Mystery Rays from Outer Space

“How to avoid influenza: Gargle Daily”

Every virus that infects a vertebrate, has to be able to deal with the vertebrate immune system. The virus’s ancestors that infected vertebrates must have been able to deal with the vertebrate immune system. Those viruses that couldn’t handle an immune response are extinct.

Some of the ways viruses handle immunity, we don’t think of as really “specific”. Rapid replication, for example, has benefits for the virus that extend past just beating the immune system to the punch. But just about every virus, even the smallest ones, also have some form of specific immune evasion gene — some way of blocking, dodging, diverting, or confusing the immune system.

In spite of this nearly universal presence, we don’t really have a good grasp of precisely what viral immune evasion genes do, as far as supporting viral pathogenesis. (For that matter, it’s only for a handful of viruses that we really have much understanding of the pathogenesis in general.) Some viruses have a huge number of genes that are clearly immune evasion genes, others apparently only have one or two. Sometimes you can knock out an immune evasion gene and virtually destroy the virus’s ability to infect; sometimes the knockout only has a modest effect; sometimes there’s no effect at all, or it may even make the virus more, rather than less, virulent.

Viruses are so different from each other¹ that there are probably few if any general rules for immune evasion. Still, we’re not even at a point yet where we have non-general rules, so the more we learn the more likely we are to see patterns.

Physicians expressing their thanks to influenza. Coloured etching attributed to Temple West, 1803.

Influenza, of course, has its own set of immune evasion genes. The most important one is the NS1 gene.² NS1 blocks the interferon pathway, and to the extent that we can generalize, it seems that blocking interferon is one of the most critical things any virus can do. Almost every virus has some way of meddling with the interferon pathways, whether by preventing interferon from being triggered or inducing resistance to the effects of interferon. It’s been known for quite a while that NS1 does this — prevents interferon from being turned on — for influenza viruses, and it’s also been known that NS1 is very, very important to the virus. Mutant influenza viruses without NS1 are much, much less virulent than wild-type virus, and even targeting NS1 after an infection has started can help treat influenza.

(A flip side of this is that influenza viruses with a particularly effective NS1 may be more virulent. The 1918 pandemic influenza, which had a very high mortality rate,³ seems to have a particularly effective NS1 that can block interferon in several ways, and it’s been shown that swapping just the NS1 from the 1918 virus can make otherwise mild flu viruses more virulent. See my previous post about that.)

But there’s a bit of a paradox here. We know that NS1, the interferon blocker, is important to influenza virus. But we also know that interferon is very important in controlling influenza virus infections. For example, mice that can’t respond to interferons are much more susceptible to infection with avian influenza.⁴ So if NS1 works by blocking interferon, why does interferon still protect?

For that matter, one of the major explanations for why some influenza viruses (like avian flu and the 1918 flu) are so virulent, is the “cytokine storm” hypothesis.  (I talked about cytokine storms here and here.)  According to this concept, these viruses are especially lethal because they induce a huge release of cytokines, such as interferon. Yet at the same time the argument is made that these viruses are the ones with especially effective interferon blockers. If they’re really good at blocking interferon, then why do people die of having too much interferon?

It turns out that part of the answer may be timing. A recent paper from Thomas Moran’s group⁵ shows that in the very earliest stages of influenza virus infection, interferons are not being produced; then, a couple of days in, there’s a sudden big bang of cytokines. Knocking NS1 out of the virus changed this; interferons were produced from the beginning of the infection, and the virus was shut down. They call this phenomenon “stealth replication”:

Our data demonstrate that the initiation of lung inflammation does not begin until almost 2 full days after infection, when virus replication reaches its apex. The migration of lung DCs to lymph nodes and the subsequent priming of naive T cells are similarly subject to this delay. We demonstrate that the delay in the generation of immediate lung inflammation is mediated by the influenza NS1 protein. We propose that the virally encoded NS1 protein establishes a time-limited “stealth phase” during which the replicating influenza virus remains undetected, thus preventing the immediate initiation of innate and adaptive immunity. ⁵

They point out that in normal human influenza virus infection, symptoms take a couple of days to kick in, which fits because most of the “flu-like symptoms” we talk about are generic effects of cytokines. They also point out that a lot of virus transmission occurs before symptoms — i.e. in the first couple days of infection.

