at segments number 4 and 7. Segment 4 codes for the protein Hemagglutinin (HA) which is responsible for virus infectivity and triggers the production of antibodies in the human immune system. Segment 7 codes for the matrix proteins (MP) M1 and M2, which help the virus to develop and maintain its structure."

 

[Mamabird]

Re: Brazil finds new strain of H1N1 virus - NOT

I posed the question about them possibly talking about the matrix earlier, and the new article states...

"They looked in particular at segments number 4 and 7. Segment 4 codes for the protein Hemagglutinin (HA) which is responsible for virus infectivity and triggers the production of antibodies in the human immune system. Segment 7 codes for the matrix proteins (MP) M1 and M2, which help the virus to develop and maintain its structure."

They also said: "they found that segment 7 appeared to be "completely conserved".

That means that the matrix protein was identical to A/California/04.

Bottom line - someone is playing a cruel joke or they are asleep at the wheel.

 

[pflu]

Re: Brazil finds new strain of H1N1 virus - NOT

The article talks about the comparison of both segments in relation to one another...

"When they compared segment 4 and segment 7 of the new A/S?o Paulo/1454/H1N1 strain against the novel swine flu reference strain A/Calif?rnia/04/H1N1 they found that segment 7 appeared to be "completely conserved" while segment 4 showed a number of discrete alterations in nucleotide and amino acid sequences."

Is there a certified virologist here or someone who isn't just puffing their chest that can give actual details about how the relationship between 7 and 4 are important and when looked at together constitute a notable mutation?

A response with new insight would be nice instead of the it's a joke because it matches in blast comments.

 

[Mamabird]

Re: Brazil finds new strain of H1N1 virus - NOT

The article talks about the comparison of both segments in relation to one another...

I'm sorry, I re-read the article in its entirity and cannot find the statement about "...comparison of both segments in relation to one another". That would indeed be a novel way to look at influenza viruses as the matrix protein is highly conserved over numerous virus subtypes, while HA is highly variable.

What I did read in the article is their patient returned from Mexico and developed Swine Flu. If the scientists had compared A/Sao Paulo to A/Mexico/4115, an isolate collected in mid April, they would would find that the two viruses were identical. No new mutation required. The variant has been around for quite some time.

 

[pflu]

Re: Brazil finds new strain of H1N1 virus - NOT

I'm assuming a relationship of some sort exists, otherwise what is the point of mentioning both, they must have compared other segments as well but did not mention those?...

"When they compared segment 4 and segment 7 of the new A/S?o Paulo/1454/H1N1 strain against the novel swine flu reference strain A/Calif?rnia/04/H1N1 they found that segment 7 appeared to be "completely conserved" while segment 4 showed a number of discrete alterations in nucleotide and amino acid sequences."


Again, as I stated earlier, I do not have expertise beyond what I read here and elsewhere. I'm simply pointing out the obvious.

Did these virologists spend 1-1/2 months working on what others here dismissed after spending a few minutes running a blast comparison? I just think there must something beyond what we understand here which let to their conclusions.

 

[Mamabird]

Re: Brazil finds new strain of H1N1 virus - NOT

I'm assuming a relationship of some sort exists, otherwise what is the point of mentioning both, they must have compared other segments as well but did not mention those?...

"When they compared segment 4 and segment 7 of the new A/S?o Paulo/1454/H1N1 strain against the novel swine flu reference strain A/Calif?rnia/04/H1N1 they found that segment 7 appeared to be "completely conserved" while segment 4 showed a number of discrete alterations in nucleotide and amino acid sequences."


Again, as I stated earlier, I do not have expertise beyond what I read here and elsewhere. I'm simply pointing out the obvious.

Did these virologists spend 1-1/2 months working on what others here dismissed after spending a few minutes running a blast comparison? I just think there must something beyond what we understand here which let to their conclusions.

They apparently did not mention the other six gene segments because they in all likelyhood did not take the time to sequence them, which is not unusual. Do to the antigenic properties of the virus, most of the importance is found in the HA, NA and MP segments.

You keep mentioning Blasts, and I'm not sure what you are talking about. Perhaps someone in an early post used that termj. However, a simple alignment using Muscle or similar tool compares the entire genome of the viruses being compared. I think the problem here is that this team made a comparison to only one other virus (A/California/04). I'm not sure why they did that, because as the CDC so eloquently pointed out in an excellent research paper, 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. That variant has been around quite a long time and can be found all over the world.

