Wednesday, June 17

Swine flu mutates in Brazil (LAST UPDATED JUNE 26)

I suggest you listen to Dr Henry Miller's discussion on Sunday's John Batchelor Show, if you're trying to make sense of seemingly contradictory accounts about the Brazilian strain.

Here is the link for the podcast; the discussion is in the second segment.

Here's my recollection of the discussion: The Brazilian researchers indeed discovered a mutation of the swine flu virus but it's not a 'significant' mutation.

Significance in this context relates to (1) transmissibility (or 'infectiousness') and (2) lethality.

Henry said that the Brazilian strain was not significantly more (or less) infectious than the one that was first isolated. And it was not more (or less) lethal.

Would the mutation then qualify for its own designation ("A/Sao/Paolo/1454/H1N1")? I don't see why not; I'd assume that every mutation of the swine flu virus that can be isolated adds to the body of knowledge about the virus, but that's a layperson talking. I don't recall for certain whether Henry addressed this part of the issue; I don't think he did because the discussion was quite brief; he was covering a lot of ground in a few minutes in the effort to update John's audience on the swine flu situation.

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.

See Also: CIDRAP
Swine flu mutates in Brazil
By Richard Reynolds
Australian Broadcast Company
Posted 6 hours 56 minutes ago
A Brazilian laboratory says it has identified the first genetic variant of the swine flu virus.

Swine flu has infected more than 30,000 people around the world but so far the new variant has only been identified in one patient. [The number is based on reported confirmed cases, of course; the actual number of infections is much higher.]

It is not known if it is a more virulent strain than the one that emerged in Mexico.

The Adolfo Lutz Institute in Sao Paulo sounded the warning, considering the information vital.

As winter arrives in the southern hemisphere, so does flu season, and as often happens with the influenza virus, it could mutate as it encounters other flu strains and they assimilate their genetic material.

This could potentially cause an even more deadly strain of the flu than the one that killed more than 100 people in Mexico.
Here's more complete information about the new strain from a June 17 report in Medical News Today. Emphasis mine:
Scientists in Brazil say they have isolated and identified a new strain of the A(H1N1) swine flu virus from a patient who was hospitalized in São Paulo in April and who has since made a complete recovery. The scientists don't know if the new strain causes more severe infections.

The new strain came from a sample isolated from a 26-year old São Paulo man who started to have symptoms of flu shortly after returning from Mexico. He was hospitalized on 24 April and has since made a full recovery. While in hospital the patient gave a sample for analysis.

A team at the Instituto Adolfo Lutz in São Paulo, led by virologist Dr Terezinha Maria de Paiva, isolated the new strain, A/São Paulo/1454/H1N1, from this sample at the end of April.

Using electron microscopes, another team at Instituto Adolfo Lutz, led by Cecília Luiza Simões, looked at nucleotide sequences in the new strain.

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.

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.

The complete nucleotide sequences for these HA and MP segments have been published in GenBank, the American open access gene sequence database, under access numbers GQ247724 (for the HA gene) and GQ250156 (for the MP).

News of the new strain, together with the newly reported deaths of two people in Argentina to the swine flu virus, have added to fears that South America is heading for a tough winter dominated by the flu pandemic.

Together with the two new deaths in Argentina, there are two in Chile, and another in Colombia, bringing the total number of officially recorded deaths to swine flu in South America to 5.

On Tuesday, Chile's reported total of lab confirmed cases leapt from 2,355 to 3,125.

Argentina has reported 733 cases, Peru 113, Brazil 69, Ecuador 84 and four other South American countries have reported nearly 120 between them, according to AFP news agency.

The Southern Hemisphere is entering the flu season now, whereas production for the swine flu virus vaccine is still months away from completion, so southern countries will have to face the pandemic without them.

While the current strain appears to cause mostly mild infections with few deaths compared to the number of cases, there are fears that it will mutate to a more severe form. And the worry is, that the more "hosts" that are present in a population without immunity, the bigger the chance that it will mutate.

The last time this happened with a pandemic strain was the 1918 Spanish flu which killed millions of people worldwide. It started as a mild version, mutated to a much deadlier form and then returned in a second wave. And like this new strain of H1N1 swine flu, the group most severely affected was healthy young adults, unlike the seasonal flu which mostly strikes the sick and the elderly.

-- GenBank

Sources: AFP, Instituto Adolfo Lutz.


Michael J. Kubat said...

Hi Pundita:

Here's something from the Israeli Ha'aretz website ( At least 10 teens contract swine flu during trip, and 18 IDF personnel get it from them.

Pundita said...

Thanks, Michael!

Michael J. Kubat said...

Le plaisir est tout a moi!

DocJim said...

"Weeks to define this strain"

This was a thorough genetic analysis, not just an antibody study to see how it cross-reacts.

What is especially bothersome is the change was in the Hemagglutinin site. This may mean that this particular strain will circulate as well as the MexiFlu. Antibodies that protect people best and prevent infection are antibodies to the Hemagglutinin site on the virus.

Funny in this situation that he became ill "shortly after returning from Mexico." Many flu cases have an "incubation period" of only 24-48 hours. That would be very "shortly" indeed.

Michael J. Kubat said...

Not to be outdone, the Czechs report three new cases in three days. One is a woman who just returned to Prague from New York.

Story is at:

That makes seven in the Czech Republic: so far, all reportedly infected in the USA or Mexico.

At this point, says Michael Vit, the chief medico of the CR, no extraordinary interventions are planned, just the standard stuff agreed to in an 09 June EU meeting of Ministers of health. (But that was on June 11, when the CR only had four cases...)