Thus, a stealth phase may also occur in humans and probably functions to maximize the probability of transmission before cytokines such as type I IFNs hamper the normal replicative cycle of influenza virus.⁵

This also helps make sense of the cytokine storm concept, I think. If avian or 1918 NS1 is especially good at preventing cytokines, then there might be a slightly longer stealth period, during which time the virus can replicate more. Then, when the immune system suddenly does become aware of an infection, there’s a huge amount of virus present, and the cytokine response would be correspondingly huge.

We might even be able to generalize to other viruses:

The stealth phase concept is not only applicable to influenza virus but can probably be extended to virtually all “real” human viral pathogens that have been shown to have an asymptomatic incubation time. For example, measles and varicella zoster viruses have a substantially prolonged evasion period that can last up to 2 wk. During this asymptomatic phase, these viruses also transmit to other susceptible hosts. Research aimed at interfering with the stealth phase may lead to the development of novel modulators as preventive treatments that target this early immune evasion mechanism. ⁵

I want to point to a previous post I made here, too, about herpes simplex virus. HSV has a wide range of immune evasion molecules, and we don’t have much understanding of what these things do in a natural infection.Frank Carbone’s group  did experiments with mouse infection that showed that HSV has a very narrow window (less than 24 hours) during which it can move from its original site of infection, in the skin, to neurons where it sets up a life-long infection. If the immune response can control HSV in this window, the virus can’t get into neurons and its life cycle is cut short. I speculated at the time that this might help explain immune evasion by HSV — it wouldn’t have to be super efficient, just keep things under control during that brief, early window. Seems quite similar to the influenza situation: Timing is critical, and perhaps immune evasion is one reason why.

1. “Virus” isn’t a natural division; it groups together things with very different, and completely unconnected, evolutionary histories[↩]
2. “NS” stands for “Non-structural”, meaning that the protein isn’t part of the virion that floats around and infects new cells — rather, the NS1 protein is produced anew in each cell after infection.[↩]
3. As influenza infections go — not close to something like smallpox or ebola, but some 20 times higher than normal seasonal flu[↩]
4. Szretter, K., Gangappa, S., Belser, J., Zeng, H., Chen, H., Matsuoka, Y., Sambhara, S., Swayne, D., Tumpey, T., & Katz, J. (2009). Early Control of H5N1 Influenza Virus Replication by the Type I Interferon Response in Mice Journal of Virology, 83 (11), 5825-5834 DOI: 10.1128/JVI.02144-08[↩]
5. Moltedo, B., Lopez, C., Pazos, M., Becker, M., Hermesh, T., & Moran, T. (2009). Cutting Edge: Stealth Influenza Virus Replication Precedes the Initiation of Adaptive Immunity The Journal of Immunology, 183 (6), 3569-3573 DOI: 10.4049/jimmunol.0900091[↩][↩][↩][↩]

Norovirus (from J Virol. 82:2079-2088 (2008))

Noroviruses cause an unpleasant, but rarely serious, diarrhea and vomiting-type disease — “cruise ship flu”¹ is one term for it.  As well as cruise ships, nursing homes and hospitals and other more or less closed systems also see outbreaks of norovirus disease fairly regularly, and as you’d expect the elderly and immune-compromised are more at risk from the disease.

Noroviruses have been around for a long time (they were first identified in the early 1970s, as “Norwalk Viruses”), but it’s in the last ten years or less that they really exploded; in 2002 there was an abrupt, worldwide upsurge of norovirus outbreaks, and more epidemics have followed almost every winter. Those outbreaks were all different mutant variants of norovirus; I talked about this earlier.² Each outbreak³ was associated with a new variant of norovirus, that is no longer controlled by the immunity that controlled the previous outbreak.

A couple of recent papers look at norovirus epidemics more closely. One⁴ analyzed the different strains involved in global outbreaks. They found that there were eight distinct variants of the GII.4 noroviruses, three of which caused global epidemics. Other strains did become epidemic, but on a more local scale (countries or continents, rather than everywhere).

My first thought was that that’s essentially the strategy that influenza viruses have used, also very effectively; each new flu season sees new variants of influenza virus, and each season’s most abundant viruses are the ones that are less well controlled by the immunity among their target population. This is the notorious “antigenic shift” that beginning virologists learn to parrot in their first class. The parallel to influenza epidemics was also noted by the authors, and they pointed out another parallel: Most of the global norovirus epidemics seem to have originated in Asia, as with influenza A.