So, unless I'm mistaken, there is simply nothing new to report here. Which if that is the case is quite good news. We get really concerned when these viruses do in fact change in some material way, as you can tell with all the rhubard that the Brazilans have caused at FT.

 

[HenryN]

Re: Brazil finds new strain of H1N1 virus - NOT

I'm assuming a relationship of some sort exists, otherwise what is the point of mentioning both, they must have compared other segments as well but did not mention those?...

"When they compared segment 4 and segment 7 of the new A/São Paulo/1454/H1N1 strain against the novel swine flu reference strain A/Califórnia/04/H1N1 they found that segment 7 appeared to be "completely conserved" while segment 4 showed a number of discrete alterations in nucleotide and amino acid sequences."


Again, as I stated earlier, I do not have expertise beyond what I read here and elsewhere. I'm simply pointing out the obvious.

Did these virologists spend 1-1/2 months working on what others here dismissed after spending a few minutes running a blast comparison? I just think there must something beyond what we understand here which let to their conclusions.

No, the story is a joke. They sequenced 2 of the 8 gene segments and saw a few changes in HA, which were not new to Brazil (which would have ben obvious to anyone who ran a BLAST, which would take a few seconds and available to anyone with internet access).

The media, who ran with this story, are as clueless as the researcher who called the press conference, which is why, at this point, the swine H1N1 has a COMMANDING lead!

 

[HenryN]

Re: Brazil finds new strain of H1N1 virus - NOT

They apparently did not mention the other six gene segments because they in all likelyhood did not take the time to sequence them, which is not unusual. Do to the antigenic properties of the virus, most of the importance is found in the HA, NA and MP segments.

You keep mentioning Blasts, and I'm not sure what you are talking about.

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

 

[Mamabird]

Re: Brazil finds new strain of H1N1 virus - NOT

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

Thank you Dr. Niman, but the inference in the post was that everyone was just doing a Blast, and in a few minutes knew more than the Brazialian researchers.

In fact, many of the folks posting to this thread have been actively involved in Swine Flu research using a variety of tools for many, many weeks (some for many, many years) and have collected a lot of usefu data. What, of course is not helpful is folks shooting from the hip without doing adequate research. That can lead to mis-information. So, I was simply questioning the Blast comment as being a generalization without factual basis.

 

[pflu]

Re: Brazil finds new strain of H1N1 virus - NOT

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

Thanks Niman,

"The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families. "


This description can be found at...


http://blast.ncbi.nlm.nih.gov/Blast.cgi

 

[HenryN]

Re: Brazil finds new strain of H1N1 virus - NOT

Thank you Dr. Niman, but the inference in the post was that everyone was just doing a Blast, and in a few minutes knew more than the Brazialian researchers.

In fact, many of the folks posting to this thread have been actively involved in Swine Flu research using a variety of tools for many, many weeks (some for many, many years) and have collected a lot of usefu data. What, of course is not helpful is folks shooting from the hip without doing adequate research. That can lead to mis-information. So, I was simply questioning the Blast comment as being a generalization without factual basis.

This is why this story is SO absurd.

BLAST is a public program that is at Genbank and is used by many to searh Genbank for similar (or IDENTICAL) sequences. If these researchers took the HA sequence they submitted to Genbank and pasted it into the BLAST search box and clicked on the "BLAST" button, in a couple of SECONDS they would have the best matches at Genbank.

If they asked how many of the 1701 HA positions were unique to their isolate, they would see that the answer was ZERO. If they asked how positions where found in 10 or less sequences, the answer would have been ZERO. If they asked how many postions were found in less than ONE HUNDRED H1N1 isolates, the answer would have been ZERO.

Thus, in a couple of SECONDS, they would know that calling a press conference to anounce a NOVEL sequence was ABSURD from an science point of view, but clearly was a success with the media.

 

[Giuseppe]

Re: Brazil finds new strain of H1N1 virus - NOT

WRONG. The only message is that the researchers are clueless (or beyond).

I appreciate your shortness.

But my post was an OPINION.

Opinions could be accepted or not, but generally don't require a further classification into CORRECT or WRONG.

