Antiviral drugs to fight the flu: yes or no?

Disclaimer: I'm not a medical doctor. I cannot recommend taking or not taking a certain drug. However, I am a human being, I've got kids who do get sick from time to time, and I work on viruses. So when I heard that people were battling the unusually nasty flu this year with antiviral drugs, well, I had to do a bit of research.

Antiviral drugs have become increasingly popular after the highly pathogenic avian flu strain emerged. The idea is that in order to be prepared for a possible pandemic, we need to stock up on drugs, enough to treat millions of people.

Let's start with a few facts about viral infections:

A virus is made of genetic material packaged in a tiny shell. Once inside a cell, the virus hijacks the cell's proteins to replicate and create thousands of copies of itself. The new virions bud out of the cell membrane and infect new cells.

However, the infected cell has one more weapon up its sleeve: it "grasps" the virions that are budding out and tries to hold them back. In more scientific terms: there's a molecule on the cell membrane (called sialic acid) that binds to a protein on the surface of the virus (called hemagglutinin). The new virions have to break this bond in order to leave the infected cell and spread the infection. How do they do that? They use an enzyme called neuraminidase: the enzyme, found on the surface of the virus, breaks the bond between hemagglutinin and siliac acid, setting the virions free to spread out and infect new cells.

Neuraminidase inhibitors are antiviral drugs that, as the name suggests, block the neuraminadase enzyme. As a consequence, the virions remain stuck to the cell membrane and thus cannot spread the infection. Supposedly, this leads to a speedier recovery. I'm saying "supposedly" because there is an ongoing debate on whether this is true or not. Here's what I found in the literature.

Jefferson et al., 2009 [1]:

"Neuraminidase inhibitors have modest effectiveness against the symptoms of influenza in otherwise healthy adults. The drugs are effective postexposure against laboratory confirmed influenza, but this is a small component of influenza-like illness, so for this outcome neuraminidase inhibitors are not effective. Neuraminidase inhibitors might be regarded as optional for reducing the symptoms of seasonal influenza. Paucity of good data has undermined previous findings for oseltamivir's prevention of complications from influenza. Independent randomised trials to resolve these uncertainties are needed."

Wang et al., 2012 [2]:

"Oseltamivir and zanamivir appear to have modest benefit in reducing duration of illness in children with influenza. However, our analysis was limited by small sample sizes and an inability to pool data from different studies. In addition, the inclusion of data from published trials only may have resulted in significant publication bias. [...] The clinical efficacy of neuraminidase inhibitors in 'at risk' children is still uncertain. Larger high-quality trials are needed with sufficient power to determine the efficacy of neuraminidase inhibitors in preventing serious complications of influenza (such as pneumonia or hospital admission), particularly in 'at risk' groups."

Jefferson et al. 2012 [3]:

"We found a high risk of publication and reporting biases in the trial programme of oseltamivir. Sub-population analyses of the influenza infected population in the oseltamivir trial programme are not possible because the two arms are non-comparable due to oseltamivir's apparent interference with antibody production. The evidence supports a direct oseltamivir mechanism of action on symptoms but we are unable to draw conclusions about its effect on complications or transmission. We expect full clinical study reports containing study protocol, reporting analysis plan, statistical analysis plan and individual patient data to clarify outstanding issues. These full clinical study reports are at present unavailable to us."

The company that manufactures the brand name drug for oseltamivir responded here, however, according to BMJ, there hasn't been any release of data yet (source).

I have two more cautionary comments.

First: viruses mutate very rapidly and as such, they rapidly find escapes to drugs. An overuse of antiviral drugs may end up selecting drug resistant strains (for example, a flu strain that carries a neuraminadase enzyme that the inhibitor drugs cannot block). I'm not saying that antiviral drugs should not be used. Some life-threatening situations require the use of such drugs (for example, in the case of patients with immunodepression). Other non life-threatening situations don't (plain and simple).

Second: the US Food and Drug Administration recommends the use of antiviral drugs and in fact, last December they expanded the recommendation to children under one year of age (source). However, if you keep browsing the FDA website you find this very interesting Q&A page, where they report some supposed (though worrisome) adverse side effects:

"In the safety review mandated by the BPCA, a number of adverse event reports were identified associated with the use of Tamiflu in children 16 years of age or younger. These adverse event reports were primarily related to unusual neurologic or psychiatric events such as delirium, hallucinations, confusion, abnormal behavior, convulsions, and encephalitis. These events were reported almost entirely in children from Japan who received Tamiflu according to Japanese treatment guidelines (very similar but not identical to U.S. treatment guidelines). The review identified a total of 12 deaths in pediatric patients since Tamiflu's approval. All of the pediatric deaths were reported in Japanese children. In many of these cases, a relationship to Tamiflu was difficult to assess because of the use of other medications, presence of other medical conditions, and/or lack of adequate detail in the reports."