What surprised me originally about the norovirus equivalent of antigenic shift was that at the time, conventional wisdom had it that immunity doesn’t play a big part in controlling seasonal norovirus outbreaks; immunity to noroviruses is weak and short-lived, and I had not thought that immunity from the previous winter would be a factor in controlling outbreaks this winter. The previous paper I talked about showed evidence, though, that immunity is a major factor in determining norovirus epidemics, and the other paper I have here⁵ looks at this in much more detail. I won’t go into their work in any detail⁶ but what they’re doing is building predictive models for norovirus epidemics. Very briefly, their overall conclusion is:

These results point to a complex interplay between host, viral and climatic factors driving norovirus epidemic patterns. Increases in norovirus are associated with cold, dry temperature, low population immunity and the emergence of novel genogroup 2 type 4 antigenic variants.⁵

The “new variant” part matches the first paper’s description of epidemics — mostly, but not always, they’re driven by a new version of the virus, but new variants don’t necessarily explode globally. It seems that a new variant may often be necessary for an outbreak, but isn’t sufficient; and in some cases, other factors may mean new variants aren’t absolutely necessary. Cool, dry weather supports an epidemic (and this is probably a big part of the highly seasonal pattern of norovirus infections, as well; it’s charmingly called “Winter vomiting disease” by some). And epidemics are possible when population immunity to a particular strain of norovirus drops under a certain level.

“Daily norovirus laboratory reports (grey circles) and predicted values (red line) from full model including temperature, relative humidity, immunity, new variants and autoregressive terms and other confounders.“

The authors point out that new variants are selected by population immunity, so two of these factors are not strictly independent. However, “Despite this, these two factors had significant effects after controlling for the other”;⁵ perhaps there’s some immunity even to variant strains of norovirus. Since immunity to norovirus does drop very quickly,⁷ perhaps a year is enough to open a window for new strains, but not for the same one; particularly if the weather cooperates. Or perhaps the arrow is going the other way — population immunity at the end of one season chokes out the prevalent strain, and only new strains that are relatively resistant survive to cause the next epidemic once the weather cooperates.

At any rate, from these parameters the authors derived a predictive model. Applied retrospectively, it looks pretty impressive (see the figure to the right; click for a larger version). ⁸  It will be interesting to see how well it actually predicts new outbreaks.

By the way, regular readers may have noticed that this is two weeks in a row with only one new post — I usually aim for two or three per week, but what with my kids starting their school this week, and my teaching schedule⁹ kicking in, I’m scrambling some to keep up.  Hopefully I’ll be in more control soon, but I make no promises.

1. It’s not flu![↩]
2. Referring to this paper: Lindesmith, L.C., Donaldson, E.F., LoBue, A.D., Cannon, J.L., Zheng, D., Vinje, J., Baric, R.S. (2008). Mechanisms of GII.4 Norovirus Persistence in Human Populations . PLoS Medicine, 5(2), e31. DOI: 10.1371/journal.pmed.0050031[↩]
3. Except for the 2007/08 outbreak, which was mainly the same strain as the previous year’s[↩]
4. Siebenga, J., Vennema, H., Zheng, D., Vinjé, J., Lee, B., Pang, X., Ho, E., Lim, W., Choudekar, A., Broor, S., Halperin, T., Rasool, N., Hewitt, J., Greening, G., Jin, M., Duan, Z., Lucero, Y., O’Ryan, M., Hoehne, M., Schreier, E., Ratcliff, R., White, P., Iritani, N., Reuter, G., & Koopmans, M. (2009). Norovirus Illness Is a Global Problem: Emergence and Spread of Norovirus GII.4 Variants, 2001–2007 The Journal of Infectious Diseases, 200 (5), 802-812 DOI: 10.1086/605127[↩]
5. Lopman, B., Armstrong, B., Atchison, C., & Gray, J. (2009). Host, Weather and Virological Factors Drive Norovirus Epidemiology: Time-Series Analysis of Laboratory Surveillance Data in England and Wales PLoS ONE, 4 (8) DOI: 10.1371/journal.pone.0006671[↩][↩][↩]
6. There are intimidating equations and everything[↩]
7. Though it’s not known exactly how quickly[↩]
8. By the way, while looking around for images to illustrate this norovirus post, I came across a lot of images of people hurling, and worse.  I decided to stick with obscure graphs instead.  No need to thank me.[↩]
9. A half-dozen classes in graduate immunology, a half dozen veterinary virology, and a dozen in veterinary immunology this year; plus a couple of guest lectures, where I’ll talk about immunity to viruses, probably focusing on swine-origin influenza virus as a particularly topical example[↩]

“Virons le virus” (Institut Merieux Benelux, 1991)

One of the important drivers of influenza virus evolution is mixed infection: Infection of the same individual with two different strains of virus, which can then reassort to generate brand-new viral genomes. This presumably what happened, for example, with the recent swine-origin influenza virus (SOIV): some pig was simultaneously infected with North American swine flu and a Eurasian swine flu, the two reassorted so that two of the Eurasian virus’s segments joined with 6 of the North American segments, and the new virus thus produced turned out, just by chance, to be good at infecting humans.