The Brazilian researcher findings can be ascertained by this method, obviously.

I continue to think about an hype driven by the perspective of a developing pharmaceutical industry.

For the other, I must accept the evaluation of specialists, as you are.

 

[pflu]

Re: Brazil finds new strain of H1N1 virus - NOT

Thank you Dr. Niman, but the inference in the post was that everyone was just doing a Blast, and in a few minutes knew more than the Brazialian researchers.

In fact, many of the folks posting to this thread have been actively involved in Swine Flu research using a variety of tools for many, many weeks (some for many, many years) and have collected a lot of usefu data. What, of course is not helpful is folks shooting from the hip without doing adequate research. That can lead to mis-information. So, I was simply questioning the Blast comment as being a generalization without factual basis.

Yes, this is what I was getting at with the blast comments. While all of us here are invested in many details of H1N1, we have not been specifically studying the strain the researches published info on, yet it was dismissed with a few blast searches.

I was just looking for some more insight into this rather then dismissing it without all the information, which is what happened early on here. Once that occurs the stage is set and most people are to proud to admit they jumped the gun.

 

[Lurker]

Re: Brazil finds new strain of H1N1 virus - NOT

The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.

Dr. Niman,

That brings me to a question I remember from a bioinformatics course. Don't BLAST searches factor in "Gap Scores" when doing the pairwise alignment calculations? I know the number given for all the isolates was identical so this point may be moot, but don't the calculations in BLAST account for slight variations.

Although, clearly by the BLAST algorithm, statistically and/or functionally these slight differences may account for no real difference in the sequence? Also, these are being done by amino acids as opposed to proteins...little things such as wobble in the third position may be a factor, but not significant?

Long story short....even if there are slight differences...for all purposes it is identical. They should know this as scientists!

Am I totally wrong, or just misguided?

Thanks

 

[pflu]

Re: Brazil finds new strain of H1N1 virus - NOT

Dr. Niman,

That brings me to a question I remember from a bioinformatics course. Don't BLAST searches factor in "Gap Scores" when doing the pairwise alignment calculations? I know the number given for all the isolates was identical so this point may be moot, but don't the calculations in BLAST account for slight variations.

Although, clearly by the BLAST algorithm, statistically and/or functionally these slight difference may account for no real difference in the sequence? Also, these are being done by amino acids as opposed to proteins...little things such as wobble in the third position may be a factor, but not significant?

Long story short....even if there are slight differences...for all purposes it is identical. They should know this as scientists!

Thanks

Thank you,

That's the insight I was talking about. This is how to dismiss something. It shows that the individual thought it out and has knowledge in the topic being discussed.

I hope you keep lurking and commenting here, we need more insight like this.

 

[Mamabird]

Re: Brazil finds new strain of H1N1 virus - NOT

we have not been specifically studying the strain the researches published info on,

I think the facts are that we have precisely been studying this strain since mid-April. The Sao Paulo isolate is not a new strain. As soon as it was released to GenBank, it was found to be identical to a large majority of all the other Swine Flu isolates using a variety of tools.

The disjunct is Brazilian scientists shooting from the hip and causing un-needed consternation. I would respectfully suggest that they retract their media statements.

 

[gsgs]

Re: Brazil finds new strain of H1N1 virus - NOT

there is another message in this:

they thought it was important but withheld it >1 month,
in a situation where a pandemic is unfolding and every week counts

 

[HenryN]

Re: Brazil finds new strain of H1N1 virus - NOT

Dr. Niman,

That brings me to a question I remember from a bioinformatics course. Don't BLAST searches factor in "Gap Scores" when doing the pairwise alignment calculations? I know the number given for all the isolates was identical so this point may be moot, but don't the calculations in BLAST account for slight variations.

Although, clearly by the BLAST algorithm, statistically and/or functionally these slight difference may account for no real difference in the sequence? Also, these are being done by amino acids as opposed to proteins...little things such as wobble in the third position may be a factor, but not significant?

Long story short....even if there are slight differences...for all purposes it is identical. They should know this as scientists!

Thanks

ALL 1701 nucleotide positions are IDENTICAL to more than 100 H1N1 public sequences at Genbank (no gaps required - there are ZERO differences). Gaps are used for sequences that have divered over centuries, not a few weeks.