There is no direct evidence that the deaths were linked to the use of the drug. In fact, often it's high risk children that need to take the drug, which means they are likely to have other conditions and take additional medications. If we can't be certain of what one drug alone can do, imagine multiple ones combined. You can read more about the Japan reports here. I also found a reference [4].

Bottom line: drugs are wonderful things. They save lives. Drugs can also mess up with our body chemistry in ways that we don't always understand. The key point is to read, be informed, and use sparingly (as needed, not just as recommended).

NOTE: I strive to make these commentaries as objective as possible. If you feel I've missed some part of the story or you have more references to add to make a rounder point, please let me know in the comments. 

[1] Jefferson, T., Jones, M., Doshi, P., & Del Mar, C. (2009). Neuraminidase inhibitors for preventing and treating influenza in healthy adults: systematic review and meta-analysis BMJ, 339 (dec07 2) DOI: 10.1136/bmj.b5106

[2] Kay Wang, Matthew Shun-Shin, Peter Gill, Rafael Perera, Anthony Harnden (2012). Neuraminidase inhibitors for preventing and treating influenza in children (published trials only) The Cochrane Library DOI: 10.1002/14651858.CD002744.pub4

[3] Tom Jefferson, Mark A Jones, Peter Doshi, Chris B Del Mar, Carl J Heneghan, Rokuro Hama, Matthew J Thompson (2012). Neuraminidase inhibitors for preventing and treating influenza in healthy adults and children The Cochrane Library DOI: 10.1002/14651858.CD008965.pub3

[4] Urushihara, H., Doi, Y., Arai, M., Matsunaga, T., Fujii, Y., Iino, N., Kawamura, T., & Kawakami, K. (2011). Oseltamivir Prescription and Regulatory Actions Vis-à-Vis Abnormal Behavior Risk in Japan: Drug Utilization Study Using a Nationwide Pharmacy Database PLoS ONE, 6 (12) DOI: 10.1371/journal.pone.0028483

The viruses inside us

One of my first and still most popular posts was on endogenous retroviruses, or ERV: these are viral sequences that got integrated in the host DNA and became part of the noncoding genome. With time, Mother Nature found a way to reuse these viral proteins, for example in the placenta, as I was explaining in the earlier post, and some of those proteins became expressed.

I was at a conference last week, and one of the talks discussed the evolution of these endogenous viral elements (EVEs) and how they have become part of a co-evolutionary process. The speaker compared the phylogenetic trees of many EVEs across different species with the phylogenetic trees of the species themselves, and these trees were topologically similar, meaning that the viruses and their hosts have developed mechanisms of coevolution. What this means is that whenever there has been a divergent event in the evolutionary history of a certain species, that event is also reflected in the evolutionary history of the virus hosted by the species. This is not surprising if you think about it: as the host evolves, the virus has to evolve too in order to survive (the Red Queen effect I talked about here).

How did these endogenous viral sequences end up in our genome? In order to replicate, retroviruses undergo reverse transcription, which turns their RNA into DNA, and then the DNA gets integrated into the host genome. When this happens in a germline cell, the germ cell doesn't undergo replication like other cells, as the integrated viral DNA may eventually be distributed throughout the genome through meiotic replication, and as a result the viral genome is stuck there and gets passed on -- as a non-coding sequence -- to the offsprings.

This explains the presence of endogenous retroviruses in our genome. More intriguing is how RNA viruses got there, given that those viruses replicate without getting integrated into the host genome. In fact, they never get trasncribed into DNA. We still don't know how such viruses could have been integrated into the host genome, though one hypothesis is that reverse transcription (as a rare event) could have been triggered by the reverse transcriptase enzyme naturally present in the cellular retroelements.