Reassortment, notoriously, can generate rapid large changes in the personality of the virus. Pandemic influenzas have been reassortants, unrecognized by the population’s immune systems. But that’s not the only possible outcome; reassortants between closely-related viruses can lead to small changes, reassortants between two circulating strains would still be recognized by the immune response, and so on. Reassortment per se isn’t inevitably devastating, the big concern is reassortment between widely-differing viruses — human and avians strains being the major issue today.

I’ve tended to think of multiple infection and reassortment as quite a rare phenomenon. Reassorted influenza viruses appear and circulate relatively often, but not, you know, daily;¹ and those are the product of millions upon millions of infected individuals. On the other hand, most reassortments are probably either dead on arrival (their different segments are simply not compatible) or at best very unfit (their different segments make them easily outcompeted by the wild flu that’s already well adapted to the individuals in question). That means we don’t know the frequency of reassortants, because most of them would be invisible to us.

I’ve also tended to think, perhaps naively, that multiple infections would be a little unusual, because the timing would have to be fairly precise. Viruses generally rely on a couple of days of relative peace (immunologically speaking) to quickly replicate and bank a virus load that then keeps pace with the increasing immune response. If Virus B tries to infect you a couple of days after Virus A is already present, Virus B is going to run right into the thick of the immune response to Virus A, never have that chance to bank its progeny virus, and you’d expect it to be quickly overwhelmed. So you probably need nearly simultaneous infections to get a real multiple infection.

“Influenza is prevalent” (Chicago, 1918)

But this is all speculation. A recent paper² went out and actually looked for evidence of mixed infection in humans.³ They used previously-collected samples, and this is going to greatly underestimate the extent of mixed infection,⁴ but they did detect evidence of several mixed infections in their collection of over 1000 influenza samples. A plausible number they offer is about 0.5% of their samples — half a dozen individuals — were potentially mixed infections.⁵

(Later they suggest, as unpublished data, that the number may be as high as 3%. An important caution, that they don’t mention here, is that the 3% number is from influenza database analysis, and we know that these databases are not high quality — see On the accuracy of the influenza databases and the paper referenced therein⁶ — in fact, about 3% of the samples in the database are contaminated, so I don’t know if the present authors took this into account when interpreting evidence for mixed infections.)

However, sticking with the 0.5% figure — which is still remarkably high, and would represent tens of thousands of cases per year — they were able to look more closely at several of these samples and confirmed that they did, in fact, represent true mixed infections. This is another spinoff of the rapid, high-throughput sequencing that’s now becoming widely available. One patient, from New Zealand, was simultaneously infected with two viruses:

…one closely related to viruses cocirculating in New Zealand during 2004 and a second lineage that clustered with A/H3N2 viruses that became dominant in the following (2005) influenza season in the southern hemisphere ²

Another, in New York, was infected with two different influenza strains that are antigenically distinct — that is, viruses that would require different vaccines for protection. Remember that influenza vaccines are customized, year by year, to match up against the dominant circulating virus of that particular year. This patient would have needed two distinct vaccines to get adequate protection from his two infections.

A third, “even more dramatic” example was another New Yorker who was infected with two viruses that were not merely antigenically different, but that came from two distinct, broad groups — influenza A and influenza B viruses. I don’t think A and B can reassort, or at least the progeny would be very unlikely to be fit, but it illustrates that very mixed infection is quite possible.

It’s important to note that they were looking for mixed infection, not reassortment. Reassortment woud be much less common than mixed infection — you need mixed infectio nfor reassortment, but it’s not inevitable following mixed infection. Still, the background of mixed infection seems to be rather higher than I thought it would be.

