HIV: genomic confusion

By Martín Bonfil Olivera

Published in Milenio Diario, August 12, 2009

On August 6, the main science note on almost all media was a study of the genetic material of the human immunodeficiency virus, HIV.

The bad news is how this discovery was reported. Some sample headlines: "HIV genome deciphered"( BBC, picked up by newspapers such as Publimetro and radio shows like Hoy por hoy en la ciencia (Today in science), from UNAM and W Radio); "HIV genome, deciphered" ( El Clarín, Argentina). What is the problem? That it is incorrect: the full genome of HIV was decoded about 10 years ago. (A Mexican blog on internet even mentioned that "it has been confirmed that HIV uses RNA -ribonucleic acid- instead of DNA -deoxyribonucleic acid", something that has been known since the eighties.)

Some other media were more precise, though still not so clear: MILENIO Diario mentioned "the first HIV full map", "to create an image, not only of RNA nucleotides, but the forms and folds of the RNA strands". Excélsior, with the information from EFE news agency, used the following header: "AIDS virus genome structure decoded". And Spanish El mundo digital headlined "HIV genome, at bird's eye", and explained that "for the first time, the complete structure of HIV's genome was decoded and they got a clear image of its internal architecture".

Let's explain briefly:

HIV, unlike most organisms, does not have genes made of DNA , the famous double helix molecule, but of RNA, formed by only one chain, not two. The chemical links that form this chain are the "letters" in which genetic information is written, and this is what was deciphered years ago.

The discovery of researchers from North Carolina University headed by Kevin Weeks (and published on Nature magazine) is that the HIV RNA strand folds in a complex way: some parts pair up with others to form double helical stretches, for example.

When the virus penetrates a cell and its genetic information is read, these "knots" and rolls (technically known as "secondary structure") can delay the reading of the genes, and this can be fundamental to control how HIV proteins are manufactured.

In other words, a kind of "hidden code" was discovered on the virus' genome, which can be important not only to fight it, but also to better understand the control of genetic information in all types of organisms.

Unfortunately, to explain this with the necessary detail, more space is required than is normally available in news media. At the very least, we should try to be as precise as possible.

(translated by Adrián Robles Benavides)

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Still, Influenza

By Martín Bonfil Olivera

Published in Milenio Diario, July 15th, 2009

Science does not reveal absolute truths, but it does have a commitment to reality.

A good example is the pandemic -started in April in Mexico as an epidemic- caused by a swine A/H1N1 influenza virus.

Mexicans remember how, after the emergency stage that forced Mexico City and other places to shut down schools, restaurants, cinemas and other gathering places, there was a curious reaction. It was said, through email and as gossip, that the epidemic was a sham. That the virus did not exist, or that the epidemic was planned by the current panista government of Mexico (or bye the American government) to influence Election Day on July 5 (or to reactivate world economy).

There were multiple versions of the rumour, but all of them had something in common: it was a way of denying reality. The traumatic experience of those secluded and inactive days, and the economic, but also social and psychological harm they left, created a fertile field for rumours that everything was a complot.

The efficacy of the health authorities was questioned, as well as the science behind their decisions. Today we can see that the epidemic, already spread around the world, is a reality that affects many other countries. Argentina and Chile in their full austral winter, already have 137 and 33 deaths, respectively, and thousands of infected people. Also, Cuba is reporting cases, and the Mexican states of Chiapas, Tabasco and Yucatan have detected an important spike, up to the point that Tabasco has decided to cancel its annual state fair.

In the meantime, research about the virus advances: a group lead by Yoshihiro Kawaoka, from Wisconsin University, reported last Monday on Nature magazine that the swine virus -which is actually a result from mutations and combinations from other already existing viruses, human, bird and swine- causes more harm to the lungs of experimental animals (mice, ferrets and macaques) than the common seasonal influenza virus, and that it can asymptomatically infect pigs (maybe that's why the epidemic was not detected until it jumped into humans).

They also found that people born before 1920 and therefore exposed to the massive epidemic of A/H1N1 influenza in 1918 (spanish flu) have antibodies that can react against the current virus, unlike people born after (thus maybe explaining the anomalous behavior of the epidemic, which affected mainly younger people).

Currently, the virus is still sensitive to tamiflu, but it is very likely that in the short term some resistant varieties will arise. Soon, we will have a vaccine, but it will take time to produce it in enough quantities to respond to the World Health Organization's request for "all countries to have access to the vaccine."

The reality of the pandemic imposes itself, beyond any belief or rumour. The countries should better pay attention to what science reveals, and they should act united in consequence.

(translated by Adrián Robles Benavides)

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Influenza and evolution

by Martín Bonfil Olivera
Published on Milenio Diario, April 29, 2009

The problem is that's what viruses are like: promiscuous and addicted to gambling. And that's what evolution is like, taking species trough twisted and unexpected roads. And that's what science is like, unable to advance on its own road, no less random, faster than it can, held up by its method, which demands it makes sure about what it knows up to that moment before taking the next step.

The influenza virus which is currently bothering us (family orthomyxoviridae, type A, the most common ones, that also infect birds, pigs and horses) is, as are all viruses, a protein capsule that contains genetic material; in this case, ribonucleic acid (RNA), the older and less stable cousin of DNA.That's part of the problem: RNA copying is less accurate: sometimes it adds, sometimes it substracts, and thus causes spontaneous mutations inside one species of viruses.

And if several different viruses infect one same cell, they can recombine, taking with them pieces of genetic information from the others. The virus that concerns us has genes from other influenza viruses that infect humans, pigs and birds. And it can continue changing. What's alarming is the fact that it has learned to jump from human to human (as was feared from bird flue in 2006).

Its last name H1N1 refers to two proteins of its surface: haemaglutinin (of which there are 15 variants; this is number 1), which the virus uses to bind to the cell it's going to infect, and neuraminidase (9 variants) which allow the new viral particles to come out of the infected cell without being stuck to it.

Oseltamivir (Tamiflu -do not self medicate!), one of the drugs that work against the current influenza virus, inhibits this enzyme, and prevents that the new viruses form disseminating.

Science, as evolution, is unpredictable. I can seem slow and expensive, but if James Watson and Francis Crick hadn’t discovered, 56 years ago, the DNA double helix, today we wouldn't have the molecular biology tools that allow us to study and fight this virus.

And if we do not widely invest in scientific investigation —as Barack Obama said, immediately backing his words by increasing his country's investing in science by 3 percent of USA's gross domestic product— we won't be able to fight future crises -whether they be health crises or any other type of crises.

(translated by Adrián Robles Benavides)

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