"The endogenous viral elements (EVEs) we know today must only be a small subset of those that have existed in the past; many others will have been lost by the chance process of genetic drift, which is the fate of most mutations at low frequency, even those that are selectively advantageous. [. . .] Other EVEs may have been removed by purifying selection because they reduce organismal fitness. In particular, human endogenous retroviruses are usually located in genomic regions away from genes, whereas the integration sites of (presumably recent) exogenous retroviruses are often close to genes, suggesting that there is a selective cost in having EVEs located too close to genic regions [1]."

Most endogenous viral elements are defective and hence are found in non-coding regions of the genome. However, like I discussed in my earlier post, it's not unusual for the sequences to find a new function and become expressed again. When this happens, the sequences could become advantageous to the host and hence get fixed in the population. For example, some endogenous viruses trigger protection in the host against similar exogenous viruses by interacting with the infecting virions and causing them to be defective.

These findings have greatly informed our understanding of viral evolution. Indeed, endogenous viral sequences represent a "fossil record" of past infections.

"The key point here is that once integrated into host genomes, EVEs cease to evolve with the very high substitution rates that characterize exogenous RNA and small DNA viruses and instead replicate using high-fidelity host DNA polymerases and probably experience fewer replications per unit time. This will result in a dramatic reduction in evolutionary rate, from the virus scale (usually around 10e-03 nucleotide substitutions per site, per year) to the host scale (~10e-09 subs/site/year)."

Basically, even though viruses evolve at a much faster rate than their hosts, once those sequences are integrated in the germline, from there on, they evolve at the same rate as the host genome, which is much slower. That's how they become "fossils" compared to their exogenous counterparts. For example, studies looking at primate lentiviruses (for example SIV and HIV) have estimated the age of these viruses to be in the thousands at maximum. However, endogenous lentivirus elements in lemurs indicate that they have been circulating for over a million years. Additionally, there is evidence of selection pressure derived from the fitness cost induced by viral infections that also points at the antiquity of some viral families.

[1] Holmes, E. (2011). The Evolution of Endogenous Viral Elements Cell Host & Microbe, 10 (4), 368-377 DOI: 10.1016/j.chom.2011.09.002

Renato Dulbecco, February 22, 1914 – February 19, 2012

Last February 19 Nobel laureate Renato Dulbecco died at age 97. Dulbecco
discovered how viruses integrate their genomes into host cells, something I've often talked about when describing the HIV life cycle. Dulbecco was mostly interested in oncoviruses, (viruses that have the potential to trigger tumors) and, in particular, the molecular mechanisms through which this could happen. He studied a virus called SV40, or simian virus 40, a polyomavirus that infects both monkeys and humans. He was also among the scientists that launched the Human Genome Project.

Over about a decade between the late '50s and the late '60s, Dulbecco and his group showed that SV40 contains DNA in a circular form and that the virus is able to permanently integrate its DNA in the cellular DNA, forming what is called a provirus. Interestingly, they found that the virus could grow in certain cell cultures, but did not grow in others, where instead it induced a cancer-like state. Dulbecco was fascinated by how the virus could achieve this as he believed the key to this mechanism could shed light on tumorigenesis in general.

In cells where the virus does not replicate, the integrated viral DNA expresses one protein in particular, the "T antigen," which the virus uses for replication. The T antigen alters the cell's replication cycle (for example by inactivating the p53 tumor suppressant proteins) favoring cell replication. Since the viral DNA is integrated in the cell's DNA, by promoting DNA replication, the virus ensures its own replication. As this happens, though, mutations start accumulating increasing the likelihood of the cell line becoming carcinogenic. In other words, it's the accumulation of mutations that eventually leads to cancer.

What about HIV? HIV is an RNA virus, not a DNA virus like SV40, and yet it uses the same mechanism that SV40 uses to replicate: integration into the host's DNA. HIV achieves this by first transforming its RNA into DNA through an enzyme called reverse transcriptase. It was Howard Temin, a graduate student in Dulbecco's laboratory, who did his Ph.D. thesis on another oncovirus, the Rous sarcoma virus, that realized that this RNA virus was able to alter the host cell DNA (edited after Dr. Racaniello's comment below). This finding led to the discovery, a few years later, of the reverse transcriptase enzyme, for which Howard Temin, David Baltimore, and Renato Dulbecco shared the 1975 Nobel Prize in Medicine (David Baltimore made the same discovery independently).

Dulbecco R (1973). Cell transformation by viruses and the role of viruses in cancer. The eleventh Marjory Stephenson Memorial Lecture. Journal of general microbiology, 79 (1), 7-17 PMID: 4359401