In sum, we propose that mixed infection of diverse influenza viruses, a necessary precursor to reassortment, is a common occurrence during seasonal influenza in humans and will in turn accelerate the rate of adaptive evolution in this virus. In addition, intrahost populations of influenza virus will harbor genetic diversity generated by de novo mutation, which we have not assessed in the current study. As a consequence, we urge that intrahost sequencing be more routinely employed to assess the degree of genotypic and phenotypic diversity in populations of acute RNA viruses. With the advent of high-throughput next-generation sequencing platforms, viral variants are being much more explicitly revealed within specimens, and this type of data can be made available on a routine basis.²

1. Offhand, actually, I don’t know how often reassortants have been identified. I’ll try to find that[↩]
2. Ghedin, E., Fitch, A., Boyne, A., Griesemer, S., DePasse, J., Bera, J., Zhang, X., Halpin, R., Smit, M., Jennings, L., St. George, K., Holmes, E., & Spiro, D. (2009). Mixed Infection and the Genesis of Influenza Virus Diversity Journal of Virology, 83 (17), 8832-8841 DOI: 10.1128/JVI.00773-09[↩][↩][↩]
3. It would probably be more interesting to look for mixed infection in swine, or wild ducks, but it’s only humans that have enough close attention to detect these relatively rare events.[↩]
4. Most samples of a mixed infection are simply going to pick up the more abundant of the viruses present[↩]
5. This comes with a large helping of caveats; it could over- or under-estimate the frequency. But it’s a reasonable starting point and they did confirm some of them.[↩]
6. Krasnitz, M., Levine, A., & Rabadan, R. (2008). Anomalies in the Influenza Virus Genome Database: New Biology or Laboratory Errors? Journal of Virology, 82 (17), 8947-8950 DOI: 10.1128/JVI.00101-08[↩]

“Some years travels into divers parts of Africa and Asia the Great” R. Everingham for R. Scot, etc.London 1677

Hepatitis C virus (HCV), one of the classic intravenous-spread viruses, was only identified about 20 years ago.  Where and when did it originate, and how did it spread?

A recent paper¹ estimates that the common ancestor of the present world-wide HCV strains was in Guinea-Bissau, around 1470.  From there:

… infections moved to the New World via Benin–Ghana, even when they originated from Guinea–Gambia. … It is therefore likely that the slave trade has played a historical role in the global dissemination of HCV genotype 2. A similar role has previously been proposed for the transcontinental transmission of yellow fever virus prior to mass global travel. ¹

The pattern of HCV spread matches the flow of the slave trade.

There’s another very interesting historical finding from this epidemiology.  HCV epidemiology is very different in Cameroon vs. Guinea-Bissau.  In Cameroon, HCV exploded in the early to mid-20th century; whereas in Guinea-Bissau, HCV spread in the 20th century was slower.  The authors here suggest that this reflects different styles of health care in the two countries — aggressive treatment vs. limited treatment.  But it’s an indirect consequence of treatment of other diseases, and the effects on HCV were the opposite of what you’d expect:

We suggest that the differential epidemic histories of HCV genotype 2 in the two countries probably result from historical differences in the large-scale administration of intravenous antimicrobial drugs, decades before the risk of transmission of blood-borne viruses was understood. After World War I, medical care in Cameroun Français was provided mostly by military doctors, and public-health interventions aimed to cover the whole population … In contrast, the health system before the mid-1940s in Portuguese Guinea (now Guinea-Bissau) was more directed towards protecting the health of the European colonists and their Guinean employees. …Thus, the 25 year delay in organizing public-health interventions in Portuguese Guinea, combined with a lower incidence of yaws and trypanosomiasis in this drier land, resulted in a much lower proportion of the population receiving intravenous injections than in Cameroun Français, and a reduced opportunity for iatrogenic HCV transmission. ¹

In other words, the aggressive treatment of diseases in Cameroon probably dramatically reduced the frequency of many diseases, but because it involved injections with non-sterile needles, the treatment also managed to spread HCV.  The more lackadaisical attitude in Portuguese Guinea may have let other diseases flourish, but accidentally restricted the spread of IV contaminants like HCV as well.

1. Markov, P., Pepin, J., Frost, E., Deslandes, S., Labbe, A., & Pybus, O. (2009). Phylogeography and molecular epidemiology of hepatitis C virus genotype 2 in Africa Journal of General Virology, 90 (9), 2086-2096 DOI: 10.1099/vir.0.011569-0[↩][↩][↩]

“Disappointed chimpanzee” – J.M. Wood (from Darwin, “The expression of the emotions in man and animals”, 1872)

Untreated HIV has very, very high mortality, but there are a few people who manage to survive for quite a long time without progressing to AIDS. These long-term non-progressors somehow keep their HIV levels quite low, and it was thought they wouldn’t develop the disease.  But:

Low-level viremia is present in the majority of elite controllers and is associated with higher HIV-1–specific antibody responses. Absolute CD4+ T cell loss is more common among viremic individuals, suggesting that even very low-level viremia has negative consequences over time.¹

So, even among these apparently-resistant people, there’s still a trend (albeit a slow trend) toward immune deficiency.

HIV is essentially simian immunodeficiency virus (SIV) that’s crossed over into humans.  Several non-human primates naturally have SIV circulating among them, and it’s usually said that in the natural hosts SIV in not harmful.  But:

SIVcpz has a substantial negative impact on the health, reproduction and lifespan of chimpanzees in the wild. … SIVcpz-infected chimpanzees in Gombe have a 10–16-fold increased death hazard compared to uninfected chimpanzees … SIVcpz infection is associated with progressive CD4⁺ T-cell loss and immune system destruction, which are hallmarks of pathogenic HIV-1 infection. … SIVcpz seems to be less pathogenic than HIV-1, but more pathogenic than HIV-2 and SIVsmm.²

So, even among this apparently-resistant species, there’s still a trend toward immune deficiency.

1. Pereyra, F., Palmer, S., Miura, T., Block, B., Wiegand, A., Rothchild, A., Baker, B., Rosenberg, R., Cutrell, E., Seaman, M., Coffin, J., & Walker, B. (2009). Persistent Low?Level Viremia in HIV?1 Elite Controllers and Relationship to Immunologic Parameters The Journal of Infectious Diseases, 200 (6), 984-990 DOI: 10.1086/605446[↩]
2. Keele, B., Jones, J., Terio, K., Estes, J., Rudicell, R., Wilson, M., Li, Y., Learn, G., Beasley, T., Schumacher-Stankey, J., Wroblewski, E., Mosser, A., Raphael, J., Kamenya, S., Lonsdorf, E., Travis, D., Mlengeya, T., Kinsel, M., Else, J., Silvestri, G., Goodall, J., Sharp, P., Shaw, G., Pusey, A., & Hahn, B. (2009). Increased mortality and AIDS-like immunopathology in wild chimpanzees infected with SIVcpz Nature, 460 (7254), 515-519 DOI: 10.1038/nature08200[↩]

This is your monkeypox infection with an adaptive immune response:	This is your monkeypox infection without an adaptive immune response:

Any questions?

(From
Osorio, J., Iams, K., Meteyer, C., & Rocke, T. (2009). Comparison of Monkeypox Viruses Pathogenesis in Mice by In Vivo Imaging PLoS ONE, 4 (8) DOI: 10.1371/journal.pone.0006592. 
Wild-type (immune-competent) mice (left) or SCID mice (no B or T cell response) were infected with monkeypox virus expressing luciferase. Mice on the left were uninfected controls.  The colors show the presence of monkeypox virus in the mice, with intensity (redder) representing more virus.  The SCID mice died on day 9, while the normal mice cleared the infection.)

We know that viruses cause a significant minority of human cancers, but we don’t know quite how many, or which, cancers are viral. It’s not as easy as you might think to tell.

The link between viruses and cancer was one of the major breakthroughs in cancer biology, but you could also make a case that that link set cancer research back several years. (Cancer viruses were shown, in chickens, in 1911¹, but it wasn’t until the 1960s that interest in the concept took off, with Epstein’s demonstration of Epstein-Barr virus (EBV)² in some human tumors. ) Studying viral oncogenesis has led to huge advances in our understanding of the fundamental biology of cancers. The problem was that there was a general assumption, in the 1960s and 1970s, that viruses were directly responsible for the vast majority of human tumors. If so, all we needed to do was to identify the viruses, develop vaccines against them, and voila! No more cancer!

Of course, it wasn’t that easy. For all the fundamental advances from this concept, it’s been relatively unproductive as far as the bedside is concerned. Most human tumors are not caused by viruses,³ and even those that are, have been really resistant to treatment via direct anti-viral approaches.⁴ The research units that were established in the 1970s to look at the virus/tumor connection have mostly either disbanded, or taken a different direction now.

Mouse polyomavirus

In spite of that, there’s still new and exciting stuff coming out. Most recently,⁵ Yuan Chang and Patrick Moore identified a new cancer-causing virus of humans. (This was their second breakthrough virus; in 1994⁶ they also found the second-most recent cancer-causing virus of humans, Kaposi’s Sarcoma Herpesvirus.)) This brings to six the number of clearly-linked human cancer viruses: papillomaviruses, HTLV-1, hepatitis B virus, EBV, Kaposi’s Sarcoma Herpesvirus, and the new one, Merkel cell polyomavirus.

I keep meaning to talk about the discovery of Merkel cell polyomavirus, but I’ll set that aside for now. Very briefly, last fall Chang and Moore showed that the presence of the virus is linked to a fairly rare tumor, Merkel cell carcinoma, and they and others have now confirmed the epidemiological association and demonstrated a mechanism for causing tumors. We’re at the stage now of trying to understand the normal biology of the virus. As with most (and all human) cancer viruses, the virus is much more widespread than the tumor. How widespread it is? How does it spread? Does it cause other disease — in particular, is it involved in other tumors?

That last is a particularly interesting question, because although Merkel cell tumors are rare, there are a number of common tumors that could, conceivably, also be caused by the virus; and if the virus causes even a subset of those, then it could be a common cause of cancer rather than an unusual one. So far, though, I think the evidence suggests that the virus is fairly limited in the damage it causes; quite a few groups have looked for the virus in other types of cancer, and although it may be occasionally found⁷, that most likely reflects general background infection with the virus rather than a causative role.

One exception is a recent paper⁸ which suggested that the virus might be associated with a subset of squamous cell carcinomas. SCC are a pretty common form of skin tumor, so if MCPyV is a cause of even a subset of SCC it might be a significant cause of cancer.

The problem is that the other studies on MCPyV have shown that it’s out there even in normal, non-diseased humans⁹ — as you’d expect; the virus must be able to spread and circulate within the human population somehow, and the version of the virus found in Merkel cell tumors is damaged and likely can’t spread, so there must be virus replicating in normal tissues. In this paper, the authors find the virus in a subset of SCC cancers, but I would like to know how many they’d find in normal human skin using the same techniques –  the 15% of positive tumor samples may or may not be significantly different. On the other hand, the SCC-associated virus did show a similar molecular signature to that found in Merkel cell cancer,¹⁰ suggesting a causative role. Right now, I’m not completely convinced, but am definitely intrigued.

One really interesting point to add is that — if MCPyV really does cause a significant number of tumors — then it’s been missed all these years, despite high interest in searching for human cancer viruses, until new techniques were applied to the right samples in the right way. Are there other human cancer viruses out there, waiting for the right technique? Is it still possible that most human cancers are caused by viruses? I think that’s pretty unlikely, but the door is still open a crack.

1. A sarcoma of the fowl transmissible by an agent separable from the tumor cells. Rous, P. 1911. J. Exp. Med. 13:397–411.[↩]
2. Virus particles in cultured lymphoblasts from Burkitt’s lymphoma. MA Epstein, BG Achong and YM Barr. Lancet 1 (1964), pp. 702–703.[↩]
3. The usual educated guess is 20%[↩]
4. One major exception, of course, being papilloma virus vaccines, which are a direct outcome of this line of research. But it’s taken a long time to come to fruition. You could also point to vaccination against hepatitis B virus, and a number of veterinary vaccines, as clinical advances arising from the virus/cancer research. But I think it’s fair to say that the energy put into this has been fundamentally, but not clinically, well spent.[↩]
5. Feng, H., Shuda, M., Chang, Y., & Moore, P. (2008). Clonal Integration of a Polyomavirus in Human Merkel Cell Carcinoma Science, 319 (5866), 1096-1100 DOI: 10.1126/science.1152586[↩]
6. Identification of herpesvirus-like DNA sequences in AIDS-associated Kaposi’s sarcoma.
   Chang Y, Cesarman E, Pessin MS, Lee F, Culpepper J, Knowles DM, Moore PS.
   Science. 1994 Dec 16;266(5192):1865-9.[↩]
7. For example, Human Merkel cell polyomavirus infection I. MCV T antigen expression in Merkel cell carcinoma, lymphoid tissues and lymphoid tumors.
   Shuda M, Arora R, Kwun HJ, Feng H, Sarid R, Fernández-Figueras MT, Tolstov Y, Gjoerup O, Mansukhani MM, Swerdlow SH, Chaudhary PM, Kirkwood JM, Nalesnik MA, Kant JA, Weiss LM, Moore PS, Chang Y.
   Int J Cancer. 2009 Sep 15;125(6):1243-9[↩]
8. Dworkin, A., Tseng, S., Allain, D., Iwenofu, O., Peters, S., & Toland, A. (2009). Merkel Cell Polyomavirus in Cutaneous Squamous Cell Carcinoma of Immunocompetent Individuals Journal of Investigative Dermatology DOI: 10.1038/jid.2009.183[↩]
9. Human Merkel cell polyomavirus infection II. MCV is a common human infection that can be detected by conformational capsid epitope immunoassays.
   Tolstov YL, Pastrana DV, Feng H, Becker JC, Jenkins FJ, Moschos S, Chang Y, Buck CB, Moore PS.
   Int J Cancer. 2009 Sep 15;125(6):1250-6[↩]
10. Shuda, M., Feng, H., Kwun, H., Rosen, S., Gjoerup, O., Moore, P., & Chang, Y. (2008). T antigen mutations are a human tumor-specific signature for Merkel cell polyomavirus Proceedings of the National Academy of Sciences, 105 (42), 16272-16277 DOI: 10.1073/pnas.0806526105 [↩]

Here we estimated the evolutionary history and inferred date of introduction to humans of each of the genes for all 20th century pandemic influenza strains. Our results indicate that genetic components of the 1918 H1N1 pandemic virus circulated in mammalian hosts, i.e., swine and humans, as early as 1911 and was not likely to be a recently introduced avian virus …. The possible generation of pandemic strains through a series of reassortment events in mammals over a period of years before pandemic recognition suggests that appropriate surveillance strategies for detection of precursor viruses may abort future pandemics.

–Smith, G., Bahl, J., Vijaykrishna, D., Zhang, J., Poon, L., Chen, H., Webster, R., Peiris, J., & Guan, Y. (2009). From the Cover: Dating the emergence of pandemic influenza viruses Proceedings of the National Academy of Sciences, 106 (28), 11709-11712 DOI: 10.1073/pnas.0904991106

(My emphasis)

Further reading: ¹

• H1N1 evolution
• Predicting influenza virulence from sequences
• Has the new H1N1 been hiding for 11 years? (No.)
• How fast can influenza change?
• 1918 flu, dinosaurs, and birds
• Viruses jumping species
• Where did avian flu come from, and where is it going?
• Cross-protection against avian influenza?
• Treatment for avian flu?
• Effective immune evasion (Influenza vs. Interferon: The grudge match)

1. Holy crap, I’ve talked a lot about influenza. I didn’t realize I had so many posts about it, and this is just a sampling![↩]

OK, maybe they call this “nanoindentation experiments”, but if this virus isn’t being SuperPoked then I give up my Web 2.0 credentials.¹

–From:
Scaffold expulsion and genome packaging trigger stabilization of herpes simplex virus capsids
Roos et al.
PNAS June 16, 2009 vol. 106 no. 24 9673-9678  doi: 10.1073/pnas.0901514106

(See also: Teenage Mutant Ninja Herpes Simplex)

1. Not that I have any.[↩]

I’m sure lots of other people will point to the new Nature paper on the history and evolution of the new H1N1 influenza.¹ (I believe this is an open-access paper, so check it out for yourself.)  Key points include:

• it was derived from several viruses circulating in swine
• the initial transmission to humans occurred several months before recognition of the outbreak.
• the reassortment of swine lineages may have occurred years before human emergence
  
• the nature and location of the genetically closest swine viruses reveal little about the immediate origin of the epidemic

A key conclusion: “Our results highlight the need for systematic surveillance of influenza in swine.”  This seems to be becoming fairly widely accepted, though I don’t know what is being done to make it happen.

They include a really helpful diagram, by far the best I’ve seen for clarifying the evolutionary history:

(Sorry for the lack of updates this week, by the way.  It’s been a rough week, nothing has gone well except for the Red Sox beating the Yankees in the first two games of their series.)

1. Smith, G., Vijaykrishna, D., Bahl, J., Lycett, S., Worobey, M., Pybus, O., Ma, S., Cheung, C., Raghwani, J., Bhatt, S., Peiris, J., Guan, Y., & Rambaut, A. (2009). Origins and evolutionary genomics of the 2009 swine-origin H1N1 influenza A epidemic Nature DOI: 10.1038/nature08182[↩]